In September 2020, an unexpected increase in Salmonella Muenchen patient isolates and notifications was observed. We investigated the outbreak to identify the vehicle of infection. RKI defined cases as patients with laboratory-confirmed S. Muenchen infections reported between September 2020 and July 2021. Genomes of clinical, food, and animal S. Muenchen isolates were analysed using cgMLST. We conducted interviews and performed a frequency-matched case-control study. We calculated frequencies and adjusted odds ratios (aOR) using logistic regression. We identified 301 cases in eight federal states in Germany. Hypothesis-generating interviews did not provide a conclusive hint of a possible vehicle. S. Muenchen strains were detected in dried coconut pieces, milk powder used for chocolate production, and a wild swan, all with a cgMLST profile indistinguishable from the prominent node comprising 116 patient isolates. Cases included in the case-control study more often consumed dried coconut pieces (22/30) than controls (2/116) (aOR: 176 (95% confidence interval: 32-954)). In this investigation, cgMLST analysis presented identical strains in three different isolate sources. The case-control study supported dried coconut pieces as vehicle of infection demonstrating the importance of interdisciplinary investigations and underscoring the potential impact of unusual vehicles.

Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is the second most common serovar causing human salmonellosis in Aotearoa New Zealand (NZ). Sequence type (ST)183, which includes phage types 9a and 11, was the second most frequently isolated S. Enteritidis strain from human cases between 2020 and 2023. This ST is considered endemic in NZ as well as in mainland Europe and Great Britain, where the European hedgehog (Erinaceus europaeus) is a recognized wildlife reservoir. Hedgehogs were introduced to NZ in the late 19th century; however, their role in the ecology of ST183 in NZ has not been formally evaluated. The aim of this study was to investigate whether hedgehogs act as a reservoir for S. Enteritidis ST183 in NZ and to assess the evolutionary history and epidemiology of this strain across human, animal and environmental contexts. We analysed human, animal and environmental ST183 isolates, including hedgehog carcasses opportunistically sampled in NZ, using Bayesian phylogenetic methods integrated with national epidemiological data. Although S. Enteritidis ST183 was isolated from three of 45 hedgehog carcasses during our study, consistent with recent prior detections of ST183 in NZ hedgehogs, Bayesian phylogenetic analysis supports a most recent common ancestor for currently circulating ST183 strains in the late 20th century, ~100 years after the introduction of hedgehogs into NZ, providing no evidence that the strain was introduced concomitantly with hedgehogs. Epidemiological analysis revealed that, unlike in Europe, ST183 infections in NZ are more common in people aged over 60 years compared with non-ST183 S. Enteritidis infections, with rural residence and contact with farm animals identified as key risk factors. Together, these findings suggest that S. Enteritidis ST183 is established within the NZ rural environment, with evidence of interspecies transmission. While hedgehogs may contribute to the maintenance of ST183, they are unlikely to represent the original source of introduction, indicating a complex, multi-host ecology.

Salmonella serotyping is shifting from slide agglutination toward whole-genome sequencing (WGS). While WGS allows for comprehensive analyses, phenotypic information about lipopolysaccharide-deficient ("LPS-rough") isolates obtained from slide agglutination is lost. This discrepancy represents a challenge for Salmonella control in livestock because in the European Union, LPS-rough Salmonella isolated from food-producing animals that are untypable using slide agglutination alone are not subject to control measures, whereas isolates of certain serovars in certain matrices would be, when based on geno-serotyping. Here, we provide an account of the relevance of this phenotype in the context of routine diagnostics and food safety by characterizing the occurrence, diversity, and isolation matrices of LPS-rough isolates among non-human Salmonella enterica subsp. enterica isolates from Germany. Using available WGS data, we examined phylogenetic relationships and associations with certain genomic features. On average, 5% of isolates exhibited an LPS-rough phenotype across 46 serovars, but clonal distribution of this phenotype along the food chain was not evident. LPS-rough isolates were more commonly found in S. Choleraesuis isolated from wild boar and in S. Typhimurium isolated from pork products, compared with other matrices. We also found associations with two virulence factors, an AMR gene, and a plasmid marker. The present work lays the foundation for future research into the role of certain matrices, environments, or genomic factors in the development of LPS-rough Salmonella isolates and will facilitate the elucidation of the genomic basis of this phenotype, which may improve recommendations regarding risk management and control measures.IMPORTANCEThe present work highlights some of the challenges associated with the recent shift from serology- to sequence-based typing of Salmonella enterica serovars and provides a national perspective on the presence and relevance of the lipopolysaccharide-deficient ("LPS-rough") phenotype in samples obtained from food, animals, and the environment, including considerations regarding the choice of typing method. We provide evidence that clonal distribution of isolates with this phenotype is unlikely, but that certain environments may favor its development, and certain genomic factors may increase survival rates of LPS-rough isolates when exposed to environmental stressors. These findings could have important implications for regulations regarding the surveillance and management of Salmonella isolated from food, feed, and animals in the future, in particular in the context of using different typing methods, and warrant further detailed research.

Background In sub-Saharan Africa, invasive non-typhoidal Salmonella disease, characterized by bloodstream infections with high mortality rates, poses a significant public health burden. In Africa, Salmonella enterica , which are typically livestock- associated pathogens in industrialised countries, have genetically evolved and anthroponotic transmission has been proposed for S . Typhimurium ST313. In this study, we investigated the hypothesis of an exclusively anthroponotic transmission reservoir of Salmonella enterica ST313 and aimed to identify reservoirs for other Salmonella spp . , shedding light on their occurrence in different ecological niches. Methods This study used a One Health approach and Salmonella were isolated from humans, livestock and the environment, in Tanzania and in Ghana. Salmonella spp. were identified by biochemical methods and antibiotic susceptibility was tested. Isolates were subjected to whole genome sequencing. Results Out of 9,086 collected samples, 222 Salmonella enterica were identified comprising 58 serovars. The highest level of antimicrobial resistance was found in humans with emerging fluroquinolone resistance and multidrug resistance being highest in isolates from blood cultures (24%, n/N = 11/46). For the invasive strains, the sequence types S . Typhimurium ST313 and ST19 were most common and ST313 was associated with multidrug resistance, followed by S . Enteritidis ST11 and ST147 and S . Dublin ST10. An overlap of sequence types amongst human-livestock and human-environmental strains was detected for S . Typhimurium ST19 but not found for ST313 and the two serovars Dublin and Enteritidis. Conclusions Our study adds further evidence of S . Typhimurium ST313 being restricted to a human reservoir and linked to multidrug resistance. Additionally, our study provides comprehensive insights into Salmonella genetic diversity and distribution among humans, animals and the environment in Ghana and in Tanzania. This sheds light on other potential reservoirs for infections, all of which show antimicrobial resistance. Further research into stool carriage is warranted, encompassing patients with invasive disease and those with and without diarrhoea, to identify transmission reservoirs in particular for invasive disease-causing strains. These findings underscore the need for integrated One Health approaches to effectively monitor and manage salmonellosis and mitigate public health risks. Continued research into the spread of Salmonella spp. and its evolution is crucial for targeted interventions and disease control.

Different laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes spanning the food, animal, and human health sectors, we aimed to assess the inter-pipeline clustering congruence across all resolution levels and perform an in-depth comparative analysis of cluster composition at outbreak level for four important foodborne pathogens: Listeria monocytogenes, Salmonella enterica, Escherichia coli, and Campylobacter jejuni. We found a general concordance between allele-based pipelines for all species, except for C. jejuni, where the different resolution power of allele-based schemas led to marked discrepancies. Still, we identified non-negligible differences in outbreak detection and demonstrated how a threshold flexibilization favors the detection of similar outbreak signals by different laboratories. These results, together with the observation that different traditional typing groups (e.g., serotypes) exhibit a remarkably different genetic diversity, represent valuable information for future outbreak case-definitions and WGS-based nomenclature design. This study reinforces the need, while demonstrating the feasibility, of conducting continuous pipeline comparability assessments, and opens good perspectives for a smoother international and intersectoral cooperation towards an efficient One Health FWD surveillance.

We report on a carbapenem-, extended spectrum β-lactam-, fluoroquinolone-, and tetracycline-resistant Salmonella enterica serovar Typhi strain in a patient returning to Germany from India. Considering the recent emergence of extensively drug-resistant Salmonella Typhi strains, further expansion of antibiotic resistance to carbapenems poses a serious threat for typhoid fever treatment.

Notifications of Salmonella Strathcona infections increased in Europe in 2023 prompting a multi-country outbreak investigation. We aimed to describe the epidemiology of S. Strathcona infections in 17 European countries 2011–2024, investigate the genetic relatedness of S. Strathcona isolates and identify the vehicle. Cases were persons residing in the study area and with a laboratory-confirmed S. Strathcona infection 2011–2024. Confirmed cases had a S. Strathcona isolate clustering with the outbreak reference strain in core genome multilocus sequence typing (cgMLST) within 7 allelic differences (AD) and possible cases within 8–13 AD. Probable cases had an epidemiological link to a confirmed case and non-outbreak cases had an isolate > 13 AD from the outbreak reference strain. Since 2011, 662 S. Strathcona infections have been identified: 469 confirmed, 161 probable, 13 possible and 19 non-outbreak cases. Median age of the cases was 34 years (IQR: 19–58 years) and 306 (47.5%) were notified in 2023–2024. Most sequenced isolates (469/496; 94.5%) were highly genetically related (≤ 7 AD) over time and across countries, compatible with a common source. Epidemiological and traceback investigations identified small tomatoes from Sicily as the suspect food vehicle. Stringent control measures at the source are needed to stop the contamination and prevent future cases.

Non-typhoidal Salmonella (NTS) presents a considerable health threat to children in low-resource settings, where clean water, sanitation, and hygiene are often inadequate. However, the environmental factors influencing NTS persistence and spread remain poorly understood. We utilized a case-control approach to investigate environmental factors associated with NTS infection in children living in Nairobi's informal settlements between August 2022 and July 2023. Stool samples were collected from febrile children, with or without diarrhea, who visited healthcare facilities. The study included 42 laboratory-confirmed NTS-positive cases and 42 NTS-negative children from the same community. Environmental samples, including drinking water, open drains, soil, and household effluent, were collected from both case and control households, in addition to raw sewage from main sewer-line convergence points. Conventional microbiological culture and quantitative Polymerase Chain Reaction techniques were employed for NTS detection, with genomic sequencing used for strain characterization. Environmental samples from case households showed a higher NTS contamination rate of 33.3% (42/126) compared to control households of 7.2% (9/126). Higher odds of NTS infection in children were associated with household environmental factors, particularly exposure to household effluent (OR = 7.7, 95% CI: 2.18-34.82, p = 0.0005), drinking water (OR = 6.4, 95% CI: 1.57-37.76, p = 0.0055), and soil (OR = 5.4, 95% CI: 1.01-54.28, p = 0.0485). Genomic analysis revealed a common strain, Salmonella Enteritidis ST11, in clinical and environmental isolates. These findings highlight the plausible role of the household environment as a reservoir for NTS, perpetuating infection cycles within the community. Addressing this challenge requires a multifaceted approach, including improved sanitation infrastructure, environmental monitoring, and integrated public health interventions to reduce NTS exposure and transmission in high-risk populations.

BACKGROUND:In February 2022, the United Kingdom (UK) detected a cluster of monophasic Salmonella Typhimurium based on whole genome sequencing (WGS). Subsequently, several countries reported cases belonging to this cluster. Epidemiological, microbiological and traceability investigations pointed toward a chocolate food business operator (FBO) in Belgium. We describe the magnitude of the outbreak, investigations performed and control measures taken. METHODS:Cases were ascertained based on internationally agreed case definitions and interviewed about food consumption prior to disease onset. Analytical epidemiological studies were conducted by the UK and Ireland. The Belgian food safety authority (FSA) coordinated microbiological and traceability investigations. RESULTS:A total of 456 cases (61% female), belonging to two genetically different WGS clusters, in 14 countries of the European Union, the UK, Switzerland, Canada and the United States were linked to the outbreak, between December 2021 and June 2022. 87% of cases were younger than 10 years. Brand A chocolate eggs, marketed for children, were reported as consumed by 168 cases (80%) with information. Analytical studies in the UK and Ireland showed a significantly higher odds of disease associated with consumption of brand A chocolate products. Retrospective investigations by the FSA revealed that routine samples (raw materials, intermediate, semi-finished and finished products as well as environmental and rinse oil samples) taken by the FBO linked to the Brand A products between December 2021 and January 2022 had tested positive for salmonella. Nine isolates were submitted to EnteroBase and matched with human isolates from both WGS clusters. The authorization for production was temporarily withdrawn on 8 April 2022 and all products of brand A were recalled worldwide, followed by a decrease in cases. CONCLUSIONS:A multi-country salmonellosis outbreak linked to chocolate occurred in the months before Easter 2022. International collaboration between stakeholders from epidemiological, microbiological and food safety entities with rapid sharing of WGS results from human and nonhuman isolates were key in containing the outbreak. Implementation of routine WGS on human and nonhuman isolates will strengthen public health responses to future outbreaks. The magnitude of the outbreak underlines the importance of timely and open communication of FBOs to FSAs in case of salmonella detection.

Background Enteric fevers (EF) are caused by infections with Salmonella Typhi (STY) or Salmonella Paratyphi (SP) A-C (except the SPB enteric pathovar) and exhibit increasing antimicrobial resistance (AMR). Notification is mandatory in Germany. Aim To describe characteristics and trends of notified EF cases in Germany. Methods We analysed German EF notifications 2001–2023 fulfilling the case definition. We calculated numbers of imported EF cases per 100,000 air travellers by country of exposure 2012–2023. Results In 2001–2023, 2,670 confirmed EF cases were notified: 56% (1,498/2,670) STY, 44% (1,172/2,670) SP, with seasonal peaks in April–May and August–September. Aside from years with COVID-19-related travel restrictions, STY notifications were stable, while SP notifications decreased. Median age of EF cases was 26 years (range: 0–93) and 55% (1,458/2,663) were male. Of cases with information, 93% (2,491/2,670) had fever, 71% (1,906/2,670) diarrhoea, 78% (2,033/2,607) were hospitalised (STY: 85% (1,234/1,459) vs SP: 70% (799/1,148), p < 0.001) and four died (two STY, one SPA, one SPB). Of STY cases, 7% (88/1,221) reported vaccination. Overall, 86% (2,251/2,613) of cases acquired EF abroad, most commonly in India, Pakistan and Türkiye. Ciprofloxacin resistance was reported for 50/59 STY and 16/18 SPA cases and cefotaxime resistance for 10/57 STY cases (exposure: Pakistan (9/10), India (1/10)) with information since 2017. We also report outbreaks and incidence among travellers. Conclusions Most cases were imported and had high hospitalisation rates and AMR. Typhoid vaccination was underutilised, highlighting that additional ways to reach at-risk travellers with information and vaccination offers are needed.

Das Ziel der interdisziplinären S2k-Leitlinie „Akute infektiöse Gastroenteritis im Säuglings-, Kindes- und Jugendalter“ ist es, den aktuellen Kenntnisstand zu klinischem Bild, Diagnostik, Therapie, Prävention und Hygiene der akuten infektiösen Gastroenteritis, einschließlich der nosokomialen gastrointestinalen Infektionen, bei Säuglingen, Kindern und Jugendlichen auf Basis der wissenschaftlichen Evidenz zusammenzufassen, im Expertenkonsens zu bewerten und daraus praxisrelevante Empfehlungen abzuleiten. Die Leitlinie liefert einen Handlungskorridor für häufige Entscheidungen. Sie dient zudem der evidenzbasierten Fort- und Weiterbildung und soll damit eine Verbesserung der medizinischen Versorgung von Kindern mit akuter Gastroenteritis erreichen. Insbesondere sollen durch die Leitlinie unnötige stationäre Aufnahmen von Kindern mit AGE vermieden und präventive Maßnahmen zur Infektionsvermeidung und -ausbreitung ergriffen werden.

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 historical and contemporary SPB PG1 isolates, obtained globally, between 1898 and 2021. We show that this pathogen existed in the 13th century, subsequently diversifying into 11 lineages and 38 genotypes with strong phylogeographic patterns. Following its discovery in 1896, it circulated across Europe until the 1970s, after which it was mostly reimported into Europe from South America, the Middle East, South Asia, and North Africa. Antimicrobial resistance recently emerged in various genotypes of SPB PG1, mostly through mutations of the quinolone-resistance-determining regions of gyrA and gyrB. This study provides an unprecedented insight into SPB PG1 and essential genomic tools for identifying and tracking this pathogen, thereby facilitating the global genomic surveillance of PTB.

Nontyphoidal Salmonella (NTS) is a predominant cause of invasive disease in sub-Saharan Africa especially among children under 5 years. Asymptomatic fecal shedding of NTS is hypothesized to contribute to the human-to-human transmission of NTS especially in low-resource settings. However, the role of pathogen shedding in invasive disease is unknown. This study aimed to investigate the prevalence and duration of fecal shedding of NTS among children under 5 years convalescing from invasive NTS disease and among healthy individuals in the community. Children presenting with fever of ≥38°C with or without diarrhea were recruited at four health facilities in Nairobi, between June 2021 and August 2023. Blood and stool samples collected were subjected to culture for the isolation of NTS (S. Enteritidis and S. Typhimurium). Children with NTS culture-positive samples (index cases) were followed up post-acute disease where household contacts and controls provided stool samples for isolation of NTS. NTS prevalence among the 3,293 individuals recruited was 1.52%. Asymptomatic shedding post-treatment was observed in almost one-third (31%) of the 42 index cases followed up. Of the 13 with intestinal shedding, 7 were shedding NTS of the same sequence type (ST) as the one recovered during acute disease. The longest duration of intestinal shedding was 3 months post-treatment. Of the 241 healthy individuals recruited, 8 had asymptomatic shedding of NTS, and 2 of these were closely related to those recovered from index cases. These findings support the hypothesis of human-to-human transmission of NTS in sub-Saharan Africa highlighting the possible benefit of vaccine introduction. IMPORTANCE:Asymptomatic fecal shedding of nontyphoidal Salmonella (NTS) is hypothesized to contribute to the human-to-human transmission of NTS especially in low-resource settings which could lead to invasive disease among high-risk populations, especially children. Our findings reiterate the hypothesis that human reservoirs could be important in the transmission of nontyphoidal Salmonella in sub-Saharan Africa. This underscores the importance of developing infection prevention measures which could include vaccine deployment and improving water, sanitation and hygiene infrastructure.

A genomic cluster of Salmonella Braenderup ST22, a serovar of Salmonella enterica subsp. enterica which causes symptoms of gastrointestinal illness, was notified by Danish authorities to the European Centre for Disease Prevention and Control (ECDC) on 3 May 2021. By 6 July 2021, S. Braenderup outbreak cases (n = 348) had been reported from 12 countries in the European Union/European Economic Area (EU/EEA) and the United Kingdom (UK), including 68 hospitalised cases. With support from affected EU/EEA countries, and in partnership with the European Food Safety Authority (EFSA), ECDC established an international outbreak investigation team to rapidly identify the source and prevent outbreak spread. Consumption information was shared with affected countries through a standard line list, revealing that 124 of 197 cases (63%) reported having eaten (any) melons within 7 days prior to disease onset. The speed and completeness of the investigation, which identified the outbreak vehicle as galia melons imported from Honduras in June 2021, was a direct result of extensive collaboration and information sharing between countries' national food safety and public health authorities. This article describes the outbreak and the benefits, successes, and challenges of multi -country collaboration for consideration in future large foodborne outbreaks across Europe.

A food-borne outbreak with about 200 Salmonella Umbilo cases occurred mainly between July and September 2024 in several European countries. Collaborative work between outbreak teams in Germany, Austria and Denmark, including epidemiological and microbiological investigations, allowed to rapidly identify rocket salad as the likely infection vehicle. Salmonella Umbilo was detected in rocket salad, and later in baby spinach. The food isolates and clinical outbreak strain were genetically closely related. Both food items originated from the same company in Italy.

Food and waterborne disease (FWD) surveillance requires Whole-Genome Sequencing (WGS)-based systems following a One Health approach. However, different laboratories employ different WGS pipelines in their routine surveillance activities, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes across seven countries and spanning the food, animal and human health sectors, we aimed to assess the inter-laboratory comparability of WGS clustering results for four important foodborne pathogens: Listeria monocytogenes, Salmonella enterica, Escherichia coli and Campylobacter jejuni. Each participating institute (n=9) applied its surveillance pipeline over the same WGS datasets (>2000 isolates per species), and, for each pipeline, genetic clusters were identified at each possible allele/SNP distance threshold. Inter-pipeline clustering congruence was assessed by calculating a Congruence Score (relying on Adjusted Wallace and Adjusted Rand coefficients) across all resolution levels, followed by an in-depth comparative analysis of cluster composition at outbreak level. An additional cluster congruence assessment was performed between WGS and traditional typing, which, depending on the species, included Sequence Type (ST), Clonal Complex (CC) and/or serotype. Our results revealed a general high concordance between allele-based pipelines at all resolution levels for all species, except for C. jejuni, where the different resolution power of available allele-based schemas led to marked discrepancies. Still, this study identified non-negligible differences in allele-based pipeline performance for outbreak cluster detection, suggesting that a threshold flexibilization is important for the detection of similar outbreak signals by different laboratories. These results, together with the observation that different STs, CCs and serotypes exhibit remarkably different genetic diversity, should inform future threshold selections for outbreak case definitions. In conclusion, this study provides valuable insights into the comparability of pipelines commonly used for routine genomics surveillance, and reinforces the need, while demonstrating the feasibility, of conducting continuous and comprehensive WGS pipeline comparability assessments. Ultimately, it opens good perspectives for a smoother international and intersectoral cooperation and communication towards a sustainable and efficient One Health FWD surveillance. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by co-funding from the European Union's Horizon 2020 Research and Innovation program under grant agreement No 773830: One Health European Joint Programme (2020 to 2022) (https://onehealthejp.eu/projects/foodborne-zoonoses/jrp-beone) and by the ISIDORe project (funding from the European Union's Horizon Europe Research & Innovation Programme, Grant Agreement no. 101046133). VM contribution was funded by national funds through FCT - Foundation for Science and Technology, I.P., in the frame of Individual CEEC 2022.00851.CEECIND/CP1748/CT0001 (2023 onwards). JDS contribution was supported by the project "Sustainable use and integration of enhanced infrastructure into routine genome-based surveillance and outbreak investigation activities in Portugal" (GENEO, https://www.insa.min-saude.pt/category/projectos/geneo/) on behalf of the EU4H programme (EU4H-2022-DGA-MS-IBA-1). Research at the National Veterinary Research Institute (PIWet) Poland was supported by the Polish Ministry of Education and Science from the funds for science in the years 2018-2022 allocated for the implementation of a co-financed international project. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Anonymized sequencing reads of the BeONE dataset are deposited in the European Nucleotide Archive (ENA) database under the BioProjects PRJEB57166, PRJEB57179, PRJEB57098 and PRJEB57119. Genome assemblies are deposited in the Zenodo repository (L. monocytogenes: 10.5281/ZENODO.7267486; S. enterica: 10.5281/ZENODO.7267785; E. coli: 10.5281/ZENODO.7267844; C. jejuni: 10.5281/ZENODO.7267879). The public dataset data was retrieved from Zenodo (L. monocytogenes: 10.5281/ZENODO.7116878; S. enterica: 10.5281/ZENODO.7119735; E. coli: 10.5281/ZENODO.7120057; C. jejuni: 10.5281/ZENODO.7120166). The collection of scripts used to conduct these analyses are available at the github repository https://github.com/insapathogenomics/WGS\_cluster\_congruence. Supplementary data are available in the Zenodo repository (https://doi.org/10.5281/zenodo.12805750).

Background In recent years, whole genome sequencing (WGS) in combination with bioinformatic analyses has become state of the art in evaluating the pathogenicity/resistance potential and relatedness of bacteria. WGS analysis thus represents a central tool in the investigation of the resistance and virulence potential of pathogens, as well as their dissemination via outbreak clusters and transmission chains within the framework of molecular epidemiology. In order to gain an overview of the available genotypic and phenotypic methods used for pathogen typing of Salmonella and Shiga toxin-producing and enterohemorrhagic Escherichia coli (STEC/EHEC) in Germany at state and federal level, along with the availability of WGS-based typing and corresponding analytical methods, a survey of laboratories was conducted.Methods An electronic survey of laboratories working for public health protection and consumer health protection was conducted from February to June 2020.Results and conclusion The results of the survey showed that many of the participating laboratories provide a wide range of phenotypic and molecular methods. Molecular typing is most commonly used for species identification of Salmonella. In many cases, WGS-based methods have already been established at federal and state institutions or are in the process of being established. The Illumina sequencing technology is the most widely used technology. The survey confirms the importance of molecular biology and whole genome typing technologies for laboratories in the diagnosis of bacterial zoonotic pathogens.