Rise in the number of notifications of Shiga toxin-producing Escherichia coli (STEC) infections probably linked to an increased use of multiplex PCR assays, Germany, 2023

Tanja Jung-Sendzik; Mareike Wollenweber; Katja Hille; Lilas Mercuriali; Gerhard Falkenhorst

doi:10.2807/1560-7917.ES.2025.30.48.2500268

. 2025 Dec 4;30(48):2500268. doi: 10.2807/1560-7917.ES.2025.30.48.2500268

Rise in the number of notifications of Shiga toxin-producing Escherichia coli (STEC) infections probably linked to an increased use of multiplex PCR assays, Germany, 2023

Tanja Jung-Sendzik ^1,^2,^3,^*, Mareike Wollenweber ^2,^3,^4,^*, Katja Hille ⁴, Lilas Mercuriali ^3,⁴, Gerhard Falkenhorst ¹

PMCID: PMC12680918 PMID: 41346319

Abstract

BACKGROUND

Shiga toxin-producing Escherichia coli (STEC) can cause illnesses ranging from self-limiting diarrhoea to severe manifestations such as haemolytic-uraemic syndrome (HUS). In 2023, an increase in notified STEC cases was observed in the German federal state of Lower Saxony and nationwide.

AIM

We aimed to investigate possible reasons for the observed increase.

METHODS

We analysed data on notified STEC cases at federal and state level. All available STEC isolates from Lower Saxony from 2023 were whole genome sequenced. We sent a survey on detection and identification methods to 25 clinical microbiology laboratories in Lower Saxony.

RESULTS

In 2023, a statistically significant increase in notified STEC cases in all ages was seen in Lower Saxony and nationwide when compared with case numbers in 2022 and the median of 2015–2019 (p < 0.01). The highest increase was observed in people aged 60–69 years: 110 cases were notified in Lower Saxony in 2023 (median 2015–2019: 26) and 471 cases nationwide (median 2015–2019: 182). No overall increase was seen in disease severity or in the number of HUS cases. No larger genetic clusters or outbreaks were identified in Lower Saxony. The survey among the 17 responding laboratories in Lower Saxony revealed an increased use of multiplex PCR assays for gastrointestinal pathogens, introduced mainly in 2023.

CONCLUSION

The increase in notified STEC cases was probably associated with the implementation of multiplex PCR assays for the analysis of gastrointestinal specimens. Our findings highlight the need to monitor diagnostic practices when assessing and evaluating surveillance data.

Keywords: STEC, case notifications, multiplex PCR, laboratory survey

Key public health message.

What did you want to address in this study and why?

Infection with Shiga toxin-producing E. coli (STEC) may be asymptomatic or lead to a diarrhoeal disease with severe complications and death. In 2023, an increase in the number of cases with STEC was seen in the German federal state of Lower Saxony and nationwide. We aimed to investigate reasons for this increase.

What have we learnt from this study?

The increase in STEC notifications was probably linked to the introduction of multiplex PCR tests in routine laboratory diagnostics, rather than a true rise in infections. The increase was mainly seen in patients aged 60–69 years. We did not observe an increase in severe cases nor an indication of major outbreaks.

What are the implications of your findings for public health?

The introduction of multiplex PCR assays in routine diagnostic practices may have led to a more frequent detection of STEC, especially in older patients with gastrointestinal infections. Our findings highlight the importance of monitoring diagnostic practices when evaluating trends in surveillance data and planning health responses.

Introduction

Shiga toxin-producing Escherichia coli (STEC) are Gram-negative bacteria that can colonise the human gastrointestinal tract and produce potent cytotoxins known as Shiga toxins (Stx1 and Stx2) with multiple subtypes. These toxins, particularly subtype Stx2a, can cause severe illnesses such as haemorrhagic colitis and haemolytic-uraemic syndrome (HUS), a potentially life-threatening condition characterised by acute kidney injury, microangiopathic haemolytic anaemia and thrombocytopenia [1]. Identification of STEC is usually done by the detection of Shiga toxins (e.g. by ELISA) or Shiga toxin genes (e.g. by PCR) [2]. Cultivation of the pathogen is recommended [2,3], but often not performed due to additional costs, time constraints and the lack of consequences for individual patient management.

Infectious disease surveillance in Germany is regulated by the Infection Protection Act (IfSG) of 2001 [4]. All laboratory-confirmed STEC cases, irrespective of the presence of symptoms, are to be notified to the local health departments [4]. From there, pseudonymised notifications are transmitted to the state health departments and further on to the National Public Health Institute, the Robert Koch Institute (RKI). Notifications of STEC include information on symptoms, hospitalisation status, possible place of infection and other variables, which are collected in the national database of notifiable diseases SurvNet@RKI [2,5]. In Germany, over 550 clinical microbiology laboratories perform microbiological diagnostics. Most of these laboratories are commercial, profit-oriented enterprises, accredited according to international standards [6,7]. Laboratories are reimbursed for PCR diagnostics of gastrointestinal pathogens since September 2022 within the statutory health insurance system [8].

According to the national guideline for acute infectious gastroenteritis in infants, children and adolescents, testing for STEC in children with gastrointestinal symptoms should be considered [9]. Independent of age, testing for STEC is recommended in severe cases with gastrointestinal symptoms and complications such as haemorrhagic colitis and HUS as well as in symptomatic people who work in the food sector or visit communal facilities [3,10]. Cases of enteropathogenic HUS are separately notifiable by treating physicians, based on clinical criteria.

We aimed to describe and analyse the observed STEC notification increase in 2023 and to identify possible reasons for the increase in Lower Saxony and Germany overall.

Methods

Data collection and analysis of STEC notifications

We extracted information of all notified STEC cases in Germany transmitted to the RKI between 2015 and 2023 from SurvNet@RKI [5].

In accordance with Section 11 (2) of the IfSG, the RKI has the task of developing surveillance case definitions for infectious diseases. Case definitions aim to ensure uniform criteria throughout Germany, thus contributing to standardised assessments and more reliable statistics. The national case definition for STEC is provided in Box.

Box. National case definition for infections of Shiga toxin-producing Escherichia coli (STEC), Germany.

Clinical criteria:

• Stomach pain or diarrhoea or vomiting or death

AND

Laboratory confirmation:

• Detection of Shiga toxin (e.g. by ELISA) from faecal specimen or stool culture

AND/OR

• Nucleic acid detection (e.g. PCR) of a Shiga toxin gene from faecal specimen or stool culture

Epidemiological confirmation:

• At least one of the following, considering the incubation period (2–10 days):

o Epidemiological link to a laboratory-confirmed human case (human-to-human transmission) of STEC

o Common source of exposure (e.g. bathing water, food, animal contact)

o Bathing in a body of water, swimming pool or bathing water, detection of STEC laboratory-confirmed

o Contact with an animal (e.g. at a petting zoo) or its faeces or consumption of its products (e.g. raw milk), detection of STEC laboratory-confirmed

o Consumption of a foodstuff (including drinking water), detection of STEC laboratory-confirmed.

We compared STEC notification data from Lower Saxony and nationwide from 2023 with data from 2022 and with the median of the five pre-COVID-19 pandemic years 2015–2019. We assessed changes over time in the following variables: case numbers, age and sex distribution, proportions of asymptomatic cases, and HUS case numbers. We excluded the pandemic years 2020 and 2021 from our analyses due to a drastic decrease in notifications for most infectious diseases [11]. We contacted local health authorities regarding results of their case investigations.

Increases in different age groups in 2023 were compared with the reference periods 2022 and 2015–2019 by two-sample Poisson test. Hospitalisation rates due to STEC among all STEC cases were analysed as a proxy for disease severity by chi-square test to assess whether 2023 rates differed significantly from those in 2018–2019 and 2022. The years 2018–2019 and 2022 were selected as reference periods based on stable hospitalisation rates. We considered p values < 0.05 statistically significant. Analyses were performed in Excel version 2019, R version 4.3.0 (https://www.r-project.org), and Stata version 19.00.20251006 (https://www.stata.com). Maps were generated in RegioGraph, version 2018 (https://regiograph.gfk.com).

Laboratory survey

To investigate whether the observed increase in STEC notifications was associated with changes in laboratory diagnostic routines and/or changes in reimbursement procedures, we conducted a laboratory survey in Lower Saxony, using the online-platform LamaPoll (https://www.lamapoll.de). The survey contained eight questions on methods and assays used for STEC diagnostics, the time of implementation of these methods and changes in diagnostic routines. The survey questionnaire is available in Supplement S1.

An invitation to the survey was sent via email to 25 clinical microbiology laboratories which participate in the Lower Saxony antimicrobial resistance monitoring network, as well as in the national network of accredited medical laboratories [12,13]. These participants represented most of the accredited clinical microbiology laboratories within the federal state. Laboratories were evenly distributed across Lower Saxony. Some were located in the neighbouring city states Bremen and Hamburg that also processed specimens from patients residing in Lower Saxony. The survey was carried out between 12 December 2023 and 8 February 2024. All participating laboratories provided their informed consent before participation.

Genomic analyses

All available STEC cases isolates (n = 120) from Lower Saxony in 2023 were characterised by whole genome sequencing (WGS) by short-read paired-end sequencing performed using MiSeq (2 × 300 bp), HiSeq 1500 (2 × 250 bp) and NextSeq 1000/2000 (2 × 150 bp) instruments (Illumina, San Diego, the United States (US)). Whole genome sequencing was performed at the National Reference Centre (NRC) for salmonellosis and other enteric pathogens at the RKI, or at the federal state laboratory of Lower Saxony. Genetic relationships were assessed by core genome multilocus sequence typing (cgMLST) according to the Enterobase scheme [14]. A genetic cluster was defined as isolates displaying < 5 allele differences in cgMLST.

Results

Spatial distribution

In Lower Saxony, 762 STEC cases were notified in 2023, equalling a 2.3-fold increase compared with 2022 (337 cases), and a 2.1-fold increase compared with the median of 2015–2019 (363 cases). Nationwide, a similar finding was observed with 4,458 notified STEC cases in 2023, equalling a 1.8-fold increase compared with 2022 (2,441 cases), and a 1.7-fold increase compared with the median of 2015–2019 (2,657 cases). These increases were statistically significant (p < 0.01). The increase in STEC notifications was not uniformly distributed across the 16 German federal states (Figure 1). Highest increases were seen in Lower Saxony (population: 8.0 million) and the neighbouring North Rhine-Westphalia (population: 18.0 million) which together account for 31% of the German population of 83.5 million [15]. Case numbers from these two federal states (2,237), constituted 50% of all STEC notifications (4,458) in Germany in 2023. Within Lower Saxony, the rise differed between districts (Figure 2). In other states, such as Baden-Wuerttemberg, Hamburg, Rhineland-Palatinate, Saxony and Saxony-Anhalt, no or only a slight increase was seen compared with the median 2015–2019, whereas in Bavaria, Berlin and Thuringia, case numbers slightly decreased (Figure 1). Detailed notification numbers for each federal state between 2015 and 2023 can be found in Supplementary Table S1.

Choropleth map illustrating how notified STEC case numbers in 2023 differed from the median of 2015–2019 per federal state. Each state is shaded according to the magnitude of change, with darker colours representing larger increases and lighter colours indicating smaller increases or decreases. Federal states boundaries and labels are shown throughout the map, and a legend indicates the value ranges used for the colour categories. A scale bar and north arrow are included for orientation. — Fold changes to notifications of cases with Shiga toxin-producing *Escherichia coli* (STEC) infection in 2023 (n = 4,458 cases) compared with the median of 2015–2019 (n = 2,657 cases), by federal state, Germany

Choropleth map showing how notified STEC case numbers in 2023 differed from the 2015–2019 median at district level. Each district is shaded according to the magnitude of change, with darker shades indicating larger increases and lighter shades indicating smaller increases or decreases. District boundaries and labels are shown throughout the map, and a legend indicates the value ranges used for the colour categories. A scale bar and north arrow are included for orientation. — Fold changes to notifications of cases with Shiga toxin-producing *Escherichia coli* (STEC) infection in 2023 (n = 762 cases) compared with the median of 2015–2019 (n = 363 cases), by district, Lower Saxony, Germany

While STEC notifications in Lower Saxony and nationwide in 2022 were at the same level as the median of 2015–2019, they were consistently higher over the course of 2023 (p < 0.01), with the most noticeable increase starting in June, reaching peaks by August–September (Figure 3).

The figures illustrate a pronounced increase in 2023 during the summer months, with the 2023 curve rising above both comparison lines. Axes labels indicate months and number of cases, the legend identifies the three data series. — Number of notified cases with Shiga toxin-producing *Escherichia coli* (STEC) infection in 2023 compared with 2022 and the median of 2015–2019, by month, Lower Saxony (A) and Germany (B)

Case interviews performed by local health authorities in Lower Saxony did not reveal any shared exposures of the STEC cases.

Age and sex distribution

Notifications of STEC increased in all age groups in 2023 compared with 2022 and the medians of 2015–2019 (p < 0.01). In Lower Saxony, compared with the 2015–2019 medians, these increases ranged from 1.5-fold in age group 20–29 years (2023: 80 cases; median 2015–2019: 54 cases), up to 4.2-fold in those aged 60–69 years (2023: 110 cases; median 2015–2019: 26 cases) (Figure 4A). The median age of cases was 40 years in 2023, 29 years in 2022 and 31 years in 2015–2019. Nationwide, the increases in 2023, when compared with the 2015–2019 medians, ranged from 1.2-fold in persons aged 0–9 years (2023: 1,143 cases; median 2015–2019: 924 cases) and 20–29 years (2023: 385 cases; median 2015–2019: 313 cases) up to 2.6-fold in those aged 60–69 years (2023: 471 cases; median 2015–2019: 182 cases) (Figure 4B). The median age of STEC cases nationwide was 36 years in 2023, 26 years in 2022 and 27 years in 2015–2019.

Histograms comparing the age distribution of notified STEC cases in Lower Saxony (Panel A) and Germany (Panel B): 2015–2019 median, 2022 and 2023. For each age group, bars display the number of cases for the three time periods. Labels indicate the fold increase in 2023 compared with the 2015–2019 median. Age groups range from 0–9 years to ≥ 70 years, and the bars illustrate higher case numbers in younger children as well as noticeable increases in older age groups in 2023. A legend identifies the three data series and the fold-increase values. — Age distribution of notified cases with Shiga toxin-producing *Escherichia coli* (STEC) infection, Lower Saxony (A) and Germany (B), 2015–2023

The proportion of female cases among notified cases in Lower Saxony was similar in 2023 (52.2%; 398/762) and in 2015–2019 (51.2%; 186/363) and slightly higher in 2022 (55.5%; 187/337). At the national level, the proportion of female cases was 53.2% (2,373/4,458) in 2023, 51.1% (1,359/2,658) in 2015–2019, and 54.1% (1,320/2,441) in 2022. Detailed results are available in Supplementary Table S2.

Clinical presentation

The number of STEC cases reported to be asymptomatic or without information on the presence of symptoms differed between the years, with a smaller proportion of asymptomatic cases in Lower Saxony in 2023 (21%; 160/762) compared with the median in 2015–2019 (32%; 117/363). However, in age groups 0–9 and 60–69 years, the proportions in 2023 (0–9 years: 22%; 33/152 and 60-69: 22%; 24/110) were comparable to the median (21% for each of the two age groups). Nationwide, similar findings were observed and are presented in Supplementary Figure S1.

Hospitalisation

Hospitalisations due to STEC increased in Lower Saxony from 29 cases in 2022 and 29 median cases in 2015–2019 to 81 cases in 2023. Nationwide, hospitalisations due to STEC increased from 382 cases in 2022 and 341 median cases in 2015–2019 to 548 in 2023 (Figure 5).

In each panel, blue bars represent the yearly number of hospitalised cases, while a line indicates the percentage of all reported STEC cases that were hospitalised. Numeric values above the bars show the annual counts. The line chart uses a secondary y-axis for the percentages. Both graphs show year-to-year variation in hospitalised case numbers and proportions across the observed period. — Number of cases hospitalised due to Shiga toxin-producing *Escherichia coli* (STEC) infection, and proportions of cases hospitalised due to STEC among all notified STEC cases, Lower Saxony (A) and Germany (B), 2015–2023

We considered proportions of cases hospitalised due to STEC of all notified STEC cases as a proxy for disease severity. The years 2018, 2019 and 2022 were selected as reference periods based on stable hospitalisation proportions. In Lower Saxony, the proportion of cases hospitalised due to STEC did not differ between these years (p > 0.05). Nationwide, the proportion of hospitalised cases in 2023 (548/4,458; 12%) was significantly lower than in 2022 (382/2,441; 16%; p < 0.05), but not lower than in 2018 (403/3,055; 13%) or 2019 (365/2,658 cases; 14%; p > 0.05) (Figure 5).

Cases with haemolytic-uraemic syndrome (HUS)

Contrary to the rise in STEC cases in 2023, we did not see a nationwide increase in HUS cases from 2022 to 2023 (77 vs 76 cases) or from the median of 2015–2019 (74 cases). A peak of 101 cases was observed in 2017 due to an outbreak of sorbitol-fermenting STEC O157 [16] (Figure 6). In Lower Saxony, 9 HUS cases were notified in 2023, six in 2022 and a median of 12 cases in 2015–2019.

The graph illustrates year-to-year variation, with values ranging from 59 to 101 cases 2015–2023. The median for 2015–2019 is shown as a separate bar for comparison. Each bar is labelled with the corresponding case count. — Number of notified Shiga toxin-producing *Escherichia coli* (STEC) infection cases with haemolytic-uraemic syndrome, Germany, 2015–2023 (n = 669)

Laboratory survey

Of the 25 invited clinical microbiology laboratories, 17 fully completed the questionnaire (response rate 68%). Multiple entries on procedures were possible.

Ten laboratories reported the use of multiplex PCR panels for gastrointestinal pathogens for STEC detection (Table). Six laboratories had introduced multiplex PCR in 2023. Five laboratories used Seegene Allplex GI-EB panel (Seegene, Seoul, South Korea) only, two laboratories used R-biopharm RIDAGENE EHEC/EPEC (R-biopharm, Darmstadt, Germany) and two laboratories used both panels. One laboratory applied the Luminex NxTAG Gastrointestinal Pathogen Panel (Luminex, Austin, the US).

Table. Laboratory methods used for detection and identification of Shiga toxin-producing Escherichia coli in clinical microbiological laboratories, Lower Saxony, Germany, 2023–2024 (n = 17).

Method	Laboratories (n)
Multiplex PCR panels for gastrointestinal illnesses	10
PCR/RT-PCR (stx1, stx2, eaeA genes) directly from faecal specimens	6
PCR/RT-PCR (stx1, stx2, eaeA genes) from colony washing	1
ELISA/EIA from enrichment broth	4
Faecal culture	2
Serotyping	1

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eae: gene coding for intimin; stx: Shiga toxin gene.

Information collected between 12 December 2023 and 8 February 2024; 17 of 25 invited laboratories responded. Multiple entries were possible.

Six laboratories used PCR assays for detection of STEC virulence genes (stx1, stx2, eaeA) directly from the stool specimens. Four of these laboratories had implemented this method in 2023. Two of the 17 laboratories cultured faecal samples.

Fifteen laboratories had not observed an increase in specific requests for STEC diagnostics. Laboratories noted that the implementation of multiplex PCRs in combination with a change in reimbursement in 2022 for PCR diagnostics may have led to an increase in STEC diagnoses.

Sequencing results

A total of 120 STEC isolates from notified cases across Lower Saxony were sequenced (WGS). Most isolates were genetically heterogenous, only six clusters consisting of two cases, each with < 5 allele differences were identified.

Discussion

In 2023, Lower Saxony observed a 2.3-fold increase in STEC notifications compared with 2022, and 2.1-fold compared with the median of 2015–2019. Nationwide, a similar finding was observed with a 1.8-fold increase compared with 2022, and a 1.7-fold increase compared with the median of 2015–2019. We aimed to investigate whether these increases in notifications were due to a true rise in infections or caused by changes in diagnostic procedures.

The nationwide case increase varied across the 16 German federal states (median 2015–2019 to 2023: 0.7–2.9-fold; 2022 to 2023: 1.1–2.3-fold). Highest increases were observed in Lower Saxony and North Rhine-Westphalia which together constituted for 50% of all STEC notifications in Germany in 2023. Case numbers increased in all age groups, both in Lower Saxony and nationwide when compared with the reference periods 2022 and 2015–2019. The strongest increase was observed in individuals aged 60–69 years. We did not detect any major changes in the sex distribution.

Nationwide, the proportion of hospitalisations due to STEC among all notified STEC cases was significantly lower in 2023 than in 2022. This could indicate a more frequent detection of non-severe STEC infections, not leading to hospitalisations. In Lower Saxony, however, we did not observe any statistically significant changes in hospitalisation proportions.

Whole genome sequencing of all available STEC isolates from 2023 from cases in Lower Saxony showed a wide genetic variety with no indication of clusters of more than two cases. Moreover, case interviews which were conducted by local health authorities as part of their routine case investigations, did not find evidence of shared exposures in Lower Saxony. Thus, a common source of infection was an unlikely explanation for the increase in case notifications.

To identify changes in diagnostic procedures that may explain the increase in STEC notifications in Lower Saxony, we performed a laboratory survey. Ten of 17 clinical microbiology laboratories performed multiplex PCR assays for testing of patients with gastroenteritis, and six of those had introduced these assays in 2023. Since September 2022, laboratories in Germany are officially reimbursed for nucleic acid detection of bacteria causing gastroenteritis, including STEC [8], which may have triggered the implementation of multiplex PCR panels. The use of multiplex PCR may also explain the higher increase of notifications in adults compared with children, since adults with gastrointestinal symptoms were previously not routinely tested for STEC, and thus would not have been diagnosed as STEC cases in the past.

Similar increases in STEC notifications after implementation of multiplex PCR have been reported from other countries such as Denmark and Norway, the US and Australia [17-22]. Norway observed an increase in low virulent STEC strains, without an increase in HUS cases [17] and Denmark an increase in STEC cases in older adults without an increase in disease severity [18,23].

The German national guideline for gastrointestinal infections [3] recommends testing for gastrointestinal infections only if the result is expected to have medical, organisational or notification consequences. Primary testing should include Campylobacter, Salmonella, rotavirus and norovirus. Infections of STEC are more frequent in the paediatric population, and children aged < 5 years are at increased risk [24]. Testing for STEC is therefore routinely recommended in symptomatic children and in severe cases with bloody diarrhoea or in symptomatic people who work in the food sector or visit communal facilities [3,9,10]. In case of a laboratory-confirmed STEC infection, children are not allowed to attend daycare or school; food industry workers are banned from work as long as they shed STEC.

Isolates are still essential for monitoring circulating STEC serotypes, cluster detection using WGS, epidemiological investigations and antimicrobial susceptibility testing [20,25,26]. The RKI and the Guideline for Gastrointestinal Infections recommend laboratories to perform bacterial culture on PCR-positive specimens [2,3], so-called reflex cultures. In our survey, 10 of the 17 participating laboratories reported the use of multiplex PCR panels, however, none of them reported to perform additional reflex cultures.

Detection of STEC by culture methods is challenging and labour-intensive due to the need for special selective media. The use of multiplex PCR allows shorter turnaround times, simplified workflows [20,21], automation of processes without deep technical knowledge and cost reductions [27]. Timely diagnosis can improve patient care and assist in infection control [20,26,28]. A drawback of PCR is that it detects the genetic material of pathogens regardless of their viability or ability to cause symptoms, which is one of the reasons the national guideline cautions against a universal use of multiplex PCRs. Instructions of commercial multiplex PCR assays stipulate that up to 45 amplification cycles should be run for nucleic acid detection. The German NRC for salmonellosis and other enteric pathogens observed that STEC cannot usually be detected by culture methods from stool specimens that were positive by PCR with quantification cycle (Cq) values > 32 (A Fruth, NRC, June 2024, personal communication). Therefore, it is questionable if positive PCR results with Cq values > 32 indicate true STEC infections or persisting infectiousness when used in follow-up stool examinations of cases. Without culture confirmation, PCR results with high Cq values may lead to unnecessary exclusions of children from daycare facilities or schools, as well as staff members, often with substantial social and economic consequences [17,21,29,30]. Moreover, the commercial multiplex PCR panels currently available in Germany do not differentiate between stx1 and stx2, possibly further contributing to unnecessary exclusions, as negative follow-up stool examinations would not be required to lift exclusions for cases with stx2-negative STEC isolates [30]. The differentiation between stx1 and stx2 would enable a more targeted patient management and follow-up, as the detection of less virulent strains could lead to fewer and/or shorter exclusions from daycares and workplaces.

Several pathogens can be detected in a single stool specimen from a patient with gastroenteritis using multiplex PCR. Studies of multiplex PCR performed in children with gastroenteritis indicated that around 20–50% of positive stool specimens were positive for more than one pathogen [21,27,28,31] but the symptom-causing pathogen was not always identified. Little is known, however, whether this also applies to adults. Contrary to the increase in STEC, notifications of other enteropathogenic bacteria, such as Campylobacter, Yersinia or Salmonella, did not increase in Germany during the study period [32].

Our analyses relied on case characteristics, such as presence of symptoms and hospitalisation status, as reported by local health authorities in the notification system. While there may be reporting errors, we have no reason to believe that the accuracy of the notification data has considerably changed over the study period. As we did not investigate other German federal states, we do not know reasons for the varying notification rates. Additional laboratory surveys may need to be carried out in other federal states to further investigate the increase in notifications. Moreover, a possible change in specimen submission behaviour by physicians could be explored.

Conclusion

We observed a marked increase in STEC notifications in 2023 in Lower Saxony and Germany nationwide, compared with 2022 and the median of 2015–2019. We consider the implementation of multiplex PCR panels for gastrointestinal pathogens in routine diagnostics to be the most plausible explanation for the observed increase. Our findings underscore the importance of monitoring diagnostic practices when evaluating trends in surveillance data.

Ethical statement

The RKI is the national public health institute and collects surveillance data on notifiable diseases according to the German Infection protection act. This study was based on anonymised surveillance data and did not require approval from an ethics committee. Laboratories participating in the survey provided their informed consent for aggregated data publishing. Names of laboratories are not published.

Use of artificial intelligence tools

Artificial intelligence was used for language editing to improve readability.

Acknowledgements

The authors would like to thank A Fruth and C Lang from the National Reference Centre for salmonellosis and other enteric pathogens, as well as R Egelkamp from the Public Health Agency of Lower Saxony for diagnostic support. Moreover, we would like to thank from the Department of Infectious Disease Epidemiology at RKI M. Faber for his support in map generation, and A Dörre for his statistical support. We also thank all laboratories participating in the survey.

Supplementary Data

Supplementary Material

25-00268_JUNG-SENDZIK_Supplement.pdf^{(468.8KB, pdf)}

Authors’ contributions: Tanja Jung-Sendzik: Conceptualisation, Formal analysis, Writing – original draft, Writing – review & editing. Mareike Wollenweber: Conceptualisation, Formal analysis, Writing – original draft, Writing – review & editing. Katja Hille: Writing – original draft, Writing – review & editing. Lilas Mercuriali: Conceptualisation, Formal analysis, Writing – original draft. Gerhard Falkenhorst: Conceptualisation, Formal analysis, Supervision, Writing – original draft, Writing – review & editing.

Conflict of interest: None declared.

Funding statement: Not applicable.

Disclaimer

Tanja Jung-Sendzik and Mareike Wollenweber were fellows of the German Postgraduate Training in Applied Epidemiology (PAE) at RKI, associated with the ECDC Fellowship Programme. Lilas Mercuriali was fellow of the of the ECDC Fellowship Programme, supported financially by the European Centre for Disease Prevention and Control (ECDC). The views and opinions expressed herein do not state or reflect those of ECDC. ECDC is not responsible for the data and information collation and analysis and cannot be held liable for conclusions or opinions drawn.

Data availability

Query of notification data in accordance with the Infection Protection Act (IfSG) via SurvNet@RKI. A limited dataset without information on individual STEC and HUS cases can be downloaded from: https://survstat.rki.de/default.aspx

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10.Müller D, Falkenhorst G, Jordans I, Heyde M, Holle J, Lange-Sperandio D, et al. Hämolytisch-urämisches Syndrom im Kindesalter. [Haemolytic-ureamic syndrom in children]. Frankfurt: Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften (AVMF); 2022. German. Available from: https://register.awmf.org/assets/guidelines/166-002l_S2k_Haemolytisch-Uraemisches-Syndrom-im-Kindesalter_2022-07.pdf
11. Ullrich A, Schranz M, Rexroth U, Hamouda O, Schaade L, Diercke M, et al. Impact of the COVID-19 pandemic and associated non-pharmaceutical interventions on other notifiable infectious diseases in Germany: An analysis of national surveillance data during week 1-2016 - week 32-2020. Lancet Reg Health Eur. 2021;6:100103. 10.1016/j.lanepe.2021.100103 [DOI] [PMC free article] [PubMed] [Google Scholar]
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24. Travert B, Rafat C, Mariani P, Cointe A, Dossier A, Coppo P, et al. Shiga toxin-associated hemolytic uremic syndrome: specificities of adult patients and Implications for critical care management. Toxins (Basel). 2021;13(5):306. 10.3390/toxins13050306 [DOI] [PMC free article] [PubMed] [Google Scholar]
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26. Teh R, Tee W, Tan E, Fan K, Koh CJ, Tambyah PA, et al. Review of the role of gastrointestinal multiplex polymerase chain reaction in the management of diarrheal illness. J Gastroenterol Hepatol. 2021;36(12):3286-97. 10.1111/jgh.15581 [DOI] [PubMed] [Google Scholar]
27. Liu J, Kabir F, Manneh J, Lertsethtakarn P, Begum S, Gratz J, et al. Development and assessment of molecular diagnostic tests for 15 enteropathogens causing childhood diarrhoea: a multicentre study. Lancet Infect Dis. 2014;14(8):716-24. 10.1016/S1473-3099(14)70808-4 [DOI] [PubMed] [Google Scholar]
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29. Elfving K, Andersson M, Msellem MI, Welinder-Olsson C, Petzold M, Björkman A, et al. Real-time PCR threshold cycle cutoffs help to identify agents causing acute childhood diarrhea in Zanzibar. J Clin Microbiol. 2014;52(3):916-23. 10.1128/JCM.02697-13 [DOI] [PMC free article] [PubMed] [Google Scholar]
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31. Enserink R, Scholts R, Bruijning-Verhagen P, Duizer E, Vennema H, de Boer R, et al. High detection rates of enteropathogens in asymptomatic children attending day care. PLoS One. 2014;9(2):e89496. 10.1371/journal.pone.0089496 [DOI] [PMC free article] [PubMed] [Google Scholar]
32.Robert Koch Institute (RKI). SURVSTAT@RKI 2.0. Berlin: RKI. [Accessed: 4 Dec 2024]. Available from: https://survstat.rki.de/Default.aspx

Associated Data

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

Supplementary Materials

Supplementary Material

25-00268_JUNG-SENDZIK_Supplement.pdf^{(468.8KB, pdf)}

Data Availability Statement

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[r8] 8. Kassenärztliche Bundesvereinigung . Beschluss des Bewertungsausschusses nach § 87 Abs. 1 Satz 1 SGB V in seiner 596. Sitzung am 15.Juni 2022 zur Änderung des Einheitlichen Bewertungsmaßstabes (EBM). [Decision of the Evaluation Committee pursuant to Section 87 Paragraph 1 Sentence 1 of the German Social Code, Book V (SGB V) at its 596th meeting on 15 June 2022 Part A on the amendment of the Uniform Assessment Scale (EBM)]. German. Dtsch Arztebl. 2022;119(26):1210-3. [Google Scholar]

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[r10] 10.Müller D, Falkenhorst G, Jordans I, Heyde M, Holle J, Lange-Sperandio D, et al. Hämolytisch-urämisches Syndrom im Kindesalter. [Haemolytic-ureamic syndrom in children]. Frankfurt: Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften (AVMF); 2022. German. Available from: https://register.awmf.org/assets/guidelines/166-002l_S2k_Haemolytisch-Uraemisches-Syndrom-im-Kindesalter_2022-07.pdf

[r11] 11. Ullrich A, Schranz M, Rexroth U, Hamouda O, Schaade L, Diercke M, et al. Impact of the COVID-19 pandemic and associated non-pharmaceutical interventions on other notifiable infectious diseases in Germany: An analysis of national surveillance data during week 1-2016 - week 32-2020. Lancet Reg Health Eur. 2021;6:100103. 10.1016/j.lanepe.2021.100103 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r12] 12.Niedersächsisches Landesgesundheitsamt. Antibiotika-Resistenz-Monitoring (ARMIN). Hannover; Niedersächsisches Landesgesundheitsamt [Monitoring of antimicrobial resistance]. [Accessed: 4 Dec 2025]. German. Available from: https://www.nlga.niedersachsen.de/antibiotika-resistenzen/antibiotikaresistenzen-197961.html

[r13] 13.Akkreditierte Labore in der Medizin e.v. (ALM). Labore unserer Mitglieder - Niedersachsen. [Member laboratories – Lower Saxony]. Berlin: ALM. [Accessed: 4 Dec 2025]. German. Available from: https://www.alm-ev.de/alm/mitglieder /

[r14] 14. Zhou Z, Alikhan NF, Mohamed K, Fan Y, Agama Study Group. Achtman M. The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res. 2020;30(1):138-52. 10.1101/gr.251678.119 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r15] 15.Statistisches Bundesamt. (Destatis). Population as of 31.12.2024 by nationality and federal states. Wiesbaden: Destatis; 20 Jun 2025. Available from: https://www.destatis.de/EN/Themes/Society-Environment/Population/Current-Population/Tables/population-by-laender-basis-2022.html

[r16] 16. Vygen-Bonnet S, Rosner B, Wilking H, Fruth A, Prager R, Kossow A, et al. Ongoing haemolytic uraemic syndrome (HUS) outbreak caused by sorbitol-fermenting (SF) Shiga toxin-producing Escherichia coli (STEC) O157, Germany, December 2016 to May 2017. Euro Surveill. 2017;22(21):30541. 10.2807/1560-7917.ES.2017.22.21.30541 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r17] 17. Jenssen GR, Veneti L, Lange H, Vold L, Naseer U, Brandal LT. Implementation of multiplex PCR diagnostics for gastrointestinal pathogens linked to increase of notified Shiga toxin-producing Escherichia coli cases in Norway, 2007-2017. Eur J Clin Microbiol Infect Dis. 2019;38(4):801-9. 10.1007/s10096-019-03475-5 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r18] 18.Statens Serum Institut (SSI). Overvågning i tal, grafer og kort - STEC/ VTEC, Laboratorieanmeldelsespligtige sygdomme. [Surveillance in numbers, graphs and maps - STEC/ VTEC, laboratory notifiable diseases]. Copenhagen: SSI. [Accessed: 4 Dec 2025]. Danish. Available from: https://statistik.ssi.dk/sygdomsdata#!/?sygdomskode=STEC&xaxis=Aar&show=Graph&datatype=Laboratory

[r19] 19. European Food Safety Authority (EFSA) European Centre for Disease Prevention and Control (ECDC) . The European Union One Health 2022 Zoonoses Report. EFSA J. 2023;21(12):e8442. [DOI] [PMC free article] [PubMed] [Google Scholar]

[r20] 20. Bording-Jorgensen M, Parsons BD, Tarr GAM, Shah-Gandhi B, Lloyd C, Chui L. Association of Ct values from real-time PCR with culture in microbiological clearance samples for Shiga toxin-producing Escherichia coli (STEC). Microorganisms. 2020;8(11):1801. 10.3390/microorganisms8111801 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r21] 21. Marder EPC, Cieslak PR, Cronquist AB, Dunn J, Lathrop S, Rabatsky-Ehr T, et al. Incidence and trends of infections with pathogens transmitted commonly through food and the effect of increasing use of culture-independent diagnostic tests on surveillance - Foodborne Diseases Active Surveillance Network, 10 U.S. sites, 2013-2016. MMWR Morb Mortal Wkly Rep. 2017;66(15):397-403. 10.15585/mmwr.mm6615a1 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r22] 22. Shrestha AC, Stafford R, Bell R, Jennison AV, Graham RMA, Field E, et al. Shiga toxin‒producing Escherichia coli diagnoses from health practitioners, Queensland, Australia. Emerg Infect Dis. 2024;30(1):199-202. 10.3201/eid3001.231202 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r23] 23.Technical University of Denmark (DTU). Annual Report on Zoonoses in Denmark 2022. Lyngby: DTU; 2023. Available from: https://www.food.dtu.dk/english/-/media/institutter/foedevareinstituttet/publikationer/pub-2023/annual-report-on-zoonoses-2022_rev18juli2023.pdf

[r24] 24. Travert B, Rafat C, Mariani P, Cointe A, Dossier A, Coppo P, et al. Shiga toxin-associated hemolytic uremic syndrome: specificities of adult patients and Implications for critical care management. Toxins (Basel). 2021;13(5):306. 10.3390/toxins13050306 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r25] 25. McAdam AJ. Unforeseen consequences: culture-independent diagnostic tests and epidemiologic tracking of foodborne pathogens. J Clin Microbiol. 2017;55(7):1978-9. 10.1128/JCM.00678-17 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r26] 26. Teh R, Tee W, Tan E, Fan K, Koh CJ, Tambyah PA, et al. Review of the role of gastrointestinal multiplex polymerase chain reaction in the management of diarrheal illness. J Gastroenterol Hepatol. 2021;36(12):3286-97. 10.1111/jgh.15581 [DOI] [PubMed] [Google Scholar]

[r27] 27. Liu J, Kabir F, Manneh J, Lertsethtakarn P, Begum S, Gratz J, et al. Development and assessment of molecular diagnostic tests for 15 enteropathogens causing childhood diarrhoea: a multicentre study. Lancet Infect Dis. 2014;14(8):716-24. 10.1016/S1473-3099(14)70808-4 [DOI] [PubMed] [Google Scholar]

[r28] 28. Macfarlane-Smith LR, Ahmed S, Wilcox MH. Molecular versus culture-based testing for gastrointestinal infection. Curr Opin Gastroenterol. 2018;34(1):19-24. 10.1097/MOG.0000000000000405 [DOI] [PubMed] [Google Scholar]

[r29] 29. Elfving K, Andersson M, Msellem MI, Welinder-Olsson C, Petzold M, Björkman A, et al. Real-time PCR threshold cycle cutoffs help to identify agents causing acute childhood diarrhea in Zanzibar. J Clin Microbiol. 2014;52(3):916-23. 10.1128/JCM.02697-13 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r30] 30. Pörtner K, Fruth A, Flieger A, Middendorf-Bauchart B, Mellmann A, Falkenhorst G. Überarbeitung der RKI Empfehlungen für die Wiederzulassung zu Gemeinschaftseinrichtungen gemäß § 34 IfSG nach EHEC-Infektion. [Revision of the RKI recommendations for readmission to community facilities according to § 34 IfSG after EHEC infection]. German. Epidemiologisches Bulletin. 2019;47:506-9. [Google Scholar]

[r31] 31. Enserink R, Scholts R, Bruijning-Verhagen P, Duizer E, Vennema H, de Boer R, et al. High detection rates of enteropathogens in asymptomatic children attending day care. PLoS One. 2014;9(2):e89496. 10.1371/journal.pone.0089496 [DOI] [PMC free article] [PubMed] [Google Scholar]

[r32] 32.Robert Koch Institute (RKI). SURVSTAT@RKI 2.0. Berlin: RKI. [Accessed: 4 Dec 2024]. Available from: https://survstat.rki.de/Default.aspx

PERMALINK

Rise in the number of notifications of Shiga toxin-producing Escherichia coli (STEC) infections probably linked to an increased use of multiplex PCR assays, Germany, 2023

Tanja Jung-Sendzik

Mareike Wollenweber

Katja Hille

Lilas Mercuriali

Gerhard Falkenhorst

Abstract

BACKGROUND

AIM

METHODS

RESULTS

CONCLUSION

Key public health message.

Introduction

Methods

Data collection and analysis of STEC notifications

Box. National case definition for infections of Shiga toxin-producing Escherichia coli (STEC), Germany.

Laboratory survey

Genomic analyses

Results

Spatial distribution

Figure 1.

Figure 2.

Figure 3.

Age and sex distribution

Figure 4.

Clinical presentation

Hospitalisation

Figure 5.

Cases with haemolytic-uraemic syndrome (HUS)

Figure 6.

Laboratory survey

Table. Laboratory methods used for detection and identification of Shiga toxin-producing Escherichia coli in clinical microbiological laboratories, Lower Saxony, Germany, 2023–2024 (n = 17).

Sequencing results

Discussion

Conclusion

Ethical statement

Use of artificial intelligence tools

Acknowledgements

Supplementary Data

Disclaimer

Data availability

References

Associated Data

Supplementary Materials

Data Availability Statement

ACTIONS

PERMALINK

RESOURCES

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Cited by other articles

Links to NCBI Databases

Table. Laboratory methods used for detection and identification of Shiga toxin-producing Escherichia coli in clinical microbiological laboratories, Lower Saxony, Germany, 2023–2024 (n = 17).