A genomic overview of the population structure of Salmonella

Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa

In Africa, the burden of illness caused by non-typhoidal Salmonella enterica is disproportionally high; however, whole-genome sequencing (WGS) efforts are overwhelmingly concentrated in world regions with lower burdens. While WGS is being increasingly employed in South Africa to characterize Salmonella enterica, the bulk of these efforts have centered on characterizing human clinical strains. Thus, very little is known about lineages circulating among animals in the country on a genomic scale. Here, we used WGS to characterize 63 Salmonella enterica strains isolated from livestock, companion animals, wildlife, and animal products in South Africa over a 60-year period. Genomes were assigned to serotypes Dublin, Hadar, Enteritidis, and Typhimurium (n = 18, 8, 13, and 24 strains, respectively) and sequence types (STs) ST10 (all S. Dublin), ST33 (all S. Hadar), ST11/ST366 (n = 12 and 1 S. Enteritidis, respectively), and ST19/ST34 (n = 23 and 1 S. Typhimurium, respectively; via seven-gene multi-locus sequence typing). Within-ST phylogenies were constructed using genomes sequenced in this study, plus publicly available genomes representative of each ST's (i) global (n = 2,802 and 1,569 S. Dublin and Hadar genomes, respectively) and (ii) African (n = 716 and 343 S. Enteritidis and Typhimurium genomes, respectively) population. For S. Dublin ST10, a largely antimicrobial-susceptible, endemic lineage circulating among humans, animals, and food in South Africa was identified, as well as a lineage that was likely recently introduced from the United States. For S. Hadar ST33, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. African S. Enteritidis ST11 could be primarily partitioned into one largely antimicrobial-susceptible and one largely multidrug-resistant (MDR) clade, with South African isolates confined to the largely antimicrobial-susceptible clade. S. Typhimurium ST19/ST34 strains sequenced here were distributed across the African S. Typhimurium ST19/ST34 phylogeny, representing a diverse range of lineages, including numerous MDR lineages. Overall, this study provides critical insights into endemic and ecdemic non-typhoidal Salmonella enterica lineages circulating among animals, foods, and humans in South Africa and showcases the utility of WGS in characterizing animal-associated strains from a world region with a high salmonellosis burden.

Heuristic and Hierarchical-Based Population Mining of Salmonella enterica Lineage I Pan-Genomes as a Platform to Enhance Food Safety

The recent incorporation of bacterial whole-genome sequencing (WGS) into Public Health laboratories has enhanced foodborne outbreak detection and source attribution. As a result, large volumes of publicly available datasets can be used to study the biology of foodborne pathogen populations at an unprecedented scale. To demonstrate the application of a heuristic and agnostic hierarchical population structure guided pan-genome enrichment analysis (PANGEA), we used populations of S. enterica lineage I to achieve two main objectives: (i) show how hierarchical population inquiry at different scales of resolution can enhance ecological and epidemiological inquiries; and (ii) identify population-specific inferable traits that could provide selective advantages in food production environments. Publicly available WGS data were obtained from NCBI database for three serovars of Salmonella enterica subsp. enterica lineage I (S. Typhimurium, S. Newport, and S. Infantis). Using the hierarchical genotypic classifications (Serovar, BAPS1, ST, cgMLST), datasets from each of the three serovars showed varying degrees of clonal structuring. When the accessory genome (PANGEA) was mapped onto these hierarchical structures, accessory loci could be linked with specific genotypes. A large heavy-metal resistance mobile element was found in the Monophasic ST34 lineage of S. Typhimurium, and laboratory testing showed that Monophasic isolates have on average a higher degree of copper resistance than the Biphasic ones. In S. Newport, an extra sugE gene copy was found among most isolates of the ST45 lineage, and laboratory testing of multiple isolates confirmed that isolates of S. Newport ST45 were on average less sensitive to the disinfectant cetylpyridimium chloride than non-ST45 isolates. Lastly, data-mining of the accessory genomic content of S. Infantis revealed two cryptic Ecotypes with distinct accessory genomic content and distinct ecological patterns. Poultry appears to be the major reservoir for Ecotype 1, and temporal analysis further suggested a recent ecological succession, with Ecotype 2 apparently being displaced by Ecotype 1. Altogether, the use of a heuristic hierarchical-based population structure analysis that includes bacterial pan-genomes (core and accessory genomes) can (1) improve genomic resolution for mapping populations and accessing epidemiological patterns; and (2) define lineage-specific informative loci that may be associated with survival in the food chain.

AT Homopolymer Strings in Salmonella enterica Subspecies I Contribute to Speciation and Serovar Diversity

Adenine and thymine homopolymer strings of at least 8 nucleotides (AT 8+mers) were characterized in Salmonella enterica subspecies I. The motif differed between other taxonomic classes but not between Salmonella enterica serovars. The motif in plasmids was possibly associated with serovar. Approximately 12.3% of the S. enterica motif loci had mutations. Mutability of AT 8+mers suggests that genomes undergo frequent repair to maintain optimal gene content, and that the motif facilitates self-recognition; in addition, serovar diversity is associated with plasmid content. A theory that genome regeneration accounts for both persistence of predominant Salmonella serovars and serovar diversity provides a new framework for investigating root causes of foodborne illness.

Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel

Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results. The BioHansel tool was developed to provide an organism-agnostic tool for hierarchical SNP-based genotyping. The tool identifies split k-mers that distinguish predefined lineages in whole genome sequencing (WGS) data using SNP-based genotyping schemes. BioHansel uses the Aho-Corasick algorithm to type isolates from assembled genomes or raw read sequence data in a matter of seconds, with limited computational resources. This makes BioHansel ideal for use by public health agencies that rely on WGS methods for surveillance of bacterial pathogens. Genotyping results are evaluated using a quality assurance module which identifies problematic samples, such as low-quality or contaminated datasets. Using existing hierarchical SNP schemes for Mycobacterium tuberculosis and Salmonella Typhi, we compare the genotyping results obtained with the k-mer-based tools BioHansel and SKA, with those of the organism-specific tools TBProfiler and genotyphi, which use gold-standard reference-mapping approaches. We show that the genotyping results are fully concordant across these different methods, and that the k-mer-based tools are significantly faster. We also test the ability of the BioHansel quality assurance module to detect intra-lineage contamination and demonstrate that it is effective, even in populations with low genetic diversity. We demonstrate the scalability of the tool using a dataset of ~8100 S. Typhi public genomes and provide the aggregated results of geographical distributions as part of the tool’s output. BioHansel is an open source Python 3 application available on PyPI and Conda repositories and as a Galaxy tool from the public Galaxy Toolshed. In a public health context, BioHansel enables rapid and high-resolution classification of bacterial pathogens with low genetic diversity.

Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts

Ancient pathogen genomics is an emerging field allowing reconstruction of past epidemics. The demise of post-contact American populations may, at least in part, have been caused by paratyphoid fever brought by Europeans. We retrieved genome-wide data from two Spanish soldiers who were besieging the city of Barcelona in 1652, during the Reapers' War. Their ancestry derived from the Basque region and Sardinia, respectively, (at that time, this island belonged to the Spanish kingdom). Despite the proposed plague epidemic, we could not find solid evidence for the presence of the causative plague agent in these individuals. However, we retrieved from one individual a substantial fraction of the Salmonella enterica serovar Paratyphi C lineage linked to paratyphoid fever in colonial period Mexico. Our results support a growing body of evidence that Paratyphi C enteric fever was more prevalent in Europe and the Americas in the past than it is today.

Prevalence, Serotypes, and Antimicrobial Resistance of Salmonella from Mink Feces and Feed in the United States

Nontyphoidal Salmonella is a leading cause of foodborne illnesses, and concentrated animal production such as commercial mink farming can be a reservoir. The objective of this study was to determine the prevalence, serotypes, antimicrobial resistance, virulence genes and mobile genetic elements, and phylogenetic characterization of Salmonella from mink fecal (n = 42) and feed (n = 8) samples at a commercial mink farm in the United States. Salmonella was detected from 11 (26.2%) fecal and 1 (12.5%) feed samples. Twelve fecal isolates obtained from the positive samples were identified into four serotypes: Salmonella Uganda (eight isolates; two isolates were obtained from one sample), Salmonella Reading (two isolates), Salmonella Heidelberg (one isolate), and Salmonella Orion (one isolate). Two isolates from the positive feed sample were identified as Salmonella Cerro. Twelve isolates, one isolate per positive sample, were whole genome sequenced for further characterization. The two Salmonella Reading isolates were multidrug resistant (MDR) with the classical ASSuT (ampicillin, streptomycin, sulfisoxazole, and tetracycline) phenotype. Genotypically, the isolates were correspondingly positive, both by polymerase chain reaction and by whole-genome sequencing (WGS), for bla_TEM-1, aph(3″)-Ib and aph(6)-Id, sul2, and tet(A). WGS additionally identified trimethoprim resistance gene dfrA8 in Salmonella Reading, and fosfomycin resistance gene fosA7 in Salmonella Heidelberg. All isolates carried Salmonella-specific multidrug resistance (mdsA/B), gold resistance, and intimin-like virulence genes. In addition, Salmonella Orion carried copper and silver resistance gene clusters. The two Salmonella Reading isolates also carried a cytolethal distension toxin (cdtB) gene. Salmonella Reading isolates belonged to ST412, a predominant sequence type among turkey and human isolates obtained in relation to recent salmonellosis outbreaks in North America. Phylogenetically, Salmonella Uganda, Salmonella Heidelberg, and Salmonella Reading were mostly associated with historic human/clinical, and poultry and swine source isolates. This study indicates that mink production can be a reservoir for foodborne pathogens such as Salmonella with MDR serovars commonly associated with human illnesses.

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, the disease with the highest economic loss for the broiler industry. However, studies focusing on the prevalence and population structure of APEC in the broiler production pyramid are scarce. Here, we used genotyping and serotyping data to elucidate the APEC population structure and its changes in different broiler production stages along with whole-genome sequencing (WGS) in a subset of APEC isolates to determine transmission patterns amongst dominant APEC sequence types (STs) and characterize them in detail. Comparison of genotypes encountered in both APEC and avian fecal E. coli (AFEC) provided further insights. Overall, APEC-related mortality, as the proportion of the total sampled mortality in the broiler production, was high (35%), while phylogroup C and serogroup O78 were predominant amongst APEC isolates. We found a low (34.0%) and high (53.3%) incidence of colibacillosis in chicks and end-cycle broilers, respectively, which may be related to a shift in APEC genotypes, suggesting a trend from commensalism to pathogenicity across different broiler production stages. Despite considerable APEC genotypic diversity, there was substantial genotype overlap (40.9%, overall) over the production stages and convergence of STs to the four clusters. Within these clusters, WGS data provided evidence of clonal transmission events and revealed an enriched virulence and resistance APEC repertoire. More specifically, sequenced APEC were assigned to defined pathotypes based on their virulence gene content while the majority (86%) was genotypically multi-drug resistant. Interestingly, WGS-based phylogeny showed that a subset of APEC, which are cephalosporin-resistant, may originate directly from cephalosporin-resistant AFEC. Finally, exploration of the APEC plasmidome indicated that the small fraction of the APEC virulome carried by IncF plasmids is pivotal for the manifestation of the APEC pathotype; thus, plasmid exchange can promote pathogenicity in strains that are at the edge of the commensal and pathogenic states.

Draft genome sequences of concurrent Escherichia coli blood and fecal isolates from a patient with bacteremia and diarrhea belie BioFire-based detection of fecal enteropathogenic E. coli

The BioFire FilmArray® Gastrointestinal panel is a multiplex PCR assay widely used to determine the etiology of infectious gastroenteritis directly from stool specimens. Recently a positive BioFire result for fecal enteropathogenic Escherichia coli (EPEC) was reported by a clinical microbiology laboratory for an adult patient with diarrhea and bacteremia. Since EPEC infrequently infects adults and rarely causes bacteremia, we isolated fecal E. coli and characterized the patient's blood and fecal E. coli isolates. Draft genome sequencing using a combination of methods indicated that the blood and fecal strains are virtually identical, are from sequence type 963 (phylogroup D) and exhibit neither the virulence genes characteristic of EPEC and extraintestinal pathogenic E. coli (ExPEC) nor classic EPEC-associated phenotypes. These findings support a gut source for the patient's bacteremia but exclude EPEC as the causative organism, and suggest that results of multiplex PCR assays from complex samples can be misleading, and should be interpreted with caution when they are discordant with clinical information. BioProject accession numbers for strains MVAST5574 and MVAST5635 genomes are PRJNA611789 and PRJNA611804, respectively.

Prevalence, Characterization, and Pathogenicity of Salmonella enterica Subspecies enterica Serovar Derby from Yaks in the Aba Tibetan Autonomous Prefecture, China

Simple Summary

Salmonella spp. is a very important pathogen in the livestock industry and public health, which poses a major threat to global public health. Yaks and their by-products have a significant economic status in the Qinghai–Tibetan Plateau. The aim of this study was to investigate the prevalence of salmonella in yak farms and to conduct a molecular characterization and tests on its pathogenicity in mice with the use of salmonella isolated from yaks with diarrhea as well as from drinking water samples. The prevalence of salmonella was 19.75% of 162 samples collected from yak farms, and all isolates were found to belong to the serovar of Salmonella Derby and ST40. All Salmonella Derby isolates from both fecal and drinking water samples from 13 farms were clonally related based on SNP alignment. Salmonella Derby was still detected positively in the feces of model mice on day 24 post-injection. This study reports the prevalence of Salmonella Derby in yaks with diarrhea and in their drinking water. In addition, the pathogenicity of the S. Derby in mice was investigated. Findings suggest that Salmonella Derby excreted by diarrheic yaks is a source of contamination for other yaks and the environment and is highly pathogenic to mice. Seeing that Salmonella Derby has become one of the most common Salmonella serovars, this situation gives rise to further risk from the potential spread of food-borne diseases.

Abstract

Salmonella enterica subsp. enterica serovar Derby (S. Derby) is one of the numerous non-typhoidal Salmonella serovars and has been recognized as a food-borne pathogen. In 2019, outbreaks of salmonellosis were reported in 13 yak farms in the Aba Tibetan Autonomous Prefecture, China. A total of 32 salmonella strains were isolated from 162 fecal samples of yaks with diarrhea as well as from drinking water samples. The isolates were subjected to serovar identification, animal experiments, and whole-genome sequencing (WGS) analyses. The serovar of all the isolates was S. Derby, and the sequence types (STs) were ST40. The analysis of the differences of single-nucleotide polymorphisms (SNPs) showed that the salmonella strains isolated from 13 farms were clonally related. Animal experiments showed that the lethal dose (LD₅₀) was 4.57 × 10⁷ CFU (colony-forming units); the shedding time of S. Derby in mice was 24 days; the bacterial loads in spleen were higher than those in other organs (ileum, liver, and cecum). Pathological analyses by hematoxylin and eosin (H&E) staining revealed obvious damage in the spleen, liver, and intestine. These results indicate that the S. Derby from yaks can cause infection in mice.

Salmonella in Chicken Meat: Consumption, Outbreaks, Characteristics, Current Control Methods and the Potential of Bacteriophage Use

The control of Salmonella in chicken processing plants is an ongoing challenge for many factories around the globe, especially with the increasing demand for poultry escalating processing throughputs. Foodborne outbreaks due to Salmonella still pose a prominent risk to public health. As chicken meat is a good reservoir for Salmonella, it is important for chicken processing plants to continuously optimize methods to reduce the incidence of Salmonella on their products. Current methods include the use of chemical antimicrobials such as chlorine-containing compounds and organic acids. However, these current methods are decreasing in popularity due to the rising rate of Salmonella resistance, coupled with the challenge of preserving the sensory properties of the meat, along with the increasing stringency of antimicrobial use. Bacteriophages are becoming more appealing to integrate into the large-scale hurdle concept. A few factors need to be considered for successful implementation, such as legislation, and application volumes and concentrations. Overall, bacteriophages show great potential because of their host specificity, guaranteeing an alternative outcome to the selective pressure for resistant traits placed by chemicals on whole microbial communities.

Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing

Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.

An evaluation of the species and subspecies of the genus Salmonella with whole genome sequence data: Proposal of type strains and epithets for novel S. enterica subspecies VII, VIII, IX, X and XI

Species and subspecies within the Salmonella genus have been defined for public health purposes by biochemical properties; however, reference laboratories have increasingly adopted sequence-based, and especially whole genome sequence (WGS), methods for surveillance and routine identification. This leads to potential disparities in subspecies definitions, routine typing, and the ability to detect novel subspecies. A large-scale analysis of WGS data from the routine sequencing of clinical isolates was employed to define and characterise Salmonella subspecies population structure, demonstrating that the Salmonella species and subspecies were genetically distinct, including those previously identified through phylogenetic approaches, namely: S. enterica subspecies londinensis (VII), subspecies brasiliensis (VIII), subspecies hibernicus (IX) and subspecies essexiensis (X). The analysis also identified an additional novel subspecies, reptilium (XI). Further, these analyses indicated that S. enterica subspecies arizonae (IIIa) isolates were divergent from the other S. enterica subspecies, which clustered together and, on the basis of ANI analysis, subspecies IIIa was sufficiently distinct to be classified as a separate species, S. arizonae. Multiple phylogenetic and statistical approaches generated congruent results, suggesting that the proposed species and subspecies structure was sufficiently biologically robust for routine application. Biochemical analyses demonstrated that not all subspecies were distinguishable by these means and that biochemical approaches did not capture the genomic diversity of the genus. We recommend the adoption of standardised genomic definitions of species and subspecies and a genome sequence-based approach to routine typing for the identification and definition of novel subspecies.

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A large-scale analysis of genomic data demonstrate Salmonella species and subspecies are genetically distinct.

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Biochemical analysis does not capture the genomic diversity of the Salmonella genus but routine species and subspecies identification can be achieved with rMLST

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Average Nucleotide Identify (ANI) with a 95% criteria was suitable to distinguish species and 98% to distinguish subspecies.

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Five novel S. enteric subspecies (VII-XI) type strains are defined.

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Reclassification of S. arizonae as a separate species is recommended.

Molecular Detection of Salmonella enterica subsp. arizonae by Quantitative PCR

Salmonella enterica subspecies arizonae (subspecies IIIa) is most frequently associated with reptiles but is also a bacterial pathogen of poultry, primarily of young turkeys where it induces septicemia, neurologic signs, and increased mortality. Arizonosis clinical cases in broiler chickens have recently been documented in the United States, driving the development of a rapid, molecular-based diagnostic for this subspecies. S. enterica subsp. arizonae is a genetically distinct subgroup of S. enterica, primarily diagnosed through culture followed by serotyping or biochemical identification, which are costly in both time and laboratory resources. Real-time/quantitative PCR offers rapid and sensitive detection of Salmonella sp. in laboratory and diagnostic samples; however, no such methodology exists to differentiate S. enterica subsp. arizonae from other Salmonella sp. In this study, we designed a quantitative PCR assay for S. enterica subsp. arizonae. The assay is able to differentiate S. enterica subsp. arizonae from other S. enterica subspecies, including S. enterica subsp. diarizonae (IIIb), and other non-Salmonella bacteria. Validation, including 56 different S. enterica subsp. arizonae serovars, demonstrated 100% sensitivity and 100% specificity. This assay provides a rapid diagnostic option for suspected cases of arizonosis in poultry.

Salmonella pathogenesis and host-adaptation in farmed animals

Salmonella is an animal and zoonotic pathogen of global importance. Depending on pathogen and host factors, infections can be asymptomatic or involve acute gastroenteritis or invasive disease. Genomic signatures associated with host-range, tissue tropism or differential virulence of Salmonella enterica serovars, and their variants, have emerged. In turn, it is becoming feasible to predict invasive potential, host-adaptation and zoonotic risk of Salmonella from sequence data to improve outbreak investigation, risk assessment and control strategies. Functional annotation of Salmonella genomes has accelerated with the screening of high-density mutant libraries, revealing host-specific, niche-specific and serovar-specific virulence factors. As natural hosts and reservoirs, farmed animals provide powerful insights into host-adaptation and pathogenesis of Salmonella not always evident from surrogate rodent or cell-based models.

Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

Objectives

Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community.

Methods

The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids.

Results

MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica.

Conclusions

MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.

Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil

Salmonella Typhimurium has been transmitted between humans and animals. Although, Brazil has been one of the largest pork meat exporters worldwide, there are few studies that characterized epidemiologically S. Typhimurium strains from swine. The aims of this work were to study the phylogenetic relationship of S. Typhimurium genomes isolated from swine in Brazil among themselves and with other genomes isolated from several sources and countries using wgMLST and cgMLST and to perform the search of Salmonella pathogenicity islands (SPIs). In addition, for S. Typhimurium strains from swine to compare the virulence and antimicrobial resistance genes by VFDB and ResFinder, genetic content by BLAST Atlas and orthologous proteins clusters by OrthoVenn. The constructed phylogenetic trees by wgMLST and cgMLST grouped the majority (92.3% and 80.7%, respectively) of the strains isolated from swine in Brazil into the same group. All the isolates contained important SPIs (SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9). A total of 100 and 31 virulence and resistance genes were detected in the S. Typhimurium strains isolated from swine, respectively. The BLAST Atlas and orthologous proteins analysis found regions of phages and differences in metabolic, regulatory and cellular processes among S. Typhimurium LT2 and S. Typhimurium isolates from swine. In conclusion, molecular typing based in the wgMLST and cgMLST suggested that the S. Typhimurium isolates from swine studied were genetically related. The pathogenic potential of the strains studied was corroborated by the presence of important SPIs and virulence genes. The high number of antimicrobial resistance genes detected is worrying and reinforced their potential risk in swine in Brazil. The comparison by BLAST Atlas suggested differences in mobile genetic elements among S. Typhimurium LT2 and S. Typhimurium isolates from swine in Brazil. The orthologous proteins analysis revealed unique genes related to important cellular processes in the strains from swine.

Contamination of street food with multidrug-resistant Salmonella, in Ouagadougou, Burkina Faso

Background

Gastrointestinal infections are a global public health problem. In Burkina Faso, West Africa, exposure to Salmonella through the consumption of unhygienic street food represents a major risk of infection requiring detailed evaluation.

Methods

Between June 2017 and July 2018, we sampled 201 street food stalls, in 11 geographic sectors of Ouagadougou, Burkina Faso. We checked for Salmonella contamination in 201 sandwiches (one per seller), according to the ISO 6579:2002 standard. All Salmonella isolates were characterized by serotyping and antimicrobial susceptibility testing, and whole-genome sequencing was performed on a subset of isolates, to investigate their phylogenetic relationships and antimicrobial resistance determinants.

Results

The prevalence of Salmonella enterica was 17.9% (36/201) and the Salmonella isolates belonged to 16 different serotypes, the most frequent being Kentucky, Derby and Tennessee, with five isolates each. Six Salmonella isolates from serotypes Brancaster and Kentucky were multidrug-resistant (MDR). Whole-genome sequencing revealed that four of these MDR isolates belonged to the emergent S. enterica serotype Kentucky clone ST198-X1 and to an invasive lineage of S. enterica serotype Enteritidis (West African clade).

Conclusion

This study reveals a high prevalence of Salmonella spp. in sandwiches sold in Ouagadougou. The presence of MDR Salmonella in food on sale detected in this study is also matter of concern.

High-Resolution Genomic Comparisons within Salmonella enterica Serotypes Derived from Beef Feedlot Cattle: Parsing the Roles of Cattle Source, Pen, Animal, Sample Type, and Production Period

Salmonella enterica is a major foodborne pathogen, and contaminated beef products have been identified as one of the primary sources of Salmonella-related outbreaks. Pathogenicity and antibiotic resistance of Salmonella are highly serotype and subpopulation specific, which makes it essential to understand high-resolution Salmonella population dynamics in cattle. Time of year, source of cattle, pen, and sample type (i.e., feces, hide, or lymph nodes) have previously been identified as important factors influencing the serotype distribution of Salmonella (e.g., Anatum, Lubbock, Cerro, Montevideo, Kentucky, Newport, and Norwich) that were isolated from a longitudinal sampling design in a research feedlot. In this study, we performed high-resolution genomic comparisons of Salmonella isolates within each serotype using both single-nucleotide polymorphism-based maximum-likelihood phylogeny and hierarchical clustering of core-genome multilocus sequence typing. The importance of the aforementioned features in clonal Salmonella expansion was further explored using a supervised machine learning algorithm. In addition, we identified and compared the resistance genes, plasmids, and pathogenicity island profiles of the isolates within each subpopulation. Our findings indicate that clonal expansion of Salmonella strains in cattle was mainly influenced by the randomization of block and pen, as well as the origin/source of the cattle, i.e., regardless of sampling time and sample type (i.e., feces, lymph node, or hide). Further research is needed concerning the role of the feedlot pen environment prior to cattle placement to better understand carryover contributions of existing strains of Salmonella and their bacteriophages. IMPORTANCE Salmonella serotypes isolated from outbreaks in humans can also be found in beef cattle and feedlots. Virulence factors and antibiotic resistance are among the primary defense mechanisms of Salmonella, and are often associated with clonal expansion. This makes understanding the subpopulation dynamics of Salmonella in cattle critical for effective mitigation. There remains a gap in the literature concerning subpopulation dynamics within Salmonella serotypes in feedlot cattle from the beginning of feeding up until slaughter. Here, we explore Salmonella population dynamics within each serotype using core-genome phylogeny and hierarchical classifications. We used machine learning to quantitatively parse the relative importance of both hierarchical and longitudinal clustering among cattle host samples. Our results reveal that Salmonella populations in cattle are highly clonal over a 6-month study period and that clonal dissemination of Salmonella in cattle is mainly influenced spatially by experimental block and pen, as well by the geographical origin of the cattle.

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BACKGROUND

Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads.

RESULTS

We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies.

CONCLUSION

The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.

ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses

Whole Genome Sequence (WGS) data from bacterial species is used for a variety of applications ranging from basic microbiological research, diagnostics, and epidemiological surveillance. The availability of WGS data from hundreds of thousands of individual isolates of individual microbial species poses a tremendous opportunity for discovery and hypothesis-generating research into ecology and evolution of these microorganisms. Flexibility, scalability, and user-friendliness of existing pipelines for population-scale inquiry, however, limit applications of systematic, population-scale approaches. Here, we present ProkEvo, an automated, scalable, reproducible, and open-source framework for bacterial population genomics analyses using WGS data. ProkEvo was specifically developed to achieve the following goals: (1) Automation and scaling of complex combinations of computational analyses for many thousands of bacterial genomes from inputs of raw Illumina paired-end sequence reads; (2) Use of workflow management systems (WMS) such as Pegasus WMS to ensure reproducibility, scalability, modularity, fault-tolerance, and robust file management throughout the process; (3) Use of high-performance and high-throughput computational platforms; (4) Generation of hierarchical-based population structure analysis based on combinations of multi-locus and Bayesian statistical approaches for classification for ecological and epidemiological inquiries; (5) Association of antimicrobial resistance (AMR) genes, putative virulence factors, and plasmids from curated databases with the hierarchically-related genotypic classifications; and (6) Production of pan-genome annotations and data compilation that can be utilized for downstream analysis such as identification of population-specific genomic signatures. The scalability of ProkEvo was measured with two datasets comprising significantly different numbers of input genomes (one with ~2,400 genomes, and the second with ~23,000 genomes). Depending on the dataset and the computational platform used, the running time of ProkEvo varied from ~3-26 days. ProkEvo can be used with virtually any bacterial species, and the Pegasus WMS uniquely facilitates addition or removal of programs from the workflow or modification of options within them. To demonstrate versatility of the ProkEvo platform, we performed a hierarchical-based population structure analyses from available genomes of three distinct pathogenic bacterial species as individual case studies. The specific case studies illustrate how hierarchical analyses of population structures, genotype frequencies, and distribution of specific gene functions can be integrated into an analysis. Collectively, our study shows that ProkEvo presents a practical viable option for scalable, automated analyses of bacterial populations with direct applications for basic microbiology research, clinical microbiological diagnostics, and epidemiological surveillance.

Investigation of the invasion mechanism mediated by the outer membrane protein PagN of Salmonella Typhimurium

BACKGROUND

Salmonella can invade host cells via a type three secretion system called T3SS-1 and its outer membrane proteins, PagN and Rck. However, the mechanism of PagN-dependent invasion pathway used by Salmonella enterica, subspecies enterica serovar Typhimurium remains unclear.

RESULTS

Here, we report that PagN is well conserved and widely distributed among the different species and subspecies of Salmonella. We showed that PagN of S. Typhimurium was sufficient and necessary to enable non-invasive E. coli over-expressing PagN and PagN-coated beads to bind to and invade different non-phagocytic cells. According to the literature, PagN is likely to interact with heparan sulfate proteoglycan (HSPG) as PagN-mediated invasion could be inhibited by heparin treatment in a dose-dependent manner. This report shows that this interaction is not sufficient to allow the internalization mechanism. Investigation of the role of β1 integrin as co-receptor showed that mouse embryo fibroblasts genetically deficient in β1 integrin were less permissive to PagN-mediated internalization. Moreover, PagN-mediated internalization was fully inhibited in glycosylation-deficient pgsA-745 cells treated with anti-β1 integrin antibody, supporting the hypothesis that β1 integrin and HSPG cooperate to induce the PagN-mediated internalization mechanism. In addition, use of specific inhibitors and expression of dominant-negative derivatives demonstrated that tyrosine phosphorylation and class I phosphatidylinositol 3-kinase were crucial to trigger PagN-dependent internalization, as for the Rck internalization mechanism. Finally, scanning electron microscopy with infected cells showed microvillus-like extensions characteristic of Zipper-like structure, engulfing PagN-coated beads and E. coli expressing PagN, as observed during Rck-mediated internalization.

CONCLUSIONS

Our results supply new comprehensions into T3SS-1-independent invasion mechanisms of S. Typhimurium and highly indicate that PagN induces a phosphatidylinositol 3-kinase signaling pathway, leading to a Zipper-like entry mechanism as the Salmonella outer membrane protein Rck.

The prevalence of the iutA and ibeA genes in Escherichia coli isolates from severe and non-severe patients with bacteremic acute biliary tract infection is significantly different

Background

Although Escherichia coli is the most frequently isolated microorganism in acute biliary tract infections with bacteremia, data regarding its virulence are limited.

Results

Information on cases of bacteremia in acute biliary tract infection in a retrospective study was collected from 2013 to 2015 at a tertiary care hospital in Japan. Factors related to the severity of infection were investigated, including patient background, phylogenetic typing, and virulence factors of E. coli, such as adhesion, invasion, toxins, and iron acquisition.

In total, 72 E. coli strains were identified in 71 cases, most of which primarily belonged to the B2 phylogroup (68.1%). The presence of the iutA gene (77.3% in the non-severe group, 46.4% in the severe group, P = 0.011) and the ibeA gene (9.1% in the non-severe group, and 35.7% in the severe group, P = 0.012) was significantly associated with the severity of infection. Among the patient characteristics, diabetes mellitus with organ involvement and alkaline phosphatase were different in the severe and non-severe groups.

Conclusions

We showed that bacteremic E. coli strains from acute biliary tract infections belonged to the virulent (B2) phylogroup. The prevalence of the iutA and ibeA genes between the two groups of bacteremia severity was significantly different.

Characterization of the emerging multidrug-resistant Salmonella enterica serotype Kentucky ST314 in China

Salmonella enterica serotype Kentucky (S. Kentucky) is an important Salmonella serotype with multiple sequence types (ST) with a worldwide incidence. We identified 8 STs from 180 strains of S. Kentucky, and ST314 emerged as the most commonly encountered ST. Drug susceptibility testing revealed that ST314 had multiple resistance properties, and 75.5% of the strains were resistant to three or more classes of antimicrobials. The rate of resistance to chloramphenicol, florfenicol, sulfafurazole and tetracycline were greater than 60%. The rates of ST314 resistance to quinolones were as follows: ciprofloxacin, 32.1%; nalidixic acid, 16%; and ofloxacin, 7.5%. Investigating the mechanism of quinolone resistance of ST314 revealed that mutations in the quinolone resistance-determining regions were rare, and resistance mainly occurred due to the resistance genes carried by plasmids. Only 1.9% (2/106) of ST314 strains had mutations in the quinolone resistance-determining regions (QRDR). The drug resistance genes of ST314 were primarily of plasmid-mediated quinolone resistance (PMQR). The detection rate of Salmonella genomic island 1 (SGI1) in ST314 was 12.3%. XbaI-pulsed-field gel electrophoresis revealed that S. enterica Kentucky ST314 was capable of cross-regional and cross-host transmission in China. We found ST314 to be the dominant S. Kentucky ST in China, and it carried multidrug resistance. This is the first report about the emergence of quinolone-resistant S. enterica Kentucky ST314 in China, which is different from previous reports, and the findings of the present study suggest that the mechanism of quinolone resistance in these strains are plasmid-mediated. Notably, plasmids carrying resistance genes may promote the rapid spread of ciprofloxacin resistance.

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch

As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for Salmonella enterica serovar Typhi (S. Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from >4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of S. Typhi high risk clones.

Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.

Prevalence, risk factors and genetic traits of Salmonella Infantis in Dutch broiler flocks

Salmonella Infantis is a poultry-adapted Salmonella enterica serovar that is increasingly reported in broilers and is also regularly identified among human salmonellosis cases. An emerging S. Infantis mega-plasmid (pESI), carrying fitness, virulence and antimicrobial resistance genes, is also increasingly found. We investigated the prevalence, genetic characteristics and risk factors for (pESI-carrying) S. Infantis in broilers. Faecal samples from 379 broiler flocks (in 198 farms with ≥3000 birds) in the Netherlands were tested. A questionnaire about farm characteristics was also administered. Sampling was performed in July 2018-May 2019, three weeks before slaughter. Fourteen flocks (in 10 farms) were S. Infantis-positive, resulting in a 3.7 % flock-level and 5.1 % farm-level prevalence. Based on multi-locus sequence typing (MLST), all isolates belonged to sequence type 32. All but one isolate carried a pESI-like mega-plasmid. Core-genome MLST showed considerable heterogeneity among the isolates, even within the same farm, with a few small clusters detected. The typical pESI-borne multi-resistance pattern to aminoglycosides, sulphonamide and tetracycline (93 %), as well as trimethoprim (71 %), was found. Additionally, resistance to (fluoro)quinolones based on gyrA gene mutations was detected. S. Infantis was found more often in flocks using salinomycin as coccidiostat, where flock thinning was applied or litter quality was poor, whereas employing external cleaning companies, wheat in feed, and vaccination against infectious bronchitis, were protective. Suggestive evidence for vertical transmission from hatcheries was found. A heterogeneous (pESI-carrying) S. Infantis population has established itself in Dutch broiler flocks, calling for further monitoring of its spread and a comprehensive appraisal of control options.

Genomic Analysis of Antibiotic-Resistant and -Susceptible Escherichia coli Isolated from Bovine Sources in Maputo, Mozambique

This study reports a genomic analysis of Escherichia coli isolates recovered from 25 bovine fecal composite samples collected from four different production units in Maputo city and around Maputo Province, Mozambique. The genomes were analyzed to determine the presence of antibiotic resistance genes (ARGs), genetic relatedness, and virulence factors known to cause diseases in humans. Whole-genome sequencing was conducted on 28 isolates using an Illumina NextSeq 500 sequencing platform. The genomes were analyzed using BLASTN for the presence of resistance genes and virulence factors, as well as to determine their phylogenetic groups, sequence types (ST), and ST complexes (ST Cplxs). The majority of the isolates (85%) were identified as members of phylogenetic groups B1, with fewer isolates identified as members of group A, and a single isolate identified as group "E/Clade I." The ST analysis demonstrated a higher level of diversity than the phylogenetic group analysis. Sixteen different STs, five ST Cplxs, and seven singleton complexes were identified. A strain identified as a novel ST (ST9215) showed a high level of similarity with an isolate recovered from a wild animal in the Gambia. Seven different ARGs were identified, with tet(B) being the most frequently detected, followed by aph(3″)-Ib, aph(6)-Id, sul2, bla_TEM-1B, and dfrA1. Three isolates encoded β-lactam-conferring point mutations in the ampC promoter (-42C>T). In total, 51 different virulence factors were identified among the genomes. This study demonstrates that E. coli from bovine sources in Mozambique encoded multiple antibiotic resistance elements, plasmids, and virulence factors. To the best of our knowledge, this is the first genomic description of antibiotic-resistant E. coli isolated from bovine sources in Mozambique.

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.

minMLST: machine learning for optimization of bacterial strain typing

MOTIVATION

High-resolution microbial strain typing is essential for various clinical purposes, including disease outbreak investigation, tracking of microbial transmission events and epidemiological surveillance of bacterial infections. The widely used approach for multilocus sequence typing (MLST) that is based on the core genome, cgMLST, has the advantage of a high level of typeability and maximal discriminatory power. Yet, the transition from a seven loci-based scheme to cgMLST involves several challenges, that include the need by some users to maintain backward compatibility, growing difficulties in the day-to-day communication within the microbiology community with respect to nomenclature and ontology, issues with typeability, especially if a more stringent approach to loci presence is used, and computational requirements concerning laboratory data management and sharing with end-users. Hence, methods for optimizing cgMLST schemes through careful reduction of the number of loci are expected to be beneficial for practical needs in different settings.

RESULTS

We present a new machine learning-based methodology, minMLST, for minimizing the number of genes in cgMLST schemes by identifying subsets of informative genes and analyzing the trade-off between gene reduction and typing performance. The results achieved with minMLST over eight bacterial species show that despite the reduction in the number of genes up to a factor of 10, the typing performance remains very high and significant with an Adjusted Rand Index that ranges between 0.4 and 0.93 in different species and a P-value < 10-3. The identification of such optimized MLST schemes for bacterial strain typing is expected to improve the implementation of cgMLST by improving interlaboratory agreement and communication.

AVAILABILITY AND IMPLEMENTATION

The python package minMLST is available at https://PyPi.org/project/minmlst/PyPI and supported on Linux and Windows.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Insights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics

BACKGROUND

Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. The aim of this work was to compare genetically 117 S. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies.

RESULTS

The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅ 90%) by the core genome multilocus sequence typing and (≅ 77%) by single copy marker genes. The phylogenetic analysis based on single nucleotide polymorphism (SNP) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were alocated into three clusters. The different orthologous protein clusters found for some S. Typhimurium isolated from humans and food are involved in metabolic and regulatory processes. For 26 isolates from swine the sequence types (ST) 19 and ST1921 were the most prevalent ones, and the ST14, ST64, ST516 and ST639 were also detected. Previous results typed the 91 S. Typhimurium isolates from humans and foods as ST19, ST313, ST1921, ST3343 and ST1649. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) strains. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes.

CONCLUSIONS

The phylogenetic trees grouped the majority of the S. Typhimurium isolates from humans into a single cluster suggesting that there is one prevalent subtype in Brazil. Regarding strains isolated from food and swine, the SNPs' results suggested the circulation of more than one subtype over 30 years in this country. The orthologous protein clusters analysis revealed unique genes in the strains studied mainly related to bacterial metabolism. S. Typhimurium strains from swine showed greater diversity of STs and prophages in comparison to strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in its virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when clinical treatment is needed.

Genomic Characterization of Salmonella typhimurium DT104 Strains Associated with Cattle and Beef Products

Salmonella enterica subsp. enterica serovar Typhimurium DT104, a multidrug-resistant phage type, has emerged globally as a major cause of foodborne outbreaks particularly associated with contaminated beef products. In this study, we sequenced three S. Typhimurium DT104 strains associated with a 2009 outbreak caused by ground beef, including the outbreak source strain and two clinical strains. The goal of the study was to gain a stronger understanding of the genomics and genomic epidemiology of highly clonal S. typhimurium DT104 strains associated with bovine sources. Our study found no single nucleotide polymorphisms (SNPs) between the ground beef source strain and the clinical isolates from the 2009 outbreak. SNP analysis including twelve other S. typhimurium strains from bovine and clinical sources, including both DT104 and non-DT104, determined DT104 strains averaged 55.0 SNPs between strains compared to 474.5 SNPs among non-DT104 strains. Phylogenetic analysis separated the DT104 strains from the non-DT104 strains, but strains did not cluster together based on source of isolation even within the DT104 phage type. Pangenome analysis of the strains confirmed previous studies showing that DT104 strains are missing the genes for the allantoin utilization pathway, but this study confirmed that the genes were part of a deletion event and not substituted or disrupted by the insertion of another genomic element. Additionally, cgMLST analysis revealed that DT104 strains with cattle as the source of isolation were quite diverse as a group and did not cluster together, even among strains from the same country. Expansion of the analysis to 775 S. typhimurium ST19 strains associated with cattle from North America revealed diversity between strains, not limited to just among DT104 strains, which suggests that the cattle environment is favorable for a diverse group of S. typhimurium strains and not just DT104 strains.

Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens

We have developed and implemented an undergraduate microbiology course in which students isolate, characterize, and perform whole genome assembly and analysis of Salmonella enterica from stream sediments and poultry litter. In the development of the course and over three semesters, successive teams of undergraduate students collected field samples and performed enrichment and isolation techniques specific for the detection of S. enterica. Eighty-eight strains were confirmed using standard microbiological methods and PCR of the invA gene. The isolates' genomes were Illumina-sequenced by the Center for Food Safety and Applied Nutrition at the FDA and the Virginia state Division of Consolidated Laboratory Services as part of the GenomeTrakr program. Students used GalaxyTrakr and other web- and non-web-based platforms and tools to perform quality control on raw and assembled sequence data, assemble, and annotate genomes, identify antimicrobial resistance and virulence genes, putative plasmids, and other mobile genetic elements. Strains with putative plasmid-borne antimicrobial resistance genes were further sequenced by students in our research lab using the Oxford Nanopore MinIONTM platform. Strains of Salmonella that were isolated include human infectious serotypes such as Typhimurium and Infantis. Over 31 of the isolates possessed antibiotic resistance genes, some of which were located on large, multidrug resistance plasmids. Plasmid pHJ-38, identified in a Typhimurium isolate, is an apparently self-transmissible 183 kb IncA/C2 plasmid that possesses multiple antimicrobial resistance and heavy-metal resistance genes. Plasmid pFHS-02, identified in an Infantis isolate, is an apparently self-transmissible 303 kb IncF1B plasmid that also possesses numerous heavy-metal and antimicrobial resistance genes. Using direct and indirect measures to assess student outcomes, results indicate that course participation contributed to cognitive gains in relevant content knowledge and research skills such as field sampling, molecular techniques, and computational analysis. Furthermore, participants self-reported a deeper interest in scientific research and careers as well as psychosocial outcomes (e.g., sense of belonging and self-efficacy) commonly associated with student success and persistence in STEM. Overall, this course provided a powerful combination of field, wet lab, and computational biology experiences for students, while also providing data potentially useful in pathogen surveillance, epidemiological tracking, and for the further study of environmental reservoirs of S. enterica.

Molecular Epidemiology of Salmonellosis in Florida, USA, 2017-2018

The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose “combination approach” comprising “HC5 clustering,” as efficient tool to trigger Salmonella outbreak investigations, and “SNP-based analysis,” for higher resolution phylogeny to confirm an outbreak. We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017–2018. Several clusters of closely related isolates (0–4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks.

Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city Lübeck

Medieval Europe was repeatedly affected by outbreaks of infectious diseases, some of which reached epidemic proportions. A Late Medieval mass burial next to the Heiligen-Geist-Hospital in Lübeck (present-day Germany) contained the skeletal remains of more than 800 individuals who had presumably died from infectious disease. From 92 individuals, we screened the ancient DNA extracts for the presence of pathogens to determine the cause of death. Metagenomic analysis revealed evidence of Salmonella enterica subsp. enterica serovar Paratyphi C, suggesting an outbreak of enteric paratyphoid fever. Three reconstructed S. Paratyphi C genomes showed close similarity to a strain from Norway (1200 CE). Radiocarbon dates placed the disease outbreak in Lübeck between 1270 and 1400 cal CE, with historical records indicating 1367 CE as the most probable year. The deceased were of northern and eastern European descent, confirming Lübeck as an important trading center of the Hanseatic League in the Baltic region.

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Salmonella enterica Paratyphi C detected in remains from a mass burial in Lübeck

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Outbreak of enteric paratyphoid fever likely occurred in 1367 CE

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Pathogen genomes showed close similarity to a strain from Norway (1200 CE)

Occurrence of Salmonella in the Cattle Production in France

Salmonella is among the most common foodborne pathogens worldwide, and can lead to acute gastroenteritis. Along with poultry, cattle production is recognized as an important source of human infection. Salmonella transmission from cattle to humans can occur through the environment, or through close contact with sick animals or their derived products. This study aimed to investigate the intestinal carriage of Salmonella spp. within French cattle production. A total of 959 cattle intestinal samples, from one of the largest French slaughterhouses, were analyzed. Isolated strains were genotyped by pulsed field gel electrophoresis (PFGE), and a sub-selection was taken by whole genome sequencing (WGS). Twenty-nine samples were positive for Salmonella spp., yielding an estimated prevalence of 3% in cattle production. Eight different Salmonella serotypes were found: Montevideo was the most prevalent (34%), followed by Mbandaka (24%) and Anatum (14%). PFGE genotyping allowed the clustering of Salmonella isolates according to their serotype. Within the clusters, some isolates presented 100% similarity. To investigate potential epidemiological links between them, WGS and core genome multilocus sequence typing (cgMLST) were used, revealing identical profiles between isolates originating from different areas and/or different animal breeds. This investigation provides new insights on Salmonella serotype epidemiology in cattle production in France.

Diversity and trends in population structure of ESBL-producing Enterobacteriaceae in febrile urinary tract infections in children in France from 2014 to 2017

BACKGROUND

The population structure of extraintestinal pathogenic Escherichia coli evolves over time, notably due to the emergence of antibiotic-resistant clones such as ESBL-producing Enterobacteriaceae (ESBL-E).

OBJECTIVES

To analyse by WGS the genetic diversity of a large number of ESBL-E isolated from urinary tract infections in children from paediatric centres across France between 2014 and 2017 and collected by the National Observatory of febrile urinary tract infection (FUTI) caused by ESBL-E.

METHODS

A total of 40 905 Enterobacteriaceae-positive urine cultures were identified. ESBL-E were found in 1983 samples (4.85%). WGS was performed on 251 ESBL-E causing FUTI. STs, core genome MLST (cgMLST), serotype, fimH allele, ESBL genes and presence of papGII key virulence factor were determined.

RESULTS

E. coli and Klebsiella pneumoniae were found in 86.9% (218/251) and 11.2% (28/251) of cases, respectively. Several STs predominate among E. coli such as ST131, ST38, ST69, ST73, ST95, ST405, ST12 and ST1193, while no ST emerged in K. pneumoniae. E. coli ST131, ST38 and ST1193 increased during the study period, with a heterogeneity in papGII prevalence (64.5%, 35% and 20% respectively). Most isolates harboured the CTX-M type (97%) with a predominance of blaCTX-M-15. blaCTX-M-27, an emerging variant in E. coli, is found in various STs. cgMLST enabled discrimination of clusters within the main STs.

CONCLUSIONS

The predominance of ST131, and the emergence of other STs such as ST38 and ST1193 combined with ESBL genes deserves close epidemiological surveillance considering their high threat in infectious disease. cgMLST could be a discriminant complementary tool for the analyses.

Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments

Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Here we show that less different E. coli sequence types (STs) are identified in wastewater than in rivers, albeit more resistant to antibiotics, and with significantly more plasmids/cell (6.36 vs 3.72). However, the genomic diversity within E. coli STs in both aquatic environments is similar. Wastewater environments favor the selection of conserved chromosomal structures associated with diverse flexible plasmids, unraveling promiscuous interplasmidic resistance genes flux. On the contrary, the key driver for river E. coli adaptation is a mutable chromosome along with few plasmid types shared between diverse STs harboring a limited resistance gene content.

Whole genome sequencing of Salmonella enterica serovar Saintpaul for elucidating the mechanisms of resistance to third generation cephalosporins

An increase in the number of Salmonella enterica serovar Saintpaul observed in Singapore in 2015-2016 in humans was accompanied by increased resistance to third generation cephalosporins. We aimed to understand the genetic mechanisms contributing to this resistance. Whole genome sequencing using MiSeq was performed on 49 S. Saintpaul isolates collected between 2014-2016. Nanopore sequencing was also performed in an attempt to obtain a full genome of the plasmids. All but one S. Saintpaul isolates sequenced belonged to a single sequence type based on an in silico 7-gene multi-locus sequence typing scheme suggesting a clonal lineage. In total 27/49 were resistant to third generation cephalosporins as confirmed by the broth microdilution method; the resistance was due to the presence of either bla_CTX-M-55 (n=23), bla_CTX-M-27 (n=1) or bla_CMY-2 (n=3) carried on a plasmid. Two isolates were also found to carry the mcr-1 gene on a different plasmid. Our study showed that all S. Saintpaul isolates resistant to third generation cephalosporins carried either bla_CTX-M-55, bla_CTX-M-27 or bla_CMY-2 on a plasmid. Continuous monitoring of Salmonella serovars is warranted to track the potential spread of these plasmids.

Salmonella nomenclature in the genomic era: a time for change

Salmonella enterica nomenclature has evolved over the past one hundred years into a highly sophisticated naming convention based on the recognition of antigens by specific antibodies. This serotyping scheme has led to the definition of over 2500 serovars which are well understood, have standing in nomenclature and, for the majority, biological relevance. Therefore, it is highly desirable for any change in naming convention to maintain backwards compatibility with the information linked to these serovars. The routine use of whole genome sequencing and the well-established link between sequence types and serovars presents an opportunity to update the scheme by incorporating the phylogenetically relevant sequence data whilst preserving the best of serotyping nomenclature. Advantages include: overcoming the variability in antibody preparations; removing the need to use laboratory animals and implementing a truly universal system. However, the issue of trying to reproduce the phenotyping gold standard needs to be relaxed if we are to fully embrace the genomic era. We have used whole genome sequence data from over 46,000 isolates of Salmonella enterica subspecies enterica to define clusters in two stages: Multi Locus Sequence Typing followed by antigen prediction. Sequence type—serotype discrepancies were resolved using core SNP clustering to determine the phylogenetic groups and this was confirmed by overlaying the antigenic prediction onto the core SNP clusters and testing the separation of clusters using cgMLST Hierarchical Clustering. This allowed us to define any major antigenic clusters within an ST—here called the MAC type and written as ST-serovar. Using this method, 99.96% of Salmonella isolates reported in the UK were assigned a MAC type and linked to a serovar name taken from the Kauffmann and White scheme. We propose a change for reporting of Salmonella enterica sub-types using the ST followed by serovar.

Exotic dried fruits caused Salmonella Agbeni outbreak with severe clinical presentation, Norway, December 2018 to March 2019

We describe an outbreak of Salmonella Agbeni sequence type (ST)2009 infections in Norway. Between 31 December 2018 and 16 March 2019, 56 cases (33 female and 23 male; median age: 50 years, range: 2-91) were reported, of which 21 were hospitalised. Cases were defined as people living in Norway, with laboratory-confirmed infection with S. Agbeni ST2009 and cluster type (CT)2489, reported between 31 December 2018 and 30 March 2019. We conducted a case-control study, with three controls per case (matched by age, sex and municipality), using the Norwegian National Registry. Cases were more likely to have consumed a commercial mix of dried exotic fruits than controls (cases = 8, controls = 31; odds ratio: 50; 95% confidence interval: 3-2,437). The outbreak strain was confirmed by whole genome sequencing (WGS) and was isolated from the fruit mix consumed by cases, resulting in withdrawal from the market on 6 March 2019.The fruit mix consisted of fruits from different countries and continents. It was packed in Italy and distributed to several European countries, including Norway. However, no other countries reported cases. This outbreak highlights that dried fruits could represent a risk in terms of food-borne infections, which is of particular concern in ready-to-eat products.

Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo

Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine. We hypothesised that plasmid properties would be the primary determinants of plasmid spread and that bacterial strain identity would also contribute. We found clinical Escherichia coli strains natively associated with ESBL-plasmids conjugated to three distinct E. coli strains and one Salmonella enterica serovar Typhimurium strain. Final transconjugant frequencies varied across plasmid, donor, and recipient combinations, with qualitative consistency when comparing transfer in vitro and in vivo in mice. In both environments, transconjugant frequencies for these natural strains and plasmids covaried with the presence/absence of transfer genes on ESBL-plasmids and were affected by plasmid incompatibility. By moving ESBL-plasmids out of their native hosts, we showed that donor and recipient strains also modulated transconjugant frequencies. This suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa

Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.

Draft Genome Sequence of Invasive Salmonella enterica Serovar Cannstatt Harboring mcr-1.1, Isolated from a Fatal Sepsis Case

Here, we report the whole-genome sequence of multidrug-resistant Salmonella enterica serovar Cannstatt harboring mcr-1.1, isolated from a fatal sepsis case. Genomic analysis revealed that the isolate was sequence type 2390 carrying mcr-1.1, bla_CTX-M-14, aac(3)IId, aac(6′)Iaa, floR, qnrS1, sul2, tetA, and tetM. Three Inc plasmids were observed, including the IncX4 plasmid containing mcr-1.1.

Here, we report the whole-genome sequence of multidrug-resistant Salmonella enterica serovar Cannstatt harboring mcr-1.1, isolated from a fatal sepsis case. Genomic analysis revealed that the isolate was sequence type 2390 carrying mcr-1.1, bla_CTX-M-14, aac(3)IId, aac(6′)Iaa, floR, qnrS1, sul2, tetA, and tetM. Three Inc plasmids were observed, including the IncX4 plasmid containing mcr-1.1.

Outbreak of Central American born Shigella sonnei in two youth camps in Belgium in the summer of 2019

In 2019, an outbreak of Shigella sonnei occurred during two youth camps in Belgium. The clustering of isolates from both camps was confirmed by next-generation sequencing, as well as a secondary infection of a technician. The outbreak strain clustered with internationally isolated strains from patients with recent travel history to Central America. This report exemplifies enhanced surveillance and international collaboration between public health institutes by enabling to link local outbreaks to region-specific sublineages circulating abroad.

Detecting High Scoring Local Alignments in Pangenome Graphs

Motivation

Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet.

Results

We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.

Availability and implementation

Source code and test data are available from https://gitlab.ub.uni-bielefeld.de/gi/plast.

Supplementary information

Supplementary data are available at Bioinformatics online.

Environmental Spread of Extended Spectrum Beta-Lactamase (ESBL) Producing Escherichia coli and ESBL Genes among Children and Domestic Animals in Ecuador

BACKGROUND

There is a significant gap in our understanding of the sources of multidrug-resistant bacteria and resistance genes in community settings where human-animal interfaces exist.

OBJECTIVES

This study characterized the relationship of third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) isolated from animal feces in the environment and child feces based on phenotypic antimicrobial resistance (AMR) and whole genome sequencing (WGS).

METHODS

We examined 3GCR-EC isolated from environmental fecal samples of domestic animals and child fecal samples in Ecuador. We analyzed phenotypic and genotypic AMR, as well as clonal relationships (CRs) based on pairwise single-nucleotide polymorphisms (SNPs) analysis of 3GCR-EC core genomes. CRs were defined as isolates with fewer than 100 different SNPs.

RESULTS

A total of 264 3GCR-EC isolates from children (n=21), dogs (n=20), and chickens (n=18) living in the same region of Quito, Ecuador, were identified. We detected 16 CRs total, which were found between 7 children and 5 domestic animals (5 CRs) and between 19 domestic animals (11 CRs). We observed that several clonally related 3GCR-EC isolates had acquired different plasmids and AMR genes. Most CRs were observed in different homes (n=14) at relatively large distances. Isolates from children and domestic animals shared the same blaCTX-M allelic variants, and the most prevalent were blaCTX-M-55 and blaCTX-M-65, which were found in isolates from children, dogs, and chickens.

DISCUSSION

This study provides evidence of highly dynamic horizontal transfer of AMR genes and mobile genetic elements (MGEs) in the E. coli community and shows that some 3GCR-EC and (extended-spectrum β-lactamase) ESBL genes may have moved relatively large distances among domestic animals and children in semirural communities near Quito, Ecuador. Child-animal contact and the presence of domestic animal feces in the environment potentially serve as important sources of drug-resistant bacteria and ESBL genes. https://doi.org/10.1289/EHP7729.

Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project

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.

Phylogeny of Salmonella enterica subspecies arizonae by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability

Salmonella enterica subspecies arizonae is frequently associated with animal reservoirs, particularly reptiles, and can cause illness in some mammals, including humans. Using whole-genome sequencing data, core genome phylogenetic analyses were performed using 112 S. enterica subsp. arizonae isolates, representing 46 of 102 described serovars. Nearly one-third of these are polyphyletic, including two serovars that appear in four and five distinct evolutionary lineages. Subspecies arizonae has a monophasic H antigen. Among the 46 serovars investigated, only 8 phase 1 H antigens were identified, demonstrating high conservation for this antigen. Prophages and plasmids were found throughout this subspecies, including five novel prophages. Polyphyly was also reflected in prophage content, although some clade-specific enrichment for some phages was observed. IncFII(S) was the most frequent plasmid replicon identified and was found in a quarter of S. enterica subsp. arizonae genomes. Salmonella pathogenicity islands (SPIs) 1 and 2 are present across all Salmonella, including this subspecies, although effectors sipA, sptP and arvA in SPI-1 and sseG and ssaI in SPI-2 appear to be lost in this lineage. SPI-20, encoding a type VI secretion system, is exclusive to this subspecies and is well maintained in all genomes sampled. A number of fimbral operons were identified, including the sas operon that appears to be a synapomorphy for this subspecies, while others exhibited more clade-specific patterns. This work reveals evolutionary patterns in S. enterica subsp. arizonae that make this subspecies a unique lineage within this very diverse species.

Bayesian Source Attribution of Salmonella Typhimurium Isolates From Human Patients and Farm Animals in England and Wales

The purpose of the study was to apply a Bayesian source attribution model to England and Wales based data on Salmonella Typhimurium (ST) and monophasic variants (MST), using different subtyping approaches based on sequence data. The data consisted of laboratory confirmed human cases and mainly livestock samples collected from surveillance or monitoring schemes. Three different subtyping methods were used, 7-loci Multi-Locus Sequence Typing (MLST), Core-genome MLST, and Single Nucleotide Polymorphism distance, with the impact of varying the genetic distance over which isolates would be grouped together being varied for the latter two approaches. A Bayesian frequency matching method, known as the modified Hald method, was applied to the data from each of the subtyping approaches. Pigs were found to be the main contributor to human infection for ST/MST, with approximately 60% of human cases attributed to them, followed by other mammals (mostly horses) and cattle. It was found that the use of different clustering methods based on sequence data had minimal impact on the estimates of source attribution. However, there was an impact of genetic distance over which isolates were grouped: grouping isolates which were relatively closely related increased uncertainty but tended to have a better model fit.