A genomic overview of the population structure of Salmonella

Abstract

For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.

Accurate reconstruction of bacterial pan- and core- genomes with PEPPAN

“…PEPPA can construct a pan-genome from thousands of genomes with high genetic diversities, and earlier versions of this pipeline were used to generate cgMLST schemes for the genera represented in EnteroBase (Alikhan et al 2018;Frentrup et al 2019;Zhou et al 2020) as well as for ancient DNA analyses (Zhou et al 2018b; Achtman and Zhou 2019). Here we address the genus Streptococcus, which includes very genetically diverse strains and highly significant zoonotic and human pathogens (Gao et al 2014), to demonstrate how to use PEPPA to construct a pan-genome from representative genomes.…”

“…This has become a common problem for core genome schemes, especially because draft genomes consist of multiple contigs, which can in turn result in the random absence of multiple genes from the genome. Core genome schemes used for cgMLST are therefore usually based on a relaxed core, consisting of single-copy genes present in the large majority of representative isolates (Moura et al 2016;Alikhan et al 2018;Zhou et al 2020). Our analyses identified 777 genes that were present in at least 3020 (95%) of the representative streptococcal genomes ( Supplemental Table S4, Fig.…”

“…5). Alikhan et al (2018) describes a pan-genome for all of Salmonella based on 537 genomes that had been derived by a precursor of PEPPA in 2015. That pan-genome had been used to develop a wgMLST scheme of 21,065 loci and a cgMLST scheme of 3002 genes.…”

“…Similarly, earlier publications indicated fewer and fewer genes within the core-genome as more and more genomes were examined, but this has also not been revisited with the larger datasets. Finally, genetic relationships that are based on single nucleotide polymorphisms are extremely difficult to calculate in real-time with very large datasets, and some large databases focus on core genome Multilocus sequence typing (cgMLST) (Mellmann et al 2011;Moura et al 2016;Alikhan et al 2018;Frentrup et al 2019;Zhou et al 2020) for genotyping and recognizing relationships. cgMLST schemes within public databases calculate the allelic variants within a fixed set of core genes.…”

Multi‐country outbreak of Salmonella Poona infections linked to consumption of infant formula

“…• with a clinical S. Poona isolate within five allelic differences by cgMLST to at least one of the representative sequences (EBI-ENA project PRJEB31267) based on the ECDC pipeline (EnteroBase scheme with 3002 loci -Annex 1) or to EnteroBase cgMLST [9] profile HC5-164707 when analysed by the Institut Pasteur.…”