Methodologies for source attribution (SA) of foodborne illnesses comprise a rapidly expanding suite of techniques for estimating the most important source or sources of human infection. Recently, the increasing availability of whole genome sequencing (WGS) data for a wide range of bacterial strains has led to the development of novel SA methods. These techniques utilize the unique features of bacterial genomes adapted to different host types and hence offer increased resolution of the outputs. Comparative studies of different SA techniques reliant on WGS data are currently lacking. Here, we critically assessed and compared the outputs of three SA methods: a supervised classification random forest machine learning algorithm (RandomForest), an Accessory genes-Based Source Attribution method (AB_SA), and a Bayesian frequency matching method (Bayesian). Each technique was applied to the WGS data of a panel of 902 reservoir host and human monophasic and biphasic Salmonella enterica subsp. enterica serovar Typhimurium isolates sampled in the British Isles (BI) and Denmark from 2012 to 2016. Additionally, for RandomForest and Bayesian, we explored whether utilization of accessory genome features as model inputs improved attribution accuracy of these methods over using the core genome derived features only. Results indicated that this was the case for RandomForest, but for Bayesian the overall attribution estimates varied little regardless of the inclusion or not of the accessory genome features. All three methods attributed the vast majority of human isolates to the Pigs primary source class, which was expected given the known high relative prevalence rates in pigs, and hence routes of infection into the human population, of monophasic and biphasic S. Typhimurium in the BI and Denmark. The accuracy of AB_SA was lower than of RandomForest when attributing the primary source classes to the 120 animal test set isolates with known primary sources. A major advantage of both AB_SA and Bayesian was a much faster execution time as compared to RandomForest. Overall, the SA method comparison presented in this study describes the strengths and weaknesses of each of the three methods applied to attributing potential monophasic and biphasic S. Typhimurium animal sources to human infections that could be valuable when deciding which SA methodology would be the most applicable to foodborne disease outbreak scenarios involving monophasic and biphasic S. Typhimurium.

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.

We present a case of carbapenemase-producing blaNDM-1-positive Salmonella Kottbus in an 82-year-old Danish man. The blaNDM-1 was also identified in Escherichia coli and Citrobacter freundii in the same patient on the same 43 kb IncN2 plasmid, suggesting in vivo inter-species plasmid transfer. A NCBI BLAST analysis of the plasmid (pAMA003584_NDM-1) identified 12 highly similar plasmids, all originating from east and south-east Asia. This case could be the first confirmed case of blaNDM-1-positive Salmonella not related to travel outside Europe.

Aquaculture systems are widely recognised as hotspots for horizontal gene transfer, and the need for screening for bacteria carrying antimicrobial resistance genes in aquaculture systems is becoming more important. In this study, we characterised seventeen bacterial strains (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and A. nosocomialis) resistant to colistin originating from retailed aquaculture products imported from Vietnam to the Czech Republic. The mcr-1.1 gene was found located on plasmid types IncHI2, IncI2, and IncX4, as well as on the rarely described plasmid types IncFIB-FIC and IncFIB(K), phage-like plasmid p0111, and on the chromosome of E. coli. One E. coli strain carried the mcr-3.5 gene on IncFII(pCoo) plasmid in addition to the mcr-1.1 gene located on IncHI2 plasmid. K. pneumoniae was found to carry the mcr-1.1 and mcr-8.2 genes on IncFIA(HI1) plasmid. The mcr-4.3 gene was found on similar untypeable plasmids of A. baumannii and A. nosocomialis strains, pointing to the possible interspecies transfer of plasmids carrying the mcr-4 gene. Our results highlight that some aquaculture products of Asian origin can represent an important source of variable plasmids carrying mcr genes. The results showed an involvement of phages in the incorporation of the mcr-1 gene into plasmids or the chromosome in E. coli strains from aquaculture. The detection of E. coli with the mcr-1 gene in the chromosome points to the risks associated with the stabilisation of the mcr genes in the bacterial chromosome.

The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3′ end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.

Salmonella enterica subspecies enterica serovar Typhimurium and its monophasic variant are among the most common Salmonella serovars associated with human salmonellosis each year. Related infections are often due to consumption of contaminated meat of pig, cattle and poultry origin. In order to evaluate novel microbial subtyping methods for source attribution, an approach based on weighted networks was applied on 141 human and 210 food and animal isolates of pigs, broilers, layers, ducks and cattle collected in Denmark from 2013 to 2014. A whole-genome SNP calling was performed along with cgMLST and wgMLST. Based on these genomic input data, pairwise distance matrices were built and used as input for construction of a weighted network where nodes represent genomes and links distances. Analyzing food and animal genomes, the coherence of source clustering was 90% for animal source, 85% for country, 82% for serotype and 65 % for year of isolation independently from the type of input data, suggesting animal source as the first driver of clustering formation. Adding human isolate genomes to the network, a percentage between 93.6% and 95% clustered with the existing component and only a percentage between 5% and 6.4% appeared as not attributed to any animal source. The majority of human genomes were attributed to pigs with probabilities ranging from 83.9 to 84.5%, followed by broilers, ducks, cattle and layers in descending order. In conclusion, weighted network approach based on pairwise SNPs, cgMLST and wgMLST matrices showed promising results for source attribution studies.

Prevention of the emergence and spread of foodborne diseases is an important prerequisite for the improvement of public health. Source attribution models link sporadic human cases of a specific illness to food sources and animal reservoirs. With the next generation sequencing technology, it is possible to develop novel source attribution models. We investigated the potential of machine learning to predict the animal reservoir from which a bacterial strain isolated from a human salmonellosis case originated based on whole-genome sequencing. Machine learning methods recognize patterns in large and complex data sets and use this knowledge to build models. The model learns patterns associated with genetic variations in bacteria isolated from the different animal reservoirs. We selected different machine learning algorithms to predict sources of human salmonellosis cases and trained the model with Danish Salmonella Typhimurium isolates sampled from broilers (n = 34), cattle (n = 2), ducks (n = 11), layers (n = 4), and pigs (n = 159). Using cgMLST as input features, the model yielded an average accuracy of 0.783 (95% CI: 0.77-0.80) in the source prediction for the random forest and 0.933 (95% CI: 0.92-0.94) for the logit boost algorithm. Logit boost algorithm was most accurate (valid accuracy: 92%, CI: 0.8706-0.9579) and predicted the origin of 81% of the domestic sporadic human salmonellosis cases. The most important source was Danish produced pigs (53%) followed by imported pigs (16%), imported broilers (6%), imported ducks (2%), Danish produced layers (2%), Danish produced cattle and imported cattle (<1%) while 18% was not predicted. Machine learning has potential for improving source attribution modeling based on sequence data. Results of such models can inform risk managers to identify and prioritize food safety interventions.

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US.Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing.Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees.Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Open Peer Review Reviewer Status AWAITING PEER REVIEW Any reports and responses or comments on the article can be found at the end of the article. Page 1 of 17 Wellcome Open Research 2020, 5:223 Last updated: 24 SEP 2020

Zoonotic Salmonella causes millions of human salmonellosis infections worldwide each year. Information about the source of the bacteria guides risk managers on control and preventive strategies. Source attribution is the effort to quantify the number of sporadic human cases of a specific illness to specific sources and animal reservoirs. Source attribution methods for Salmonella have so far been based on traditional wet-lab typing methods. With the change to whole genome sequencing there is a need to develop new methods for source attribution based on sequencing data. Four European datasets collected in Denmark (DK), Germany (DE), the United Kingdom (UK) and France (FR) are presented in this descriptor. The datasets contain sequenced samples of Salmonella Typhimurium and its monophasic variants isolated from human, food, animal and the environment. The objective of the datasets was either to attribute the human salmonellosis cases to animal reservoirs or to investigate contamination of the environment by attributing the environmental isolates to different animal reservoirs.

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.

EFSA and ECDC were requested by the European Commission to jointly evaluate the possible solutions for the collection and analysis of whole genome sequencing (WGS) data for at least Listeria monocytogenes, Salmonella and Escherichia coli by: (1) analysing the outcome of the surveys on the status of the use of WGS of food-borne pathogens in EU/EEA countries in both the food and public health sectors; (2) conducting a consultation of relevant actors to assess state-of-the-art pipelines for collecting and analysing WGS data in Europe; (3) involving relevant stakeholders to assess the needs and requirements for the analysis of WGS data and their comparability; and (4) preparing a technical report on the identification and comparison of potential solutions for the set-up and running of a joint EFSA–ECDC pipeline to collect and analyse WGS data. Logical components of the overall system were identified and technical requirements were prioritised and grouped according to functionality. Eleven platforms (solutions) that integrate the relevant functionalities for collecting, analysing and visualising WGS data were thoroughly described. The degree to which the requirements are met by the different solutions (as of 31 December 2018) was evaluated. The assessment made clear that no single solution meets all the critical requirements and each solution has significant gaps regarding the unmet critical requirements. Therefore, scenarios consisting of a combination of several solutions were considered. As there may be many suitable scenarios, and the choice among them will depend on strategic or financial elements that are not within the scope of this report, it contains the scientific and technical elements necessary to generate scenarios, rather proposing individual scenarios. A scenario builder is presented which includes the significant gaps for each solution/functionality and the limitations and risks to be considered when setting up a joint ECDC–EFSA database for the collection and analysis of WGS data. © European Centre for Disease Control and European Food Safety Authority, 2019

In April 2019, a cross-border outbreak of Yersinia entercolitica O-3 was identified in Sweden and Denmark and confirmed using whole genome sequencing. Close cross-border collaboration with representatives from human and food authorities helped direct resources and investigations. Combined epidemiological and trace-back investigations pointed to imported fresh spinach as the outbreak vehicle and highlight that other vehicles of Y. enterocolitica outbreaks than pork should be considered.

Currently, there are multiple variants of mcr-mediated colistin resistance in Gram-negative bacteria from different sources around the whole world. The most prevalent gene in Enterobacteriaceae mcr-1 has been located on several types of plasmids. This study was focused on plasmid characteristics of Enterobacteriaceae isolates with mcr-1 gene and one Aeromonas spp. isolate carrying both mcr-3 and mcr-7-like genes obtained from retailed raw meat products. Altogether, 17 colistin resistant isolates carrying mcr genes originated from 12 meat samples (turkey, rabbit and quail meat). Twelve Escherichia coli isolates carrying mcr-1 gene were isolated from turkey meat and liver from the Czech Republic (n=3), Poland (n=5), Germany (n=3) and Brazil (n=1). Two Klebsiella pneumoniae carrying mcr-1 originated from turkey meat and liver from the Czech Republic (n=1) and Brazil (n=1). One isolate of E. coli with mcr-1 and one Citrobacter braakii isolate with mcr-1 were obtained from the same rabbit meat sample from China. Aeromonas spp. with mcr-3 and mcr-7-like genes was isolated from quail meat sample from France. The sequencing was performed using Illumina MiSeq and Oxford Nanopore MinION platform and the whole sequences of plasmids carrying mcr genes were obtained by hybrid assembly. The content of plasmid sequences was analysed using ResFinder and PlasmidFinder, the annotation of genes was done by Prokka (Galaxy Version 1.13). The comparison of plasmid sequences was done using BLAST Ring Image Generator (BRIG). The hybrid assembly of the genomes showed three plasmid types (IncX4, IncHI2 and IncI2) carrying the mcr-1 gene in tested isolates. The most prevalent plasmid type carrying mcr-1 was IncX4 detected in E. coli (n=8) and K. pneumoniae (n=2) isolated from meat products of different origin (Czech Republic, Poland, Germany, Brazil). The size of IncX4 varied between ~33 to ~34 kb with two exceptions of ~38 kb and ~188 kb large plasmids. The IncX4 plasmids with size ~33 to ~34 kb did not carry any other antimicrobial resistance genes except for mcr-1 gene. Four E. coli isolates from turkey meat of Polish origin had localized mcr-1 on plasmid type IncHI2 which varied in their size (between ~153 kb to 284 kb) and carried other resistance genes. The isolates of E. coli and C. braakii from one rabbit meat sample from China carried mcr-1 gene on IncI2 plasmid (~60 kb). The comparison of both IncI2 plasmids showed their high identity. Similarly, in case of E. coli and K. pneumoniae isolates obtained from one meat sample, the IncX4 plasmids carrying mcr-1 gene were almost identical. These results support a transmission capability of these plasmids among different species of Enterobacteriaceae. On the other hand, the mcr-3.8 and mcr-7-like genes in colistin resistant Aeromonas spp. were found to be located in the chromosome and the isolate did not contain any plasmids. The mcr-7-like gene was found twice in the chromosome and had 86% and 82% identity, respectively, with the mcr-7.1 gene described in the NCBI database. These results are consistent with the estimated origin of mcr-3 and mcr-7 genes from Aeromonas species. The results of this study indicate a possible spread of plasmid mediated colistin resistance via raw meat market between bacteria of different genus. IncX4 plasmids carrying mcr-1 gene were found to be conserved among species of Enterobacteriaceae isolated from raw meat products of different origin. While the most of tested IncX4 and IncI2 plasmids had similar size and carried only mcr-1, the tested IncHI2 plasmids carrying mcr-1 gene were diverse in size and in the content of resistance genes. The presence of mcr-3 and mcr-7-like genes on plasmids in colistin resistant Aeromonas spp. isolate was not confirmed.

Background Salmonella Infantis ( S . Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S . Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar. Results We sequenced a global collection of 100 S . Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S . Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed. Conclusions This study analysed a global S . Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage. We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.

Currently, there are described several types of horizontally transmitted plasmids carrying multiple variants of mcr genes encoding colistin resistance, the most prevalent is mcr 1. This study was focused on plasmid characteristics of Enterobacteriaceae carrying mcr 1 gene obtained from retailed raw meat products. In total 16 isolates carrying mcr-1 were obtained from 11 meat samples. They belonged to various species - Escherichia coli (12), Klebsiella pneumoniae (2) and Citrobacter braakii (1). The sequencing was performed using Illumina MiSeq and Oxford Nanopore MinION platforms and the sequences of plasmids carrying mcr-1 gene were obtained by hybrid assembly. The content of plasmid sequences was analysed and the comparison of plasmid sequences was performed. The outcome showed three plasmid types (IncX4, IncHI2 and IncI2) carrying mcr-1 gene. The most prevalent plasmid type was IncX4 detected in E. coli (8) and K. pneumoniae (2) with size between ~33 to ~34 kb with two exceptions. IncHI2 plasmid was isolated from E. coli (4), it varied in size (~153 kb to 284 kb) and carried also other resistance genes. E. coli (1) and C. braakii (1) isolates from one meat sample carried mcr-1 on IncI2 plasmid (~60 kb). The results of this study indicate a possible spread of plasmid mediated colistin resistance genes via bacteria contained in raw meat. While most of the tested IncX4 and IncI2 plasmids were found to be conserved and carried only mcr-1, the tested IncHI2 plasmids carrying mcr-1 were diverse in size and in the content of genes encoding resistance to other antibiotics.

In 2017, an outbreak of gastroenteritis in England attributed to Salmonella Adjame was detected and investigated. With the introduction of whole genome sequencing (WGS) for microbial typing, methods for comparing international outbreak data require evaluation. A case was defined as a person resident in England with a clinical sample from 1 June 2017 to 27 July 2017 from whom S. Adjame was isolated. Cases were interviewed and exposures analysed. Backward tracing of food provenance was undertaken. WGS was performed on isolates from cases and historical isolates and compared using Public Health England's SnapperDB high-quality SNP pipeline and Enterobase's Salmonella core genome multi-locus sequence typing (cgMLST) scheme. In total, 14 cases were identified. The majority were vegetarian, probably of South Asian descent, with a median age of 66.5 years with no recent international travel reported. Cases consumed a range of fresh food products including herbs and spices bought from South Asian grocers. Backward tracing did not identify a common source. WGS typing showed sub-clustering and considerable genetic variation across human samples. cgMLST allele-based analysis was comparable to SNP-derived phylogenetic analysis and clusters were defined using each method. Imported herbs or spices were suspected vehicles. The cases were linked in time and place but WGS showed marked heterogeneity, atypical of a point source Salmonella outbreak. The application of incorporating SNP or allelic differences into the case definition may not always be appropriate. With further validation, cgMLST could be used for international outbreak alerts when WGS analysis is being undertaken to facilitate comparison.

In Denmark, outbreaks of salmonella with more than 20 cases have become rare. In November 2018, an outbreak of monophasic Salmonella Typhimurium was detected and an investigation initiated with the aim of identifying the source and controlling the outbreak. Outbreak cases were defined based on core genome multilocus sequence types. We conducted hypothesis-generating interviews, a matched case-control study, food sampling and trace-back investigations. We identified 49 cases distributed across Denmark. In univariable analyses a traditional form of raw Danish pork sausage (medister sausage), pork chops and ground veal/pork showed matched odds ratio of 26 (95% CI 3-207), 4 (95% CI 1-13) and 4 (95% CI 1-10), respectively. In a multivariable analysis, only medister sausage remained significant. Several patients described tasting or eating the sausage raw or undercooked. Samples of medister sausage analysed were negative for salmonella and investigations at the production site did not reveal the mechanism of contamination. In conclusion, in spite of having eliminated salmonella in the egg and broiler industry, Denmark is still at risk of major salmonella outbreaks. We identified a raw pork sausage as a particular risk product that needs to be thoroughly cooked before consumption. Tasting raw meat or eating undercooked pork should be discouraged.

Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link possible food and veterinary sources to the outbreaks. Isolates clustered according to sequence types (STs) 19, 34, and 36. Our study shows that core-genome single-nucleotide polymorphism analysis is suitable for surveillance and outbreak investigation for Salmonella Typhimurium (ST19 and ST36), but whole genome-wide analysis may be required for the tight genetic clone of monophasic variants (ST34).