Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks
Abstract 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...
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| Format: | Article |
| Language: | English |
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BMC
2022-03-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08439-2 |
| _version_ | 1818321007728918528 |
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| author | Emeline Cherchame Laurent Guillier Renaud Lailler Marie-Leone Vignaud Nathalie Jourdan-Da Silva Simon Le Hello François-Xavier Weill Sabrina Cadel-Six |
| author_facet | Emeline Cherchame Laurent Guillier Renaud Lailler Marie-Leone Vignaud Nathalie Jourdan-Da Silva Simon Le Hello François-Xavier Weill Sabrina Cadel-Six |
| author_sort | Emeline Cherchame |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-13T10:34:04Z |
| format | Article |
| id | doaj.art-9ca9e674d32c43f0a33d2148010348ef |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T10:34:04Z |
| publishDate | 2022-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-9ca9e674d32c43f0a33d2148010348ef2022-12-21T23:50:47ZengBMCBMC Genomics1471-21642022-03-0123111310.1186/s12864-022-08439-2Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaksEmeline Cherchame0Laurent Guillier1Renaud Lailler2Marie-Leone Vignaud3Nathalie Jourdan-Da Silva4Simon Le Hello5François-Xavier Weill6Sabrina Cadel-Six7Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES)Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES)Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES)Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES)Santé Publique FranceCentre National de Référence Des Escherichia Coli, Institut Pasteur, Unité Des Bactéries Pathogènes EntériquesCentre National de Référence Des Escherichia Coli, Institut Pasteur, Unité Des Bactéries Pathogènes EntériquesLaboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES)Abstract 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.https://doi.org/10.1186/s12864-022-08439-2Salmonella WelikadeReference genomeOutbreak characterizationEnteroBase analysisCore genome SNP analysisClonalFrameML |
| spellingShingle | Emeline Cherchame Laurent Guillier Renaud Lailler Marie-Leone Vignaud Nathalie Jourdan-Da Silva Simon Le Hello François-Xavier Weill Sabrina Cadel-Six Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks BMC Genomics Salmonella Welikade Reference genome Outbreak characterization EnteroBase analysis Core genome SNP analysis ClonalFrameML |
| title | Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks |
| title_full | Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks |
| title_fullStr | Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks |
| title_full_unstemmed | Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks |
| title_short | Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks |
| title_sort | salmonella enterica subsp enterica welikade guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks |
| topic | Salmonella Welikade Reference genome Outbreak characterization EnteroBase analysis Core genome SNP analysis ClonalFrameML |
| url | https://doi.org/10.1186/s12864-022-08439-2 |
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