Unraveling the impact of genome assembly on bacterial typing: a one health perspective
Abstract Background In the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approa...
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BMC
2024-11-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-10982-z |
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| author | Déborah Merda Meryl Vila-Nova Mathilde Bonis Anne-Laure Boutigny Thomas Brauge Marina Cavaiuolo Amandine Cunty Antoine Regnier Maroua Sayeb Noémie Vingadassalon Claire Yvon Virginie Chesnais |
| author_facet | Déborah Merda Meryl Vila-Nova Mathilde Bonis Anne-Laure Boutigny Thomas Brauge Marina Cavaiuolo Amandine Cunty Antoine Regnier Maroua Sayeb Noémie Vingadassalon Claire Yvon Virginie Chesnais |
| author_sort | Déborah Merda |
| collection | DOAJ |
| description | Abstract Background In the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approaches available to generate bacterial cgMLST, our research used an assembly-based approach (chewBBACA tool). Methods Simulations of short-read sequencing were conducted for 5 genomes of 27 pathogens of interest in animal, plant, and human health to evaluate the repeatability and reproducibility of cgMLST. Various quality parameters, such as read quality and depth of sequencing were applied, and several read simulations and genome assemblies were repeated using three tools: SPAdes, Unicycler and Shovill. In vitro sequencing were also used to evaluate assembly impact on cgMLST results, for six bacterial species: Bacillus thuringiensis, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, Vibrio parahaemolyticus and Xylella fastidiosa. Results The results highlighted variability in cgMLST, which not only related to the assembly tools, but also induced by the intrinsic composition of the genomes themselves. This variability observed in simulated sequencing was further validated with real data for six of the bacterial pathogens studied. Conclusion This highlights that the intrinsic genome composition affects assembly and resulting cgMLST profiles, and that variability in bioinformatics tools can induce a bias in cgMLST profiles. In conclusion, we propose that the completeness of cgMLST schemes should be considered when clustering strains. |
| format | Article |
| id | doaj-art-bf2b66771b624a7fbc6df9da9ea2d65c |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-bf2b66771b624a7fbc6df9da9ea2d65c2024-11-10T12:09:31ZengBMCBMC Genomics1471-21642024-11-0125111310.1186/s12864-024-10982-zUnraveling the impact of genome assembly on bacterial typing: a one health perspectiveDéborah Merda0Meryl Vila-Nova1Mathilde Bonis2Anne-Laure Boutigny3Thomas Brauge4Marina Cavaiuolo5Amandine Cunty6Antoine Regnier7Maroua Sayeb8Noémie Vingadassalon9Claire Yvon10Virginie Chesnais11Université Paris Est, ANSES, Laboratory for Food Safety, SPAAD unitUniversité Paris Est, ANSES, Laboratory for Food Safety, SPAAD unitUniversité Paris Est, ANSES, Laboratory for Food Safety, SBCL unitANSES, Plant Health Laboratory, Bacteriology Virology GMO UnitANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit (B3PA)Université Paris Est, ANSES, Laboratory for Food Safety, SBCL unitANSES, Plant Health Laboratory, Bacteriology Virology GMO UnitANSES, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit (B3PA)Université Paris Est, ANSES, Laboratory for Food SafetyUniversité Paris Est, ANSES, Laboratory for Food Safety, SBCL unitUniversité Paris Est, ANSES, Laboratory for Food SafetyUniversité Paris Est, ANSES, Laboratory for Food Safety, SPAAD unitAbstract Background In the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approaches available to generate bacterial cgMLST, our research used an assembly-based approach (chewBBACA tool). Methods Simulations of short-read sequencing were conducted for 5 genomes of 27 pathogens of interest in animal, plant, and human health to evaluate the repeatability and reproducibility of cgMLST. Various quality parameters, such as read quality and depth of sequencing were applied, and several read simulations and genome assemblies were repeated using three tools: SPAdes, Unicycler and Shovill. In vitro sequencing were also used to evaluate assembly impact on cgMLST results, for six bacterial species: Bacillus thuringiensis, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, Vibrio parahaemolyticus and Xylella fastidiosa. Results The results highlighted variability in cgMLST, which not only related to the assembly tools, but also induced by the intrinsic composition of the genomes themselves. This variability observed in simulated sequencing was further validated with real data for six of the bacterial pathogens studied. Conclusion This highlights that the intrinsic genome composition affects assembly and resulting cgMLST profiles, and that variability in bioinformatics tools can induce a bias in cgMLST profiles. In conclusion, we propose that the completeness of cgMLST schemes should be considered when clustering strains.https://doi.org/10.1186/s12864-024-10982-zcgMLSTGenome assemblyBioinformatics tool variabilityData comparability |
| spellingShingle | Déborah Merda Meryl Vila-Nova Mathilde Bonis Anne-Laure Boutigny Thomas Brauge Marina Cavaiuolo Amandine Cunty Antoine Regnier Maroua Sayeb Noémie Vingadassalon Claire Yvon Virginie Chesnais Unraveling the impact of genome assembly on bacterial typing: a one health perspective BMC Genomics cgMLST Genome assembly Bioinformatics tool variability Data comparability |
| title | Unraveling the impact of genome assembly on bacterial typing: a one health perspective |
| title_full | Unraveling the impact of genome assembly on bacterial typing: a one health perspective |
| title_fullStr | Unraveling the impact of genome assembly on bacterial typing: a one health perspective |
| title_full_unstemmed | Unraveling the impact of genome assembly on bacterial typing: a one health perspective |
| title_short | Unraveling the impact of genome assembly on bacterial typing: a one health perspective |
| title_sort | unraveling the impact of genome assembly on bacterial typing a one health perspective |
| topic | cgMLST Genome assembly Bioinformatics tool variability Data comparability |
| url | https://doi.org/10.1186/s12864-024-10982-z |
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