Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 10: Suitability of taxonomic units notified to EFSA until March 2019

Abstract

The qualified presumption of safety (QPS) procedure was developed to provide a harmonised generic pre‐evaluation to support safety risk assessments of biological agents performed by EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance were assessed. Safety concerns identified for a taxonomic unit (TU) are, where possible and reasonable in number, reflected by ‘qualifications’ which should be assessed at the strain level by the EFSA's Scientific Panels. During the current assessment, no new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA from applications for market authorisation was updated with 47 biological agents, received between October 2018 and March 2019. Of these, 19 already had QPS status, 20 were excluded from the QPS exercise by the previous QPS mandate (11 filamentous fungi) or from further evaluations within the current mandate (9 notifications of Escherichia coli). Sphingomonas elodea, Gluconobacter frateurii, Corynebacterium ammoniagenes, Corynebacterium casei, Burkholderia ubonensis, Phaeodactylum tricornutum, Microbacterium foliorum and Euglena gracilis were evaluated for the first time. Sphingomonas elodea cannot be assessed for a possible QPS recommendation because it is not a valid species. Corynebacterium ammoniagenes and Euglena gracilis can be recommended for the QPS list with the qualification ‘for production purposes only’. The following TUs cannot be recommended for the QPS list: Burkholderia ubonensis, due to its potential and confirmed ability to generate biologically active compounds and limited of body of knowledge; Corynebacterium casei, Gluconobacter frateurii and Microbacterium foliorum, due to lack of body of knowledge; Phaeodactylum tricornutum, based on the lack of a safe history of use in the food chain and limited knowledge on its potential production of bioactive compounds with possible toxic effects.

Summary

The European Food Safety Authority (EFSA) asked the Panel on Biological Hazards (BIOHAZ) to deliver a Scientific Opinion on the maintenance of the list of qualified presumption of safety (QPS) biological agents intentionally added to food or feed. The request included three specific tasks as mentioned in the Terms of Reference (ToR).

The QPS process was developed to provide a harmonised generic pre‐evaluation procedure to support safety risk assessments of biological agents performed by EFSA's scientific Panels and Units. The taxonomic identity, body of knowledge and safety of biological agents are assessed. Safety concerns identified for a taxonomic unit (TU) are, where possible and reasonable in number, reflected as ‘qualifications’ that should be assessed at the strain level by the EFSA's scientific Panels. A generic qualification for all QPS bacterial TUs applies in relation to the absence of acquired genes conferring resistance to clinically relevant antimicrobials (EFSA, 2008).

The overall summary of the re‐evaluation of TUs previously recommended for the QPS list is undertaken every 3 years in a scientific Opinion of the BIOHAZ Panel. Meanwhile, the list of microorganisms is maintained and re‐evaluated approximately every 6 months in a Panel Statement. If new information is retrieved from extended literature searches that would change the QPS status of a microbial species or its qualifications, this is published in the Panel Statement. The Panel Statement also includes the evaluation of microbiological agents newly notified to EFSA within the 6‐month period for an assessment for use as feed additives, food enzymes, food additives and flavourings, novel foods or plant protection products (PPPs). The main results of the assessments completed from 2017 onwards will be included in the scientific Opinion of the BIOHAZ Panel to be published by the end of the current mandate in December 2019. In the interim, as a result of each Panel Statement, the ‘2016 updated list of QPS status recommended biological agents for safety risk assessments carried out by EFSA scientific Panels and Units’ is extended by the inclusion of new recommendations for QPS status, and appended to the Opinion adopted in December 2016 (Appendix E).

The first ToR requires ongoing updates of the list of biological agents notified to EFSA, in the context of a technical dossier, for intentional use in food and/or feed or as sources of food and feed additives, enzymes and PPPs for safety assessment. The list was updated with the notifications received since the latest review in October 2018. Within this period, 47 notifications were received by EFSA, of which 32 were for feed additives, two for food enzymes, food additives and flavourings, 10 for novel foods and 3 for PPPs. The new notifications, received between October 2018 and March 2019, are included in a table appended to the current Statement (Appendix F).

The second ToR concerns the revision of the TUs previously recommended for the QPS list and their qualifications when new information has become available, and the updating of the information provided in the previous Opinion adopted in December 2016. According to the articles retrieved through an extensive literature search (ELS), for articles published from October 2018 to March 2019 no new information was found that would affect the QPS status of those TUs and their qualifications.

The third ToR requires a (re)assessment of TUs notified to EFSA, but not present in the current QPS list, for their suitability for inclusion in the updated list. The current Statement focuses on the assessments of the TUs that were notified to EFSA between October 2018 and March 2019. Of the 47 notifications received, 19 biological agents already had QPS status and did not require further evaluation in this Statement and 20 were not included because: 11 were notifications of filamentous fungi that were excluded from the QPS exercise; nine were notifications of Escherichia coli that were excluded from further QPS evaluations within the current QPS mandate. Eight new TUs were considered for the QPS assessment within this Statement: Sphingomonas elodea, Corynebacterium ammoniagenes, Corynebacterium casei, Gluconobacter frateurii, Burkholderia ubonensis, Phaeodactylum tricornutum, Euglena gracilis and Microbacterium foliorum which were evaluated for the first time.

Sphingomonas elodea could not be assessed for a possible QPS recommendation because it is currently not a valid species. Corynebacterium ammoniagenes and Euglena gracilis can be recommended for the QPS list with the qualification ‘for production purposes only’. The following TUs cannot be recommended for the QPS list: Burkholderia ubonensis, due to its potential ability to generate biologically active compounds and limited body of knowledge; Corynebacterium casei, Gluconobacter frateurii and Microbacterium foliorum, due to lack of body of knowledge; Phaeodactylum tricornutum, based on the lack of a safe history of use in the food chain and limited knowledge on its potential production of bioactive compounds with toxic effects.

Pediococcus dextrinicus (Coster and White, 1964) Back, 1978 species has been changed to Lactobacillus dextrinicus (Coster and White, 1964) Haakensen et al., 2009, comb. nov. It will be updated in the QPS list.

1. Introduction

The qualified presumption of safety (QPS) approach was developed by the EFSA Scientific Committee to provide a generic concept to prioritise and to harmonise risk assessment within the European Food Safety Authority (EFSA) of microorganisms intentionally introduced into the food chain, in support of the respective Scientific Panels and Units in the frame of market authorisations (EFSA, 2007). The list, first established in 2007, has been continuously revised and updated. The publication of the overall assessment of the taxonomic units (TUs) previously recommended for the QPS list is to be evaluated every 3 years through a scientific Opinion by the Panel on Biological Hazards (BIOHAZ). Intermediate deliverables in the form of a Panel Statement are produced and published for periods of around 6 months, should an assessment for a QPS classification of a microbiological agent notified to EFSA be requested by the Units dealing with feed additives, food enzymes, food additives and flavourings, novel foods, or plant protection products. These Panel Statements also include the results of the assessment of the relevant new papers related to the TUs with QPS status.

1.1. Background and Terms of Reference as provided by EFSA

1.1.1. Background as provided by EFSA

A wide variety of microorganisms are intentionally added at different stages into the food and feed chain. In the context of applications for market authorisation of these biological agents, used either directly or as sources of food and feed additives, food enzymes and plant protection products, EFSA is requested to assess their safety.

Several taxonomic units (usually species for bacteria and yeasts, families for viruses) have been included in the qualified presumption of safety (QPS) list either following notifications to EFSA or proposals made initially by stakeholders during a public consultation in 2005, even if they were not yet notified to EFSA (EFSA, 2005).1 The EFSA Scientific Committee reviewed the range and numbers of microorganisms likely to be the subject of an EFSA Opinion and published in 2007 a list of microorganisms recommended for the QPS list.2

In 2007, the Scientific Committee recommended that a QPS approach should provide a generic concept to prioritise and to harmonise safety risk assessment of microorganisms intentionally introduced into the food chain, in support of the respective Scientific Panels and EFSA Units in the frame of the market authorisations. The same Committee recognised that there would have to be continuing provision for reviewing and modifying the QPS list and in line with this recommendation, the EFSA Scientific Panel on Biological Hazards (BIOHAZ) took the prime responsibility for this and started reviewing annually the existing QPS list. The first annual QPS update3 was published in 2008 and EFSA's initial experience in applying the QPS approach was included. The potential application of the QPS approach to microbial plant protection products was discussed in the 2009 update.4 Also in 2009, bacteriophages were assessed and were not considered appropriate for the QPS list. After consecutive years of reviewing the existing scientific information, the filamentous fungi (2008 to 2013 updates) and enterococci (2010 to 2013 updates) were not recommended for the QPS list. The 2013 update5 of the recommended QPS list included 53 species of Gram‐positive non‐spore‐forming bacteria, 13 Gram‐positive spore forming bacteria (Bacillus species), one Gram‐negative bacterium (Gluconobacter oxydans), 13 yeast species, and three virus families.

In 2014 the BIOHAZ Panel, in consultation with the Scientific Committee, decided to change the revision procedure: the overall assessment of the taxonomic units previously recommended for the QPS list is no longer carried out annually but over 3‐year periods. From 2017, the search and revision of the possible safety concerns linked to those taxonomic units start to be done every 6 months period. The revision of the 2013 update (EFSA Biohaz Panel, 2013) was updated in 2016 (EFSA BIOHAZ Panel, 2017a) and the next update will be published in a scientific Opinion of the BIOHAZ Panel after its adoption in December 2019.6 The QPS list of microorganisms has been maintained and frequently checked, based on the evaluation of extensive literature searches. In the meantime and every 6 months, a Panel Statement, compiling the assessments for a QPS status of the microbiological agents notified to EFSA requested by the Feed Unit, the Food Ingredients and Packaging (FIP) Unit, the Nutrition Unit or by the Pesticides Unit, has been produced and published. In the follow up of the 2013 update5 the Scientific Committee agreed to exclude some biological groups (filamentous fungi, bacteriophages and Enterococcus faecium 7) notified to EFSA from the QPS assessment because it was considered unlikely that any taxonomical units within these groups would be granted QPS status in the foreseeable future. Thus, the assessment of members of these biological groups needs to be done at a strain level, on a case‐by‐case basis, by the relevant EFSA Unit.

The QPS provides a generic safety pre‐assessment approach for use within EFSA that covers risks for human, animals and the environment. In the QPS concept a safety assessment of a defined taxonomic unit is considered independently of any particular specific notification in the course of an authorisation process. The QPS concept does not address hazards linked to the formulation or other processing of the products containing the microbial agents and added into the food or feed chain. Although general human safety is part of the evaluation, specific issues connected to type and level of exposure of users handling the product (e.g. dermal, inhalation, ingestion) are not addressed. In the case Genetically Modified Microorganisms (GMMs) for which the species of the recipient strain qualifies for the QPS status, and for which the genetically modified state does not give rise to safety concerns, the QPS approach can be extended to genetically modified production strains (EFSA BIOHAZ Panel, 2018a).8 Assessment of potential allergenicity to microbial residual components is beyond the QPS remit; if there is however, science‐based evidence for some microbial species it is reported. Where applicable these aspects are assessed, separately by the EFSA Panel responsible for assessing the notification. Antimicrobial resistance was introduced as a possible safety concern for the assessment of the inclusion of bacterial species in the QPS list published in 2008 QPS Opinion (EFSA, 2008)³. In the 2009 QPS Opinion (EFSA BIOHAZ Panel, 2009)⁴ a qualification regarding the absence of antimycotic resistance for yeasts was introduced.

1.1.2. Terms of Reference as provided by EFSA

The Terms of Reference, as provided by EFSA are as follows:

ToR 1: Keep updated the list of biological agents being notified in the context of a technical dossier to EFSA Units such as Feed, Pesticides, Food Ingredients and Packaging (FIP) and Nutrition, for intentional use directly or as sources of food and feed additives, food enzymes and plant protection products for safety assessment.

ToR 2: Review taxonomic units previously recommended for the QPS list and their qualifications when new information has become available. The latter is based on a review of the updated literature aiming at verifying if any new safety concern has arisen that could require the removal of the taxonomic unit from the list, and to verify if the qualifications still efficiently exclude safety concerns.

ToR 3: (Re) assess the suitability of new taxonomic units notified to EFSA for their inclusion in the QPS list. These microbiological agents are notified to EFSA and requested by the Feed Unit, the FIP Unit, the Nutrition Unit or by the Pesticides Unit.

1.2. Interpretation of the Terms of Reference

The absence of acquired genes conferring resistance to clinically relevant antimicrobials is a qualification9 applied to all QPS bacterial TUs. The verification of such qualification is under the remit of the Unit conducting the safety assessment of the organism notified to EFSA for market authorisation, and is therefore done at strain level (EFSA BIOHAZ Panel, 2017a).

In June 2017 (EFSA BIOHAZ Panel, 2017b), the BIOHAZ Panel has agreed to exclude Escherichia coli and any species of the genus Streptomyces from QPS evaluation within this mandate.

In June 2018 (EFSA BIOHAZ Panel, 2018b), the BIOHAZ Panel clarified that the qualification ‘for production purpose only’ implies the absence of viable cells of the production organism in the final product and can also be applied for food and feed products based on microbial biomass.

2. Data and methodologies

2.1. Data

Only valid TUs covered by the relevant international committees on the nomenclature for microorganisms are considered for the QPS assessment.

In reply to ToR 3, (re)assessment of the suitability of TUs notified within the time period covered by this Statement (from October 2018 to March 2019) is carried out. The literature review considered the identification, the body of knowledge, the potential safety concerns, and the knowledge on acquired antimicrobial resistance (AMR). Relevant databases, such as PubMed, Web of Science, Cases Database, CAB Abstracts or Food Science Technology Abstracts (FSTA) and Scopus, were searched. More details on the search strategy, search keys, and approach are described in Appendix A.

In reply to ToR 2, concerning the revision of the TUs previously recommended for the QPS list and their qualifications, an extensive literature search (ELS) was conducted as described in Appendices B and C.

2.2. Methodologies

2.2.1. Evaluation of a QPS recommendation for taxonomic units notified to EFSA

In response to ToR 1, the EFSA Units were asked to update the list of biological agents being notified to EFSA. A total of 47 notifications were received between October 2018 and March 2019, of which 32 were for a feed additive, 2 for food enzymes, 10 for novel foods and 3 for plant protection products (Table 1).

Table 1.

Notifications received by EFSA, per risk assessment area and by biological group, from October 2018 and March 2019

Risk assessment area	Not evaluated in this Statement		Evaluated in this Statement	Total
Biological group	Already QPS	Excluded in QPSa
Feed additives	15	13	4	32
Bacteria	9	4	4	17
Filamentous fungi	0	9	0	9
Yeasts	6	0	0	6
Novel foods	2	5	3	10
Bacteria	0	5	1	4
Yeasts	2	0	0	2
Algae	0	0	2	2
Plant protection products	2	1	0	3
Bacteria	1	0	0	1
Filamentous fungi	0	1	0	1
Viruses	1	0	0	1
Food enzymes, food additives and flavourings	0	1	1	2
Bacteria	0	0	1	1
Filamentous fungi	0	1	0	1
Total	19	20	8	47

QPS: qualified presumption of safety.

^aThe number includes 11 notifications of filamentous fungi excluded from QPS evaluation in the 2013 QPS Opinion and 9 notifications of E. coli (bacterium) already excluded in the Panel Statement adopted in December 2016 (EFSA BIOHAZ Panel et al., 2017a).

In response to ToR 3, out of the 47 notifications, 19 were related to TUs that already had QPS status and did not require further evaluation. Of the remaining 26 notifications, 20 were related to TUs not evaluated for a QPS status for the following reasons:

• eleven notifications related to filamentous fungi, which were excluded from QPS evaluations in the follow‐up of a recommendation of the QPS 2013 and 2016 updates (EFSA BIOHAZ Panel, 2013, 2014, 2016);

• nine notifications related to E. coli, which were recently excluded from the current mandate by the BIOHAZ Panel.

The TUs corresponding to the remaining eight notifications evaluated for a possible QPS recommendation:

• Sphingomonas elodea, Gluconobacter frateurii, Corynebacterium ammoniagenes, Corynebacterium casei, Burkholderia ubonensis, Phaeodactylum tricornutum, Microbacterium foliorum and Euglena gracilis, all evaluated for the first time.

The notifications received by EFSA, per risk assessment area, by biological group from October 2018 to March 2019, are presented in Table 1.

2.2.2. Use of MLT in the context of the yeasts and Bacillus taxonomic units

To explore the potential application of a machine learning technique (MLT) for screening papers in the context of the QPS project the performances of such technique were assessed against the previous batch of papers retrieved for the Bacillus and Yeasts taxonomic units.

To that purpose, the DistillerAI Toolkit included in the DistillerSR online software was used.

DistillerAI ‘Preview and Rank’ function was used mapping the papers from ‘Title screening’ to ‘Article evaluation’. The SVM algorithm with 100% training set and 100% references to preview was used and the references were subsequently tagged. The algorithm was trained on the combined results of the 2 reviewers in the QPS rounds from 1 June 2016 to 31 December 2017. This is considered a conservative approach since, in the case of conflicts among the experts, the algorithm considers the paper as relevant.

The MLT predicted screening results on the batch of papers corresponding to the period January–June 2018 were obtained and compared with the results obtained by the two reviewers in the real exercise.

The results of the exercise showed that, in the case of yeasts, MLT had around 88% and 80% of sensitivity and specificity, respectively, while, in the case of Bacillus, MLT had 100% and about 82% of sensitivity and specificity, respectively. Moreover, it was found that in case of using the MLT algorithm as a reviewer in parallel with a human reviewer, in both projects no information relevant for the QPS status would have been missed.

On the basis of these results and considering the high number of papers retrieved for both yeasts and Bacillus in the context of the QPS exercise, it was decided to use the MLT in parallel with a human reviewer to screen the current batch of papers in these two TUs.

As expected, considering its specificity, the application of the MLT algorithm resulted in a high number of potentially relevant papers at the end of the screening phase. On the other hand, the algorithm did not miss any paper identified as potentially relevant by the human reviewer.

2.2.3. Monitoring of new safety concerns related to the QPS list

The aim of the ELS carried out in response to ToR 2 (review of the recommendations for the QPS list and specific qualifications) was to identify any publicly available studies reporting on safety concerns for humans, animals or the environment caused by QPS organisms since the previous QPS review (i.e. publications from July to December 2018). For a detailed protocol of the process and search strategies, refer to Appendices B and C.

After removal of duplicates, 3,710 records were submitted to the title screening step, which led to the exclusion of 3,179 of them. The remaining 531 records were found eligible for the Title and abstract screening step, which led to the exclusion of 39 of these. Of the 492 articles that finally reached the Article evaluation step (full text), 85 were considered to be relevant for the QPS project.

The flow of records from their identification by the different search strategies (as reported in Appendix C) to their consideration as potentially relevant papers for QPS is shown in Table 2.

Table 2.

Flow of records by search strategy

Species	No of papers
	Title screening step	Title/abstract screening step	Article evaluation step (screening for potential relevance)a	Article evaluation step (identification of potential safety concerns)
Bacteria	2,244	258	224	11
Bacillus spp.	804	199	199b	2
Geobacillus stearothermophilus			0	0
Bifidobacterium spp.	206	21	3	1
Carnobacterium divergens			0	0
Corynebacterium glutamicum	45	0	0	0
Gluconobacter oxydans	115	1	0	0
Xanthomonas campestris			0	0
Lactobacillus spp.	555	22	12	3
Lactococcus lactis	173	6	4	3
Leuconostoc spp.	68	5	4	1
Microbacterium imperiale			0	0
Oenococcus oeni	24	1	0	0
Pasteuria nishizawae			0	0
Pediococcus spp.	146	2	2	1
Propionibacterium spp.	27	0	0	0
Streptococcus thermophilus	81	1	0	0
Viruses	108	0	0	0
Alphaflexiviridae	39	0	0	0
Potyviridae				0
Baculoviridae	69	0	0	0
Yeasts	1,358	273	268 b	30 c
Candida famata (teleomorph = Debaryomyces hansenii)	1,358	273	268	10
Candida kefyr (teleomorph = Kluyveromyces marxianus)				16
Candida pelliculosa (synonymus = Pichia anomala) (teleomorph = Wickerhamomyces anomalus)				6
Candida utilis (teleomorph = Lindnera jadinii)				1
Hanseniaspora uvarum				1
Saccharomyces cerevisiae including Saccharomyces boulardii				8
Kluyveromyces lactis				1
Schizosaccharomyces pombe				1
Total	3,710	531	492	85
Excluded	3,179	39	407

^aRelevant references in Appendix D.

^bThe relatively high number of hits is linked to the procedure followed for the screening of references using machine learning techniques (MLT) in parallel with experts’ selection.

^c30 articles describing 45 studies related to different yeast species. In one case, there was no reference to any particular species.

3. Assessment

3.1. Taxonomic units evaluated during the previous QPS mandate and re‐evaluated in the current Statement

None.

3.2. Taxonomic units to be evaluated for the first time

3.2.1. Bacteria

3.2.1.1. Burkholderia ubonensis

Identity

B. ubonensis is a species with Standing in Nomenclature. B. ubonensis belongs to the Burkholderia cepacia complex (Martina et al., 2018) that was first described as Burkholderia uboniae (Yabuuchi et al., 2000) and later on renamed as B. ubonensis (Anonymous, 2000).

Body of knowledge

There are only a limited number of scientific papers published on this TU. B. ubonensis as well as other Burkholderia species, produce lipases, which are used in a broad range of industrial applications.

Safety concerns

B. ubonensis is considered to be non‐pathogenic, although its virulence potential has not been extensively tested. It appears to be innocuous after a subcutaneous challenge to mice (Price et al., 2017).

Whole genome characterisation of strains within the species revealed the presence of numerous genes encoding secondary, biologically active, metabolites such as polyketides, non‐ribosomal peptides, quinolines and pyrrolnitrins (Loveridge et al., 2017). Some produce monobactams (Imada et al., 1981), bulgecins (Horsman et al., 2017), which enhance the bactericidal effect of β‐lactams on Gram negative bacteria, and bacteriocin‐like compounds (Marshall et al., 2010).

Antimicrobial resistance aspects

Different features, namely the external membrane structure and an inducible class A β‐lactamase contributes to the intrinsic resistance to diverse antibiotics (Rhodes and Schweizer, 2016)

Conclusions on a recommendation for the QPS list

B. ubonensis cannot be recommended for the QPS list due to its ability to generate biologically active compounds and limited body of knowledge.

3.2.1.2. Corynebacterium ammoniagenes

Identity

C. ammoniagenes is a species with Standing in Nomenclature. It was first described by Cooke and Keith (1927) as Brevibacterium ammoniagenes, an urea‐splitting bacterium isolated from the human intestinal tract. It was transferred to the genus Corynebacterium by Collins (1987).

Body of knowledge

C. ammoniagenes is used for the industrial production of nucleotides, nucleosides and riboflavin (Koizumi et al., 2000; Serrano et al., 2017).

C. ammoniagenes derived single‐cell protein10 can also be used as a non‐conventional protein source in animal diet such as in broilers (An et al., 2018) and growing pigs (Wang et al., 2013), without any negative effects on blood, bone characteristics or meat quality (An et al., 2018).

Safety concerns

No information was found in relation to pathogenicity of the organism, including when used for production of SCP for feed (Oliveira et al., 2017).

Antimicrobial resistance aspects

No information was found in relation to the AMR.

Conclusions on a recommendation for the QPS list

C. ammoniagenes can be recommended for QPS list with the qualification ‘for production purposes only’.

3.2.1.3. Corynebacterium casei

Identity

C. casei was first isolated from the surface of a smear‐ripened cheese (Brennan et al., 2001) and is a valid species according to the list of prokaryotic names with Standing in Nomenclature.

Body of knowledge

There are only a limited number of articles published on this TU. Most of the relevant articles described the microbial communities and activities in ripened cheese where C. casei contributes as a spontaneous contaminant to the production of the desired organoleptic properties (Brennan et al., 2002; Hannon et al., 2004; Mounier et al., 2005; Rea et al., 2007; Bockelmann, 2011; Cogan et al., 2014; Bertuzzi et al., 2017).

Safety concerns

One article described the identification of C. casei among 57 bacterial strains isolated during the screening of blood samples of patients with cardiovascular diseases and not having any active infection (Dinakaran et al., 2012), so no proven connection with the ongoing diseases was identified.

Antimicrobial resistance aspects

No information was found in the literature.

Conclusions on a recommendation for the QPS list

C. casei cannot be recommended to the QPS list due to lack of body of knowledge.

3.2.1.4. Gluconobacter frateurii

Identity

It is a species with Standing in Nomenclature (Mason and Claus, 1989). It was separated from Acetobacter in 1989. It has been classified as a separate cluster in the Gluconobacter genus according to 16S rRNA gene sequence analysis (Sievers et al., 1995) and to restriction analysis of 16S‐23S rDNA internal transcribed spacer regions (Malimas et al., 2006).

Body of knowledge

There are only a limited number of articles published on this TU. It can produce high amounts of fructans and can efficiently produce glyceric acid from raw glycerol (Poljungreed and Boonyarattanakalin, 2018). It is an obligate aerobic acetic acid bacterium that is found as a spontaneous contaminant as part of the microbial community in some food processes (e.g. vinegar production and kefir, cocoa and coconut water fermentation) (Korsak et al., 2015; Ho et al., 2018). Although these foods are consumed and exposure of humans and animals to this microorganism is expected, the scientific knowledge on this species is limited.

Safety concerns

The literature search retrieved no hits on virulence, pathogenicity or disease related to this TU.

Antimicrobial resistance aspects

No information is available in the scientific literature.

Conclusions on a recommendation for the QPS list

Gl. frateurii cannot be recommended for the QPS list due to lack of body of knowledge.

3.2.1.5. Microbacterium foliorum

Identity

M. foliorum is a valid species name according to the List of Prokaryotic Names with Standing in Nomenclature. It was first isolated as a plant associated bacterium (Behrendt et al., 2001).

Body of knowledge

There are only a limited number of articles published on this TU. M. foliorum is a saprophytic organism that may become endophytic and allow cruciferous plants to grow on oil seep soils, due to its capacity to process hydrocarbons such as catechol, toluene, naphthalene, octanol and others (Lumactud et al., 2016, 2017). In addition, it is, as a spontaneous contaminant, part of the microbiota involved in production of flavour and aroma in surface‐ripened cheeses, such as Limburger and Munster, due to its caseinolytic, aminopeptidase and deaminase activities (Deetae et al., 2007, 2009). Although these foods are consumed and exposure of humans to this microorganism is expected, the scientific knowledge on this species is still limited.

Safety concerns

M. foliorum has been associated with clinical samples. Laffineur et al. (2003) reported the isolation of 30 Microbacterium spp. specimens ‘during the past decades’ one of which was classified as M. foliorum, with no further indication of its source or the conditions of the patient. Gneiding et al. (2008) identified 50 isolates as belonging to the genus Microbacterium in a survey of bacteria obtained during the previous 5 years from pathological samples and processed in a German Coryneform reference laboratory. Unfortunately, only the origin of the samples was reported, with no indication of the patient conditions or the procedures to which they were subjected. Of these isolates, seven were ascribed to M. foliorum, their origin being wound swabs (5), pleural fluid (1) and blood (1).

A toxicological study was made on lysed cultures from a single strain without adverse effects, but the results cannot be extrapolated to the species (Kim et al., 2018a).

Antimicrobial resistance aspects

One paper (Gneiding et al., 2008) reported susceptibility profiles of M. foliorum but without reference to transmissibility of resistances.

Conclusions on a recommendation for the QPS list

M. foliorum cannot be recommended for the QPS list due to lack of body of knowledge.

3.2.1.6. Sphingomonas elodea

Identity

S. elodea was described as a Gram‐negative bacterium, initially named as Pseudomonas elodea (Kang et al., 1982). This species has not been taxonomically validated according to the List of Prokaryotic Names with Standing in Nomenclature (LPSN) (Euzéby, 2013) ( http://www.bacterio.net/-allnamesdl.html) and the modifications that appear in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) (Oren and Garrity, 2015).

Body of knowledge

Not applicable.

Safety concerns

Not applicable.

Antimicrobial resistance aspects

Not applicable.

Conclusions on a recommendation for the QPS list

S. elodea could not be assessed for a possible QPS recommendation because it is not a valid species.

3.2.2. Algae

3.2.2.1. Euglena gracilis

Identity

E. gracilis belongs to the genus Euglena, phototrophic euglenoid flagellates possessing complex chloroplasts. The taxonomy of E. gracilis and closely related species has not been amended so far based on molecular phylogenetic analyses (Zakryś et al., 2017). The whole genome of the E. gracilis strain Z1 was recently sequenced (Ebenezer et al., 2019).

Body of knowledge

There are an extended amount of scientific papers published on this TU. E. gracilis is found in many freshwater habitats, especially in shallow eutrophic ponds. The species is able to synthesise biotechnologically relevant compounds such as polyunsaturated fatty acids, vitamins, β‐glucans and tyrosine used in cosmetics and food supplements. E. gracilis is also used for bioremediation of heavy metals in contaminated water and as a toxicity bioindicator (Krajčovič et al., 2015).

E. gracilis biomass, generally based on dried cells, is used as a feed additive in aquaculture and in animal feed as well as in human food (Suzuki, 2017). Food products containing E. gracilis are marketed in Japan as cookies, cereal bars and nutritional drinks.

Safety concerns

Using dried preparations of non‐viable E. gracilis, no genotoxicity was observed in bacterial reverse mutation and mammalian micronucleus tests. Moreover, subchronic toxicity tests in rats did not show any adverse effect and a no‐observed‐adverse‐effect‐level (NOAEL) of 50,000 ppm was determined. (Simon et al., 2016).

Literature searches did not provide any evidence for a safety concern for human or animal health for any use of E. gracilis.

Antimicrobial resistance aspects

Not applicable.

Conclusions on a recommendation for the QPS list

E. gracilis may be recommended for the QPS list with the qualification ‘for production purposes only’.

3.2.2.2. Phaeodactylum tricornutum

Identity

The unicellular, photosynthetic alga P. tricornutum was first isolated and described as a new species by the end of the 19th century (Bohlin, 1897). It is a pennate diatom (class Bacillariophyceae) and the only known species in the genus. It is an unusual diatom since it is pleiomorphic (fusiform, oval or triradiate morphology) and production of a silica frustule is facultative. Identification has recently been made by 18S rRNA gene sequencing (Demirel, 2016; Haro et al., 2017). The genome of one isolate has been sequenced (Bowler et al., 2008; Rastogi et al., 2018).

Body of knowledge

There are an extended amount of scientific papers published on the TU. P. tricornutum has been isolated from marine or brackish locations, often in benthic habitats, and appears to have a global distribution (De Martino et al., 2007). However, it is not a dominant species of algal communities and relatively little is known about its ecology.

It is of biotechnological interest, for studies within algal physiology and metabolism and as a model test species in toxicology. The potential of P. tricornutum as a source of biomass for biofuels, antimicrobial agents, health‐promoting substances and food or feed components in general is subject to intensive study (Bajpai, 2016; Garcia et al., 2017; Haro et al., 2017; Shah et al., 2018). For example, the alga produces many compounds of high nutritional value, such as essential fatty acids and carotenoids (Zhang et al., 2015; Garcia et al., 2017). It has also been shown that P. tricornutum biomass can be used as a feed supplement (Skrede et al., 2011; Cerezuela et al., 2012; Sørensen et al., 2016).

Although several scientific studies are available, there appears to be no history of use of P. tricornutum in food or feed in practice, since no evidence was found that P. tricornutum, or substances produced by it, have yet been commercialised and/or widely consumed.

Safety concerns

The literature search did not reveal any studies reporting infection or intoxication by P. tricornutum.

Niccolai et al. (2017) tested in vitro toxicity of water‐ or methanol extracts of P. tricornutum (strain F&M‐M40) and found them to be toxic to fibroblasts. Neumann et al. (2018a) showed cytotoxic effects on human peripheral mononuclear cells.

In another study, Neumann et al. (2018b) investigated the bioavailability and toxicity of disrupted and freeze‐dried cells of P. tricornutum in a mouse model and no adverse effect was reported.

Recent studies suggest that P. tricornutum can produce β‐N‐methylamino‐l‐alanine (BMAA) (Réveillon et al., 2016; Lage et al., 2019), which is a neurotoxin produced by certain cyanobacteria, diatoms and dinoflagellates. BMAA occurs ubiquitously in marine environments and can be transferred in food‐webs to fish and seafood (Salomonsson et al., 2015; Lance et al., 2018).

Antimicrobial resistance aspects

Not applicable.

Conclusions on a recommendation for the QPS list

P. tricornutum is not recommended for QPS status based on the lack of a safe history of use in the food chain and on its potential for production of bioactive compounds with toxic effects.

3.3. Monitoring of new safety concerns related to organisms on the QPS list

The summaries of the evaluation of the possible safety concerns for humans, animals or the environment caused by QPS organisms described and published since the previous ELS (i.e. between January and June 2018, as described in Appendices B and C) and the references selected as potentially relevant for the QPS exercise (Appendix D) for each of the TUs or groups of TUs that are part of the QPS list (Appendix E) are presented below.

3.3.1. Gram‐positive non‐sporulating bacteria

3.3.1.1. Bifidobacterium spp.

A search for papers potentially relevant for the QPS consideration of Bifidobacterium spp. and Carnobacterium divergens 11 provided 206 references. The analysis of their title left 21 articles; the rest were discarded because they did not deal with safety concerns. Three articles were found relevant for the QPS consideration of Bifidobacterium spp. at the level of title and abstract screening. For one article, the full text was not available (conference proceedings) (Magistrelli et al., 2018). For one of the two other articles (Suzuki et al., 2018), the study was not considered because of study design shortcomings in relation to QPS assessment. For the third article (Kim et al., 2018a,b), no safety concern was identified for both Bifidobacterium bifidum and Bifidobacterium longum.

Based on the available evidence as described above, the QPS status of Bifidobacterium spp. is not changed.

3.3.1.2. Carnobacterium divergens

A search for papers potentially relevant for the QPS consideration of Bifidobacterium spp. and Carnobacterium divergens provided 206 references. The analysis of their title/abstracts left 21 articles; the rest were discarded because they did not deal with safety concerns. No article arrived to the final stage for this TU. Consequently, the QPS status of C. divergens is not changed.

3.3.1.3. Corynebacterium glutamicum

A search for papers potentially relevant for the QPS consideration of Corynebacterium glutamicum provided 45 references. No paper reached the final selection phase, therefore no new safety concerns were identified.

3.3.1.4. Lactobacillus spp.

A search for papers potentially relevant for the QPS consideration of any of the 35 Lactobacillus species included in the list provided 555 references. Analysis of their title left 22 articles; the rest were discarded because they did not deal with safety concerns. Inspection of their abstracts allowed the selection of 12 papers that might raise safety concerns. After analysing the full texts, nine were considered to be not relevant, while the other three described safety concerns linked to L. paracasei (Kao et al., 2018) and L. rhamnosus (Naqvi et al., 2018; Zeba et al., 2018). In one case (Kao et al., 2018), no indication is provided on how the identification of the pathogen was done, while in Zeba et al. (2018) an automated phenotypical method was used, known not to reliably identify lactobacilli. Patients in the three studies (Kao et al., 2018; Naqvi et al., 2018; Zeba et al., 2018) presented with clear predisposing conditions.

Based on the available evidence as described above, the QPS status of the lactobacilli involved in the reported cases and, by extension, of all others included in the QPS list, is not changed.

3.3.1.5. Lactococcus lactis

A search for papers potentially relevant for the QPS consideration of Lactococcus lactis provided 173 references. Analysis of their title/abstracts left six articles; the rest were discarded because they did not deal with safety concerns. Analysis of the abstracts allowed selection of four papers that might raise safety concerns. After analysing the full texts, one was found not to deal with safety concerns (Kato et al., 2018) while the other three (Chen et al., 2018; Kaboré et al., 2018; Shimizu et al., 2019) did. In two of them (Chen et al., 2018; Kaboré et al., 2018) phenotypical methods for identification of the etiological agent were used, which are known not to be reliable for this species. In addition, two of the papers (Chen et al., 2018; Shimizu et al., 2019) described cases in which clear predisposing conditions were identified. Shimizu et al. (2019) describes a patient suffering from a cholangiocarcinoma that blocked bile evacuation, reason why a bilioduodenal catheter was inserted. This might have been the source of the L. lactis cholangitis (predisposing condition) that appeared just 2 days later. The last reference (Kaboré et al., 2018) described the microbiota associated to 125 cases of endodontitis, out of which five contained L. lactis as part of a polymicrobial community, which is suggestive of colonisation of the oral cavity rather than aetiology of the infections.

Based on the available evidence as described above, the QPS status of Lactococcus lactis is not changed.

3.3.1.6. Leuconostoc citreum, Leuconostoc lactis, Leuconostoc mesenteroides, Leuconostoc pseudomesenteroides

A search for papers potentially relevant for the QPS consideration of Leuconostoc spp. and Microbacterium imperiale ¹¹ provided 68 references. The analysis of their title left five articles; the rest were discarded because they did not deal with safety concerns. One paper lacked information on the identification procedures used to identify the infectious agents. Four papers arrived to the full text phase. Three were immediately excluded as they were not dealing with a safety concern or with these TUs. In the article of Menegueti et al. (2018), a 67‐year‐old female patient with chronic Chagas disease was submitted to several surgical interventions, and presented complications such as hypotension and hypoxemia. The identification of cultures was performed using automated phenotypical method known not to reliably identify Leuconostoc spp.

The safety concern identified was linked to severe underlying health conditions and the identification of strain was not reliable due to the use of phenotypic tests. Consequently the QPS status of Leuconostoc spp. is not changed.

3.3.1.7. Microbacterium imperiale

A search for papers potentially relevant for the QPS consideration of Leuconostoc and Microbacterium imperiale ¹¹ provided 68 references. The analysis of their title left five articles; one paper lacked information on the identification procedures used to identify the infectious agents. The rest were discarded because they did not deal with safety concerns. None of the remaining four articles dealt with this TU. Consequently, the QPS status of M. imperiale is not changed.

3.3.1.8. Oenococcus oeni

A search for papers potentially relevant for the QPS consideration of Oenococcus oeni and Pasteuria nishizawae ¹¹ provided 24 references. The analysis of their title/abstracts left one article for consideration. No paper reached the final selection phase, no new safety concern was found. Consequently, the QPS status of O. oeni is not changed.

3.3.1.9. Pasteuria nishizawae

A search for papers potentially relevant for the QPS consideration of Oenococcus oeni and Pasteuria nishizawae ¹¹ provided 24 references. The analysis of their title/abstracts left one article for consideration. No paper reached the final selection phase, no new safety concern was found. Consequently, the QPS status of P. nishizawae is not changed.

3.3.1.10. Pediococcus spp.

A search for papers potentially relevant for the QPS consideration of Pediococcus spp. provided 146 references. The analysis of their title left two articles (Chen et al., 2018; Singla et al., 2018). The latter does not describe a safety concern. Chen et al. (2018) describes an infectious endocarditis caused by L. lactis subsp. Lactis and Pediococcus pentosaceus. P. pentosaceus was identified after levofloxacin treatment in blood cultures, but the phenotypical method used for its identification is known not to be reliable for this species. In addition, the papers describe a case in which clear predisposing conditions were identified.

Consequently, the QPS status of Pediococcus spp. is not changed.

Pediococcus dextrinicus (Coster and White, 1964) Back, 1978, species, the name was changed to Lactobacillus dextrinicus (Coster and White, 1964) Haakensen et al., 2009, comb. nov. It will be updated in the QPS list.

3.3.1.11. Propionibacterium spp.

A search for papers potentially relevant for the QPS consideration of Propionibacterium spp. provided 27 references. Following the analysis of their title/abstracts, no articles were selected for the final selection phase, thus no new safety concerns were identified. Consequently, the QPS status of Propionibacterium spp. is not changed.

3.3.1.12. Streptococcus thermophilus

A search for papers potentially relevant for the QPS consideration of Streptococcus thermophilus provided 81 references. The analysis of their title/abstracts left one article that did not reach the final selection phase; thus, no new safety concern was found. Therefore, the QPS status of S. thermophilus is not changed.

3.3.2. Gram‐positive spore‐forming bacteria

3.3.2.1. Bacillus spp.

A search for papers potentially relevant for the QPS consideration of Bacillus spp. and Geobacillus stearothermophilus ¹¹ provided 804 references. The analysis of their titles left 199 articles. A first round has been conducted using the MLT as a co‐assistant; the second round of analysis of the 199 articles by two experts left two articles for more in‐depth analysis. The remaining articles were discarded because they did not deal with safety concerns. The paper of Osman et al. (2018) concerns the enterotoxinogenic potential of Bacillus pumilus strains, a topic covered by the current qualification for Bacillus spp. The paper of Tsonis et al. (2018) concerns the description of a cerebral abscess due to Bacillus subtilis in an immunocompetent patient. For both papers there were methodological shortcomings on the identification methods of the bacterial strains and therefore the data presented were not included for further assessment.

The ELS did not come up with any information that would change the status of the Bacillus species included in the QPS list.

3.3.2.2. Geobacillus stearothermophilus

A search for papers potentially relevant for the QPS consideration of Bacillus spp. and Geobacillus stearothermophilus ¹¹ provided 804 references. The analysis of their titles/abstract left 199 articles. None was dealing with this species. Consequently, the QPS status Geobacillus stearothermophilus is not changed.

3.3.3. Gram‐negative bacteria

3.3.3.1. Gluconobacter oxydans

A search for papers potentially relevant for the QPS consideration of Gluconobacter oxidans and Xanthomonas campestris ¹¹ provided 115 references. The analysis of their titles left one article; the rest were discarded because they did not deal with safety concerns. No paper reached the final selection phase for this TU. Consequently, the QPS status of G. oxydans is not changed.

3.3.3.2. Xanthomonas campestris

A search for papers potentially relevant for the QPS consideration of Gluconobacter oxidans and Xanthomonas campestris ¹¹ provided 115 references. The analysis of their titles left one article; the rest were discarded because they did not deal with safety concerns. No paper reached the final selection phase for this TU. Consequently, the QPS status of X. campestris is not changed.

3.3.4. Yeasts

A search for papers potentially relevant for the QPS consideration of the yeasts’ species included in the QPS list provided 1,358 references. The analysis of their titles left 268 articles. A first round has been conducted using the MLT as a co‐assistant; 229 of these were immediately excluded because they were not in English or because they were not dealing with safety concerns. Thus, the ELS identified 30 articles relevant for different yeast species with QPS status (please refer to Appendix D for the complete list of references).

These 30 articles included description of 45 studies related to different yeast species with QPS status, of which 16 referred to Candida kefyr (teleomorph = Kluyveromyces marxianus) (Afsarian et al., 2018; Awad et al., 2018; Bharathi, 2018; Diba et al., 2018; García‐Agudo et al., 2018; Hasan and Yassein, 2018; Kaur et al., 2018; Kesmen et al., 2018; Khedri et al., 2018; Nagy et al., 2018; Okmen et al., 2018; Omran and Mansori, 2018; de Paula et al., 2018; Sadrossadati et al., 2018; Shokohi et al., 2018; Simi et al., 2019), 8 to Saccharomyces cerevisiae including Saccharomyces boulardii (corresponding to 7 articles: Lazo‐Vélez et al., 2018; Ruelle et al., 2018; Hasan and Yassein, 2018; Kara et al., 2018; Kesmen et al., 2018; Ochiai et al., 2018; Teblick et al., 2018), 10 to Candida famata (teleomorph = Debaryomyces hansenii) (Afsarian et al., 2018; Alobaid and Khan, 2018; Awad et al., 2018; Cen et al., 2018; Das et al., 2018; Diba et al., 2018; Hasan and Yassein, 2018; Kesmen et al., 2018; de Paula et al., 2018; Simi et al., 2019), 6 to Candida pelliculosa (synonymus = Pichia anomala, teleomorph = Wickerhamomyces anomalus) (Ahmadsah et al., 2018; Arendrup et al., 2018; Cen et al., 2018; Jung et al., 2018; Kesmen et al., 2018; Soman et al., 2018), 1 to Candida utilis (teleomorph = Lindnera jadinii) (Treguier et al., 2018), 1 to Hanseniaspora uvarum (Kesmen et al., 2018), 1 Kluyveromyces lactis (Kesmen et al., 2018) and 1 to Schizosaccharomyces pombe (Kesmen et al., 2018). One of these articles was considered relevant (Pfaller et al., 2018) to evaluate since it presented new data on antimycotic MIC breakpoints for azoles but it is not associated to any specific yeast TU.

For the other yeast species with QPS status, no relevant studies were identified through the ELS.

Methodological problems were identified in 30 out of those 45 studies (corresponding to 22 articles – see Table 3). In 17 of those 30 studies (corresponding to 11 articles: Alobaid and Khan, 2018; Awad et al., 2018; Bharathi, 2018; de Paula et al., 2018; Hasan and Yassein, 2018; Kaur et al., 2018; Okmen et al., 2018; Ruelle et al., 2018; Soman et al., 2018; Treguier et al., 2018; Simi et al., 2019), a problem was found in respect to the methodology used for identity confirmation of the microorganism, therefore the value of these results and conclusions were very limited. In 2 of those 30 studies (corresponding to 1 article, Awad et al., 2018), the problem was due to a lack of information regarding the source attribution. In 19 studies (corresponding to 15 articles: Afsarian et al., 2018; Alobaid and Khan, 2018; Bharathi, 2018; Diba et al., 2018; Das et al., 2018; Hasan and Yassein, 2018; Jung et al., 2018; Kara et al., 2018; Khedri et al., 2018; Kaur et al., 2018; Nagy et al., 2018; Omran and Mansori, 2018; Sadrossadati et al., 2018; Shokohi et al., 2018; Teblick et al., 2018), the problem was due to predisposing factors in the exposed subject.

Table 3.

Articles that arrived to the evaluation phase (final step of the extensive literature search) for the QPS status yeasts group (30 articles with 45 studies)

Relevant to the QPS exercise a , b	Articles not describing safety concerns	19 articles (32 studies)	Any methodological problem identified?	Yes	11 articles (17 studies)	Methodology used for identity confirmation of the microorganism	11 articles (17 studies)	Alobaid and Khan (2018); Awad et al. (2018); Bharathi (2018); de Paula et al. (2018); Hasan and Yassein (2018); Kaur et al. (2018); Okmen et al. (2018); Ruelle et al. (2018); Simi et al. (2019); Soman et al. (2018); Treguier et al. (2018)
						Reliability of the source attribution	1 article (2 studies)	Awad et al. (2018)
						Misuse of the microorganism	None
						Predisposing factors in the exposed subjects	4 articles (6 studies)	Alobaid and Khan (2018); Bharathi (2018); Hasan and Yassein (2018); Kaur et al. (2018)
						Other reasons	1 article (2 studies)	de Paula et al. (2018)
				No	8 articles (15 studies)			Arendrup et al. (2018); Ahmadsah et al. (2018); Cen et al. (2018); García‐Agudo et al. (2018); Lazo‐Vélez et al. (2018); Kesmen et al. (2018); Ochiai et al. (2018); Pfaller et al. (2018)
	Articles dealing with safety concerns	11 articles (13 studies)	Any methodological problem identified?	Yes	11 articles (13 studies)	Methodology used for identity confirmation of the microorganism	None
						Reliability of the source attribution	None
						Misuse of the microorganism	None
						Predisposing factors in the exposed subjects	11 articles (13 studies)	Afsarian et al. (2018); Diba et al. (2018); Das et al. (2018); Jung et al. (2018); Kara et al. (2018); Khedri et al. (2018); Nagy et al. (2018); Omran and Mansori (2018); Sadrossadati et al. (2018); Shokohi et al. (2018); Teblick et al. (2018)
						Other reasons	None
				No	None

^aPlease refer to Appendix D for the complete list of references.

^bNumber of references (articles and studies) indicated for each step.

For 32 of those 45 studies, no potential safety concern was reported, while a potential safety concern was described in the other 13 studies (corresponding to 11 articles: Diba et al., 2018; Das et al., 2018; Jung et al., 2018; Kara et al., 2018; Khedri et al., 2018; Nagy et al., 2018; Omran and Mansori, 2018; Sadrossadati et al., 2018; Afsarian et al., 2018; Shokohi et al., 2018; Teblick et al., 2018): 3 for C. famata (Das et al., 2018; Diba et al., 2018; Shokohi et al., 2018), 7 for C. kefyr (Afsarian et al., 2018; Diba et al., 2018; Khedri et al., 2018; Nagy et al., 2018; Omran and Mansori, 2018; Sadrossadati et al., 2018; Shokohi et al., 2018), 1 for C. pelliculosa (Jung et al., 2018) and 2 for Saccharomyces cerevisiae (Kara et al., 2018; Teblick et al., 2018). All these studies reported isolation of the QPS yeasts from opportunistic infections in patients with serious predisposing factors.

In short, the ELS did not identify any information that would change the status for the yeast species included in the QPS list.

3.3.5. Viruses used for plant protection

3.3.5.1. Alphaflexiviridae

A search for papers potentially relevant for the QPS consideration of Alphaflexiviridae and Potyviridae ¹¹ provided 39 references. No paper reached the final selection phase, thus no new safety concern was found.

3.3.5.2. Potyviridae

A search for papers potentially relevant for the QPS consideration of Alphaflexiviridae and Potyviridae ¹¹ provided 39 references. No paper reached the final selection phase, thus no new safety concern was found.

3.3.5.3. Baculoviridae

A search for papers potentially relevant for the QPS consideration of Baculoviridae provided 69 references. No article reached the final selection phase, thus no new safety concern was found.

The ELS did not come up with any information that would change the current QPS status of any of the above virus families.

4. Conclusions

ToR 1: Keep updated the list of biological agents being notified, in the context of a technical dossier to EFSA Units (such as Feed, Food Ingredients and Packaging (FIP), Nutrition Unit and Pesticides Unit), for intentional use in feed and/or food or as sources of food and feed additives, enzymes and plant protection products for safety assessment:

• Between October 2018 and March 2019, the list was updated with 47 notifications that were received by EFSA, of which 32 were for feed additives, 2 for food enzymes, food additives and flavourings, 10 for novel foods and 3 for plant protection products.

ToR 2: Review taxonomic units previously recommended for the QPS list and their qualifications when new information has become available:

• In relation to the results of the monitoring of possible new safety concerns related to the QPS list, there were no results that justify removal of any TU from the QPS list or changes in their respective qualifications.

ToR 3: (Re)assess the suitability of taxonomic units notified to EFSA not present in the current QPS list for their inclusion in that list:

• The TUs corresponding to 19 out of the 47 notifications received, already had a QPS status.

• Of the 28 notifications without a QPS status, 11 notifications related to filamentous fungi which were excluded from QPS activities in the follow‐up of a recommendation of the QPS 2013 update (EFSA BIOHAZ Panel, 2013, 2014, 2016), 9 notifications related to E. coli, which was recently excluded from the current mandate by the BIOHAZ Panel (EFSA BIOHAZ Panel, 2018a).

• The remaining eight TUs, Burkholderia ubonensis, Corynebacterium ammoniagenes, Corynebacterium casei, Euglena gracilis, Gluconobacter frateurii, Microbacterium foliorum, Phaeodactylum tricornutum and Sphingomonas elodea, were evaluated for potential QPS recommendation for the first time.

5. Recommendations

• Burkholderia ubonensis cannot be recommended for the QPS list due to its ability to generate biologically active compounds and limited of body of knowledge.

• Corynebacterium ammoniagenes can be recommended for QPS list status with the qualification ‘for production purposes only’.

• Corynebacterium casei cannot be recommended to the QPS list due to lack of body of knowledge.

• Euglena gracilis may be recommended for the QPS list with the qualification ‘for production purposes only’.

• Gluconobacter frateurii cannot be recommended to the QPS list due to lack of body of knowledge.

• Microbacterium foliorum cannot be recommended to the QPS list due to lack of body of knowledge.

• Phaeodactylum tricornutum cannot be recommended for QPS status, based on the lack of a safe history of use in the food chain and on its potential production of bioactive compounds with toxic effects based on the lack of a safe history of use in the food chain and a limited knowledge on its potential production of bioactive compounds with toxic effects.

• Sphingomonas elodea could not be assessed for a possible QPS recommendation because it is not a valid species.

Pediococcus dextrinicus (Coster and White, 1964) Back, 1978 species has been changed to Lactobacillus dextrinicus (Coster and White, 1964) Haakensen et al., 2009, comb. nov.

This new QPS recommendation will be included as an addition to the list of QPS status recommended biological agents (EFSA BIOHAZ Panel, 2016), published both as an update to the Scientific Opinion (EFSA BIOHAZ Panel, 2016) and as supporting information available on the Knowledge Junction at https://doi.org/10.5281/zenodo.1146566.

Glossary and Abbreviations

Antimicrobial compounds

Antibiotics, bacteriocins and/or small peptides with antimicrobial activity

AMR

antimicrobial resistance

BIOHAZ

EFSA Panel on Biological Hazards

BMAA

β‐N‐methylamino‐l‐alanine

ELS

Extensive Literature Search

FIP

EFSA Food Ingredients and Packaging Unit

FSTA

Food Science Technology Abstracts

GMM

genetically modified microorganism

IJSEM

International Journal of Systematic and Evolutionary Microbiology

LPSN

List of Prokaryotic Names with Standing in Nomenclature

MLT

machine learning technique

NOAEL

no‐observed‐adverse‐effect‐level

QPS

qualified presumption of safety

PPP

plant protection product

SCP

single cell protein

ToR

Terms of Reference

TU

taxonomic unit

WG

Working Group

Appendix A – Search strategy followed for the (re)assessment of the suitability of TUs notified to EFSA not present in the current QPS list for their inclusion in the updated list (reply to ToR 3)

1.

Burkholderia ubonensis

A literature search was performed in PubMed database using the search term: “Burkholderia ubonensis”: 18 citations were identified and screened.

Corynebacterium ammoniagenes

A literature search was performed in PubMed database using the search term: “Corynebacterium ammoniagenes”: 112 citations were identified and screened.

Corynebacterium casei

A literature search was performed in Scopus database using the search term: “Corynebacterium casei”: 125 citations were identified and screened from which, 40 were relevant for the assessment.

Euglena gracilis

Pub Med search; “Euglena gracilis”, taxonomy; 88 references screened for relevance; two selected: Zakryś et al. (2017) for taxonomy and Krajčovič et al. (2015) for body of knowledge as review article

A literature search was performed in PubMed database using the search term:

• “E. gracilis” biotechnology 49 references.

• “E. gracilis” biomass 26 references.

• “E. gracilis” and safety, 5 references, Simon et al. (2016) as relevant.

• “E. gracilis” and illness: no references.

• “E. gracilis” and hospitalization: no references

• “E. gracilis” and infectivity: 6 references, Ebenezer et al. (2019) as relevant.

• “E. gracilis” and tox: 1 reference, not relevant.

• “E. gracilis” and health: 30 references, none relevant.

• “E. gracilis” and environment and concern: 1 reference, not relevant.

• “E. gracilis” and environment: 245 references, Suzuki et al. (2018) as relevant.

Gluconobacter frateurii

A literature search was performed in Web of Science core collection and in Pubmed using the search term: “Gluconobacter frateurii”: 74 and 45 citations were identified and screened respectively.

Microbacterium foliorum

A search using the species name “Microbacterium foliorum” in the Web of Science core collection provided 29 hits.

Phaeodactylum tricornutum

Literature searches were performed in the Web of Science Core Collection. Using only the species name “Phaeodactylum tricornutum” gave 2,917 references. Using refined search terms gave the following numbers of references, which were all scanned at title level:

• “Phaeodactylum tricornutum” and (species characterization): 55 references.

• “Phaeodactylum tricornutum” and taxonom*: 55 references.

• “Phaeodactylum tricornutum” and ecology: 50 references.

• “Phaeodactylum tricornutum” and (secondary metabolit*): 17 references.

• “Phaeodactylum tricornutum” and infect*: 14 references.

• “Phaeodactylum tricornutum” and toxi*: 299 references.

• “Phaeodactylum tricornutum” and safety: 14 references.

• “Phaeodactylum tricornutum” and BMAA: 3 references.

Sphingomonas elodea

A literature search was performed in PubMed database using the search term: “Sphingomonas elodea”: 26 hits were identified and screened, mainly dealing with the gellan gun production and the molecular characterisation of the enzymes and genes involved in this production.

Appendix B – Protocol for Extensive literature search (ELS), relevance screening, and article evaluation for the maintenance and update of list of QPS‐recommended biological agents (reply to ToR 2)

1.

The following protocol for extensive literature search (ELS) will be used in the context of the EFSA self‐task mandate on the list of QPS‐recommended biological agents intentionally added to the food or feed (EFSA‐Q‐2016‐00684).

B.1. Description of the process

An ELS of studies related to safety concerns for humans, animals, plants and/or the environment of microorganisms recommended for the Qualified Presumption of Safety (QPS) 2019 list will be performed.

The process will be performed according to the following main steps:

• ELS for potentially relevant citations;

• Relevance screening to select the citations identified by the literature search, based on titles and abstract and then full‐text;

• Evaluation of articles according to pre‐specified categories of possible safety concerns;

• Discussion between experts to come to collective expert evaluation of the outcome, reflected in the QPS Opinion and Panel Statements.

Considering the purpose of the QPS approach, a broad search will be performed.

The review questions will be broken down into key elements using the PECO conceptual model:

• Population of interest (P);

• Exposure of interest (E);

• Comparator (C);

• Outcomes of interest (O).

B.1.1. Objective

The aim is to identify any publicly available studies reporting on safety concerns for humans, animals or the environment caused by microorganisms on the QPS recommended list (see Appendix E).

B.1.2. Target population

The populations of interest are humans, animals, plants and the environment.

B.1.3. Exposure

Citations must report on at least one species included in one of the five groups of named species specified in the EFSA QPS recommended list of the QPS 2016 update ((see Table A.1 in Appendix A to (EFSA BIOHAZ Panel, 2017a)):

1. Gram‐positive non‐spore‐forming bacteria;

2. Gram‐positive spore‐forming bacteria;

3. Gram‐negative bacteria;

4. Viruses used for plant protection;

5. Yeasts.

In more detail:

• aGram‐positive non‐spore forming bacteria:

Bifidobacterium adolescentis, Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Carnobacterium divergens, Corynebacterium glutamicum, Lactobacillus acidophilus, Lactobacillus amylolyticus, Lactobacillus animalis, Lactobacillus amylovorus, Lactobacillus alimentarius, Lactobacillus aviaries, Lactobacillus brevis, Lactobacillus buchneri, Lactobacillus casei, Lactobacillus cellobiosus, Lactobacillus collinoides, Lactobacillus coryniformis, Lactobacillus crispatus, Lactobacillus curvatus, Lactobacillus delbrueckii, Lactobacillus diolivorans Lactobacillus farciminis, Lactobacillus fermentum, Lactobacillus gallinarum, Lactobacillus gasseri, Lactobacillus helveticus, Lactobacillus hilgardii, Lactobacillus johnsonii, Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus mucosae, Lactobacillus panis, Lactobacillus paracasei, Lactobacillus paraplantarum, Lactobacillus pentosus, Lactobacillus plantarum, Lactobacillus pontis, Lactobacillus reuteri, Lactobacillus rhamnosus, Lactobacillus sakei, Lactobacillus salivarius, Lactobacillus sanfranciscensis, Lactococcus lactis, Leuconostoc citreum, Leuconostoc lactis, Leuconostoc mesenteroides, Leuconostoc pseudomesenteroides, Microbacterium imperiale, Oenococcus oeni, Pasteuria nishizawae, Pediococcus acidilactici, Pediococcus dextrinicus, Pediococcus parvulus, Pediococcus pentosaceus, Propionibacterium freudenreichii, Propionibacterium acidopropionici, Streptococcus thermophilus;

• bGram‐positive spore‐forming bacteria:

Bacillus amyloliquefaciens, Bacillus atrophaeus, Bacillus clausii, Bacillus coagulans, Bacillus flexus, Bacillus fusiformis, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus mojavensis, Bacillus pumilus, Bacillus smithii, Bacillus subtilis, Bacillus vallismortis, Geobacillus stearothermophilus;

• cGram‐negative bacteria:

Gluconobacter oxydans; Xanthomonas campestris;

• dViruses used for plant protection:

Plant viruses (Family): Alphaflexiviridae, Potyviridae;

Insect viruses (Family): Baculoviridae;

• eYeasts:

Candida cylindracea, Debaryomyces hansenii, Hanseniaspora uvarum, Kluyveromyces lactis, Kluyveromyces marxianus, Komagataella pastoris, Lindnera jadinii, Ogataea angusta, Saccharomyces bayanus, Saccharomyces cerevisiae, Saccharomyces pastorianus, Schizosaccharomyces pombe, Wickerhamomyces anomalus, Xanthophyllomyces dendrorhous.

For the yeast species, as previously, the name of the teleomorphic form is used in the list of QPS species, when available. Important synonyms and older names were also included in the searches. For instance, names of the anamorphic growth forms were included, when such a form is known:

• Debaryomyces hansenii: anamorph Candida famata;

• Hanseniaspora uvarum: anamorph Kloeckera apiculata;

• Kluyveromyces lactis: anamorph Candida spherica;

• Kluyveromyces marxianus: anamorph Candida kefyr;

• Komagataella pastoris: synonym Pichia pastoris;

• Lindnera jadinii: synonyms Pichia jadinii, Hansenula jadinii, Torulopsis utilis, anamorph Candida utilis;

• Ogataea angusta: synonym Pichia angusta;

• Saccharomyces cerevisiae: synonym Saccharomyces boulardii;

• Saccharomyces pastorianus: synonym Saccharomyces carlsbergensis;

• Wickerhamomyces anomalus: synonyms Hansenula anomala, Pichia anomala, Saccharomyces anomalus, anamorph Candida pelliculosa;

• Xanthophyllomyces dendrorhous: anamorph Phaffia rhodozyma.

B.1.4. Comparator

It is expected that the prevalent study designs will be case reports or case series and studies based on surveys or isolate collections. The remaining study designs may include: studies using laboratory isolates; randomised controlled trials, field trials or experimental designs in the laboratory; experimental designs in live animals with a deliberate disease challenge; observational study designs; animal or insect models; investigations to identify or to understand the causes of safety concerns (e.g. identification, characterisation of toxic factors, virulence mechanisms); studies to demonstrate beneficial effects but with reporting of unwanted side‐effects.

Since it is expected that in the majority of the study designs relevant for the review question, the comparator will not be available, the latter will not be included as a key element in the search strategy.

B.1.5. Outcomes of interest

The outcomes of interest to this ELS are:

Question 1:

• potential harms;

• safety issues;

• virulence or infectivity;

• intoxication.

Question 2:

• (acquired/intrinsic) antimicrobial resistance (AMR) covering phenotypic and genotypic aspects.

The QPS concept does not address hazards linked to the formulation or processing of the products based on biological agents added into the food or feed chain. Neither the safety of users handling the product nor the genetic modifications are taken into account.

B.1.6. Identification of the review questions

The following research questions will be addressed:

• Is there evidence of any safety concerns, including virulence features and toxin production, for humans, animals, plants and/or the environment associated with microbial species currently recommended for the QPS list since the previous QPS review (i.e. published from June 2016 until June 2019)?

• Is there evidence related to the presence or absence of antimicrobial resistance or antimicrobial resistance genes for the same microbial species published during the same time period?

B.2. Eligibility criteria for study selection

The selection of studies relevant to questions 1 and 2 will be performed applying the eligibility criteria described in Table B.1 below.

Table B.1.

Eligibility criteria for questions 1 and 2

	Criteria
Study design	No specific type of study design will be used to include/exclude relevant studies, although it is expected that the prevalent study designs will be case reports or case series and studies based on surveys or isolate collections
Study characteristics:	No exclusion will be based on study characteristics
Population	Humans, animals, plants, environment
Exposure	Studies must report on at least one TU as identified in Section B.1.3
Outcome of interest	Outcomes as listed in Section B.1.5
Language	English
Time	From June 2016 until end June 2019
Publication type	Primary research studies and secondary studies reporting previously unpublished primary studies

B.3. Literature searches

Searches will be conducted in a range of relevant information sources to identify any evidence of safety concerns and AMR regarding the target microbial species.

Considering the results of the previous QPS exercise, to handle the high number of studies identified in each group, 20 search strategies were prepared: three for yeasts, one for insect viruses, one for plant viruses, 13 for Gram‐positive bacteria and two for Gram‐negative bacteria according to named species specified by EFSA in the QPS recommended list of the QPS 2016 update (see Table A.1 in Appendix A to (EFSA BIOHAZ Panel, 2017a)).

The 20 subgroups of target microbial species will be searched separately.

Each search strategy will comprise two elements: the search terms (Section B.3.1) and the information sources (Section B.3.2) to be searched.

B.3.1. Search terms

The search strategies used to identify studies are given in Appendix C.

Each strategy will comprise two key elements:

• Target microbial species as described in Section B.1.3 (‘Exposure’)

• Safety issues as described in Section B.1.5 (‘Outcomes’).

In order to maximise the sensitivity of the search for the species for which the number of overall publications in the relevant time period is expected to be low, the search strategy will not include outcome‐related terms.

The population of interest (humans, animals, plants or the environment) will not be included as a key element in the search strategies, as it is often not explicitly described within a title or abstract. It would also have been difficult to describe adequately such a broad population using title/abstract words and/or subject headings. Population information will be captured at the time of evaluating the articles (see Section B.1 above).

Search terms for safety issues were identified in close collaboration with the information specialist; example of such terms, are the following: ‘toxin*’, ‘disease*’, ‘infection*’, ‘clinical*’, ‘virulen*’, ‘antimicrobial resistan*’, ‘endocarditis’.

The 20 subgroups of target microbial species will be entered on separate search lines. The search line for each group will be combined with the safety terms individually.

The searches will not be limited by language or study design.

The review period will be from June 2016 to June 2019.

B.3.2. Information sources searched

The same information sources used for the previous QPS exercise (EFSA BIOHAZ Panel et al., 2017a) will be searched for studies reporting safety concerns regarding the target microbial species (see Table B.2 below).

Table B.2.

Information sources to be searched to identify relevant studies

Information source	Interface
Web of Science Core Collection	Web of Science, Thomson Reuters 2018
CAB Abstracts	Web of Science, Thomson Reuters 2018
BIOSIS Citation Index	Web of Science, Thomson Reuters 2018
MEDLINE	Web of Science, Thomson Reuters 2018
Food Science Technology Abstracts (FSTA)	Web of Science, Thomson Reuters 2018

Search results will be downloaded from the information sources and imported into EndNote^® X8 bibliographic management software. For each of the 20 species groups, within‐group removal of duplicate entries will be done in EndNote^® X8. Following uploading of the species groups into the DistillerSR12 online software, removal of duplicates will again be undertaken, using the Duplicate Detection feature.

B.4. Study selection and article evaluation

To identify potentially relevant studies to be included in the review the studies will be selected by a three ‐step procedure using the DistillerSR online software.

The results of the different phases of the study selection process will be reported in a flowchart as recommended in the PRISMA statement on preferred reporting items for systematic reviews and meta‐analyses (Moher et al., 2009).

B.4.1. Screening for potential relevance at title level

Articles will initially be screened at title level in parallel by two Working Group (WG) expert reviewers and, if needed, EFSA staff.

If the information in the title is not relevant for the research objectives, the article will not proceed to the next step (Section B.4.2).

Articles that will be excluded during screening at this step will be stored in Distiller SR.

In case of doubts or divergences between the reviewers, the paper will proceed to step 2.

B.4.2. Screening for potential relevance at title and abstract level

The articles passing the first step will undergo a screening at abstract level in parallel by two experts.

If the information in title and abstract is not relevant for the research objectives, the article will not proceed to the next step (Section B.4.3).

Articles that will be excluded during screening at this step will be stored in Distiller SR.

In case of doubts or divergences between the reviewers, the paper will proceed to step 3.

B.4.3. Article evaluation

The aim of this step will be to confirm that the article is relevant for the QPS project and, in case it is, to evaluate it. It will be carried out at full text level.

The articles passing the second step will undergo a validation procedure carried out by two experts. One reviewer will initially be tasked with the evaluation of a paper. The evaluation will be then forwarded to another reviewer for the validation of the appraisal received.

In case of disagreement with the initial appraisal, the second reviewer will write down their comments. The reviewers will initially try to solve the disagreement. In case this will not be possible, the conflicting information will be presented for collective expert evaluation of the ELS outcome (see Section B.5).

If the information contained in the article is not relevant for the research objectives, the article will not be evaluated. Articles that will not be considered relevant will be stored in Distiller SR.

B.4.3.1. Questions for study selection and article evaluation

STEP 1 (Screening for potential relevance):

Question 1: Is the full‐text available, in English and dealing with safety concerns?

• Yes: Include and continue to Article evaluation form;

• Full text not available: Exclude;

• Full text not in English: Exclude;

• Full text in English but not dealing with safety concerns: Exclude.

STEP 2 (Article evaluation):

Question 2: Identification of the microorganisms

• The article will be characterised in terms of the microorganisms involved;

  Single choice question: the Experts will identify the microorganism/s described in the article. In case more than one microorganism is described in the paper, the form will be repeated for each microorganism.

Question 3: Is there any “methodological” problem identified in the paper under consideration?

• No problems identified;

• Yes some problems were identified.

Question 4: Which “methodological” problems were identified in the paper under consideration? (this question will appear in case in question 3 the option “Yes some problems were identified” will be selected)

• Methodology used for identity confirmation of the microorganism;

• Reliability of the source attribution;

• Misuse of the microorganism (e.g. parenteral exposure);

• Predisposing factors in the exposed subjects;

• Others.

When one of the above options will be selected a dedicated free text box will appear to describe the problem identified.

Question 5: Is there any safety concern identified? (this question will appear in case in question 3 the option “No problems identified” will be selected)

• No safety concerns identified;

• Yes some safety concerns were identified.

Question 6: Which safety concerns were identified? (this question will appear in case in question 5 the option “Yes some safety concerns were identified” will be selected)

• On human health;

• On animal health;

• On the environment;

• On AMR;

• On other aspects.

When one of the above options will be selected a dedicated free text box will appear to describe the safety concern identified.

Question 7: Overall, is there any information that could potentially lead to a change in the QPS status of the microorganism? (this question will appear in case in question 5 the option “Yes some safety concerns were identified” will be selected)

• No;

• Yes.

In case the option “Yes” will be selected a dedicated free text box will appear to describe the information that could potentially lead to a change in the QPS status of the microorganism.

B.5. Collective expert evaluation of the ELS outcome and presentation in the QPS opinion

The overall results of the searches and evaluations of individual articles will be presented in tabular format for each group/subgroup and species. These results will be further evaluated collectively by the working group and the outcome will be reflected in the QPS opinion.

B.6. Update of the process

The literature search, study selection and collective expert evaluation will be repeated every 6 months.

References

EFSA BIOHAZ Panel (EFSA Panel on Biological Hazards), 2017. Scientific Opinion on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA. EFSA Journal 2017;15(1):4664, 177 pp. https://doi.org/10.2903/j.efsa.2017.4664

Moher D, Liberati A, Tetzlaff J, Altman DG and the PRISMA Group, 2009. Preferred reporting items for systematic reviews and meta‐analyses: the PRISMA statement. PLoS Med, 6, e1000097.

Appendix C – Search strategies for the maintenance and update of list of QPS‐recommended biological agents (reply to ToR 2)

1.

Gram‐Positive Non‐Spore‐forming Bacteria

Bifidobacterium spp.

String for species
“Bifidobacterium adolescentis” OR “Bifidobacterium animalis” OR “Bifidobacterium bifidum” OR “Bifidobacterium breve” OR “Bifidobacterium longum” OR “B adolescentis” OR “B animalis” OR “B bifidum” OR “B breve” OR “B longum”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antibiotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR bacteremia OR bacteraemia OR toxin*
3. Type of disease	endocarditis OR abscess OR meningitis
4. Mortality/Morbidity	clinical* OR death* OR morbidit* OR mortalit* OR disease* OR illness*
5. Disease Risk	opportunistic OR virulen*

Carnobacterium divergens

String for species
“Carnobacterium divergens” OR “C divergens”
OUTCOME	String
6. Antimicrobial/Antibiotic/Antimycotic	Not applied
7. Infection/Bacteremia/Fungemia/Sepsis	Not applied
8. Type of disease	Not applied
9. Mortality/Morbidity	Not applied
10. Disease Risk	Not applied

Corynebacterium glutamicum

String for species
“Corynebacterium glutamicum” OR “C glutamicum” OR “Brevibacterium lactofermentum” OR “B lactofermentum”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antibiotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR bacteremia OR bacteraemia OR toxin* OR pathogen*
3. Type of disease	Not applied
4. Mortality/Morbidity	clinical* OR death* OR morbidit* OR mortalit* OR disease* OR illness*
5. Disease Risk	opportunistic OR virulen*

Lactobacillus spp.

String for species
“Lactobacillus acidophilus” OR “Lactobacillus amylolyticus” OR “Lactobacillus amylovorus” OR “Lactobacillus alimentarius” OR “Lactobacillus animalis” OR “Lactobacillus aviaries” OR “Lactobacillus brevis” OR “Lactobacillus buchneri” OR “Lactobacillus casei” OR “Lactobacillus zeae” OR “Lactobacillus cellobiosus” OR “Lactobacillus coryniformis” OR “Lactobacillus crispatus” OR “Lactobacillus curvatus” OR “Lactobacillus delbrueckii” OR “Lactobacillus diolivorans” OR “Lactobacillus farciminis” OR “Lactobacillus fermentum” OR “Lactobacillus gallinarum” OR “Lactobacillus gasseri” OR “Lactobacillus helveticus” OR “Lactobacillus hilgardii” OR “Lactobacillus johnsonii” OR “Lactobacillus kefiranofaciens” OR “Lactobacillus kefiri” OR “Lactobacillus mucosae” OR “Lactobacillus panis” OR “Lactobacillus collinoides” OR “Lactobacillus paracasei” OR “Lactobacillus paraplantarum” OR “Lactobacillus pentosus” OR “Lactobacillus plantarum” OR “Lactobacillus pontis” OR “Lactobacillus reuteri” OR “Lactobacillus rhamnosus” OR “Lactobacillus sakei” OR “Lactobacillus salivarius” OR “Lactobacillus sanfranciscensis” OR “L acidophilus” OR “L amylolyticus” OR “L amylovorus” OR “L alimentarius” OR “L animalis” OR “L aviaries” OR “L brevis” OR “L buchneri” OR “L casei” OR “L zeae” OR “L cellobiosus” OR “L coryniformis” OR “L crispatus” OR “L curvatus” OR “L delbrueckii” OR “L diolivorans” OR “L farciminis” OR “L fermentum” OR “L gallinarum” OR “L gasseri” OR “L helveticus” OR “L hilgardii” OR “L johnsonii” OR “L kefiranofaciens” OR “L kefiri” OR “L mucosae” OR “L panis” OR “L collinoides” OR “L paracasei” OR “L paraplantarum” OR “L pentosus” OR “L plantarum” OR “L pontis” OR “L reuteri” OR “L rhamnosus” OR “L sakei” OR “L salivarius” OR “L sanfranciscensis”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antibiotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR bacteremia OR bacteraemia OR toxin*
3. Type of disease	endocarditis OR abscess OR meningitis
4. Mortality/Morbidity	Not applied
5. Disease Risk	opportunistic OR virulen*

Lactococcus lactis

String for species
“Lactococcus lactis” OR “L lactis”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antibiotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR bacteremia OR bacteraemia OR toxin*
3. Type of disease	endocarditis OR abscess OR meningitis
4. Mortality/Morbidity	clinical* OR death* OR morbidit* OR mortalit* OR disease* OR illness*
5. Disease Risk	opportunistic OR virulen*

Leuconostoc spp.

String for species
“Leuconostoc mesenteroides” OR “Leuconostoc lactis” OR “Leuconostoc pseudomesenteroides” OR “Leuconostoc citreum” OR “L mesenteroides” OR “L lactis” OR “L pseudomesenteroides” OR “L citreum”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antibiotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR bacteremia OR bacteraemia OR toxin*
3. Type of disease	Not applied
4. Mortality/Morbidity	clinical* OR death* OR morbidit* OR mortalit* OR disease* OR illness*
5. Disease Risk	opportunistic OR virulen*

Microbacterium imperiale

String for species
“Microbacterium imperiale” OR “M imperiale”
OUTCOME	String
6. Antimicrobial/Antibiotic/Antimycotic	Not applied
7. Infection/Bacteremia/Fungemia/Sepsis	Not applied
8. Type of disease	Not applied
9. Mortality/Morbidity	Not applied
10. Disease Risk	Not applied

Oenococcus spp.

String for species
“Oenococcus oeni” OR “O oeni”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	Not applied
2. Infection/Bacteremia/Fungemia/Sepsis	Not applied
3. Type of disease	Not applied
4. Mortality/Morbidity	Not applied
5. Disease Risk	Not applied

Pasteuria nishizawae

String for species
“Pasteuria nishizawae” OR “P nishizawae”
OUTCOME	String
11. Antimicrobial/Antibiotic/Antimycotic	Not applied
12. Infection/Bacteremia/Fungemia/Sepsis	Not applied
13. Type of disease	Not applied
14. Mortality/Morbidity	Not applied
15. Disease Risk	Not applied

Pediococcus spp.

String for species
“Pediococcus pentosaceus” OR “Pediococcus dextrinicus” OR “Pediococcus acidilactici” OR “Pediococcus parvulus” OR “P pentosaceus” OR “P dextrinicus” OR “P acidilactici” OR “P parvulus”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	Not applied
2. Infection/Bacteremia/Fungemia/Sepsis	Not applied
3. Type of disease	Not applied
4. Mortality/Morbidity	Not applied
5. Disease Risk	Not applied

Propionibacterium spp.

String for species	Number papers retrieved and notes
“Propionibacterium acidipropionici” OR “Propionibacterium freudenreichii” OR “P acidipropionici” OR “P freudenreichii”	176
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	Not applied
2. Infection/Bacteremia/Fungemia/Sepsis	Not applied
3. Type of disease	Not applied
4. Mortality/Morbidity	Not applied
5. Disease Risk	Not applied

Streptococcus thermophilus

String for species
“Streptococcus thermophilus” OR “S thermophilus” “Streptococcus thermophilus” OR “S thermophilus”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antibiotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR bacteremia OR bacteraemia OR toxin*
3. Type of disease	Not applied
4. Mortality/Morbidity	clinical* OR death* OR morbidit* OR mortalit* OR disease* OR illness*
5. Disease Risk	opportunistic OR virulen*

Gram‐positive spore‐forming bacteria

Bacillus spp.

String for species
“Bacillus amyloliquefaciens” OR “Bacillus coagulans” OR “Bacillus clausii” OR “Bacillus atrophaeus” OR “Bacillus flexus” OR “Bacillus fusiformis” OR “Lysinibacillus fusiformis” OR “Bacillus licheniformis” OR “Bacillus lentus” OR “Bacillus mojavensis” OR “Bacillus megaterium” OR “Bacillus vallismortis” OR “Bacillus smithii” OR “Bacillus subtilis” OR “Bacillus pumilus” OR “Geobacillus stearothermophilus” OR “B amyloliquefaciens” OR “B coagulans” OR “B clausii” OR “B atrophaeus” OR “B flexus” OR “B fusiformis” OR “L fusiformis” OR “B licheniformis” OR “B lentus” OR “B mojavensis” OR “B megaterium” OR “B vallismortis” OR “B smithii” OR “B subtilis” OR “B pumilus” OR “G stearothermophilus”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antibiotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR bacteremia OR bacteraemia OR toxin*
3. Type of disease	endocarditis OR abscess OR meningitis
4. Mortality/Morbidity	Not applied
5. Disease Risk	opportunistic OR virulen*

Gram‐negative bacteria

Gluconobacter oxydans

String for species
“Gluconobacter oxydans” OR “G oxydans”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	Not applied
2. Infection/Bacteremia/Fungemia/Sepsis	Not applied
3. Type of disease	Not applied
4. Mortality/Morbidity	Not applied
5. Disease Risk	Not applied

Xanthomonas campestris

String for species
“Xanthomonas campestris” OR “X campestris”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	Not applied
2. Infection/Bacteremia/Fungemia/Sepsis	Not applied
3. Type of disease	Not applied
4. Mortality/Morbidity	Not applied
5. Disease Risk	Not applied

Yeasts

TUs without keywords for OUTCOME

String for species
“Candida cylindracea” OR “Debaryomyces hansenii” OR “Candida famata” OR “Hanseniaspora uvarum” OR “Kloeckera apiculata” OR “Ogataea angusta” OR “Pichia angusta” OR “Saccharomyces bayanus” OR “Saccharomyces pastorianus” OR “Saccharomyces carlsbergensis” OR “Wickerhamomyces anomalus” OR “Hansenula anomala” OR “Pichia anomala” OR “Saccharomyces anomalus” OR “Candida pelliculosa” OR “Xanthophyllomyces dendrorhous” OR “Phaffia rhodozyma” OR “C cylindracea” OR “D hansenii” OR “C famata” OR “H uvarum” OR “K apiculata” OR “O angusta” OR “P angusta” OR “S bayanus” OR “S pastorianus” OR “S carlsbergensis” OR “W anomalus” OR “H anomala” OR “P anomala” OR “S anomalus” OR “C pelliculosa” OR “X dendrorhous” OR “P rhodozyma”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	Not applied
2. Infection/Bacteremia/Fungemia/Sepsis	Not applied
3. Type of disease	Not applied
4. Mortality/Morbidity	Not applied
5. Disease Risk	Not applied

TUs with keywords for OUTCOME except for type of disease and morbility/mortality

String for species
“Kluyveromyces lactis” OR “Candida spherica” OR “Kluyveromyces marxianus” OR “Candida kefyr” OR “Komagataella pastoris” OR “Pichia pastoris” OR “Lindnera jadinii” OR “Pichia jadinii” OR “Hansenula jadinii” OR “Torulopsis utilis” OR “Candida utilis” OR “Schizosaccharomyces pombe” OR “K lactis” OR “C spherica” OR “K marxianus” OR “C kefyr” OR “K pastoris” OR “P pastoris” OR “L jadinii” OR “P jadinii” OR “H jadinii” OR “T utilis” OR “C utilis” OR “S pombe”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antimycotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR fungemia OR fungaemia OR mycos*
3. Type of disease	Not applied
4. Mortality/Morbidity	Not applied
5. Disease Risk	opportunistic OR virulen*

TUs with keywords for OUTCOME except for type of disease

String for species
“Saccharomyces cerevisiae” OR “Saccharomyces boulardii” OR “Scerevisiae” OR “Sboulardii”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	antimicrobial resistan* OR antimycotic resistan* OR antimicrobial susceptibil*
2. Infection/Bacteremia/Fungemia/Sepsis	infection* OR abscess* OR sepsis* or septic* OR fungemia OR fungaemia OR mycos*
3. Type of disease	Not applied
4. Mortality/Morbidity	clinical* OR death* OR morbidit* OR mortalit* OR disease* OR illness*
5. Disease Risk	opportunistic OR virulen*

Viruses used for plant protection

Alphaflexiviridae

String for species
“Alphaflexiviridae” OR “Potyviridae”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	Not applied
2. Infection/Bacteremia/Fungemia/Sepsis	necros*
3. Type of disease	Not applied
4. Mortality/Morbidity	mortalit* OR safety concern* OR “health hazard”
5. Disease Risk	virulen*

Baculoviridae

String for species
“Nuclear polyhedrosis virus” OR “granulovirus” OR “baculoviridae”
OUTCOME	String
1. Antimicrobial/Antibiotic/Antimycotic	Not applied
2. Infection/Bacteremia/Fungemia/Sepsis	Not applied
3. Type of disease	“nuclear polyhedrosis” OR granulosis
4. Mortality/Morbidity	mortalit* OR safety concern* OR “health hazard”
5. Disease Risk	Not applied

Appendix D – References selected from the ELS exercise as relevant for the QPS for searches from July to December 2018 (reply to ToR 2)

Gram‐Positive Non‐Sporulating Bacteria

Bifidobacterium spp.

Kim MJ, Seockmo K, Sun Young K, Hyun Ha L, Hui J, Sini K, Rui L, Johnston TV, Myeong Soo P and Geun Eog J, 2018. Safety evaluations of Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI. International Journal of Molecular Sciences, 19, 1422–1422.

Magistrelli L, Amoruso A, Milner AV, Mogna L, Cantello R, Pane M and Comi C, 2018. Effects of probiotic bacterial strains on peripheral inflammation in Parkinson's disease. European Journal of Neurology, 25, 428–428.

Suzuki S, Campos‐Alberto E, Morita Y, Yamaguchi M, Toshimitsu T, Kimura K, Ikegami S, Katsuki T, Kohno Y and Shimojo N, 2018. Low Interleukin 10 Production at Birth Is a Risk Factor for Atopic Dermatitis in Neonates with Bifidobacterium Colonization. International Archives of Allergy and Immunology, 177, 342–349.

Carnobacterium divergens

None

Corynebacterium glutamicum

None

Lactobacilli spp.

Arokiyaraj S, Seo SS, Kwon M, Lee JK and Kim MK, 2018. Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study. Scientific Reports, 8, 15479.

Costa RL, Moreira J, Lorenzo A and Lamas CC, 2018. Infectious complications following probiotic ingestion: a potentially underestimated problem? A systematic review of reports and case series. Bmc Complementary and Alternative Medicine, 18, 329.

Esaiassen E, Hjerde E, Cavanagh JP, Pedersen T, Andresen JH, Rettedal SI, Stoen R, Nakstad B, Willassen NP and Klingenberg C, 2018. Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants. Frontiers in Pediatrics, 6, 347.

Griff PM, Schleper A, Lynch CA, Sun Y and Butler TR, 2018. CHRONIC ADMINISTRATION OF PROBIOTIC L. RHAMNOSUS AFFECTS ANXIETY‐LIKE BEHAVIOR IN A MODEL OF ALCOHOL USE DISORDER VULNERABILITY. Alcoholism‐Clinical and Experimental Research, 42, 35A–35A.

Hojsak I, Fabiano V, Pop TL, Goulet O, Zuccotti GV, Cokugras FC, Pettoello‐Mantovani M and Kolacek S, 2018. Guidance on the use of probiotics in clinical practice in children with selected clinical conditions and in specific vulnerable groups. Acta Paediatrica, 107, 927–937.

Kao, B‐Z, Lin H‐J, Chen M‐Y, Wu C‐S, Lin S‐T, Lee M‐H, Lai Y‐X and Hu P‐J, 2018. Lactobacillus paracasei as cause of liver abscess: Case report. Journal of Gastroenterology and Hepatology, 33, 433–433.

Kawai K, Kamochi R, Oiki S, Murata K and Hashimoto W, 2018. Probiotics in human gut microbiota can degrade host glycosaminoglycans. Scientific Reports, 8, 10674.

Maillet F, Passeron A, Podglajen I, Ranque B and Pouchot J, 2018. Lactobacillus delbrueckii urinary tract infection in a male patient. Medecine et maladies infectieuses.

Naqvi SSB, Nagendra V and Hofmeyr A, 2018. Probiotic related Lactobacillus rhamnosus endocarditis in a patient with liver cirrhosis. IDCases, 13, e00439–e00439.

Okba A, Shahin R, Attallah A, Sheha D, Mkawy M and Farag M, 2018. ROLE OF INTESTINAL MICROBIOTA IN CARDIOVASCULAR DISEASE RISK IN END STAGE RENAL DISEASE PATIENTS. Nephrology Dialysis Transplantation, 33, 573–574.

Zawistowska‐Rojek A and Tyski S, 2018. Are Probiotic Really Safe for Humans? Polish Journal of Microbiology, 67, 251–258.

Zeba F, Yirerong J, Assali M, Tewary G and Noska A, 2018. A Double Whammy: Lactobacillus acidophilus Bacteremia and Subsequent Lactobacillus rhamnosus Prosthetic Valve Infective Endocarditis in an Elderly Diabetic Patient. Rhode Island Medical Journal (2013), 101, 32–35.

Lactococcus lactis

Chen F, Zhang Z and Chen J, 2018. Infective endocarditis caused by Lactococcus lactis subsp. lactis and Pediococcus pentosaceus: A case report and literature review. Medicine, 97, e13658–e13658.

Kabore WAD, Dembele R, Bagre TS, Konate A, Boisrame S, Chevalier V, Konsem T, Traore AS and Barro N, 2018. Characterization and Antimicrobial Susceptibility of Lactococcus lactis Isolated from Endodontic Infections in Ouagadougou, Burkina Faso.” Dentistry Journal, 6.

Kato Y, Kanayama M, Yanai S, Nozawa H, Kanauchi O and Suzuki S, 2018. Safety evaluation of excessive intake of Lactococcus lactis subsp. lactis JCM 5805: a randomized, double‐blind, placebo‐controlled, parallel‐group trial. Food and Nutrition Sciences, 9, 403–419.

Shimizu A, Hase R, Suzuki D, Toguchi A, Otsuka Y, Hirata N and Hosokawa N, 2019. Lactococcus lactis cholangitis and bacteremia identified by MALDI‐TOF mass spectrometry: A case report and review of the literature on Lactococcus lactis infection. Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy, 25, 141–146.

Leuconostoc spp.

Chen F, Zhang Z and Chen J, 2018. Infective endocarditis caused by Lactococcus lactis subsp. lactis and Pediococcus pentosaceus: A case report and literature review. Medicine, 97, e13658–e13658.

Coton M, Lebreton M, Salas ML, Garnier L, Navarri M, Pawtowski A, Le Blay G, Valence F, Coton E and Mounier J, 2018. Biogenic amine and antibiotic resistance profiles determined for lactic acid bacteria and a propionibacterium prior to use as antifungal bioprotective cultures. International Dairy Journal, 85, 21–26.

Menegueti MG, Gaspar GG, Laus AM, Basile‐Filho A, Bellissimo‐Rodrigues F and Auxiliadora‐Martins M, 2018. Bacteremia by Leuconostoc mesenteroides in an immunocompetent patient with chronic Chagas disease: a case report. BMC Infectious Diseases, 18.

Mussano F, Ferrocino I, Gavrilova N, Genova T, Dell'Acqua A, Cocolin L and Carossa S, 2018. Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing. BMC Oral Health, 18.

Shimizu A, Hase R, Suzuki D, Toguchi A, Otsuka Y, Hirata N and Hosokawa N, 2019. Lactococcus lactis cholangitis and bacteremia identified by MALDI‐TOF mass spectrometry: a case report and review of the literature on Lactococcus lactis infection. Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy, 25, 141–146.

Ting C, Qianwen L, Wenliang X, Qing Z, Qisheng Z, Gong C and Yimin C, 2017. Antibiotic resistance evaluation and resistance gene profile of epibiotic lactic acid bacteria on red bell peppers used for Sichuan pickle fermentation. Food Science, China, 38, 27–33.

Microbacterium imperiale

None

Oenococcus oeni

None

Pasteuria nishizawae

None

Pediococci spp.

Chen F, Zhang Z and Chen J, 2018. Infective endocarditis caused by Lactococcus lactis subsp. lactis and Pediococcus pentosaceus: A case report and literature review. Medicine, 97, e13658–e13658.

Han A, Mehta J and Pauly RR, 2016. Septic shock secondary to a urinary tract infection with Pediococcus pentosaceus. Missouri Medicine, 113, 179–181.

Propionibacterium spp.

None

Streptococcus thermophilus

None

Gram‐Positive Spore‐forming Bacteria

Bacillus spp.

(2018). Selection of Potential Probiotic Lactic Acid Bacteria Isolated from Palm Sap (Borassus flabellifer Linn.) Origin Kupang, East Nusa Tenggara. Inventing Prosperous Future through Biological Research and Tropical Biodiversity Management 2002.

Abdelgani AM, Rukayadi Y, Shaari K and Safinar I, 2018. Antibacterial and sporicidal activities of methanolic Sygygium polyanthum L. Leaf extract against vegetative cells and spores of Bacillus pumilus and Bacillus megaterium. Journal of Pure and Applied Microbiology, 12, 1047‐1053.

Abreo E, Valle D, Mujica V and Altier N, 2018. Pathogenicity and virulence factors of Lysinibacillus xylanilyticus and Bacillus spp. towards Argyrotaenia sphaleropa larvae (Lepidoptera). Journal of Applied Entomology, 142, 882–892.

Aditya K, Babu PPS and Roy SD, 2018. Assessment of immune response in post‐probiotic treated Litopenaeus vannamei challenged with Vibrio harveyi. Proceedings of the National Academy of Sciences India. Section B, Biological Sciences, 88, 797–802.

Agerso Y, Stuer‐Lauridsen B, Bjerre K, Jensen MG, Johansen E, Bennedsen M, Brockmann E and Nielsen B, 2018. Antimicrobial susceptibility testing and tentative epidemiological cutoff values for five Bacillus species relevant for use as animal feed additives or for plant protection. Applied and Environmental Microbiology, 84.

Ali M, Boonerjee S, Islam MN, Saha ML, Hoque MI and Sarker RH, 2018. Endogenous bacterial contamination of plant tissue culture materials: identification and control strategy. Plant Tissue Culture & Biotechnology, 28, 99–108.

Al‐Khalaifah HS, 2018. Benefits of probiotics and/or prebiotics for antibiotic‐reduced poultry. Poultry Science, 97, 3807–3815.

Al‐Marzooq F, Al Bayat S, Sayyar F, Ishaq H, Nasralla H, Koutaich R and Al Kawas S, 2018. Can probiotic cleaning solutions replace chemical disinfectants in dental clinics? European Journal of Dentistry, 12, 532‐539.

Alonso Lucero‐Velasco E, Judith Molina‐Garza Z and Galaviz‐Silva L, 2018. First survey of cultivable bacteria from Rhipicephalus sanguineus sensu lato and assessment of the antagonism against five microorganisms of clinical importance. International Journal of Acarology, 44, 204–209.

Alsanie WF, Felemban EM, Farid MA, Hassan MM, Sabry A and Gaber A, 2018. Molecular identification and phylogenetic analysis of multidrug‐resistant bacteria using 16S rDNA sequencing. Journal of Pure and Applied Microbiology, 12, 489–496.

Amman F, D'Halluin A, Antoine R, Huot L, Bibova I, Keidel K, Slupek S, Bouquet P, Coutte L, Caboche S, Locht C, Vecerek B and Hot D, 2018. Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis. RNA Biology, 15, 967–975.

Ansari A, Zohra RR, Tarar OM, Ul Qader SA and Aman A, 2018. Screening, purification and characterization of thermostable, protease resistant Bacteriocin active against methicillin resistant Staphylococcus aureus (MRSA). BMC Microbiology, 18.

Bao L, Fang Q, Lou B, Wu D, Chen Y and Liu J, 2018. Diagnostic value of inflammatory factors in patients with sepsis caused by infections. Chinese Journal of Nosocomiology, 28, 547–550.

Ben Abdallah D, Frikha‐Gargouri O and Tounsi S, 2018. Rizhospheric competence, plant growth promotion and biocontrol efficacy of Bacillus amyloliquefaciens subsp plantarum strain 32a. Biological Control, 124, 61–67.

Berger P, Messner MJ, Crosby J, Renwick DV and Heinrich A, 2018. On the use of total aerobic spore bacteria to make treatment decisions due to Cryptosporidium risk at public water system wells. International Journal of Hygiene and Environmental Health, 221, 704–711.

Beric T, Biocanin M, Stankovic S, Dimkic I, Janakiev T, Fira D and Lozo J, 2018. Identification and antibiotic resistance of Bacillus spp. isolates from natural samples. Archives of Biological Sciences, 70, 581–588.

Bjelic D, Ignjatov M, Marinkovic J, Milosevic D, Nikolic Z, Gvozdanovic‐Varga J and Karaman M, 2018. Bacillus isolates as potential biocontrol agents of Fusarium clove rot of garlic. Zemdirbyste‐Agriculture, 105, 369–376.

Carles L, Joly M, Bonnemoy F, Leremboure M, Donnadieu F, Batisson I and Besse‐Hoggan P, 2018. Biodegradation and toxicity of a maize herbicide mixture: mesotrione, nicosulfuron and S‐metolachlor. Journal of Hazardous Materials, 354, 42–53.

Caselli E, Pancaldi S, Baldisserotto C, Petrucci F, Impallaria A, Volpe L, D'Accolti M, Soffritti I, Coccagna M, Sassu G, Bevilacqua F, Volta A, Bisi M, Lanzoni L and Mazzacane S, 2018. Characterization of biodegradation in a 17th century easel painting and potential for a biological approach. Plos One, 13.

Cerioli MF, Moliva MV, Cariddi LN and Reinoso EB, 2018. Effect of the essential oil of Minthostachys verticillata (Griseb.) epling and limonene on biofilm production in pathogens causing Bovine Mastitis. Frontiers in Veterinary Science, 5.

Chen B‐C, Lin C‐X, Chen N‐P, Gao C‐X, Zhao Y‐J and Qian C‐D, 2018. Phenanthrene antibiotic targets bacterial membranes and kills Staphylococcus aureus with a low propensity for resistance development. Frontiers in Microbiology, 9.

Chen Q, He W, Yan X, Zhang T, Jiang B, Stressler T, Fischer L and Mu W, 2018. Construction of an enzymatic route using a food‐grade recombinant Bacillus subtilis for the production and purification of epilactose from lactose. Journal of Dairy Science, 101, 1872–1882.

Cheng Y‐H, Zhang N, Han J‐C, Chang C‐W, Hsiao FS‐H and Yu Y‐H, 2018. Optimization of surfactin production from Bacillus subtilis in fermentation and its effects on Clostridium perfringens‐induced necrotic enteritis and growth performance in broilers. Journal of Animal Physiology and Animal Nutrition, 102, 1232–1244.

Cho BC, Hardies SC, Jang GI and Hwang CY, 2018. Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL‐TW6(T) adapted to coastal planktonic lifestyle. BMC Genomics, 19.

Chomwong S, Charoensapsri W, Amparyup P and Tassanakajon A, 2018. Two host gut‐derived lactic acid bacteria activate the proPO system and increase resistance to an AHPND‐causing strain of Vibrio parahaemolyticus in the shrimp Litopenaeus vannarnei. Developmental and Comparative Immunology, 89, 54–65.

Costa EM, Silva S, Veiga M, Tavaria FK and Pintado MM, 2018. Chitosan's biological activity upon skin‐related microorganisms and its potential textile applications. World Journal of Microbiology & Biotechnology, 34.

Coullon H, Rifflet A, Wheeler R, Janoir C, Boneca IG and Candela T, 2018. N‐Deacetylases required for muramic–lactam production are involved in Clostridium difficile sporulation, germination, and heat resistance. Journal of Biological Chemistry, 293, 18040–18054.

Crowe‐McAuliffe C, Graf M, Huter P, Takada H, Abdelshahid M, Novacek J, Murina V, Atkinson GC, Hauryliuk V and Wilson DN, 2018. Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. Proceedings of the National Academy of Sciences of the United States of America, 115, 8978–8983.

Dalvand LF, Hosseini F, Dehaghi SM and Torbati ES, 2018. Inhibitory effect of bismuth oxide nanoparticles produced by Bacillus licheniformis on methicillin‐resistant Staphylococcus aureus strains (MRSA). Iranian Journal of Biotechnology, 16, 279–286.

Dasgupta D, Jasmine J and Mukherj S, 2018. Characterization, phylogenetic distribution and evolutionary trajectories of diverse hydrocarbon degrading microorganisms isolated from refinery sludge. 3 Biotech, 8.

Demirhan B, Guragac FT, Er‐Demirhan B, Tastan H and Kupeli‐Akkol E, 2018. A PRECLINICAL STUDY: EFFECT OF NEW PROBIOTIC PRODUCTS, “BACILLUS SUBTILIS AND BACILLUS AMYLOLIQUEFACIENS”, ON DIARRHEA. Fresenius Environmental Bulletin, 27, 4139–4148.

Doroteo AM, Pedroso FL, Lopez JDM and Apines‐Amar MJS, 2018. Evaluation of potential probiotics isolated from saline tilapia in shrimp aquaculture. Aquaculture International, 26, 1095–1107.

De Melo Pereira GV, Coelho BdO, Magalhaes Junior AI, Thomaz‐Soccol V and Soccol CR, 2018. How to select a probiotic? A review and update of methods and criteria. Biotechnology Advances, 36, 2060–2076.

Efimenko TA, Efremenkova OV, Demkina EV, Petrova MA, Sumarukova IG, Vasilyeva BF and El’‐Registan GI, 2018. Bacteria isolated from antarctic permafrost are efficient antibiotic producers. Microbiology, 87, 692–698.

Erler S, Lewkowski O, Poehlein A and Forsgren E, 2018. The curious case of achromobacter eurydice, a gram‐variable pleomorphic bacterium associated with European foulbrood disease in honeybees. Microbial Ecology, 75, 1–6.

Escribano‐Viana R, Portu J, Garijo P, Rosa Gutierrez A, Santamaria P, Lopez‐Alfaro I, Lopez R and Gonzalez‐Arenzana L, 2018. Evaluating a preventive biological control agent applied on grapevines against Botrytis cinerea and its influence on winemaking. Journal of the Science of Food and Agriculture, 98, 4517–4526.

Etminani F and Harighi B, 2018. Isolation and identification of endophytic bacteria with plant growth promoting activity and biocontrol potential from wild pistachio trees. Plant Pathology Journal, 34, 208–217.

Farlow J, Bolkvadze D, Leshkasheli L, Kusradze I, Kotorashvili A, Kotaria N, Balarjishvili N, Kvachadze L, Nikolich M and Kutateladze M, 2018. Genomic characterization of three novel Basilisk‐like phages infecting Bacillus anthracis. BMC Genomics, 19.

Fernanda Villarreal‐Delgado M, Daniel Villa‐Rodriguez E, Alberto Cira‐Chavez L, Isabel Estrada‐Alvarado M, Isela Parra‐Cota F and e los Santos‐Villalobos S, 2018. The genus Bacillus as a biological control agent and its implications in the agricultural biosecurity. Revista Mexicana de Fitopatologia, 36, 95–130.

Fu G, Wang L, Li L, Liu J, Liu S and Zhao X, 2018. Bacillus licheniformis CK1 alleviates the toxic effects of zearalenone in feed on weaned female Tibetan piglets. Journal of Animal Science, 96, 4471–4480.

Fuchs S, Mehlan H, Bernhardt J, Hennig A, Michalik S, Surmann K, Pane‐Farre J, Giese A, Weiss S, Backert L, Herbig A, Nieselt K, Hecker M, Voelker U and Maeder U, 2018. AureoWiki‐The repository of the Staphylococcus aureus research and annotation community. International Journal of Medical Microbiology, 308, 558–568.

Galaviz‐Silva L, Mario Iracheta‐Villarreal J and Judith Molina‐Garza Z, 2018. Bacillus and Virgibacillus strains isolated from three Mexican coasts antagonize Staphylococcus aureus and Vibrio parahaemolyticus. Fems Microbiology Letters, 365.

Galvan DD and Yu Q, 2018. Surface‐enhanced raman scattering for rapid detection and characterization of antibiotic‐resistant bacteria. Advanced Healthcare Materials, 7.

Gangola S, Sharma A, Bhatt P, Khati P and Chaudhary P, 2018. Presence of esterase and laccase in Bacillus subtilis facilitates biodegradation and detoxification of cypermethrin. Scientific Reports, 8.

Garcia‐Ramon DC, Berry C, Tse C, Fernandez‐Fernandez A, Osuna A and Vilchez S, 2018. The parasporal crystals of Bacillus pumilus strain 15.1: a potential virulence factor? Microbial Biotechnology, 11, 302–316.

Ghosh K, Kang HS, Hyun WB and Kim K‐P, 2018. High prevalence of Bacillus subtilis‐infecting bacteriophages in soybean‐based fermented foods and its detrimental effects on the process and quality of Cheonggukjang. Food Microbiology, 76, 196–203.

Ghosh K, Senevirathne A, Kang HS, Hyun WB, Kim JE and Kim K‐P, 2018. Complete nucleotide sequence analysis of a Novel Bacillus subtilis‐infecting bacteriophage BSP10 and its effect on poly‐gamma‐glutamic acid degradation. Viruses‐Basel, 10.

Goldner NK, Bulow C, Cho K, Wallace M, Hsu F‐F, Patti GJ, Burnham C‐A, Schlesinger P and Dantas G, 2018. Mechanism of high‐level daptomycin resistance in Corynebacterium striatum. Msphere, 3.

Golkar T, Zielinski M and Berghuis AM, 2018. Look and outlook on enzyme‐mediated macrolide resistance. Frontiers in Microbiology, 9.

Gosavi SM, Kharat SS, Kumkar P and Navarange SS, 2018. Interplay between behavior, morphology and physiology supports lepidophagy in the catfish Pachypterus khavalchor (Siluriformes: Horabagridae). Zoology, 126, 185–191.

Goto E, Haga Y, Kubo M, Itoh T, Kasai C, Shoji O, Yamamoto K, Matsumura C, Nakano T and Inui H, 2018. Metabolic enhancement of 2,3 ‘,4,4 ‘,5‐pentachlorobiphenyl (CB118) using cytochrome P450 monooxygenase isolated from soil bacterium under the presence of perfluorocarboxylic acids (PFCAs) and the structural basis of its metabolism. Chemosphere, 210, 376–383.

Gotzmann G, Portillo J, Wronski S, Kohl Y, Gorjup E, Schuck H, Roegner FH, Mueller M, Chaberny IF, Schoenfelder J and Wetzel C, 2018. Low‐energy electron‐beam treatment as alternative for on‐site sterilization of highly functionalized medical products ‐ A feasibility study. Radiation Physics and Chemistry, 150, 9–19.

Grohmann E, Keller W and Muth G, 2018. Mechanisms of conjugative transfer and type IV secretion‐mediated effector transport in gram‐positive bacteria. Type Iv Secretion in Gram‐Negative and Gram‐Positive Bacteria, 413, 115–141.

Haditomo AHC and Prayitno SB, 2018. Probiotic candidates from fish pond water in central java Indonesia. 3rd International Conference on Tropical and Coastal Region Eco Development 2017 116.

Halami PM, 2018. Sublichenin, a new subtilin‐like lantibiotics of probiotic bacterium Bacillus licheniformis MCC 2512T with antibacterial activity. Microbial Pathogenesis, 128, 139–146.

Hamdache A, Ezziyyani M and Lamarti A, 2018. Effect of preventive and simultaneous inoculations of Bacillus amyloliquefaciens (Fukumoto) strains on conidial germination of Botrytis cinerea Pers.:Fr. Anales de Biologia, 40, 65–72.

Hamzah TNT, Lee SY, Hidayat A, Terhem R, Faridah‐Hanum I and Mohamed R, 2018. Diversity and characterization of endophytic fungi isolated from the tropical mangrove species, Rhizophora mucronata, and identification of potential antagonists against the soil‐borne fungus, Fusarium solani. Frontiers in Microbiology, 9.

Hao X, Zhang X, Duan B, Huo S, Lin W, Xia X and Liu K, 2018. Screening and genome sequencing of deltamethrin‐degrading bacterium ZJ6. Current Microbiology, 75, 1468–1476.

Hasan SMZ, Hossain F, Zaoti ZF, Hasan F, Islam A and Sikdar B, 2018. PCR amplification of DNA sequence related to the hrpD gene of Xanthomonas cucurbitae in leaf spot disease of pumpkin and their antagonism by soil bacteria. Archives of Phytopathology and Plant Protection, 51, 252–266.

He S, Feng K, Ding T, Huang K, Yan H, Liu X and Zhang Z, 2018. Complete genome sequence Bacillus licheniformis BL‐010. Microbial Pathogenesis, 118, 199–201.

Hill AJ, Leys JE, Bryan D, Erdman FM, Malone KS, Russell GN, Applegate RD, Fenton H, Niedringhaus K, Miller AN, Allender MC and Walker DM, 2018. Common cutaneous bacteria isolated from snakes inhibit growth of Ophidiomyces ophiodiicola. Ecohealth, 15, 109–120.

Ho K, Huo W, Pas S, Dao R and Palmer KL, 2018. Loss‐of‐function mutations in epaR confer resistance to phi NPV1 infection in Enterococcus faecalis OG1RF. Antimicrobial Agents and Chemotherapy, 62.

Hoelzer K, Bielke L, Blake DP, Cox E, Cutting SM, Devriendt B, Erlacher‐Vindel E, Goossens E, Karaca K, Lemiere S, Metzner M, Raicek M, Surinach MC, Wong NM, Gay C and Van Immerseel F, 2018. Vaccines as alternatives to antibiotics for food producing animals. Part 2: new approaches and potential solutions. Veterinary Research, 49.

Hosseini S, Curilovs A and Cutting SM, 2018. Biological containment of genetically modified Bacillus subtilis. Applied and Environmental Microbiology, 84.

Huang Y, Xiao X, Huang H, Jing J, Zhao H, Wang L and Long X‐E, 2018. Contrasting beneficial and pathogenic microbial communities across consecutive cropping fields of greenhouse strawberry. Applied Microbiology and Biotechnology, 102, 5717–5729.

Imarhiagbe EE and Ikhajiagbe B, 2018. Antibiotic susceptibility of bacterial isolates and water quality index of water sourced from closed ground water and open hand dug well in Koko Community, Delta State, Nigeria. Studia Universitatis Babes‐Bolyai Biologia, 63, 47–57.

Iseppi R, e Niederhausern S, Bondi M, Messi P and Sabia C, 2018. Extended‐Spectrum ‐Lactamase, AmpC, and MBL‐Producing Gram‐Negative Bacteria on Fresh Vegetables and Ready‐to‐Eat Salads Sold in Local Markets. Microbial Drug Resistance, 24, 1156–1164.

Ivanko OG and Solianyk OV, 2018. Antibiotic‐associated disorders of prothrombin synthesis and their probiotic correction with B. clausii in breastfeed infants. Zaporozhye Medical Journal, 384–387.

Javed MT, Akram MS, Abid A, Shahid M, Ali Q and Iqbal N, 2018. Bacillus pumilus enhances the safflower (Carthamus tinctorius L.) growth under chromium stress by an antioxidative potential and nutrient acquisition. Phytopathology, 108, 43–43.

Jebakumar RM and Selvarajan R, 2018. Biopriming of micropropagated banana plants at pre‐ or post‐BBTV inoculation stage with rhizosphere and endophytic bacteria determines their ability to induce systemic resistance against BBTV in cultivar Grand Naine. Biocontrol Science and Technology, 28, 1074–1090.

Jeong D‐E, So Y, Lim H, Park S‐H and Choi S‐K, 2018. Scarless genomic point mutation to construct a Bacillus subtilis strain displaying increased antibiotic plipastatin production. Journal of Microbiology and Biotechnology, 28, 1030–1036.

Jeong J‐J, Moon H‐J, Pathiraja D, Park B, Choi I‐G and Kim KD, 2018. Draft genome sequences of Bacillus megaterium KU143, Microbacterium testaceum KU313, and Pseudomonas protegens AS15, Isolated from Stored Rice Grains. Microbiology Resource Announcements 6.

Ji H, Wu L, Pu F, Ren J and Qu X, 2018. Point‐of‐care identification of bacteria using protein‐encapsulated gold nanoclusters. Advanced Healthcare Materials, 7.

Jiang Y, Zhang Z, Wang Y, Jing Y, Liao M, Rong X, Li B, Chen G and Zhang H, 2018. Effects of probiotic on microfloral structure of live feed used in larval breeding of turbot Scophthalmus maximus. Journal of Oceanology and Limnology, 36, 1002–1012.

Jimenez‐Tototzintle M, Ferreira IJ, Duque SdS, Guimaraes Barrocas PR and Saggioro EM, 2018. Removal of contaminants of emerging concern (CECs) and antibiotic resistant bacteria in urban wastewater using UVA/TiO2/H2O2 photocatalysis. Chemosphere, 210, 449–457.

Jujjavarapu SE and Dhagat S, 2018. In silico discovery of novel ligands for antimicrobial lipopeptides for computer‐aided drug design. Probiotics and Antimicrobial Proteins, 10, 129–141.

Jujjavarapu SE, Dhagat S and Kurrey V, 2018. Identification of novel ligands for therapeutic lipopeptides: daptomycin, surfactin and polymyxin. Current Drug Targets, 19, 1589–1598.

Ka‐ot AL, Banerjee S, Haldar G and Joshi SR, 2018. Acid and heavy metal tolerant Bacillus sp from rat‐hole coal mines of Meghalaya, India. Proceedings of the Indian National Science Academy Part B Biological Sciences, 88, 1187–1198.

Kapoor Y, Sharma R and Kumar A, 2018. Repurposing of existing drugs for the bacterial infections: An In silico and In vitro study. Infectious disorders drug targets.

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Zhou S‐Y, Hu Y‐J, Meng F‐C, Qu S‐Y, Wang R, Andersen RJ, Liao Z‐H and Chen M, 2018. Bacillamidins A‐G from a Marine‐Derived Bacillus pumilus. Marine Drugs, 16.

Zommiti M, Bouffartigues E, Maillot O, Barreau M, Szunerits S, Sebei K, Feuilloley M, Connil N and Ferchichi M, 2018. In vitro Assessment of the Probiotic Properties and Bacteriocinogenic Potential of Pediococcus pentosaceus MZF16 Isolated From Artisanal Tunisian Meat Dried Ossban. Frontiers in Microbiology, 9.

Geobacillus stearothermophilus

None

Gram‐negative bacteria

Gluconobacter oxydans

None

Xanthomonas campestris

None

Yeasts

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Acs‐Szabo L, Papp LA, Antunovics Z, Sipiczki M and Miklos I, 2018. Assembly of Schizosaccharomyces cryophilus chromosomes and their comparative genomic analyses revealed principles of genome evolution of the haploid fission yeasts. Scientific Reports 8.

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Alassane‐Kpembi I, Pinton P, Hupe J‐F, Neves M, Lippi Y, Combes S, Castex M and Oswald IP, 2018. Saccharomyces cerevisiae boulardii Reduces the Deoxynivalenol‐Induced Alteration of the Intestinal Transcriptome. Toxins, 10(5).

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Argy N, Le Gal S, Coppee R, Song Z, Vindrios W, Massias L, Kao W‐C, Hunte C, Yazdanpanah Y, Lucet J‐C, Houze S, Clain J and Nevez G, 2018. Pneumocystis Cytochrome b Mutants Associated With Atovaquone Prophylaxis Failure as the Cause of Pneumocystis Infection Outbreak Among Heart Transplant Recipients. Clinical Infectious Diseases, 67, 913–919.

Awad L, Tamim H, Abdallah D, Salameh M, Mugharbil A, Jisr T, Zahran K, Droubi N, Ibrahim A and Moghnieh R, 2018. Correlation between antifungal consumption and the distribution of Candida species in different hospital departments of a Lebanese medical Centre. BMC Infectious Diseases, 18.

Awais MM, Jamal MA, Akhtar M, Hameed MR, Anwar MI and Ullah MI, 2018. Immunomodulatory and ameliorative effects of Lactobacillus and Saccharomyces based probiotics on pathological effects of eimeriasis in broilers. Microbial pathogenesis, 126, 101–108.

Baeza M, Fernandez‐Lobato M, Alcaino J and Cifuentes V, 2018. Isolation and Characterization of Extrachromosomal Double‐Stranded RNA Elements from Carotenogenic Yeasts. Microbial Carotenoids: Methods and Protocols, 1852, 327–339.

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Beauvais A and Latge J‐P, 2018. Special Issue: Fungal Cell Wall. Journal of Fungi, 4.

Belinato de Souza JR, Kupper KC and Augusto F, 2018. In vivo investigation of the volatile metabolome of antiphytopathogenic yeast strains active against Penicillium digitatum using comprehensive two‐dimensional gas chromatography and multivariate data analysis. Microchemical Journal, 141, 204–209.

Beyer R, Jandric Z, Zutz C, Gregori C, Willinger B, Jacobsen ID, Kovarik P, Strauss J and Schuller C, 2018. Competition of Candida glabrata against Lactobacillus is Hog1 dependent. Cellular Microbiology, 20.

Bhakt P, Shivarathri R, Choudhary DK, Borah S and Kaur R, 2018. Fluconazole‐induced actin cytoskeleton remodeling requires phosphatidylinositol 3‐phosphate 5‐kinase in the pathogenic yeast Candida glabrata. Molecular Microbiology, 110, 425–443.

Bharathi R, 2018. Comparison of Chromogenic Media with the Corn Meal Agar for Speciation of Candida. Journal of Pure and Applied Microbiology, 12, 1617–1622.

Bhatt RS, Sahoo A, Karim SA and Gadekar YP, 2018. Effects of Saccharomyces cerevisiae and rumen bypass‐fat supplementation on growth, nutrient utilisation, rumen fermentation and carcass traits of lambs. Animal Production Science, 58, 530–538.

Biagiotti C, Ciani M, Canonico L and Comitini F, 2018. Occurrence and involvement of yeast biota in ripening of Italian Fossa cheese. European Food Research and Technology, 244, 1921–1931.

Biasucci G, 2018. Gut perturbation and probiotics in neonatology. Journal of Pediatric and Neonatal Individualized Medicine, 7.

Bijelic B, Matic IZ, Besu I, Jankovic L, Juranic Z, Marusic S and Andrejevic S, 2018. Celiac disease‐specific and inflammatory bowel disease‐related antibodies in patients with recurrent aphthous stomatitis. Immunobiology.

Bonciani T, De Vero L, Giannuzzi E, Verspohl A and Giudici P, 2018. Qualitative and quantitative screening of the ‐glucosidase activity in Saccharomyces cerevisiae and Saccharomyces uvarum strains isolated from refrigerated must. Letters in Applied Microbiology, 67, 72–78.

Buckova M, Puskarova A, Zenisova K, Krakova L, Piknova L, Kuchta T and Pangallo D, 2018. Novel insights into microbial community dynamics during the fermentation of Central European ice wine. International Journal of Food Microbiology, 266, 42–51.

Burr R and Espenshade PJ, 2018. Oxygen‐responsive transcriptional regulation of lipid homeostasis in fungi: Implications for anti‐fungal drug development. Seminars in Cell & Developmental Biology, 81, 110–120.

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Calahorra M, Sanchez NS and Pena A, 2018. Influence of phenothiazines, phenazines and phenoxazine on cation transport in Candida albicans. Journal of Applied Microbiology, 125, 1728–1738.

Caldara M and Marmiroli N, 2018. Tricyclic antidepressants inhibit Candida albicans growth and biofilm formation. International Journal of Antimicrobial Agents, 52, 500–505.

Cassilly CD and Reynolds TB, 2018. PS, It's Complicated: The Roles of Phosphatidylserine and Phosphatidylethanolamine in the Pathogenesis of Candida albicans and Other Microbial Pathogens. Journal of Fungi, 4.

Castilho DG, Alencar Chaves AF, Navarro MV, Conceicao PM, Ferreira KS, Silva LS, Xander P and Batista WL, 2018. Secreted aspartyl proteinase (PbSap) contributes to the virulence of Paracoccidioides brasiliensis infection. Plos Neglected Tropical Diseases, 12.

Cen Q‐W, Chen T, Zheng W, Zhang Y, Ying R‐F, Tang Z‐X and Shi L‐E, 2018. Isolation, Identification and Partial Characterization of Film‐forming Microorganisms from Chinese Homemade Pickle, a Traditional Fermented Vegetable Product. Chiang Mai Journal of Science, 45, 2283–2293.

Chen J, Wan C‐M, Gong S‐T, Fang F, Sun M, Qian Y, Huang Y, Wang B‐X, Xu C‐D, Ye L‐Y, Dong M, Jin Y, Huang Z‐H, Wu Q‐B, Zhu C‐M, Fang Y‐H, Zhu Q‐R and Dong Y‐S, 2018. Chinese clinical practice guidelines for acute infectious diarrhea in children. World Journal of Pediatrics, 14, 429–436.

Cioch‐Skoneczny M, Satora P, Skotniczny M and Skoneczny S, 2018. Quantitative and qualitative composition of yeast microbiota in spontaneously fermented grape musts obtained from cool climate grape varieties ‘Rondo’ and ‘Regent’. FEMS Yeast Research, 18.

Cohen PA, 2018. Probiotic Safety‐No Guarantees. Jama Internal Medicine, 178, 1577–1578.

Corbaci C and Ucar FB, 2018. Purification, characterization and in vivo biocontrol efficiency of killer toxins from Debaryomyces hansenii strains. International Journal of Biological Macromolecules, 119, 1077–1082.

Cristina dos Reis K, Arrizon J, Amaya‐Delgado L, Gschaedler A, Freitas Schwan R and Ferreira Silva C, 2018. Volatile compounds flavoring obtained from Brazilian and Mexican spirit wastes by yeasts. World Journal of Microbiology & Biotechnology, 34.

Csoma H, Acs‐Szabo L, Papp LA and Sipiczki M, 2018. Application of different markers and data‐analysis tools to the examination of biodiversity can lead to different results: a case study with Starmerella bacillaris (synonym Candida zemplinina) strains. Fems Yeast Research, 18.

Cully M, 2018. ANTIFUNGAL DRUGS Small molecules targeting a tertiary RNA structure fight fungi. Nature Reviews Drug Discovery, 17.

Cummings D, Cruise M, Lopez R, Roggenbuck D, Jairath V, Wang Y, Shen B and Rieder F, 2018. Loss of tolerance to glycoprotein 2 isoforms 1 and 4 is associated with Crohn's disease of the pouch. Alimentary Pharmacology & Therapeutics, 48, 1251–1259.

Czech A, Smolczyk A, Ognik K, Wlazlo L, Nowakowicz‐Debek B and Kiesz M, 2018. Effect of dietary supplementation with Yarrowia lipolytica or Saccharomyces cerevisiae yeast and probiotic additives on haematological parameters and the gut microbiota in piglets. Research in Veterinary Science, 119, 221–227.

Dalhoff A, 2018. Does the use of antifungal agents in agriculture and food foster polyene resistance development? A reason for concern. Journal of Global Antimicrobial Resistance, 13, 40–48.

Daliri EB‐M, Tango CN, Lee BH and Oh D‐H, 2018. Human microbiome restoration and safety. International Journal of Medical Microbiology, 308, 487–497.

Das S, Rai G, Tigga RA, Srivastava S, Singh PK, Sharma R, Datt S, Singh NP and Dar SA, 2018. Candida auris in critically ill patients: Emerging threat in intensive care unit of hospitals. Journal De Mycologie Medicale, 28, 514–518.

Davis SE, Tams RN, Solis NV, Wagner AS, Chen T, Jackson JW, Hasim S, Montedonico AE, Dinsmore J, Sparer TE, Filler SG and Reynolds TB, 2018. Candida albicans Cannot Acquire Sufficient Ethanolamine from the Host To Support Virulence in the Absence of De Novo Phosphatidylethanolamine Synthesis. Infection and Immunity, 86.

De Marco S, Sichetti M, Muradyan D, Piccioni M, Traina G, Pagiotti R and Pietrella D, 2018. Probiotic Cell‐Free Supernatants Exhibited Anti‐Inflammatory and Antioxidant Activity on Human Gut Epithelial Cells and Macrophages Stimulated with LPS. Evidence‐Based Complementary and Alternative Medicine.

Demirhan B, Guragac FT, Er‐Demirhan B, Tastan H and Kupeli‐Akkol E, 2018. A PRECLINICAL STUDY: EFFECT OF NEW PROBIOTIC PRODUCTS, “BACILLUS SUBTILIS AND BACILLUS AMYLOLIQUEFACIENS”, ON DIARRHEA. Fresenius Environmental Bulletin, 27, 4139–4148.

Demuyser L, Van Genechten W, Mizuno H, Colombo S and Van Dijck P, 2018. Introducing fluorescence resonance energy transfer‐based biosensors for the analysis of cAMP‐PKA signalling in the fungal pathogen Candida glabrata. Cellular Microbiology, 20.

Devi G, Harikrishnan R, Paray BA, Al‐Sadoon MK, Hoseinifar SH and Balasundaram C, 2018. Comparative immunostimulatory effect of probiotics and prebiotics in Channa punctatus against Aphanomyces invadans. Fish & Shellfish Immunology, 86, 965–973.

Diazid TG, Branco AF, Jacovaci FA, Jobim CC, Pratti Daniel JL, Iank Bueno AV and Ribeiro MG, 2018. Use of live yeast and mannan‐oligosaccharides in grain‐based diets for cattle: Ruminal parameters, nutrient digestibility, and inflammatory response. Plos One, 13.

Diba K, Makhdoomi K, Nasri E, Vaezi A, Javidnia J, Gharabagh DJ, Jazani NH, Chavshin AR, Badiee P, Badali H and Fakhim H, 2018. Emerging Candida species isolated from renal transplant recipients: Species distribution and susceptibility profiles. Microbial Pathogenesis, 125, 240–245.

Dudzicz S, Kujawa‐Szewieczek A, Kwiecien K, Wiecek A and Adamczak M, 2018. Lactobacillus plantarum 299v Reduces the Incidence of Clostridium difficile Infection in Nephrology and Transplantation Ward‐Results of One Year Extended Study. Nutrients, 10.

Duo Saito RA, Connell L, Rodriguez R, Redman R, Libkind D and e Garcia V, 2018. Metabarcoding analysis of the fungal biodiversity associated with Castano Overa Glacier ‐ Mount Tronador, Patagonia, Argentina. Fungal Ecology, 36, 8–16.

De Paula Menezes R, Silva FF, Melo SGO, Alves PGV, Brito MO, e Souza Bessa MA, Amante Penatti MP, Pedroso RS, Abdallah VOS and Roder DvDB, 2018. Characterization of Candida species isolated from the hands of the healthcare workers in the neonatal intensive care unit. Medical Mycology.

El Khoury S, Rousseau A, Lecoeur A, Cheaib B, Bouslama S, Mercier P‐L, Demey V, Castex M, Giovenazzo P and Derome N, 2018. Deleterious Interaction Between Honeybees (Apis mellifera) and its Microsporidian Intracellular Parasite Nosema ceranae Was Mitigated by Administrating Either Endogenous or Allochthonous Gut Microbiota Strains. Frontiers in Ecology and Evolution, 6.

El Kurdi B, Khatua B, Snozek C and Singh VP, 2018. ADMISSION SERUM UNBOUND FATTY ACIDS CORRELATE WITH LENGTH OF HOSPITAL STAY IN PATIENTS WITH ACUTE PANCREATITIS (AP). Gastroenterology, 154, S294–S295.

El Mouzan MI, Korolev KS, Al Mofarreh MA, Menon R, Winter HS, Al Sarkhy AA, Dowd SE, Al Barrag AM and Assiri AA, 2018. Fungal dysbiosis predicts the diagnosis of pediatric Crohn's disease. World Journal of Gastroenterology, 24, 4510–4516.

Eldarov MA, Beletsky AV, Tanashchuk TN, Kishkovskaya SA, Ravin NV and Mardanov AV, 2018. Whole‐Genome Analysis of Three Yeast Strains Used for Production of Sherry‐Like Wines Revealed Genetic Traits Specific to Flor Yeasts. Frontiers in Microbiology, 9.

Ene LV, Farrer RA, Hirakawa MP, Agwamba K, Cuomo CA and Bennett RJ, 2018. Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen. Proceedings of the National Academy of Sciences of the United States of America, 115, E8688–E8697.

Fan G, Xu D, Fu Z, Xu C, Teng C, Sun B and Li X, 2018. Screen of aroma‐producing yeast strains from Gujinggong Daqu and analysis of volatile flavor compounds produced by them. Journal of Chinese Institute of Food Science and Technology, 18, 220–229.

Ferraz Dellias, MdT, Borges CD, Lopes ML, Cruz SH, e Amorim HV and Tsai SM, 2018. Biofilm formation and antimicrobial sensitivity of lactobacilli contaminants from sugarcane‐based fuel ethanol fermentation. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 111, 1631–1644.

Ferreira RM, Aguiar F, Rocha TM, Ganhao S, Agueda A, Guerra M, Pimenta S, Bernardes M and Costa L, 2018. ANTI‐SACCHAROMYCES CEREVISIAE ANTIBODIES IN SPONDYLARTHROPATHIES: PREVALENCE AND ASSOCIATIONS WITH DISEASE PHENOTYPE. Annals of the Rheumatic Diseases, 77, 856–856.

Florencia Perez M, Sofia Isas A, Aladdin A, El Enshasy HA and Rafael Dib J, 2018. Killer Yeasts as Biocontrol Agents of Postharvest Fungal Diseases in Lemons. Sustainable Technologies for the Management of Agricultural Wastes, 87–98.

Florez ID, Veroniki A‐A, Al Khalifah R, Yepes‐Nunez JJ, Sierra JM, Vernooij RWM, Acosta‐Reyes J, Granados CM, Perez‐Gaxiola G, Cuello‐Garcia C, Zea AM, Zhang Y, Foroutan N, Guyatt GH and Thabane L, 2018. Comparative effectiveness and safety of interventions for acute diarrhea and gastroenteritis in children: A systematic review and network meta‐analysis. Plos One, 13.

Forche A, Cromie G, Gerstein AC, Solis NV, Pisithkul T, Srifa W, Jeffery E, Abbey D, Filler SG, Dudley AM and Berman J, 2018. Rapid Phenotypic and Genotypic Diversification After Exposure to the Oral Host Niche in Candida albicans. Genetics, 209, 725–741.

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Gallone B, Mertens S, Gordon JL, Maere S, Verstrepen KJ and Steensels J, 2018. Origins, evolution, domestication and diversity of Saccharomyces beer yeasts. Current Opinion in Biotechnology, 49, 148–155.

Gao J, Wang H, Li Z, Wong AH‐H, Wang Y‐Z, Guo Y, Lin X, Zeng G, Wang Y and Wang J, 2018. Candida albicans gains azole resistance by altering sphingolipid composition. Nature Communications 9.

Garcia MD, Chua SMH, Low Y‐S, Lee Y‐T, Agnew‐Francis K, Wang J‐G, Nouwens A, Lonhienne T, Williams CM, Fraser JA and Guddat LW, 2018. Commercial AHAS‐inhibiting herbicides are promising drug leads for the treatment of human fungal pathogenic infections. Proceedings of the National Academy of Sciences of the United States of America, 115, E9649–E9658.

Garcia‐Agudo L, Rodriguez‐Iglesias M and Carranza‐Gonzalez R, 2018. Nosocomial Candiduria in the Elderly: Microbiological Diagnosis. Mycopathologia, 183, 591–596.

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Ghodhbane H, Ben Hamed K, Alesendria V, Abdelly C, Cocolin L and Regaya I, 2018. ANTIBACTERIAL AND ANTIFUNGAL ACTIVITY OF LAB BACTERIOCINS DERIVED FROM THE VALORIZATION OF DAIRY BYPRODUCTS USING AWDA ASSAY. Toxicon, 149, 96–96.

Glinka P, Nowacka K, Kulesza K, Ejdys E and Dynowska M, 2018. Share of the Saccharomyces genus in the mycobiota of the gastrointestinal tract of oncology patients ‐ potential effects of a fruit‐based diet. Annals of Parasitology, 64, 199–202.

Gobesso, A. A. O., G. V. Pombo, R. L. Costa, Y. S. Pereira and K. Feltre (2018). Effect of yeast supplementation on digestibility, fecal microbiota and serum endotoxin levels in non‐exercising and exercising horses. Livestock Science 215: 21‐24.

Gonzalez T, Malagon C, Guarnizo P, Mosquera AC, Chila‐Moreno L and Romero‐Sanchez C, 2018. Autoantibodies and Gastrointestinal Symptoms in Colombian Children with Juvenile Idiopathic Arthritis. Current Rheumatology Reviews, 14, 163–171.

Gordun E, Puig A, Pinol L and Carbo R, 2018. Identification of yeast isolated from laboratory sourdoughs prepared with grape, apple, and yogurt. Journal of Microbiology, Biotechnology and Food Sciences, 7, 399–403.

Goren I, Godny L, Reshef L, Yanai H, Gophna U, Tulchinsky H and Dotan I, 2018. Starch Consumption May Modify Antiglycan Antibodies and Fecal Fungal Composition in Patients With Ileo‐Anal Pouch. Inflammatory bowel diseases.

Gorgel A, Cankaya C and Tecellioglu M, 2018. Anti‐Saccharomyces cerevisiae as Unusual Antibody in Autoimmune Polyglandular Syndrome Type III: A Case Report. Endocrine, metabolic & immune disorders drug targets.

Gress A, Serratorre N and Briggs SD, 2018. Determining the role of the epigenetic factor SET4 in antifungal drug resistance in budding yeast. Faseb Journal, 32.

Gupta S, Bhathena ZP, Kumar S, Srivastava PP and Jadhao SB, 2018. Quantification and Characterization of Mannan Oligosaccharide Producing Yeasts isolated from Various Food Products. Proceedings of the Indian National Science Academy Part B Biological Sciences, 88, 1237–1247.

Gurina OP, Stepanova AA, Dementieva EA, Blinov AE, Varlamova ON and Blinov GA, 2018. TITLE. Klinicheskaia laboratornaia diagnostika, 63, 44–50.

Gut AM, Vasiljevic T, Yeager T and Donkor ON, 2018. Salmonella infection ‐ prevention and treatment by antibiotics and probiotic yeasts: a review. Microbiology‐Sgm, 164, 1327–1344.

Gutierrez A, Boekhout T, Gojkovic Z and Katz M, 2018. Evaluation of non‐Saccharomyces yeasts in the fermentation of wine, beer and cider for the development of new beverages. Journal of the Institute of Brewing, 124, 389–402.

Haastrup MK, Johansen P, Malskaer AH, Castro‐Mejia JL, Kot W, Krych L, Arneborg N and Jespersen L, 2018. Cheese brines from Danish dairies reveal a complex microbiota comprising several halotolerant bacteria and yeasts. International Journal of Food Microbiology, 285, 173–187.

Hardwick JM, 2018. Do Fungi Undergo Apoptosis‐Like Programmed Cell Death? Mbio, 9.

Hasan KAM and Yassein SN, 2018. Prevalence and type of fungi in milk from goats with sub clinical mastitis. Online Journal of Veterinary Research, 22, 669–674.

Hayashi K, Yamaguchi Y, Ogita A, Tanaka T, Kubo I and Fujita K‐I, 2018. Effect of nagilactone E on cell morphology and glucan biosynthesis in budding yeast Saccharomyces cerevisiae. Fitoterapia, 128, 112–117.

Healey KR, Kordalewska M, Ortigosa CJ, Singh A, Berrio I, Chowdhary A and Perlin DS, 2018. Limited ERG11 Mutations Identified in Isolates of Candida au ris Directly Contribute to Reduced Azole Susceptibility. Antimicrobial Agents and Chemotherapy, 62.

Hernandez A, Perez‐Nevado F, Ruiz‐Moyano S, Serradilla MJ, Villalobos MC, Martin A and Cordoba MG, 2018. Spoilage yeasts: What are the sources of contamination of foods and beverages? International Journal of Food Microbiology, 286, 98–110.

Hernandez‐Chavez MJ, Franco B, Clavijo‐Giraldo DM, Hernandez NV, Estrada‐Mata E and Manuel Mora‐Montes H, 2018. Role of protein phosphomannosylation in the Candida tropicalis‐macrophage interaction. Fems Yeast Research, 18.

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Horn MP, Peter AM, Grunder FR, Leichtle AB, Spalinger J, Schibli S and Sokollik C, 2018. PR3‐ANCA and panel diagnostics in pediatric inflammatory bowel disease to distinguish ulcerative colitis from Crohn's disease. Plos One, 13.

Hu L, Wang J, Ji X, Liu R, Chen F and Zhang X, 2018. Selection of non‐Saccharomyces yeasts for orange wine fermentation based on their enological traits and volatile compounds formation. Journal of Food Science and Technology‐Mysore, 55, 4001–4012.

Hu XQ, Liu Q, Hu JP, Zhou JJ, Zhang X, Peng SY, Peng LJ and Wang XD, 2018. Identification and characterization of probiotic yeast isolated from digestive tract of ducks. Poultry Science, 97, 2902–2908.

Ienascu IMC, Balaes T, Petre CV, Pop RO, Cata A, Stefanut MN, Albu P and Poenaru M, 2018. Novel N‐(2‐bromo‐phenyl)‐2‐hydroxy‐benzamide Derivatives with Antifungal Activity. Revista De Chimie, 69, 1876–1880.

Imarhiagbe EE and Ikhajiagbe B, 2018. Antibiotic susceptibility of bacterial isolates and water quality index of water sourced from closed ground water and open hand dug well in Koko Community, Delta State, Nigeria. Studia Universitatis Babes‐Bolyai Biologia, 63, 47–57.

Jakopovic Z, Cica KH, Mrvcic J, Pucic I, Canak I, Frece J, Pleadin J, Stanzer D, Zjalic S and Markov K, 2018. Properties and Fermentation Activity of Industrial Yeasts Saccharomyces cerevisiae, S. uvarum, Candida utilis and Kiuyveromyces marxianus Exposed to AFB(1), OTA and ZEA. Food Technology and Biotechnology, 56, 208–217.

Jiang L and Yang Y, 2018. The putative transient receptor potential channel protein encoded by the orf19.4805 gene is involved in cation sensitivity, antifungal tolerance, and filamentation in Candida albicans. Canadian Journal of Microbiology, 64, 727–731.

Johnston BC, Lytvyn L, Lo CK‐F, Allen SJ, Wang D, Szajewska H, Miller M, Ehrhardt S, Sampalis J, Duman DG, Pozzoni P, Colli A, Lonnermark E, Selinger CP, Wong S, Plummer S, Hickson M, Pancheva R, Hirsch S, Klarin B, Goldenberg JZ, Wang L, Mbuagbaw L, Foster G, Maw A, Sadeghirad B, Thabane L and Mertz D, 2018. Microbial Preparations (Probiotics) for the Prevention of Clostridium difficile Infection in Adults and Children: An Individual Patient Data Meta‐analysis of 6,851 Participants. Infection Control and Hospital Epidemiology, 39, 771–781.

Jung J, Moon YS, Yoo JA, Lim J‐H, Jeong J and Jun J‐B, 2018. Investigation of a nosocomial outbreak of fungemia caused by Candida pelliculosa (Pichia anomala) in a Korean tertiary care center. Journal of Microbiology Immunology and Infection, 51, 794–801.

Kara I, Yildirim F, Ozgen O, Erganis S, Aydogdu M, Dizbay M, Gursel G and Kalkanci A, 2018. Saccharomyces cerevisiae fungemia after probiotic treatment in an intensive care unit patient. Journal De Mycologie Medicale, 28, 218–221.

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Su H, Han L and Huang X, 2018. Potential targets for the development of new antifungal drugs. Journal of Antibiotics, 71, 978–991.

Sulik‐Tyszka B, Snarski E, Niedzwiedzka M, Augustyniak M, Myhre TN, Kacprzyk A, Swoboda‐Kopec E, Roszkowska M, Dwilewicz‐Trojaczek J, Jedrzejczak WW and Wroblewska M, 2018. Experience with Saccharomyces boulardii Probiotic in Oncohaematological Patients. Probiotics and Antimicrobial Proteins, 10, 350–355.

Sun Z and Xiao D, 2018. Review in metabolic modulation of higher alcohols in top‐fermenting yeast. Advances in Applied Biotechnology, 444, 767–773.

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Tao F, Xuzeng W, Yifei W, Min S, Lingyun Y and Zhimin X, 2018. Isolation and identification of yeast strains from vineyard soils and aroma compounds of wines fermented by them. Food Science, China, 39, 213–220.

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Yang Y, 2018. Regulatory effect of Saccharomyces boulardii combined with Lactulose on serum brain‐gut peptides in children with functional constipation. Zhongguo Weishengtaxixue Zazhi/Chinese Journal of Microecology, 30, 441–447.

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Zhang F, Tang Y, Ren Y, Yao K, He Q, Wan Y and Chi Y, 2018. Microbial composition of spoiled industrial‐scale Sichuan paocai and characteristics of the microorganisms responsible for paocai spoilage. International Journal of Food Microbiology, 275, 32–38.

Viruses used for plant protection

Alphaflexiviridae

Potyviridae

Baculoviridae

None.

Appendix E – The 2016 updated list of QPS Status recommended biological agents in support of EFSA risk assessments

1.

The list of QPS status recommended biological agents (EFSA BIOHAZ Panel, 2016) is being maintained in accordance with the self‐task mandate of the BIOHAZ Panel (2017–2019). Possible additions to this list are included around every 6 months, with the first Panel Statement adopted in June 2017 and the last Panel Statement planned for adoption in December 2019. These additions are published as updates to the Scientific Opinion (EFSA BIOHAZ Panel, 2016); the latest update is available at https://doi.org//10.2903/j.efsa.2018.5315 and, as of January 2018, also as supporting information linked to every Panel Statement available on the Knowledge Junction at https://doi.org/10.5281/zenodo.1146566.

Appendix F – Microbial species as notified to EFSA, received between October 2018 and March 2019 (reply to ToR 1)

1.

EFSA risk assessment area	Microorganism species/strain	Intended use	EFSA Question numbera and EFSA webpage linkb	Additional information provided by the EFSA Scientific Unit	Previous QPS status of the respective TU?c	To be evaluated? yes or nod
Bacteria
Feed additives	Bacillus amyloliquefaciens CBS143954	Zootechnical additives/Digestibility enhancer endo‐1,4‐beta‐xylanase (EC 3.2.1.8) produced by GMM Trichoderma reesei, subtilisin protease (EC 3.4.21.62) produced by GMM Bacillus subtilis and alpha‐amylase (EC 3.2.1.1) produced by GMM Bacillus amyloliquefaciens	EFSA‐Q‐2018‐01040		Yes	No
Plant protection products	Bacillus amyloliquefaciens FZB42	Fungicide	EFSA‐Q‐2019‐00096		Yes	No
Feed additives	Bacillus licheniformis DSM 19670	Zootechnical additives/Digestibility enhancers RONOZYME® ProAct (serine protease produced by a GMM strain of Bacillus licheniformis DSM 19670)	EFSA‐Q‐2019‐00156		Yes	No
Feed additives	Bacillus licheniformis ENV01/DSM 32457	Technological additives/Silage additive	EFSA‐Q‐2018‐00690		Yes	No
Feed additives	Bacillus subtilis CBS143946	Zootechnical additives/Digestibility enhancer? endo‐1,4‐beta‐xylanase (EC 3.2.1.8) produced by GMM Trichoderma reesei, subtilisin protease (EC 3.4.21.62) produced by GMM Bacillus subtilis and alpha‐amylase (EC 3.2.1.1) produced by GMM Bacillus amyloliquefaciens	EFSA‐Q‐2018‐01040		Yes	No
Feed additives	Bacillus subtilis DSM32324, Bacillus subtilis DSM32325 and Bacillus amyloliquefaciens DSM25840	Zootechnical feed additive/Flora stabiliser	EFSA‐Q‐2019‐00117	Bacillus subtilis DSM32324, Bacillus subtilis DSM32325 and Bacillus amyloliquefaciens DSM25840 are non‐GMM, and are all three of natural origin	Yes	No
Food enzymes, food additives and flavourings	Burkholderia ubonensis	Food enzyme triacylglycerol lipase produced by Burkholderia ubonensis	EFSA‐Q‐2019‐00056	Burkholderia ubonensis has been used for over 20 years for the production of the food enzyme	No	Yes
Feed additives	Corynebacterium ammoniagenes KCCM 80161	Sensory additives/ Flavouring compounds IMP (disodium 5’‐inosinate) produced by fermentation with Corynebacterium ammoniagenes KCCM 80161	EFSA‐Q‐2019‐00040	Disodium 5’‐inosinate feed grade is a highly purified product and does not contain any microorganisms. After the fermentation, the cells of the production strain Corynebacterium ammoniagenes KCCM80161 are eliminated by filtration and centrifugation from the fermentation broth	No	Yes
Feed additives	Corynebacterium casei KCCM80190	Nutritional Additives/Amino Acids, their salts and analogues. l‐lysine produced by fermentation with a GMM Corynebacterium casei KCCM80190	EFSA‐Q‐2019‐00195		No	Yes
Feed additives	Corynebacterium glutamicum KCCM 80184	Nutritional additives/Amino acids/Production of l‐methionine	EFSA‐Q‐2018‐01017		Yes	No
Feed additives	Corynebacterium glutamicum KCCM80188	Sensory additives/ Flavouring compounds MSG (monosodium l‐glutamate) produced by fermentation with Corynebacterium glutamicum KCCM80188	EFSA‐Q‐2019‐00037		No	No
Feed additives	Corynebacterium glutamicum KFCC11043	Nutritional Additives/Amino Acids, their salts and analogues l‐lysine sulphate feed grade produced by fermentation with Corynebacterium glutamicum KFCC11043 (GMM)	EFSA‐Q‐2019‐00194		Yes	No
Novel foods	Escherichia coli BL21 (DE3) strain	Production of a recombinant protein (novel food) for food supplements	EFSA‐Q‐2018‐00316	GMM E. coli Summary of the application under “APOAEQUORIN” at https://ec.europa.eu/food/safety/novel_food/authorisations/summary-ongoing-applications-and-notifications_en	No	No
Novel foods	Escherichia coli DSM 32833	Production of novel food 6‐SL (6’‐sialyllactose sodium salt)	EFSA‐2019‐0169	GMM E. coli (K12‐DH1 derivative)	No	No
Novel foods	Escherichia coli DSM 32834	Production of novel food 3‐SL (3’‐sialyllactose sodium salt)	EFSA‐2019‐0204	GMM E. coli (K12‐DH1 derivative)	No	No
Feed additives	Escherichia coli K12 KCCM 80096	Nutritional additives/Amino acids/Production of l‐methionine	EFSA‐Q‐2018‐01017		No	No
Feed additives	Escherichia coli KCCM 80109 Escherichia coli KCCM 80197	Sensory additives/ Flavouring compounds/ l‐cysteine hydrochloride monohydrate by fermentation with Escherichia coli KCCM 80109 and Escherichia coli KCCM 80197	EFSA‐Q‐2019‐00041	l‐cysteine hydrochloride monohydrate feed grade is a highly purified product and does not contain any microorganisms. After the fermentation, the cells of the production strain E. coli K12 KCCM 80109 and KCCM 80197 are removed by filtration and centrifugation from the fermentation broth	No	No
Novel foods	Escherichia coli strain K12 DH1 (DSM 32774)	Production of 2’‐fucosyllactose/difucosyllactose (novel food)	EFSA‐Q‐2018‐00374 http://www.efsa.europa.eu/en/efsajournal/pub/5717	GMM E. coli (K12‐DH1 derivative) Summary of application: https://ec.europa.eu/food/sites/food/files/safety/docs/novel-food_sum_ongoing-app_2fl-dfl.pdf	No	No
Novel foods	Escherichia coli K12 derivative	For the production of allulose (novel food); a recombinant derivative of Escherichia coli strain K‐12 is used in the fermentation process to produce d‐psicose 3‐epimerase	EFSA‐Q‐2018‐00756	Summary of application: https://ec.europa.eu/food/sites/food/files/safety/docs/novel-food_sum_ongoing-app_allulose_sum.pdf	No	No
Feed additives	Escherichia coli K12 KCCM 80159 (C 001)	Nutritional additives/Amino acids/Production of l‐valine	EFSA‐Q‐2018‐00712		No	No
Feed additives	Escherichia coli NITE BP‐02526	Nutritional additives/Amino acids/Flavouring compounds/Sensory additives/Production of l‐histidine monohydrochloride monohydrate	EFSA‐Q‐2018‐00782		No	No
Feed additives	Gluconobacter frateurii NBRC 103465	Zootechnical additives/Gluconobacter frateurii NBRC 103465 is a glyceric acid producing strain. Used for the production of the active ingredient: 2,3‐dihydroxy propanoic acid/glyceric acid (GA), d‐enantiomer (d‐GA)	EFSA‐Q‐2018‐00999	Other Zootechnical additives/Draft Genome Sequence of Gluconobacter frateurii NBRC 103465, has been published online by Sato et al. in 2013 Jul 25. https://doi.org/10.1128/genomea.00369-13	No	Yes
Feed additives	Lactobacillus buchneri DSM 29026	Technological Additives/Silage Additives	EFSA‐Q‐2019‐00180	This is a non‐holder specific additive. The strain has also been designated MFLBU1 or LBU1	Yes	No
Feed additives	Microbacterium foliorum SYG27B‐MF	Production of the novel food d‐allulose	EFSA‐Q‐2018‐00797	Non‐GMM strain of Microbacterium foliorum	No	Yes
Feed additives	Sphingomonas elodea PS‐60 ATCC 31461	Technological additives/Gelling agents, Stabilisers, Thickeners/Production of Gellan Gum	EFSA‐Q‐2018‐00815		No	Yes
Filamentous fungi
Food enzymes, food additives and flavourings	Aspergillus niger (DSM 25770)	Zootechnical additives Digestibility enhancers 6‐phytase produced by a GMM strain of Aspergillus niger (DSM 25770)	EFSA‐Q‐2019‐00042	Natuphos® E is a preparation of 6‐phytase produced by Aspergillus niger, LU17257 (DSM 25770)
Food enzymes, food additives and flavourings	Aspergillus niger DSM 32805	Food enzyme chymosin IUBMB name and number of the enzyme protein: 3.4.23.4; Chymosin from GMM strain of Aspergillus niger DSM 32805. This strain was previously known under the name A. niger var. awamori	EFSA‐Q‐2019‐00125		No	No
Feed additives	Aspergillus niger strain ATCC 26550 and NRC A‐1‐233	Zootechnical functional group/Performance enhancer AviPlus® is a preparation based on a mixture of sorbic acid, citric acid, thymol and vanillin	EFSA‐Q‐2019‐00154	The production of citric acid process is via fermentation of a stable non‐GMM Aspergillus niger strain	No	No
Feed additives	Aspergillus niger strain ATCC 26550/NRC A‐1‐233	Zootechnical additive/Performance enhancer AviPlus® is a preparation based on a mixture of sorbic acid, citric acid, thymol and vanillin	EFSA‐Q‐2019‐00157	The production of citric acid process is via fermentation of a stable non‐GMM Aspergillus niger strain	No	No
Plant protection products	Trichoderma atroviride AGR2	Plant protection product	EFSA‐Q‐2018‐00476	Pesticide risk assessment and peer review of Trichoderma atroviride AGR2 in accordance with Article 12 of Regulation (EC) No 1107/2009 (application for approval)	No	No
Feed additives	Trichoderma longibrachiatum MUCL 49754 /Trichoderma longibrachiatum MUCL 49755	Zootechnical additives/Production of endo‐1,4‐beta‐xylanase and endo‐1,3(4)‐beta‐glucanase	EFSA‐Q‐2018‐00762		No	No
Feed additives	Trichoderma reesei CBS143953	Zootechnical additives/endo‐1,4‐beta‐xylanase (EC 3.2.1.8) produced by GMM Trichoderma reesei, subtilisin protease (EC 3.4.21.62) produced by GMM Bacillus subtilis and alpha‐amylase (EC 3.2.1.1) produced by GMM Bacillus amyloliquefaciens	EFSA‐Q‐2018‐01040		No	No
Feed additives	Trichoderma reesei DSM 32338	Zootechnical additives/Production of muramidase	EFSA‐Q‐2018‐00952		No	No
Feed additives	Trichoderma reesei MUCL 49755	Zootechnical additives/Digestibility enhancers Used for the production of endo‐1,4‐beta‐xylanase (Bergazym® P 100)	EFSA‐Q‐2019‐00097	The strain used for the production of the xylanase is Trichoderma reesei MUCL 49755
Feed additives	Trichoderma reesei RF5427 strain	Zootechnical additives/Digestibility enhancers/Production of endo‐1,4‐beta‐xylanase	EFSA‐Q‐2018‐00824		No	No
Feed additives	Trichoderma reesei strain Morph‐Y5#2 (CBS143953)	Zootechnical additives/Digestibility enhancers/Production of Xylanase by GMM Trichoderma reesei	EFSA‐Q‐2018‐01039		No	No
Yeasts
Feed additives	Komagataella pastoris appaT75 (CGMCC 12056) previously known as Pichia pastoris	Zootechnical feed additive/Digestibility enhancer APSA PHYTAFEEDR 20,000 is a preparation of 6‐phytase produced in two formulations. APSA PHYTAFEEDR 20,000 is produced by fermentation of a GMM yeast	EFSA‐Q‐2019‐00188		Yes	No
Feed additives	Komagataella pastoris appaT75 (CGMCC 12056) previously known as Pichia pastoris	Zootechnical feed additive/Digestibility enhancer APSA PHYTAFEEDR 20,000 is a preparation of 6‐phytase produced in two formulations. APSA PHYTAFEEDR 20,000 is produced by fermentation of a GMM yeast	EFSA‐Q‐2019‐00192		Yes	No
Feed additives	Pichia pastoris	Nutrase P (6‐phytase) belongs to the category 4 ‘zootechnical additives’ in its functional group ‘digestibility enhancers’	EFSA‐Q‐2019‐00155	The strain used for the production is a GMM Pichia pastoris	Yes	No
Feed additives	Saccharomyces cerevisiae	Nutritional additives/vitamins, pro‐vitamins and chemically well‐defined substances having a similar effect 25‐hydroxycholecalciferol (25‐OH‐D3)	EFSA‐Q‐2019‐00155	25‐OH‐D3 is obtained from the raw material 5,7,24‐cholestatrienol (‘trienol’). Trienol is produced by a fermentation process using a GMM Saccharomyces cerevisiae strain number SC0639
Feed additives	Saccharomyces cerevisiae CBS 493.94	Zootechnical additives/Digestibility enhancers	EFSA‐Q‐2018‐00893		Yes	No
Feed additives	Saccharomyces cerevisiae CNCM I‐3399	Nutritional additives/Selenium‐enriched yeast	EFSA‐Q‐2018‐00908	Trace elements	Yes	No
Novel foods	Yarrowia lipolytica A‐101	As a novel food production of yeast biomass/Chromium enriched	EFSA‐Q‐2018‐00769	Application from same applicant as Yarrowia lipolytica biomass (see above)/Summary of application: NA Qualification: ‘for production purpose only’ implies the absence of viable cells of the production organism in the final product and can also be applied for food and feed products based on microbial biomass	Yes	No
Novel foods	Yarrowia lipolytica A‐101	As a novel food production of yeast biomass/Selenium enriched	EFSA‐Q‐2018‐00796	Application from same applicant as Yarrowia lipolytica biomass (See above)/Summary of application: NA Qualification: ‘for production purpose only’ implies the absence of viable cells of the production organism in the final product and can also be applied for food and feed products based on microbial biomass	Yes	No
Viruses
Plant protection products	Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV)	Plant protection product	EFSA‐Q‐2018‐00726	Pesticide risk assessment and peer review of Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) in accordance with Article 12 of Regulation (EC) No 1107/2009 (application for approval)	Yes	No
Algae
Novel foods	Euglena gracilis	As a novel food consisting on dried whole cells of Euglena gracilis	EFSA‐Q‐2019‐00043	A minimally processed dried biomass of E. gracilis preparation, containing a minimum of 50% algae beta‐glucan	No	Yes
Novel foods	Phaeodactylum tricornutum	PhaeoSOL is a novel food consisting on an extract of the microalgae Phaeodactylum tricornutum to be uses as a source of the naturally occurring carotenoid, fucoxanthin	EFSA‐Q‐2019‐00091	PhaeoSOL consists of an ethanolic extraction of microalgae dried biomass	No	Yes

^aTo find more details on specific applications please access the EFSA website ‐ Register of Questions: http://registerofquestions.efsa.europa.eu/roqFrontend/ListOfQuestionsNoLogin?0&panel=ALL

^bWhere no link is given this means that the risk assessment has not yet been published at the time of the publication of this Panel Statement.

^cIncluded in the QPS list as adopted in December 2016 (EFSA BIOHAZ Panel, 2017) and respective updates which include new additions (latest: EFSA BIOHAZ Panel, 2018).

^dIn the current Panel Statement.

Suggested citation: EFSA BIOHAZ Panel (EFSA Panel on Biological Hazards) , Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S and Herman L, 2019. Statement on the update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 10: Suitability of taxonomic units notified to EFSA until March 2019. EFSA Journal 2019;17(7):5753, 79 pp. 10.2903/j.efsa.2019.5753