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. 2021 Mar 22;10(3):339. doi: 10.3390/antibiotics10030339

Clonal Clusters, Molecular Resistance Mechanisms and Virulence Factors of Gram-Negative Bacteria Isolated from Chronic Wounds in Ghana

Denise Dekker 1,2,*, Frederik Pankok 3, Thorsten Thye 1, Stefan Taudien 3, Kwabena Oppong 4, Charity Wiafe Akenten 4, Maike Lamshöft 1,2, Anna Jaeger 1, Martin Kaase 3, Simone Scheithauer 3, Konstantin Tanida 5, Hagen Frickmann 5,6, Jürgen May 1,2,7, Ulrike Loderstädt 3
Editor: Manuela Oliviera
PMCID: PMC8004795  PMID: 33810142

Abstract

Wound infections are common medical problems in sub-Saharan Africa but data on the molecular epidemiology are rare. Within this study we assessed the clonal lineages, resistance genes and virulence factors of Gram-negative bacteria isolated from Ghanaian patients with chronic wounds. From a previous study, 49 Pseudomonas aeruginosa, 21 Klebsiella pneumoniae complex members and 12 Escherichia coli were subjected to whole genome sequencing. Sequence analysis indicated high clonal diversity with only nine P. aeruginosa clusters comprising two strains each and one E. coli cluster comprising three strains with high phylogenetic relationship suggesting nosocomial transmission. Acquired beta-lactamase genes were observed in some isolates next to a broad spectrum of additional genetic resistance determinants. Phenotypical expression of extended-spectrum beta-lactamase activity in the Enterobacterales was associated with blaCTX-M-15 genes, which are frequent in Ghana. Frequently recorded virulence genes comprised genes related to invasion and iron-uptake in E. coli, genes related to adherence, iron-uptake, secretion systems and antiphagocytosis in P. aeruginosa and genes related to adherence, biofilm formation, immune evasion, iron-uptake and secretion systems in K. pneumonia complex. In summary, the study provides a piece in the puzzle of the molecular epidemiology of Gram-negative bacteria in chronic wounds in rural Ghana.

Keywords: wounds, Gram-negative bacteria, colonization, infection, clonal lineages, resistance genes, virulence factors

1. Introduction

The microbiology of chronic infected wounds, also on a molecular level, is poorly understood in sub-Saharan Africa (SSA) [1]. However, studies highlight the importance of antibiotic resistant Gram-negative bacteria [2,3,4,5,6].

From other parts in the world, in particular from industrialized countries, information on the microbiology and the role of biofilm-forming microorganisms causing such infections are well established [7,8,9,10].

In chronic wounds, Pseudomonas aeruginosa is amongst the most frequently isolated Gram-negative bacteria, associated with biofilm formation [11,12]. Tightly adhering biofilms pose a challenge in the diagnosis of P. aeruginosa using standard culturing methods [13].

In comparison, the role of Enterobacterales in chronic wounds has been much less characterized [14,15,16,17]. Studies have shown that geography seems to play a role in the estimation of their etiological relevance [18]. It was shown that skin colonization with Gram-negative bacteria is frequent in resource-limited (sub)tropical settings [19,20,21], in contrast to skin colonization of individuals from industrialized countries, where Gram-positive bacteria dominate [19]. Temperature and moisture have been discussed as likely reasons for the difference seen [22].

Isolation of potentially pathogenic bacteria from non-sterile sites like wounds does not necessarily indicate clinical relevance, which poses challenge to clinical interpretation.

In a recent study that focused on the overall bacterial composition of chronic wound infections in Ghana, from which the isolates for the present molecular analysis were taken, Enterobacterales and Pseudomonas aeruginosa constituted the majority of isolated bacterial strains [23]. A moderate proportion of ESBL-positive Enterobacterales suggests lower frequencies of antibiotic resistance [23] than what was recorded from other Ghanaian hospitals [5,24].

Within this study, we aim at characterizing clonal lineages, resistance-associated genetic elements and virulence genes of P. aeruginosa, the Klebsiella pneumoniae complex and Escherichia coli, which were recently isolated from chronic wounds of Ghanaian adult patients [23]. The molecular epidemiology of dominating clonal lineages and associated resistance genes will be assessed. Further, analysis of highly abundant virulence factors will be conducted.

2. Results

2.1. Clustering Based on Core Genome Multilocus Sequence Typing (cgMLST) Results

Of the 49 P. aeruginosa analyzed, a total of nine clusters comprising isolates without any recorded differences (n = 2) or with one or two alleles difference (n = 7) were found, suggesting closely related phylogeny (Figure 1). In addition to the clusters, 31 singletons with differences ranging from 80 to 3584 alleles were observed. MLST sequence types (ST) are indicated in Figure 1 and Table A1 and Table A2. Cluster sequence types included the following: ST244, ST245, ST381, ST554, ST856, ST1485, ST2033, ST3227 and ST3590.

Figure 1.

Figure 1

Minimum spanning tree of P. aeruginosa based on 3867 targets (core genome). Isolate numbers are found within the nodes, and numbers between nodes indicate the number of different alleles. Isolates within clusters are colored based on MLST sequence type (ST). The ST types of white nodes are indicated in Table A1.

No clusters were identified among the 21 assessed K. pneumonia complex members, which were all singletons with differences ranging from 647 to 2244 alleles. K. pneumoniae complex sequence types are summarized in Figure 2. From the 12 E. coli isolates, three isolates in a cluster of close phylogenetic relationship were found (1× no allelic differences, 1 × 1 allele difference) (Figure 3). In addition to the cluster observed, nine singletons with differences ranging from 41 to 2365 alleles were recorded. The sequence type of the cluster was ST132 (Pasteur MLST scheme). Sequence types of all E. coli isolates are illustrated in Figure 3.

Figure 2.

Figure 2

Minimum spanning tree of K. pneumoniae complex based on 2358 targets (core genome). Isolate numbers are found within the nodes, and the numbers between the nodes indicate the number of different alleles. Colors demonstrate the MLST sequence type of the isolates.

Figure 3.

Figure 3

Minimum spanning tree of E. coli based on 2513 targets (core genome). Isolate numbers are found within the nodes, and the numbers between the nodes indicate the number of different alleles. Colors demonstrate the Pasteur sequence type of the isolates.

2.2. Identified Molecular Resistance Mechanisms in Correlation to Previous Phenotypic Antibiotic Resistance

Table 1 summarizes acquired antimicrobial resistance determinants for E. coli and acquired genes mediating tolerance to disinfectants. Data for P. aeruginosa and K. pneumoniae are presented in Table A1 and Table A2. Table A3, Table A4, Table A5, Table A6, Table A7 and Table A8 summarize the phenotypic resistance results as previously recorded [23].

Table 1.

Analysis of antimicrobial resistance determinants, ordered by strain and MLST type, of the assessed E. coli isolates. ST = Sequence type.

Sample ID ST-Type Acquired Resistance Determinants Against
Beta lacatams Sulfonamids Trimethoprim Makrodlids Tetracyclins Fluoroquinolones Chloramphenicol Aminoglycosides Efflux pumps Amino acid exchanges due to point mutations Disinfectant resistance genes *
041 ST 2 blaOXA-1, blaTEM-1B, blaCTX-M-15 sul1 dfrA17 mph(A) tet(B) aac(6′)-Ib-cr, aac(6′)-Ib-cr catB3,
catA1
aac(3)-IId, aac(6′)-Ib-cr, aadA5, aac(6′)-Ib-cr mdf(A) parE p.S458A, gyrA p.S83L, gyrA p.D87N, parC p.S80I sitABCD, qacE
049 ST 3 bla TEM-1B sul2, sul1, dfrA12 mph(A) tet(A) aadA2, aph(3″)-Ib, aph(6)-Id mdf(A) sitABCD-like,
qacE
068 ST 632 bla TEM-1B sul3 dfrA12 tet(A) cmlA1 aadA1, aadA2 mdf(A)-like parE p.S458A, gyrA p.S83L, gyrA p.D87N, parC p.S80I
117 ST 4 bla TEM-1B sul1, sul2 dfrA7 tet(A) catA1 aph(6)-Id, aph(3 ″)-Ib mdf(A)-like sitABCD-like, qacE
152 ST 22 blaCARB-2, blaTEM-1B sul1 dfrA1 ere(B) tet(B) catA1 aadA1, aadA2b mdf(A)-like gyrA p.S83L qacE, sitABCD
176 ST 132 bla TEM-1B sul1 dfrA7 tet(A) catA1 aph(3 ″)-Ib, aph(6)-Id mdf(A) qacE, sitABCD
221 ST 132 bla TEM-1B sul1 dfrA7 tet(A) catA1 aph(6)-Id, aph(3 ″)-Ib mdf(A) qacE, sitABCD
222 ST 132 bla TEM-1B sul1, sul2 dfrA7 tet(A) catA1 aph(3 ″)-Ib, aph(6)-Id mdf(A) qacE, sitABCD
225 ST 506 blaTEM-1D, blaCTX-M-15 sul1, sul2 dfrA17 mph(A) tet(A) catA1 aadA5, aph(6)-Id, aph(3″)-Ib mdf(A)-like gyrA p.S83L, parE p.I529L sitABCD-like, qacE
245 ST 2 bla TEM-1B sul1 dfrA12 mph(A) tet(B) qepA4 (neu) catA1 aadA2, aac(3)-IId mdf(A) parE p.S458A, gyrA p.S83L, gyrA p.D87N, parC p.S80I qacE
270 ST 2 bla CTX-M-15 tet(B) catA1 mdf(A) gyrA p.S83L, gyrA p.D87N, parE p.S458A, parC p.S80I
299 ST 1018 bla TEM-1B sul3 dfrA14 tet(A) qnrS1 mdf(A)

* sitABCD = peroxides resistance, qacE = quaternary ammonium compounds resistance.

In the present study, phylogenetically identical or almost identical isolates also carried the same resistomes. All E. coli strains harbored acquired beta-lactamase genes with the majority coding for small spectrum beta-lactamases such as blaTEM-1 or blaOXA-1. Only four strains carried the gene for an ESBL, in all cases blaCTX-M-15. Among the K. pneumoniae complex strains, two belonged to the species K. variicola, one to the species K. quasipneumoniae and the remaining to the species K. pneumoniae sensu stricto as reflected by intrinsic blaLEN, blaOKP and blaSHV-1 like, respectively. Genes coding for ESBL (blaCTX-M-15) were found solely in four out of 18 K. pneumoniae sensu stricto strains that also displayed resistance to oxyimino cephalosporins. In addition, several K. pneumoniae complex strains harbored blaTEM-1, single strains also contained blaOXA-1 and blaSCO-1.

With respect to P. aeruginosa, only one strain harbored acquired beta-lactamase genes (blaTEM-1 and blaSCO-1). Increased minimum inhibitory concentrations (MICs) for carbapenems as observed in some P. aeruginosa strains were neither explained by matching acquired carbapenemase genes nor by full sequence analysis of the oprD gene. The associated amino acid sequences are shown in Figure A1. As indicated, the complete oprD gene was found in all 49 P. aeruginosa isolates; there was no evidence of protein truncation by premature stop of translation. The 49 isolates could be divided into 7 subgroups according to the protein sequence of the oprD protein, which differ in a total of 30 individual amino acid exchanges and in a single 12aa/10aa-stretch. Therefore, genotypic assessment could not identify the reason for the single carbapenem-resistant P. aeuroginosa isolate 088 (ST 1682).

Other frequently detected resistance genes in P. aeruginosa were the fosfomycin resistance gene fosA, the chloramphenicol resistance gene catB7, the aminoglycoside resistance gene aph(3′)-IIb and the fluoroquinolone-resistance gene crpP. In the Klebsiella pneumoniae complex isolates, single amino acid exchanges and the fosmomycin resistance gene fosA were frequent. Various fluoroquinolone resistance genes and disinfectant tolerance mediating genes also quantitatively dominated. Finally, a broad spectrum of acquired genes causing resistance to the assessed classes of antimicrobial drugs and tolerance to disinfectants was observed in the E. coli strains.

2.3. Identified Molecular Virulence Mechanisms

Table 2 summarizes the analysis of virulence-related genes in E. coli (without genes mediating enteropathogenicity). Data for P. aeruginosa and K. pneumoniae are presented in Table A9 and Table A10.

Table 2.

Analysis of virulence determinants, ordered by strain and MLST type, of the assessed E. coli isolates. ST = Sequence type.

Sample ID ST-Type Pathogenicity Factor Groups
Adherence Invasion Toxin Immune Evasion Iron Uptake Protease
041 ST 2 fdeC aslA, ompA entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG,
049 ST 3 aslA, kpsC, kpsD, kpsE, kpsF, kpsM, kpsU, kpsS-like, ompA chuS, chuU, chuV, chuW, chuY, entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG
068 ST 632 ompA entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG
117 ST 4 aslA, kpsC, kpsD, kpsE, kpsF, kpsM, kpsU; kpsS-like, ompA hlyB, hlyC, hlyD, tcpC chuA, chuS, chuT, chuU, chuV, chuW, chuX, chuY, entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG, hlyA, iroN, pic, sat, vat
152 ST 22 sfaB, sfaC, sfaD, sfaE, sfaF, sfaG, sfaH, sfaS, sfaX, sfaY aslA, kpsC, kpsD, kpsE, kpsF, kpsM, kpsU; kpsS-like, ompA cnf1; hlyA, hlyB, hlyC, hlyD, tcpC chuA, chuS, chuT, chuU, chuV, chuW, chuX, chuY, entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG, iroN, vat
176 ST 132 aslA, kpsC, kpsD, kpsE, kpsF, kpsM, kpsU; kpsS-like, ompA entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG, sat
221 ST 132 aslA, kpsC, kpsD, kpsE, kpsM, kpsU; kpsS-like, ompA entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG, sat
222 ST 132 aslA, kpsC, kpsD, kpsE, kpsF, kpsM, kpsU; kpsS-like, ompA entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG, sat
225 ST 506 aslA, kpsC, kpsD, kpsE, kpsF, kpsM, kpsU; kpsS-like, ompA chuA, chuS, chuT, chuU, chuV, chuW, chuX, chuY, entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepC, fepD, fepG, sat
245 ST 2 aslA, ompA entA-like, entB, entC, entE, entF, entS, fepB, fepC, fepD, fepG
270 ST 2 aslA, ompA entA-like, entB, entC, entE, entS, fepA, fepB, fepC, fepD, fepG
299 ST 1018 ompA entA-like, entB, entC, entE, entF, entS, fepA, fepB, fepD, fepG

The virulence-associated gene exoU, which has been described in association with the P. aeruginosa high-risk clone ST 135 [25], was recorded three times, associated with ST 135 (sample ID 296), ST 532 (sample ID 310) and ST 2483 (sample ID 22), respectively. Based on a Kleborate assessment, a positive virulence score was calculated for 7 out of 21 K. pneumoniae strains, comprising the known high-risk clones ST 17 (sample IDs 177, 199) and ST 152 (sample ID 100) [26], next to the clones ST 4 (sample ID 146), ST 6 (sample ID 214), ST 36 (sample ID 267) and ST 39 (sample ID 73), respectively. With focus on some important virulence associated genes in Klebsiella spp., ybt genes were detected in the abovementioned 7 samples, iroE was recorded in all 21 strains, while clb or rpmA genes were not detected.

Iron-uptake-related genes were numerous in all analyzed bacterial strains. For P. aeruginosa and K. pneumoniae, various secretion system-associated genes were found. Immune evasion-related genes were highly abundant in K. pneumoniae but not in E. coli isolates. Adherence-related genes were numerous in P. aeruginosa and in K. pneumoniae but not in E. coli.

Numerous invasion-associated genes were detected in E. coli, antiphagocytosis-associated genes were found in P. aeruginosa, and biofilm-associated genes in K. pneumoniae.

Less frequently detected were: toxin genes in E. coli and K. pneumoniae, protease genes in E. coli and P. aeruginosa, regulation genes in P. aeruginosa and K. pneumoniae, biosurfactant and pigment genes in P. aeruginosa and nutrition factor, efflux pumps and serum resistance genes in K. pneumoniae.

3. Discussion

Within this study, we aimed at filling information gaps on the molecular epidemiology of Gram-negative bacteria from chronic infected wounds in rural Ghana. Phylogenetic analyses based on core genome comparison indicated a high clonal diversity of the wound-associated isolates. Clonal clusters were restricted to nine P. aeruginosa clusters and one E. coli cluster, most likely indicating nosocomial transmission, which has most likely occurred in the wound dressing room that patients’ visit on a weekly basis.

ST 135 and ST 244, which are among the worldwide top 10 P. aeruginosa high-risk clones [25], were found among the P. aeruginosa wound isolates. In detail, one ST 135 Pseudomonas aeruginosa isolate was detected, carrying the beta-lactamase-encoding genes blaTEM-1B and blaSCO-1 and an exoU gene, next to five ST 244 without acquired beta-lactamases. Focusing on known pathogenic K. pneumoniae clones [26], two ST 17 strains, a clone reported to be associated with carbapenem-resistance, and one ST 152 strain, a clone known from the Caribbean as common carrier of multiple resistance genes, were detected. Strains carrying the ybt and iro genes were also identified as high-risk clones by the Kleborate software. From the observed E. coli ST types, none have been previously reported as being associated with pathogenic clones so far [27].

In line with the phenotypical antibiotic resistance results previously published [23], numerous acquired resistance determinants were detected in the bacterial strains under investigation. Focusing on the few observed clusters, comparable resistome compositions point towards recent nosocomial transmission. The gene blaCTX-M-15 was identified as the determinant of the detected extended spectrum beta-lactamase (ESBL) expression in ESBL positive Enterobacterales [23]. This is in line with previous reports from both human and livestock-associated ESBL positive Enterobacterales in Ghana [28,29,30,31,32,33,34]. In P. aeruginosa and K. pneumoniae, blaSCO-1, which has initially been described from an Acinetobacter baumannii isolate from Argentina [35], was observed. Beta-lactamases with high hydrolytic effects on carbapenems were lacking, the same applies to protein truncation by premature stop of translation of the oprD gene in P. aeruginosa. Accordingly, the genetic background of carbapenem resistance of a single P. aeruginosa strain could not be resolved, although downregulation of oprD expression due to mutations outside of the gene or ampC (class C betalactamase) overexpression could not be excluded as likely reasons.

Substance-specific genes and genes encoding efflux pumps mediating tolerance to disinfectants were observed in Enterobacterales. Therefore, further monitoring of the spread of disinfectant tolerance-associated genes and the effects of their abundance on disinfectant-based skin and wound decolonization strategies [36] seem advisable.

The importance of highly abundant virulence factors like iron-uptake- and secretion system-related genes in P. aeruginosa is comprehensively described in the literature [37,38]. Other genes reported in the literature like regulation-associated virulence genes, recently reported, were less frequently observed in our isolates [39,40]. However, due to lacking information on the individual etiological relevance of each isolate, any association with clinical effects remains speculative.

Further limitations of this study include a rather small sample size and the lack of a comparison strain collection containing isolates from other clinical specimens and environmental strains. Accordingly, the interpretation of the etiological relevance of individual strains remains challenging and is clearly beyond the scope of this work.

In summary, a broad spectrum of Gram-negative clones was isolated from the chronic wounds of the Ghanaian patients. Thereby, known high-risk clones [25,26,27] played only a minor role. Observed resistance patterns and mechanisms were in line with the spectrum expected from previous reports [23,28,29,30,31,32,33,34].

4. Materials and Methods

4.1. Sample Collection, Bacterial Culture and Antibiotic Susceptibility Testing

Single patient strains of P. aeruginosa, E. coli and K. pneumoniae complex were isolated from patients ≥15 years with an infected chronic wound at the Outpatient Department (OPD) of the Agogo Presbyterian Hospital, in the Asante Akim North District of rural Ghana. Patients typically visit the wound dressing room of the OPD on a weekly basis. Sampling was performed from January 2016 to November 2016. Sample collection and microbiological investigations were reported previously [23]. Antibiotic susceptibility was tested by the disk diffusion method and interpreted following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines v.6.0 (http://www.eucast.org (accessed on 15 January 2016)). Bacterial strains and antibiotic susceptibility were confirmed using the VITEK2 System. Those data have been published before [23].

4.2. DNA Isolation and Whole Genome Sequencing

Bacterial DNA was isolated using the MasterPure Complete DNA and RNA Purification Kit (LGC standards GmbH, Wesel, Germany) and sent for whole genome sequencing (WGS) to BGI Europe, Denmark, Copenhagen. A BGISEQ-500 device was used for sequencing, generating 2 × 150 bp paired-end reads with an aimed coverage of 100×. Original raw data were upload for public use to the short-read archive (SRA, NCBI) under the accession number PRJNA699140. Details on the strain-specific SRA accession numbers are provided in Table A11.

4.3. Whole Genome Sequencing and Data Analysis

All raw data passed quality control using FASTQC v.0.11.4 [41] and were used for further analysis. Taxonomic classification and contamination check of raw-reads was performed using KRAKEN2 v.2.0.8-beta [42]. Phylogenetic analysis based on core genome multi locus sequence typing (cgMLST) analysis was performed using the commercial software SeqSphere+ v. 7.2.0 (Ridom GmbH, Münster, Germany) [43]. The software pipeline included assessment of read data and adapter control using FASTQC followed by genome assembly using the internally provided assembler Velvet, applying default settings. The reference genomes NC_000913.3 (E. coli), NC_002516.2 (P. aeruginosa) and NC_01273.1 (K. pneumoniae species complex) were used for cgMLST analyses. Only samples with a ration of “good cgMLST targets” higher than 90% were included in the phylogenetic analysis. Novel cgMLST-based complex types (CT) were automatically assigned by the SeqSphere software. Unknown alleles and profiles of MLST genes were submitted to pubmlst.org or Institute Pasteur to establish novel sequence types (ST). Isolates were defined to be clonally identical with allele differences less than four. Moreover, raw data were assembled with SPAdes v3.13.11 [44] using the careful option. Scaffolds shorter than 500 bp or with a coverage smaller than ten were sorted out, using an in-house script. Abricate v.0.9.9 [45] was used to screen for resistance and virulence genes in SPAdes assembly files, using NCBI AMRFinderPlus [46] and VFDB [47] as reference databases (both updated 6 November 2020), respectively. Additionally, SPAdes assemblies were uploaded to ResFinder4.1 [48] to obtain WGS predicted phenotypes against different antimicrobials by using default settings (%ID > 90, minimum length > 60%) and to Kleborate to predict virulence genes in Klebsiella isolates.

4.4. Ethical Considerations

The Committee on Human Research, Publications and Ethics, School of Medical Science, Kwame Nkrumah University of Science and Technology in Kumasi, Ghana, approved this study (approval number CHRPE/AP/078/16).

5. Conclusions

In conclusion, this study provides a molecular insight into the epidemiology of Gram-negative bacteria isolated from chronic wound infections from patients in rural Ghana. Epidemiological data that focus on the distribution and spread of antimicrobial resistance determinants and associated virulence factors in resource-limited settings are scarce. Although the study is a small cross-sectional assessment, which cannot replace continuous surveillance programs, it might provide a glimpse of prevailing Gram-negative bacteria isolated from wound infections in this area of Ghana. Considering the ongoing need for resistance and virulence surveillance in tropical regions, larger future studies are desirable.

Acknowledgments

We thank all patients that participated in this study and the staff at the Agogo Presbyterian Hospital. Without their support, this research study would not have been possible. We thank the team of curators pubmlst.org and the Institute Pasteur MLST and whole genome MLST databases for curating the data and making them publicly available at http://bigsdb.pasteur.fr/ (accessed on 22 March 2021).

Appendix A

Table A1.

Analysis of antimicrobial resistance determinants, ordered by strain and MLST type, of the assessed P. aeruginosa isolates. ST = Sequence type.

Sample ID ST-Type Acquired Resistance Determinants Against
Beta Lacatams Sulfonamids Fosfomycin Trimethoprim Makrolides Tetracyclinws Fluoroquinolones Chloramphenicol Rifampicin Aminoglycosides Efflux Pumps Amino Acid Exchanges Due to Point Mutations Disinfectant Resistance Genes
017 ST 381 fosA catB7 aph(3′)-IIb
022 ST 2483 fosA catB7 aph(3′)-IIb
032 ST 3587 sul1 fosA dfrA15 tet(G) catB7 aph(3′)-IIb
069 ST 360 fosA crpP-like catB7 aph(3′)-IIb
081 ST 244 fosA catB7 aph(3′)-IIb
082 ST 514 fosA catB7 aph(3′)-IIb
088 ST 1682 fosA catB7 aph(3′)-IIb
099 ST 244 fosA catB7 aph(3′)-IIb
106 ST 1521 fosA catB7 aph(3′)-IIb
114 ST 244 fosA crpP-like catB7 aph(3′)-IIb-like
137 ST 3014 fosA crpP-like catB7 aph(3′)-IIb-like
144 ST 245 fosA crpP-like catB7 aph(3′)-IIb
147 ST 245 fosA crpP-like catB7 aph(3′)-IIb
149 ST 381 fosA crpP-like catB7 aph(3′)-IIb
153 ST 704 fosA-like crpP-like catB7-like aph(3′)-IIb- like
154 ST 244 , fosA crpP-like catB7 aph(3′)-IIb-like
157 ST 2616 fosA catB7-like aph(3′)-IIb
160 ST 170 fosA-like aph(3′)-IIb
162 ST 274 fosA crpP-like catB7 aph(3′)-IIb
180 ST 856 fosA catB7 aph(3′)-IIb
183 ST 244 fosA catB7 aph(3′)-IIb-like
186 ST 3588 fosA-like catB7-like aph(3′)-IIb-like
190 ST 871 fosA catB7-like aph(3′)-IIb
195 ST 988 fosA crpP-like catB7-like aph(3′)-IIb-like
196 ST 2475 fosA crpP-like catB7 aph(3′)-IIb
198 ST 2476 fosA crpP-like catB7 aph(3′)-IIb
204 ST 639 fosA crpP catB7 aph(3′)-IIb-like
208 ST 132 fosA crpP-like catB7 aph(3′)-IIb
218 ST 856 fosA catB7 aph(3′)-IIb
229 ST 270 fosA crpP-like catB7 aph(3′)-IIb
233 ST 3227 fosA catB7 aph(3′)-IIb
236 ST 266 fosA catB7 aph(3′)-IIb
238 ST 3589 fosA-like crpP-like catB7-like aph(3′)-IIb-like
242 ST 3590 fosA-like
243 ST 3590 fosA-like catB7-like aph(3′)-IIb-like
272 ST 2033 fosA catB7-like aph(3′)-IIb-like
274 ST 2033 fosA catB7-like aph(3′)-IIb
278 ST 988 fosA crpP-like catB7-like
282 ST 554 fosA crpP-like catB7 aph(3′)-IIb
285 ST 554 fosA catB7 aph(3′)-IIb
289 ST 1485 fosA catB7 aph(3′)-IIb
290 ST 1485 fosA catB7 aph(3′)-IIb
296 ST 235 blaTEM-1B, blaSCO-1 sul1 fosA tet(G) catB7-like aph(3′)-IIb-like, aac(3)-IIa
298 ST 3227 fosA catB7 aph(3′)-IIb
301 ST 3593 fosA-like catB7-like aph(3′)-IIb-like
302 ST 1755 fosA catB7 aph(3′)-IIb
309 ST 3592 fosA like crpP-like catB7-like aph(3′)-IIb-like
310 ST 532 sul1 fosA catB7-like aph(3″)-Ib, aph(6)-Id, aph(3′)-IIb
312 ST 381 fosA catB7 aph(3′)-IIb

Acquired resistance genes for macrolides, rifampicin, resistance-associated point mutations, genes for efflux pumps or genes mediating tolerance against disinfectants were not detected.

Table A2.

Analysis of antimicrobial resistance determinants, ordered by strain and MLST type, of the assessed K. pneumoniae isolates. ST = Sequence type.

Sample ID ST-Type Acquired Resistance Determinants Against
Beta Lacatams Sulfonamids Fosfomycin Trimethoprim Macrolides Tetracyclines Fluoroquinolones Chloramphenicol Rifampicin Aminoglycosides Efflux Pumps Amino Acid Exchanges Due to Point Mutations Disinfectant Resistance Genes *
044 ST 327 fosA oqxB, oqxA ompK37 p.I70M, ompK37 p.I128M,ompK37 p.I128M, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R, ompK36 p.T254S, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxB, oqxA
060 ST 5379 bla TEM-1C sul1, sul2 fosA dfrA12 mph(A) oqxA, oqxB, qnrS1 catA2-like aph(6)-Id, aph(3″)-Ib, aph(3′)-Ia, aadA2, aac(3)-IIa acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.T184P, ompK37 p.I70M, ompK37 p.I128M oqxA, qacE, oqxB
073 ST 39 blaTEM-1B , bla CTX-M-15 sul1, fosA dfrA27 erm(B), mph(A) tet(D) oqxB, oqxA, aac(6′)-Ib-cr, qnrB2, aac(6′)-Ib-cr catA2-like ARR-3 aac(6′)-Ib-cr, aadA16, aac(3)-IIa, aac(6′)-Ib-cr, aph(3″)-Ib, aph(6)-Id acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK37 p.I70M, ompK37 p.I128M, ompK37 p.N230G, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R, ompK36 p.T254S oqxB, oqxA, qacE
100 ST 152 blaCTX-M-15 , bla OXA-1 , bla TEM-1B sul2, sul1 fosA dfrA1, dfrA27 mph(A) tet(D) aac(6′)-Ib-cr, oqxB, qnrB6, oqxA, aac(6′)-Ib-cr catB3, catA1, catB3 ARR-3 aac(3)-IIa, aph(6)-Id, aph(3″)-Ib, aadA1, aadA16, aph(3′)-Ia, aac(6′)-Ib-cr, aac(6′)-Ib-cr ompK36 p.N49S, ompK36 p.L59V, ompK36 p.G189T, ompK36 p.F198Y, ompK36 p.F207Y, ompK36 p.A217S, ompK36 p.T222L, ompK36 p.D223G, ompK36 p.E232R, ompK36 p.N304E, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK37 p.I70M, ompK37 p.I128M, ompK37 p.N230G oqxB, oqxA
102 ST 514 fosA tet(C) oqxB, oqxA catA1 ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R, ompK36 p.T254S, ompK37 p.I70M, ompK37 p.I128M, ompK37 p.N230G, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxB, oqxA
124 ST 399 fosA oqxA, oqxB catA1 ompK36 p.N49S, ompK36 p.L59V, ompK36 p.G189T, ompK36 p.F198Y, ompK36 p.F207Y, ompK36 p.A217S, ompK36 p.T222L, ompK36 p.D223G, ompK36 p.E232R, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.F197I, acrR p.K201M, ompK37 p.I70M, ompK37 p.I128M oqxA, oqxB
146 ST 4 sul2 fosA tet(D) oqxA, oqxB catA2-like oqxA, oqxB
177 ST 17 sul1, sul2 fosA dfrA15 tet(A) oqxA, oqxB-like catA1 aadA1, aph(3″)-Ib, aph(6)-Id ompK37 p.I70M, ompK37 p.I128M, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK36 p.N49S, ompK36 p.L59V,ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232RompK36 p.T254S qacE, oqxB-like, oqxA
181 ST 5380 fosA oqxA, oqxB ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R, ompK36 p.T254S,ompK37 p.I70M, ompK37 p.I128M, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxA, oqxB
184 ST 5381 fosA oqxA-like, oqxB-like ompK37 p.I70M, ompK37 p.I128M, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191Q, ompK36 p.F198Y,ompK36 p.A217S, ompK36 p.N218H, ompK36 p.Q227N, ompK36 p.L229V, ompK36 p.N304E, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxA-like, oqxB-like
199 ST 17 blaCTX-M-15 , bla TEM-1B sul2, sul1 fosA-like dfrA16 oqxA, oqxB aadA2b, aac(3)-IIa acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK37 p.I70M, ompK37 p.I128M, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.T86V, ompK36 p.S89T, ompK36 p.D91K, ompK36 p.A93S, ompK36 p.L191Q, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.Q227N, ompK36 p.L229V, ompK36 p.E232R,ompK36 p.H235D, ompK36 p.T254S oqxA, oqxB, qacE
214 ST 6 sul1 fosA-like dfrA14 oqxB-like, oqxA catA1 aph(3′)-Ia ompK37 p.I70M, ompK37 p.I128M, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.G189T, ompK36 p.F198Y, ompK36 p.F207Y, ompK36 p.A217S, ompK36 p.T222L, ompK36 p.D223G, ompK36 p.E232R, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxB- like, oqxA
217 ST 3154 blaSCO-1 , bla TEM-1B sul1, sul2 fosA dfrA12, dfrA14 tet(A) oqxA, oqxB-like catA2-like aph(6)-Id, aph(3″)-Ib, aac(3)-IIa, aadA2 acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK37 p.I70M, ompK37 p.I128M, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.G189T, ompK36 p.F198Y, ompK36 p.F207Y, ompK36 p.A217S, ompK36 p.T222L, ompK36 p.D223G, ompK36 p.E232R, ompK36 p.N304E oqxA, qacE, oqxB-like
220 ST 5382 fosA-like oqxB-like, oqxA-like catA1 ompK37 p.I70M, ompK37 p.I128M, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191Q, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.Q227N, ompK36 p.L229V, ompK36 p.N304E, acrR p.P161R, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxB-like, oqxA-like
234 ST 109 fosA oqxA, oqxB-like ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R, ompK36 p.T254S, acrR p.P161R, acrR p.G164A, acrR p.F172S,acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK37 p.I70M, ompK37 p.I128M oqxA, oqxB-like
240 ST 5383 fosA-like tet(D) oqxA, oqxB-like ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R, ompK37 p.I70M, ompK37 p.I128M, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I,acrR p.K201M oqxA, oqxB-like
248 ST 5384 fosA-like tet(A) oqxB-like, oqxA-like catA1 ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F198Y, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R, ompK37 p.I70M, ompK37 p.I128M, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxB-like, oqxA-like
252 ST 607 bla TEM-1B sul2, sul1 fosA-like dfrA7 tet(A) oqxB-like, oqxA catA1 aph(3″)-Ib, aph(6)-Id ompK37 p.I70M, ompK37 p.I128M, ompK37 p.N230G, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R, ompK36 p.T254S, acrR p.P161R,acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxB-like, oqxA, qacE
267 ST 36 blaCTX-M-15 , bla TEM-1B sul2, sul1 fosA dfrA27 tet(D) aac(6′)-Ib-cr, oqxA, oqxB catA2-like ARR-3 aph(6)-Id, aph(3″)-Ib, aac(6′)-Ib-cr, aadA16, aac(3)-IIa, aph(6)-Id ompK36 p.N49S, ompK36 p.L59V, ompK36 p.T184P, ompK37 p.I70M, ompK37 p.I128M, ompK37 p.N230G, acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M oqxA, qacE, oqxB
277 ST 530 bla TEM-35 sul2 fosA-like dfrA14 tet(D) oqxA, oqxB-like aph(3″)-Ib, aph(6)-Id acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.L191S, ompK36 p.F207W, ompK36 p.A217S, ompK36 p.N218H, ompK36 p.D224E, ompK36 p.L228V, ompK36 p.E232R,ompK36 p.T254S, ompK37 p.I70M, ompK37 p.I128M oqxA, oqxB-like
279 ST 5385 fosA oqxA, oqxB acrR p.P161R, acrR p.G164A, acrR p.F172S, acrR p.R173G, acrR p.L195V, acrR p.F197I, acrR p.K201M, ompK36 p.N49S, ompK36 p.L59V, ompK36 p.T184P, ompK37 p.I70M, ompK37 p.I128M oqxA, oqxB

* qacE = quaternary ammonium compounds resistance and oqxB and oqxA = efflux pumps mediating resistance against disinfectants.

Table A3.

Phenotypic resistance the P. aeruginosa strains. Data are missing for strains 198, 218 and 312, due to loss during subcultivation. MIC = minimum inhibitory concentration. N.a. = value missing due to loss of strain or failed reaction.

Sample ID Piperacillin Piperacillin/Tazobactam Ceftrazidime Cefepime Imipenem Meropenem Gentamicin
MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation
17 ≤4 S ≤4 S ≤1 S ≤1 S ≤0.25 S ≤0.25 S ≤1 S
22 ≤4 S ≤4 S ≤1 S ≤1 S ≤0.25 S ≤0.25 S ≤1 S
32 ≤4 S 8 S 2 S 2 S 1 S ≤0.25 S ≤1 S
69 ≤4 S ≤4 S 4 S 2 S 1 S ≤0.25 S ≤1 S
81 ≤4 S 8 S 2 S ≤1 S 1 S 1 S ≤1 S
82 16 S 8 S 4 S 2 S 2 S ≤0.25 S ≤1 S
88 ≥128 R ≥128 R ≥64 R 32 R ≥16 R 4 I ≤1 S
99 8 S 8 S 4 S 2 S 2 S 1 S ≤1 S
106 ≤4 S 8 S 2 S 2 S 2 S 1 S ≤1 S
114 ≤4 S 8 S 2 S ≤1 S 2 S 1 S ≤1 S
137 16 S 8 S 4 S 2 S 2 S 2 S ≤1 S
144 16 S 8 S 4 S 2 S 2 S 1 S ≤1 S
147 8 S ≤4 S 4 S 8 S 2 S 0.5 S 4 S
149 8 S 8 S 4 S 2 S ≤0.25 S ≤0.25 S ≤1 S
153 ≤4 S 8 S 2 S ≤1 S 1 S ≤0.25 S ≤1 S
154 64 R ≤4 S ≤1 S ≤1 S 2 S 0.5 S ≤1 S
157 16 S 8 S 4 S 4 S 2 S ≤0.25 S 2 S
160 ≥128 R 32 R 16 R 32 R 8 I 8 I 8 R
162 64 R 32 R 8 S 8 S 2 S 1 S 2 S
180 16 S 8 S 4 S 2 S 2 S ≤0.25 S ≤1 S
183 8 S 8 S 4 S 2 S 2 S 0.5 S ≤1 S
186 16 n.a. n.a. S 4 S 2 S 2 S ≤0.25 S ≤1 S
190 16 S 8 S 4 S 2 S 2 S 0.5 S ≤1 S
195 8 S 8 S 4 S ≤1 S 2 S ≤0.25 S ≤1 S
196 ≤4 S ≤4 S 2 S ≤1 S 2 S 0.5 S ≤1 S
198 n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a.
204 8 S 8 S 2 S ≤1 S 2 S ≤0.25 S ≤1 S
208 8 S 8 S 4 S 2 S 2 S ≤0.25 S ≤1 S
218 n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a.
229 8 S 8 S 4 S 2 S 1 S ≤0.25 S ≤1 S
233 ≥128 R ≥128 R 32 R 8 S 8 I 4 I ≤1 S
236 16 S 16 S 4 S 2 S 2 S 0.5 S 2 S
238 8 S 16 S 4 S 2 S 2 S ≤0.25 S ≤1 S
242 8 S 8 S 4 S 2 S 1 S ≤0.25 S ≤1 S
243 16 S 8 S 4 S 2 S 1 S ≤0.25 S ≤1 S
272 64 R 64 R 8 S 4 S 2 S 1 S ≤1 S
274 16 S 8 S 4 S 2 S 2 S 0.5 S ≤1 S
278 ≤4 S ≤4 S 2 S ≤1 S 2 S ≤0.25 S ≤1 S
282 ≤4 S 8 S ≤1 S ≤1 S 2 S 1 S ≤1 S
285 ≤4 S ≤4 S ≤1 S ≤1 S 2 S 1 S ≤1 S
289 ≤4 S 8 S ≤1 S ≤1 S 2 S 1 S ≤1 S
290 8 S 8 S ≤1 S ≤1 S 2 S 1 S ≤1 S
296 ≥128 R 64 R 4 S 8 S 1 S 1 S ≥16 R
298 ≥128 R ≥128 R ≥64 R 8 S 8 I 4 I ≤1 S
301 16 S 8 S 4 S 2 S 2 S 0.5 S ≤1 S
302 8 S 8 S 4 S ≤1 S 2 S 0.5 S ≤1 S
309 16 S 8 S 4 S 4 S 2 S 1 S ≤1 S
310 32 R 16 S 4 S 4 S 2 S 1 S ≤1 S
312 n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a.

Table A4.

Phenotypic resistance of P. aeruginosa strains. Data are missing for strains 198, 218 and 312 due to loss during subcultivation. MIC = minimum inhibitory concentration. N.a. = value missing due to loss of strain or failed reaction.

Sample ID Ciprofloxacin Moxifloxacin Aztreonam Amikacin Tobramycin Fosfomycin Colistin
MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation
17 ≤0.25 S 1 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
22 ≤0.25 S 1 R 2 I ≤2 S ≤1 S 128 R 1 S
32 ≤0.25 S 2 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
69 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
81 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S ≥256 R ≤0.5 S
82 ≤0.25 S 1 R 16 I ≤2 S ≤1 S ≤16 R ≤0.5 S
88 2 R ≥8 R 32 R ≤2 S ≤1 S 128 R ≤0.5 S
99 ≤0.25 S 2 R 16 I ≤2 S ≤1 S 128 R ≤0.5 S
106 2 R 1 R 8 I ≤2 S ≤1 S ≥256 R ≤0.5 S
114 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
137 ≤0.25 S 1 R 16 I ≤2 S ≤1 S ≥256 R ≤0.5 S
144 ≤0.25 S 1 R 16 I ≤2 S ≤1 S ≥256 R ≤0.5 S
147 ≤0.25 S 2 R 4 I 8 S ≤1 S ≥256 R ≤0.5 S
149 ≤0.25 S 1 R 16 I ≤2 S ≤1 S ≥256 R ≤0.5 S
153 ≤0.25 S 2 R 4 I ≤2 S ≤1 S ≤16 R ≤0.5 S
154 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S ≥256 R ≤0.5 S
157 ≤0.25 S 1 R 16 I ≤2 S ≤1 S ≥256 R ≤0.5 S
160 1 R ≥8 R ≥64 R 16 I ≤1 S 64 R ≤0.5 S
162 0.5 S 2 R 32 R 4 S ≤1 S 128 R ≤0.5 S
180 ≤0.25 S 1 R 16 I ≤2 S ≤1 S ≥256 R ≤0.5 S
183 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S ≥256 R ≤0.5 S
186 ≤0.25 S 1 R 16 I ≤2 S ≤1 S 32 R ≤0.5 S
190 ≤0.25 S 1 R 16 I 4 S ≤1 S 32 R ≤0.5 S
195 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S 64 R ≤0.5 S
196 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S 64 R ≤0.5 S
198 n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a.
204 ≤0.25 S 1 R 2 I ≤2 S ≤1 S 32 R 2 S
208 ≤0.25 S 1 R 8 I ≤2 S ≤1 S 128 R ≤0.5 S
218 n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a.
229 ≤0.25 S 1 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
233 ≤0.25 S 2 R 16 I ≤2 S ≤1 S ≤16 R ≤0.5 S
236 ≤0.25 S 1 R 16 I 8 S ≤1 S 64 R ≤0.5 S
238 ≤0.25 S 2 R 8 I ≤2 S ≤1 S ≤16 R ≤0.5 S
242 ≤0.25 S 1 R 8 I ≤2 S ≤1 S 128 R ≤0.5 S
243 ≤0.25 S 2 R 16 I ≤2 S ≤1 S 64 R ≤0.5 S
272 ≤0.25 S 2 R 32 R ≤2 S ≤1 S ≥256 R ≤0.5 S
274 ≤0.25 S 2 R 16 I ≤2 S ≤1 S ≥256 R ≤0.5 S
278 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
282 ≤0.25 S 1 R 2 I ≤2 S ≤1 S 128 R ≤0.5 S
285 ≤0.25 S 1 R 2 I ≤2 S ≤1 S 128 R ≤0.5 S
289 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
290 ≤0.25 S 0.5 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
296 ≥4 R ≥8 R 32 R ≤2 S ≥16 R 64 R ≤0.5 S
298 ≤0.25 S 2 R 16 I ≤2 S ≤1 S ≤16 R ≤0.5 S
301 ≤0.25 S 2 R 16 I ≤2 S ≤1 S ≤16 R ≤0.5 S
302 ≤0.25 S 1 R 4 I ≤2 S ≤1 S 128 R ≤0.5 S
309 ≤0.25 S 1 R 4 I ≤2 S ≤1 S ≤16 R ≤0.5 S
310 ≤0.25 S 2 R 16 I ≤2 S ≤1 S 128 R ≤0.5 S
312 n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a. n.a.

Table A5.

Phenotypic resistance of the Klebsiella strains. MIC = minimum inhibitory concentration. ESBL = signal in phenotypic testing for extended-spectrum beta-lactamases.

Sample ID ESBL Ampicillin Ampicillin/Sulbactam Piperacillin/Tazobactam Cefuroxime Cefuroxime Axetil Cefpodoxime Cefotaxime Ceftrazidime
MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation
44 negative ≥32 R 16 R ≤4 S 4 I 4 I ≤0.25 S ≤1 S ≤1 S
60 negative ≥32 R 16 R ≤4 S ≤1 I ≤1 S ≤0.25 S ≤1 S ≤1 S
73 positive ≥32 R ≥32 R ≥128 R ≥64 R ≥64 R ≥8 R ≥64 R 8 R
100 positive ≥32 R ≥32 R ≥128 R ≥64 R ≥64 R ≥8 R ≥64 R 16 R
102 negative ≥32 R ≤2 I 8 S 8 I 8 I ≤0.25 S ≤1 S ≤1 S
124 negative ≥32 R ≤2 I ≤4 S 2 I 2 I ≤0.25 S ≤1 S ≤1 S
146 negative ≥32 R ≤2 I 8 S 2 I 2 I ≤0.25 S ≤1 S ≤1 S
177 positive ≥32 R ≥32 R ≥128 R 2 I 2 S ≤0.25 S ≤1 S ≤1 I
181 negative ≥32 R ≤2 I ≤4 S 2 I 2 I ≤0.25 S ≤1 S ≤1 S
184 negative 16 R ≤2 I ≤4 S 2 I 2 S ≤0.25 S ≤1 S ≤1 S
199 positive ≥32 R ≥32 R 8 R ≥64 R ≥64 R ≥8 R ≥64 R 16 R
214 negative ≥32 R ≤2 I ≤4 S ≤1 I ≤1 S ≤0.25 S ≤1 S ≤1 S
217 negative ≥32 R ≥32 R ≥128 R 4 I 4 I ≤0.25 S ≤1 S ≤1 S
220 negative ≥32 R ≤2 I ≤4 S 4 I 4 I ≤0.25 S ≤1 S ≤1 S
234 negative ≥32 R ≤2 I ≤4 S 2 I 2 I ≤0.25 S ≤1 S ≤1 S
240 negative ≥32 R ≤2 I ≤4 S ≤1 I ≤1 S ≤0.25 S ≤1 S ≤1 S
248 negative ≥32 R ≤2 I ≤4 S 2 I 2 I ≤0.25 S ≤1 S ≤1 S
252 negative ≥32 R 16 R ≤4 S 2 I 2 I ≤0.25 S ≤1 S ≤1 S
267 positive ≥32 R ≥32 R 32 R ≥64 R ≥64 R ≥8 R ≥64 R 16 R
277 negative ≥32 R ≥32 R 64 R 2 I 2 I ≤0.25 S ≤1 S ≤1 S
279 negative ≥32 R ≤2 I ≤4 S 2 I 2 I ≤0.25 S ≤1 S ≤1 S

Table A6.

Phenotypic resistance of the Klebsiella strains. MIC = minimum inhibitory concentration. ESBL = signal in phenotypic testing for extended-spectrum beta-lactamases.

Sample ID ESBL Ertapenem Imipenem Meropenem Gentamicin Ciprofloxacin Moxifloxacin Tigecycline Trimethoprim/Sulfamethoxazole
MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation
44 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≤20 S
60 negative ≤0.5 S ≤0.25 S ≤0.25 S ≥16 R 1 R 2 R ≤0.5 S ≥320 R
73 positive ≤0.5 S ≤0.25 S ≤0.25 S ≥16 R 1 R 2 R ≤0.5 S ≥320 R
100 positive ≤0.5 S ≤0.25 S ≤0.25 S ≥16 R ≥4 R ≥8 R ≤0.5 S ≥320 R
102 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S 0.5 R 4 R ≤20 S
124 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≤20 S
146 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S 1 S ≤20 S
177 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S 2 I ≥320 R
181 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≤20 S
184 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≤20 S
199 positive ≤0.5 S ≤0.25 S ≤0.25 S ≥16 R ≤0.25 S ≤0.25 S ≤0.5 S ≥320 R
214 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≥320 R
217 negative ≤0.5 S ≤0.25 S ≤0.25 S ≥16 R ≤0.25 S ≤0.25 S 2 I ≥320 R
220 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S 0.5 R 1 S ≤20 S
234 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S 0.5 R 1 S ≤20 S
240 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≤20 S
248 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S 2 I ≤20 S
252 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S 1 S ≥320 R
267 positive ≤0.5 S ≤0.25 S ≤0.25 S ≥16 R ≤0.25 S ≤0.25 S ≤0.5 S ≥320 R
277 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S 1 S ≥320 R
279 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≤20 S

Table A7.

Phenotypic resistance of Escherichia coli strains. MIC = minimum inhibitory concentration. ESBL = signal in phenotypic testing for extended-spectrum beta-lactamases.

Sample ID ESBL Ampicillin Ampicillin/Sulbactam Piperacillin/Tazobactam Cefuroxime Cefuroxime Axetil Cefpodoxime Cefotaxime Ceftrazidime
MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation
41 positive ≥32 R ≥32 R 64 R ≥64 R ≥64 R ≥8 R ≥64 R 16 R
49 negative ≥32 R 16 R ≤4 S 4 I 4 S ≤0.25 S ≤1 S ≤1 S
68 negative ≥32 R 16 R ≤4 S ≤1 I ≤1 S ≤0.25 S ≤1 S ≤1 S
117 negative ≥32 R ≥32 R 64 R 4 I 4 S ≤0.25 S ≤1 S ≤1 S
152 negative ≥32 R ≥32 R ≥128 R 4 I 4 S 0.5 S ≤1 S ≤1 S
176 negative ≥32 R ≥32 R ≤4 I 2 I 2 S ≤0.25 S ≤1 S ≤1 S
221 negative ≥32 R ≥32 R ≤4 I 2 I 2 S ≤0.25 S ≤1 S ≤1 S
222 negative ≥32 R ≥32 R ≤4 I 4 I 4 S ≤0.25 S ≤1 S ≤1 S
225 positive ≥32 R ≥32 R ≤4 R ≥64 R ≥64 R ≥8 R ≥64 R 16 R
245 positive ≥32 R ≥32 R 16 I 16 R 16 R 1 S 2 I ≤1 S
270 positive ≥32 R 16 R ≤4 R ≥64 R ≥64 R ≥8 R ≥64 R ≥64 R
299 negative ≥32 R ≤2 I ≤4 S 4 I 4 S ≤0.25 S ≤1 S ≤1 S

Table A8.

Phenotypic resistance of Escherichia coli strains. MIC = minimum inhibitory concentration. ESBL = signal in phenotypic testing for extended-spectrum beta-lactamases.

Sample ID ESBL Ertapenem Imipenem Meropenem Gentamicin Ciprofloxacin Moxifloxacin Tigecycline Trimethoprim/Sulfamethoxazole
MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation MIC Interpretation
41 positive ≤0.5 S ≤0.25 S ≤0.25 S ≥16 R ≥4 R ≥8 R ≤0.5 S ≥320 R
49 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≥320 R
68 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≥4 R ≥8 R ≤0.5 S ≥320 R
117 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≥320 R
152 negative ≤0.5 S ≤0.25 S ≤0.25 S 2 S 1 R 2 R ≤0.5 S ≥320 R
176 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≥320 R
221 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≥320 R
222 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≤0.25 S ≤0.25 S ≤0.5 S ≥320 R
225 positive ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S 0.5 I 1 R ≤0.5 S ≥320 R
245 positive ≤0.5 S 0.5 S ≤0.25 S ≥16 R ≥4 R ≥8 R ≤0.5 S ≥320 R
270 positive ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S ≥4 R ≥8 R ≤0.5 S ≤20 S
299 negative ≤0.5 S ≤0.25 S ≤0.25 S ≤1 S 0.5 I 2 R ≤0.5 S ≥320 R

Figure A1.

Figure A1

Clustal omega multiple alignment of oprD proteins—one example for the 7 detected subgroups.

Table A9.

Analysis of virulence determinants, ordered by strain and MLST type, of the assessed P. aeruginosa isolates. ST = Sequence type.

Sample ID ST-Type Pathogenicity Factor Groups
Adherence Anti-Phagocytosis Biosurfactant Iron Uptake Pigment Protease Toxin Regulation Secretion System
017 ST 381 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimV, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algP/algR3 algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdD, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
022 ST 2483 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
032 ST 3587 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
069 ST 360 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
081 ST 244 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW like, xcpX, xcpY, xcpZ
082 ST 514 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimV, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
088 ST 1682 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
099 ST 244 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
106 ST 1521 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdD, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
114 ST 244 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW like, xcpX, xcpY, xcpZ
137 ST 3014 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
144 ST 245 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
147 ST 245 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
149 ST 381 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimV, pilA, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
153 ST 704 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA plcH lasI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
154 ST 244 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW like, xcpX, xcpY, xcpZ
157 ST 2616 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimV, pilA, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
160 ST 170 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimV, pilA, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
162 ST 274 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimV, pilA, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
180 ST 856 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
183 ST 244 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW like, xcpX, xcpY, xcpZ
186 ST 3588 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
190 ST 871 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
195 ST 988 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
196 ST 2475 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
198 ST 2476 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimV, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
204 ST 639 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
208 ST 132 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
218 ST 856 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
229 ST 270 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdD, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
233 ST 3227 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimV, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
236 ST 266 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
238 ST 3589 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA plcH lasI, rhlI xcpP, xcpQ, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
242 ST 3590 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3 like, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
243 ST 3590 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
272 ST 2033 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
274 ST 2033 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
278 ST 988 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
282 ST 554 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
285 ST 554 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilA like, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
289 ST 1485 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdD, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
290 ST 1485 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdD, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
296 ST 235 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW like, xcpX, xcpY, xcpZ
298 ST 3227 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimV, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
301 ST 3593 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
302 ST 1755 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
309 ST 3592 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimT, fimU, fimV, pilB, pilD, pilE, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilV, pilW, pilX pilY1, pilY2, pilC, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdE phzM, phzS aprA, lasA plcH lasI, rhlI xcpP, xcpQ, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
310 ST 532 waaA, waaC, waaF, waaG, waaP, chpA, chpB, chpC, chpD, chpE, fimV, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, fpvA pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA phzM, phzS aprA lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ
312 ST 381 waaA, waaC, waaF, waaG, waaP, wzy, wzz, chpA, chpB, chpC, chpD, chpE, fimV, pilB, pilD, pilF, pilG, pilH, pilI, pilK, pilM, pilN, pilO, pilP, pilQ, pilR, pilS, pilT, pilU, pilC like, xcpA/pilD alg44, alg8, algA, algB, algC, algD, algE, algF, algG, algI, algJ, algK, algL, algP/algR3, algQ, algR, algU, algW, algX, algZ, mucA, mucB, mucC rhlA, rhlB fptA, pchA, pchB, pchC, pchD, pchE, pchF, pchG, pchH, pchI, pchR, pvdA, pvdD, pvdE phzM, phzS aprA, lasA toxA, plcH lasI, rhlI xcpP, xcpQ, xcpR, xcpS, xcpT, xcpU, xcpV, xcpW, xcpX, xcpY, xcpZ

Table A10.

Analysis of virulence determinants, ordered by strain and MLST type, of the assessed K. pneumoniae isolates. ST = Sequence type.

Sample ID ST-Type Pathogenicity Factor Groups
Adherence Biofilm Formation Efflux Pump Immune Evasion Iron Uptake Nutritional Factor Regulation Secretion System Serum Resistance Toxin
044 ST 327 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, ugd, wza like, wzi entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE like rcsA, rcsB impA/tssA like, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
060 ST 5379 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB impA/tssA, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC
073 ST 39 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE, irp1, irp2, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX rcsA, rcsB impA/tssA, sciN/tssJ, tle1, tli1, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
100 ST 152 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, ugd, wza like, wzi entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE, irp1, irp2, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX rcsA, rcsB impA/tssA like, sciN/tssJ, tssF, tssG
102 ST 514 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB impA/tssA like, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
124 ST 399 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkF, mrkH, mrkJ acrA, acrB cpsACP, galF, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB glf, wbbM, wbbN, wbbO, wzm, wzt
146 ST 4 fimA, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE, irp1, irp2, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX rcsA, rcsB impA/tssA like, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
177 ST 17 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza like, wzi entA, entB, entC, entD, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX rcsA, rcsB impA/tssA, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
181 ST 5380 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gmd like, gnd, manB, manC, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB, impA/tssA, sciN/tssJ, tle1, tli1, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
184 ST 5381 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, ugd, wza like, wzi entA, entB, entC, entD like, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE like rcsA, rcsB impA/tssA, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC
199 ST 17 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB like, manC, ugd, wza, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE, irp1, irp2, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX rcsA, rcsB impA/tssA, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC
214 ST 6 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE, irp1, irp2, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX rcsA, rcsB impA/tssA like, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
217 ST 3154 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB impA/tssA like, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
220 ST 5382 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB like, manC, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE, allA, allB, allC, allD, allR, allS rcsA, rcsB
234 ST 109 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB, impA/tssA, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
240 ST 5383 fimC, fimD, fimF, fimG, fimH, fimI, fimK mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB glf, wbbM, wbbN, wbbO, wzm, wzt
248 ST 5384 mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
252 ST 607 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, wza like, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
267 ST 36 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE, irp1, irp2, ybtA, ybtE, ybtP, ybtQ, ybtS, ybtT, ybtU, ybtX rcsA, rcsB impA/tssA, sciN/tssJ, tle1, tli1, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
277 ST 530 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, manB, manC, ugd, wza, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB impA/tssA like, sciN/tssJ, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC glf, wbbM, wbbN, wbbO, wzm, wzt
279 ST 5385 fimA, fimB, fimC, fimD, fimE, fimF, fimG, fimH, fimI, fimK mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ acrA, acrB cpsACP, galF, gnd, ugd, wza, wzi entA, entB, entC, entE, entF, fepA, fepB, fepC, fepD, fepG, fes, ybdA, iroE rcsA, rcsB, impA/tssA, sciN/tssJ, tle1, tli1, tssF, tssG, vasE/tssK, vgrG/tssI, vipA/tssB, vipB/tssC wzm, wzt

Table A11.

Details on the strain-specific short-read archive (SRA) accession numbers.

Sample ID Percentage of Good Targets (SeqSphere+) Average Coverage (Assembled) (SeqSphere+) Approximated Genome Size (Megabases) (SeqSphere+) Species (Kraken2) Sequence Type Complex Type (SeqSphere+) SRA Accession
Iso00017 99.4 105 6.7 Pseudomonas aeruginosa 381 1791 SRR13617317
Iso00022 99.4 102 6.9 Pseudomonas aeruginosa 2483 1792 SRR13617316
Iso00032 99.2 106 6.6 Pseudomonas aeruginosa 3587 1793 SRR13617305
Iso00041 99.4 97 5.0 Escherichia coli 2 (Pasteur) 11349 SRR13617294
Iso00044 99.7 116 5.1 Klebsiella pneumoniae 327 5462 SRR13617283
Iso00049 98.7 94 5.2 Escherichia coli 3 (Pasteur) 11350 SRR13617272
Iso00060 99.6 112 5.3 Klebsiella pneumoniae 5379 5463 SRR13617261
Iso00068 99.6 109 4.9 Escherichia coli 632 (Pasteur) 11351 SRR13617250
Iso00069 99.6 104 6.8 Pseudomonas aeruginosa 360 1794 SRR13617239
Iso00073 99.4 104 5.8 Klebsiella pneumoniae 39 5464 SRR13617236
Iso00081 98.7 108 6.6 Pseudomonas aeruginosa 244 1795 SRR13617315
Iso00082 99.4 112 6.3 Pseudomonas aeruginosa 514 1796 SRR13617314
Iso00088 97.8 105 6.8 Pseudomonas aeruginosa 1682 1797 SRR13617313
Iso00099 99.4 106 6.6 Pseudomonas aeruginosa 244 1798 SRR13617312
Iso00100 99.2 108 5.5 Klebsiella pneumoniae 152 5465 SRR13617311
Iso00102 99.2 111 5.4 Klebsiella pneumoniae 514 5466 SRR13617310
Iso00106 99.5 110 6.4 Pseudomonas aeruginosa 1521 1799 SRR13617309
Iso00114 99.4 105 6.7 Pseudomonas aeruginosa 244 1800 SRR13617308
Iso00117 99.2 95 5.3 Escherichia coli 4 (Pasteur) 11352 SRR13617307
Iso00124 99.4 112 5.3 Klebsiella pneumoniae 399 5467 SRR13617306
Iso00137 99.4 110 6.4 Pseudomonas aeruginosa 3014 1801 SRR13617304
Iso00144 99.6 109 6.5 Pseudomonas aeruginosa 245 1802 SRR13617303
Iso00146 99.4 110 5.5 Klebsiella pneumoniae 4 5468 SRR13617302
Iso00147 99.5 108 6.6 Pseudomonas aeruginosa 245 1802 SRR13617301
Iso00149 99.6 104 6.9 Pseudomonas aeruginosa 381 1803 SRR13617300
Iso00152 99.4 98 5.2 Escherichia coli 22 (Pasteur) 11353 SRR13617299
Iso00153 98.5 111 6.4 Pseudomonas aeruginosa 704 ? SRR13617298
Iso00154 99.4 102 7.0 Pseudomonas aeruginosa 244 1805 SRR13617297
Iso00157 99.6 114 6.3 Pseudomonas aeruginosa 2616 1806 SRR13617296
Iso00160 99.2 115 6.2 Pseudomonas aeruginosa 170 1807 SRR13617295
Iso00162 99.1 111 6.5 Pseudomonas aeruginosa 274 1808 SRR13617293
Iso00176 99.0 98 5.1 Escherichia coli 132 (Pasteur) 11354 SRR13617292
Iso00177 99.6 108 5.5 Klebsiella pneumoniae 17 5469 SRR13617291
Iso00180 99.8 110 6.5 Pseudomonas aeruginosa 856 1809 SRR13617290
Iso00181 99.9 107 5.6 Klebsiella pneumoniae 5380 5470 SRR13617289
Iso00183 99.5 107 6.7 Pseudomonas aeruginosa 244 1795 SRR13617288
Iso00184 98.3 104 5.6 Klebsiella variicola subsp. variicola 5381 5471 SRR13617287
Iso00186 98.7 113 6.3 Pseudomonas aeruginosa 3588 1810 SRR13617286
Iso00190 99.7 114 6.3 Pseudomonas aeruginosa 871 1811 SRR13617285
Iso00195 99.5 111 6.5 Pseudomonas aeruginosa 988 1812 SRR13617284
Iso00196 99.5 101 7.1 Pseudomonas aeruginosa 2475 1813 SRR13617282
Iso00198 99.6 112 6.4 Pseudomonas aeruginosa 2476 1814 SRR13617281
Iso00199 99.4 108 5.6 Klebsiella pneumoniae 17 5472 SRR13617280
Iso00204 99.5 104 6.9 Pseudomonas aeruginosa 639 1815 SRR13617279
Iso00208 99.7 109 6.5 Pseudomonas aeruginosa 132 1816 SRR13617278
Iso00214 99.7 108 5.5 Klebsiella pneumoniae 6 5473 SRR13617277
Iso00217 99.8 104 5.7 Klebsiella pneumoniae 3154 5474 SRR13617276
Iso00218 99.7 109 6.5 Pseudomonas aeruginosa 856 1809 SRR13617275
Iso00220 97.8 110 5.4 Klebsiella quasipneumoniae subsp. similipneumoniae 5382 5475 SRR13617274
Iso00221 99.0 94 5.1 Escherichia coli 132 (Pasteur) 11354 SRR13617273
Iso00222 99.0 96 5.1 Escherichia coli 132 (Pasteur) 11354 SRR13617271
Iso00225 99.1 99 5.2 Escherichia coli 506 (Pasteur) 11355 SRR13617270
Iso00229 99.6 109 6.5 Pseudomonas aeruginosa 270 1817 SRR13617269
Iso00233 97.8 114 6.1 Pseudomonas aeruginosa 3227 1818 SRR13617268
Iso00234 99.7 111 5.5 Klebsiella pneumoniae 109 5476 SRR13617267
Iso00236 99.7 112 6.4 Pseudomonas aeruginosa 266 1819 SRR13617266
Iso00238 98.7 108 6.6 Pseudomonas aeruginosa 3589 1820 SRR13617265
Iso00240 98.9 112 5.4 Klebsiella pneumoniae 5383 5477 SRR13617264
Iso00242 98.9 111 6.4 Pseudomonas aeruginosa 3590 1821 SRR13617263
Iso00243 98.9 111 6.4 Pseudomonas aeruginosa 3590 1821 SRR13617262
Iso00245 99.3 107 4.8 Escherichia coli 2 (Pasteur) 11356 SRR13617260
Iso00248 97.2 108 5.5 Klebsiella quasivariicola 5384 5478 SRR13617259
Iso00252 99.6 112 5.3 Klebsiella pneumoniae 607 5479 SRR13617258
Iso00267 99.6 103 5.7 Klebsiella pneumoniae 36 5480 SRR13617257
Iso00270 99.2 100 4.9 Escherichia coli 2 (Pasteur) 11358 SRR13617256
Iso00272 99.5 109 6.5 Pseudomonas aeruginosa 2033 1822 SRR13617255
Iso00274 99.4 109 6.5 Pseudomonas aeruginosa 2033 1822 SRR13617254
Iso00277 99.4 109 5.5 Klebsiella pneumoniae 530 5481 SRR13617253
Iso00278 99.6 110 6.5 Pseudomonas aeruginosa 988 1823 SRR13617252
Iso00279 99.7 111 5.5 Klebsiella pneumoniae 5385 5482 SRR13617251
Iso00282 99.3 108 6.6 Pseudomonas aeruginosa 554 1824 SRR13617249
Iso00285 99.3 109 6.5 Pseudomonas aeruginosa 554 1824 SRR13617248
Iso00289 99.6 112 6.3 Pseudomonas aeruginosa 1485 1825 SRR13617247
Iso00290 99.7 113 6.3 Pseudomonas aeruginosa 1485 1825 SRR13617246
Iso00296 99.7 106 6.7 Pseudomonas aeruginosa 235 1826 SRR13617245
Iso00298 97.8 116 6.1 Pseudomonas aeruginosa 3227 1818 SRR13617244
Iso00299 99.3 108 4.6 Escherichia coli 1018 (Pasteur) 11357 SRR13617243
Iso00301 98.6 112 6.3 Pseudomonas aeruginosa 3593 1827 SRR13617242
Iso00302 99.6 113 6.3 Pseudomonas aeruginosa 1755 1828 SRR13617241
Iso00309 98.6 109 6.5 Pseudomonas aeruginosa 3592 1829 SRR13617240
Iso00310 99.3 105 6.8 Pseudomonas aeruginosa 532 1830 SRR13617238
Iso00312 99.4 106 6.7 Pseudomonas aeruginosa 381 1791 SRR13617237

Author Contributions

U.L., D.D. and J.M. designed and coordinated this study. T.T., F.P. and S.T. performed bioinformatic analysis. M.L. supported the management of this study. A.J. managed the data collection. H.F., D.D. and U.L. wrote the first draft of this manuscript. K.O. conducted and supervised fieldwork. C.W.A. and K.T. conducted and supervised lab work. M.K. and S.S. supported the interpretation of the results, writing and editing the manuscript. All authors read and approved the final manuscript.

Funding

This study was funded by institutional funds of the Bernhard Nocht Institute for Tropical Medicine (BNITM).

Institutional Review Board Statement

The study was conducted according to guidelines of the Declaration of Helsinki. The Committee on Human Research, Publications and Ethics, School of Medical Science, Kwame Nkrumah University of Science and Technology in Kumasi, Ghana, approved this study (approval number CHRPE/AP/078/16).

Informed Consent Statement

Informed consent was obtained from all study participants.

Data Availability Statement

All relevant data have been provided in the paper and its Appendix A materials. Raw data are available applying the links as indicated in the methods chapter and can also be provided by the authors on reasonable request.

Conflicts of Interest

The authors declare no conflict of interest.

Footnotes

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

References

  • 1.Lai P.S., Bebell L.M., Meney C., Valeri L., White M.C. Epidemiology of antibiotic-resistant wound infections from six countries in Africa. BMJ Glob. Health. 2018;2(Suppl. 4):e000475. doi: 10.1136/bmjgh-2017-000475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Mama M., Abdissa A., Sewunet T. Antimicrobial susceptibility pattern of bacterial isolates from wound infection and their sensitivity to alternative topical agents at Jimma University Specialized Hospital, South-West Ethiopia. Ann. Clin. Microbiol. Antimicrob. 2014;13:14. doi: 10.1186/1476-0711-13-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Moremi N., Mushi M.F., Fidelis M., Chalya P., Mirambo M., Mshana S.E. Predominance of multi-resistant gram-negative bacteria colonizing chronic lower limb ulcers (CLLUs) at Bugando Medical Center. BMC Res. Notes. 2014;7:211. doi: 10.1186/1756-0500-7-211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Kassam N.A., Damian D.J., Kajeguka D., Nyombi B., Kibiki G.S. Spectrum and antibiogram of bacteria isolated from patients presenting with infected wounds in a Tertiary Hospital, northern Tanzania. BMC Res. Notes. 2017;10:757. doi: 10.1186/s13104-017-3092-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Janssen H., Janssen I., Cooper P., Kainyah C., Pellio T., Quintel M., Monnheimer M., Groß U., Schulze M.H. Antimicrobial-Resistant Bacteria in Infected Wounds, Ghana, 2014. Emerg. Infect. Dis. 2018;24:916–919. doi: 10.3201/eid2405.171506. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Kazimoto T., Abdulla S., Bategereza L., Juma O., Mhimbira F., Weisser M., Utzinger J., von Müller L., Becker S.L. Causative agents and antimicrobial resistance patterns of human skin and soft tissue infections in Bagamoyo, Tanzania. Acta Trop. 2018;186:102–106. doi: 10.1016/j.actatropica.2018.07.007. [DOI] [PubMed] [Google Scholar]
  • 7.Høiby N., Ciofu O., Johansen H.K., Song Z.J., Moser C., Jensen P.Ø., Molin S., Givskov M., Tolker-Nielsen T., Bjarnsholt T. The clinical impact of bacterial biofilms. Int. J. Oral. Sci. 2011;3:55–65. doi: 10.4248/IJOS11026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Percival S.L., Hill K.E., Williams D.W., Hooper S.J., Thomas D.W., Costerton J.W. A review of the scientific evidence for biofilms in wounds. Wound Repair Regen. 2012;20:647–657. doi: 10.1111/j.1524-475X.2012.00836.x. [DOI] [PubMed] [Google Scholar]
  • 9.Rahim K., Saleha S., Zhu X., Huo L., Basit A., Franco O.L. Bacterial Contributionin Chronicity of Wounds. Microb. Ecol. 2017;73:710–721. doi: 10.1007/s00248-016-0867-9. [DOI] [PubMed] [Google Scholar]
  • 10.Xu Z., Hsia H.C. The Impact of Microbial Communities on Wound Healing: A Review. Ann. Plast. Surg. 2018;81:113–123. doi: 10.1097/SAP.0000000000001450. [DOI] [PubMed] [Google Scholar]
  • 11.Mulcahy L.R., Isabella V.M., Lewis K. Pseudomonas aeruginosa biofilms in disease. Microb. Ecol. 2014;68:1–12. doi: 10.1007/s00248-013-0297-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Serra R., Grande R., Butrico L., Rossi A., Settimio U.F., Caroleo B., Amato B., Gallelli L., de Franciscis S. Chronic wound infections: The role of Pseudomonas aeruginosa and Staphylococcus aureus. Expert. Rev. Anti. Infect. Ther. 2015;13:605–613. doi: 10.1586/14787210.2015.1023291. [DOI] [PubMed] [Google Scholar]
  • 13.Kirketerp-Møller K., Jensen P.Ø., Fazli M., Madsen K.G., Pedersen J., Moser C., Tolker-Nielsen T., Høiby N., Givskov M., Bjarnsholt T. Distribution, organization, and ecology of bacteria in chronic wounds. J. Clin. Microbiol. 2008;46:2717–2722. doi: 10.1128/JCM.00501-08. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Kohler J.E., Hutchens M.P., Sadow P.M., Modi B.P., Tavakkolizadeh A., Gates J.D. Klebsiella pneumoniae necrotizing fasciitis and septic arthritis: An appearance in the Western hemisphere. Surg. Infect. 2007;8:227–232. doi: 10.1089/sur.2006.007. [DOI] [PubMed] [Google Scholar]
  • 15.Dana A.N., Bauman W.A. Bacteriology of pressure ulcers in individuals with spinal cord injury: What we know and what we should know. J. Spinal Cord. Med. 2015;38:147–160. doi: 10.1179/2045772314Y.0000000234. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Washington M.A., Barnhill J.C., Duff M.A., Griffin J. Recovery of Bacteria and Fungi from a Leg Wound. J. Spec. Oper. Med. 2015;15:113–116. doi: 10.55460/DW1G-SZNG. [DOI] [PubMed] [Google Scholar]
  • 17.Vyas K.S., Wong L.K. Detection of Biofilm in Wounds as an Early Indicator for Risk for Tissue Infection and Wound Chronicity. Ann. Plast. Surg. 2016;76:127–131. doi: 10.1097/SAP.0000000000000440. [DOI] [PubMed] [Google Scholar]
  • 18.Wetterslev M., Rose-Larsen K., Hansen-Schwartz J., Steen-Andersen J., Møller K., Møller-Sørensen H. Mechanism of injury and microbiological flora of the geographical location are essential for the prognosis in soldiers with serious warfare injuries. Dan. Med. J. 2013;60:A4704. [PubMed] [Google Scholar]
  • 19.Yun H.C., Murray C.K., Roop S.A., Hospenthal D.R., Gourdine E., Dooley D.P. Bacteria recovered from patients admitted to a deployed U.S. military hospital in Baghdad, Iraq. Mil. Med. 2006;171:821–825. doi: 10.7205/MILMED.171.9.821. [DOI] [PubMed] [Google Scholar]
  • 20.Micheel V., Hogan B., Rakotoarivelo R.A., Rakotozandrindrainy R., Razafimanatsoa F., Razafindrabe T., Rakotondrainiarivelo J.P., Crusius S., Poppert S., Schwarz N.G., et al. Identification of nasal colonization with β-lactamase-producing Enterobacteriaceae in patients, health care workers and students in Madagascar. Eur. J. Microbiol. Immunol. 2015;5:116–125. doi: 10.1556/EuJMI-D-15-00001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Frickmann H., Podbielski A., Kreikemeyer B. Resistant Gram-Negative Bacteria and Diagnostic Point-of-Care Options for the Field Setting during Military Operations. Biomed. Res. Int. 2018;2018:9395420. doi: 10.1155/2018/9395420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.McBride M.E., Duncan W.C., Knox J.M. Physiological and environmental control of Gram negative bacteria on skin. Br. J. Dermatol. 1975;93:191–199. doi: 10.1111/j.1365-2133.1975.tb06740.x. [DOI] [PubMed] [Google Scholar]
  • 23.Krumkamp R., Oppong K., Hogan B., Strauss R., Frickmann H., Wiafe-Akenten C., Boahen K.G., Rickerts V., McCormick Smith I., Groß U., et al. Spectrum of antibiotic resistant bacteria and fungi isolated from chronically infected wounds in a rural district hospital in Ghana. PLoS ONE. 2020;15:e0237263. doi: 10.1371/journal.pone.0237263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Codjoe F.S., Donkor E.S., Smith T.J., Miller K. Phenotypic and Genotypic Characterization of Carbapenem-Resistant Gram-Negative Bacilli Pathogens from Hospitals in Ghana. Microb. Drug. Resist. 2019;25:1449–1457. doi: 10.1089/mdr.2018.0278. [DOI] [PubMed] [Google Scholar]
  • 25.Del Barrio-Tofiño E., López-Causapé C., Oliver A. Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired β-lactamases: 2020 update. Int. J. Antimicrob. Agents. 2020;56:106196. doi: 10.1016/j.ijantimicag.2020.106196. [DOI] [PubMed] [Google Scholar]
  • 26.Wyres K.L., Lam M.M.C., Holt K.E. Population genomics of Klebsiella pneumoniae. Nat. Rev. Microbiol. 2020;18:344–359. doi: 10.1038/s41579-019-0315-1. [DOI] [PubMed] [Google Scholar]
  • 27.Denamur E., Clermont O., Bonacorsi S., Gordon D. The population genetics of pathogenic Escherichia coli. Nat. Rev. Microbiol. 2021;19:37–54. doi: 10.1038/s41579-020-0416-x. [DOI] [PubMed] [Google Scholar]
  • 28.Eibach D., Belmar Campos C., Krumkamp R., Al-Emran H.M., Dekker D., Boahen K.G., Kreuels B., Adu-Sarkodie Y., Aepfelbacher M., Park S.E., et al. Extended spectrum beta-lactamase producing Enterobacteriaceae causing bloodstream infections in rural Ghana, 2007–2012. Int. J. Med. Microbiol. 2016;306:249–254. doi: 10.1016/j.ijmm.2016.05.006. [DOI] [PubMed] [Google Scholar]
  • 29.Eibach D., Dekker D., Gyau Boahen K., Wiafe Akenten C., Sarpong N., Belmar Campos C., Berneking L., Aepfelbacher M., Krumkamp R., Owusu-Dabo E., et al. Extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in local and imported poultry meat in Ghana. Vet. Microbiol. 2018;217:7–12. doi: 10.1016/j.vetmic.2018.02.023. [DOI] [PubMed] [Google Scholar]
  • 30.Labi A.K., Bjerrum S., Enweronu-Laryea C.C., Ayibor P.K., Nielsen K.L., Marvig R.L., Newman M.J., Andersen L.P., Kurtzhals J.A.L. High Carriage Rates of Multidrug-Resistant Gram-Negative Bacteria in Neonatal Intensive Care Units from Ghana. Open Forum Infect. Dis. 2020;7:ofaa109. doi: 10.1093/ofid/ofaa109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Agyepong N., Govinden U., Owusu-Ofori A., Amoako D.G., Allam M., Janice J., Pedersen T., Sundsfjord A., Essack S. Genomic characterization of multidrug-resistant ESBL-producing Klebsiella pneumoniae isolated from a Ghanaian teaching hospital. Int. J. Infect. Dis. 2019;85:117–123. doi: 10.1016/j.ijid.2019.05.025. [DOI] [PubMed] [Google Scholar]
  • 32.Falgenhauer L., Imirzalioglu C., Oppong K., Akenten C.W., Hogan B., Krumkamp R., Poppert S., Levermann V., Schwengers O., Sarpong N., et al. Detection and Characterization of ESBL-Producing Escherichia coli from Humans and Poultry in Ghana. Front. Microbiol. 2019;9:3358. doi: 10.3389/fmicb.2018.03358. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Donkor E.S., Horlortu P.Z., Dayie N.T., Obeng-Nkrumah N., Labi A.K. Community acquired urinary tract infections among adults in Accra, Ghana. Infect. Drug. Resist. 2019;12:2059–2067. doi: 10.2147/IDR.S204880. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Obeng-Nkrumah N., Labi A.K., Blankson H., Awuah-Mensah G., Oduro-Mensah D., Anum J., Teye J., Kwashie S.D., Bako E., Ayeh-Kumi P.F., et al. Household cockroaches carry CTX-M-15-, OXA-48- and NDM-1-producing enterobacteria, and share beta-lactam resistance determinants with humans. BMC Microbiol. 2019;19:272. doi: 10.1186/s12866-019-1629-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Poirel L., Corvec S., Rapoport M., Mugnier P., Petroni A., Pasteran F., Faccone D., Galas M., Drugeon H., Cattoir V., et al. Identification of the novel narrow-spectrum beta-lactamase SCO-1 in Acinetobacter spp. from Argentina. Antimicrob. Agents Chemother. 2007;51:2179–2184. doi: 10.1128/AAC.01600-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Münch J., Hagen R.M., Müller M., Kellert V., Wiemer D.F., Hinz R., Schwarz N.G., Frickmann H. Colonization with Multidrug-Resistant Bacteria—On the Efficiency of Local Decolonization Procedures. Eur. J. Microbiol. Immunol. 2017;7:99–111. doi: 10.1556/1886.2017.00008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Cornelis P., Dingemans J. Pseudomonas aeruginosa adapts its iron uptake strategies in function of the type of infections. Front. Cell. Infect. Microbiol. 2013;3:75. doi: 10.3389/fcimb.2013.00075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 38.Hasannejad-Bibalan M., Jafari A., Sabati H., Goswami R., Jafaryparvar Z., Sedaghat F., Sedigh Ebrahim-Saraie H. Risk of type III secretion systems in burn patients with Pseudomonas aeruginosa wound infection: A systematic review and meta-analysis. Burns. 2020 doi: 10.1016/j.burns.2020.04.024. [DOI] [PubMed] [Google Scholar]
  • 39.Rumbaugh K.P., Griswold J.A., Hamood A.N. Contribution of the regulatory gene lasR to the pathogenesis of Pseudomonas aeruginosa infection of burned mice. J. Burn Care Rehabil. 1999;20(Pt 1):42–49. doi: 10.1097/00004630-199901001-00008. [DOI] [PubMed] [Google Scholar]
  • 40.Colmer-Hamood J.A., Dzvova N., Kruczek C., Hamood A.N. In Vitro Analysis of Pseudomonas aeruginosa Virulence Using Conditions That Mimic the Environment at Specific Infection Sites. Prog. Mol. Biol. Transl. Sci. 2016;142:151–191. doi: 10.1016/bs.pmbts.2016.05.003. [DOI] [PubMed] [Google Scholar]
  • 41.Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. 2010. [(accessed on 15 December 2020)]; Available online: http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
  • 42.Wood D.E., Lu J., Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20:257. doi: 10.1186/s13059-019-1891-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 43.Jünemann S., Sedlazeck F.J., Prior K., Albersmeier A., John U., Kalinowski J., Mellmann A., Goesmann A., von Haeseler A., Stoye J., et al. Updating benchtop sequencing performance comparison. Nature Biotechnol. 2013;31:294–296. doi: 10.1038/nbt.2522. [DOI] [PubMed] [Google Scholar]
  • 44.Prjibelski A., Antipov D., Meleshko D., Lapidus A., Korobeynikov A. Using SPAdes de novo assembler. Curr. Protoc. Bioinform. 2020;70:e102. doi: 10.1002/cpbi.102. [DOI] [PubMed] [Google Scholar]
  • 45.Seemann T. Abricate, Github. [(accessed on 22 March 2021)]; Available online: https://github.com/tseemann/abricate.
  • 46.Feldgarden M., Brover V., Haft D.H., Prasad A.B., Slotta D.J., Tolstoy I., Tyson G.H., Zhao S., Hsu C.H., McDermott P.F., et al. Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob. Agents Chemother. 2019;63:e00483-19. doi: 10.1128/AAC.00483-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Chen L., Zheng D., Liu B., Yang J., Jin Q. VFDB 2016: Hierarchical and refined dataset for big data analysis—10 years on. Nucleic Acids Res. 2016;44:D694–D697. doi: 10.1093/nar/gkv1239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 48.Bortolaia V., Kaas R.S., Ruppe E., Roberts M.C., Schwarz S., Cattoir V., Philippon A., Allesoe R.L., Rebelo A.R., Florensa A.F., et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 2020;75:3491–3500. doi: 10.1093/jac/dkaa345. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

All relevant data have been provided in the paper and its Appendix A materials. Raw data are available applying the links as indicated in the methods chapter and can also be provided by the authors on reasonable request.


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