Around the World in 1,475<i>Salmonella</i>Geo-serotypes

Gossner, Céline M; Hello, Simon Le; Jong, B de; Rolfhamre, Per; Faensen, Daniel; Weill, François‐Xavier; Giesecke, Johan

doi:10.3201/eid2207.141678

Cited by 10 publications

(7 citation statements)

References 13 publications

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“…The 14 strains originating from the NRC included (i) the historical S . Welikade strain, isolated for the first time in Sri Lanka in 1956 [ 21 ], (ii) 12 strains corresponding to all the clinical S . Welikade cases that occurred in metropolitan France since 2012, and (iii) one strain isolated from goat’s cheese in 2016.…”

Section: Resultsmentioning

confidence: 99%

Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks

et al. 2022

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Background Salmonella spp. is a major foodborne pathogen with a wide variety of serovars associated with human cases and food sources. Nevertheless, in Europe a panel of ten serovars is responsible for up to 80% of confirmed human cases. Clustering studies by single nucleotide polymorphism (SNP) core-genome phylogenetic analysis of outbreaks due to these major serovars are simplified by the availability of many complete genomes in the free access databases. This is not the case for outbreaks due to less common serovars, such as Welikade, for which no reference genomes are available. In this study, we propose a method to solve this problem. We propose to perform a core genome MLST (cgMLST) analysis based on hierarchical clustering using the free-access EnteroBase to select the most suitable genome to use as a reference for SNP phylogenetic analysis. In this study, we applied this protocol to a retrospective analysis of a Salmonella enterica serovar Welikade (S. Welikade) foodborne outbreak that occurred in France in 2016. Finally, we compared the cgMLST and SNP analyses. SNP phylogenetic reconstruction was carried out considering the effect of recombination events identified by the ClonalFrameML tool. The accessory genome was also explored by phage content and virulome analyses. Results Our findings revealed high clustering concordance using cgMLST and SNP analyses. Nevertheless, SNP analysis allowed for better assessment of the genetic distance among strains. The results revealed epidemic clones of S. Welikade circulating within the poultry and dairy sectors in France, responsible for sporadic and non-sporadic human cases between 2012 and 2019. Conclusions This study increases knowledge on this poorly described serovar and enriches public genome databases with 42 genomes from human and non-human S. Welikade strains, including the isolate collected in 1956 in Sri Lanka, which gave the name to this serovar. This is the first genomic analysis of an outbreak due to S. Welikade described to date.

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Section: Resultsmentioning

confidence: 99%

Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks

et al. 2022

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“…Of those, a total of 235, including 147 (83 in 2015 and 64 in 2016) clinical and 88 (62 and 26, respectively) non-human isolates, were extensively studied by WGS and/or MLVA. We also analysed 54 ‘historical’ subtyped S. Dublin isolates collected between 1929 and 2014, 31 from humans and 22 from non-human specimens, as well as the human isolate which gave the name to the serotype in 1929 (number 65k) [18]. In total, we included 289 isolates in this study (Figure 1).…”

Section: Methodsmentioning

confidence: 99%

Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016

et al. 2019

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On 18 January 2016, the French National Reference Centre for Salmonella reported to Santé publique France an excess of Salmonella enterica serotype Dublin (S. Dublin) infections. We investigated to identify the source of infection and implement control measures. Whole genome sequencing (WGS) and multilocus variable-number tandem repeat analysis (MLVA) were performed to identify microbiological clusters and links among cases, animal and food sources. Clusters were defined as isolates with less than 15 single nucleotide polymorphisms determined by WGS and/or with identical MLVA pattern. We compared different clusters of cases with other cases (case–case study) and controls recruited from a web-based cohort (case–control study) in terms of food consumption. We interviewed 63/83 (76%) cases; 2,914 controls completed a questionnaire. Both studies’ findings indicated that successive S. Dublin outbreaks from different sources had occurred between November 2015 and March 2016. In the case–control study, cases of distinct WGS clusters were more likely to have consumed Morbier (adjusted odds ratio (aOR): 14; 95% confidence interval (CI): 4.8–42) or Vacherin Mont d’Or (aOR: 27; 95% CI: 6.8–105), two bovine raw-milk cheeses. Based on these results, the Ministry of Agriculture launched a reinforced control plan for processing plants of raw-milk cheeses in the production region, to prevent future outbreaks.

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“…Together with the roman numeral abbreviation for the S. enterica subspecies, the combination of O- and H-antigens antigens is what defines the serotype (also known as a serovar) of a given Salmonella strain. Salmonella serovars also have common names that are often the name of the geographical location where they were first isolated (Gossner et al, 2016), to accompany their antigenic formulae (Brenner et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen

2019

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Not all Salmonella enterica serovars cause the same disease. S. enterica represents an incredibly diverse species comprising >2,600 unique serovars. While some S. enterica serovars are host-restricted, others infect a wide range of hosts. The diseases that nontyphoidal Salmonella (NTS) serovars cause vary considerably, with some serovars being significantly more likely to cause invasive disease in humans than others. Furthermore, while genomic analyses have advanced our understanding of the genetic diversity of these serovars, they have not been able to fully account for the observed clinical differences. One overarching challenge is that much of what is known about Salmonella ’s general biology and virulence strategies is concluded from studies examining a select few serovars, especially serovar Typhimurium. As targeted control strategies have been implemented to control select serovars, an increasing number of foodborne outbreaks involving serovars that are less frequently associated with human clinical illness are being detected. Harnessing what is known about the diversity of NTS serovars represents an important factor in achieving the ultimate goal of reducing salmonellosis-associated morbidity and mortality worldwide. In this review we summarize the current understanding of the differences and similarities among NTS serovars, highlighting the virulence mechanisms, genetic differences, and sources that characterize S. enterica diversity and contribute to its success as a foodborne pathogen.

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Around the World in 1,475SalmonellaGeo-serotypes

Abstract: Most Salmonella serotypes are named after geographic locations; a few others have surprisingly humorous origins.

Cited by 10 publications

References 13 publications

Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks

Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks

Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016

Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen

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