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

Abstract

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.

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature

“…cgSTs are automatically assigned to multiple levels of single linkage hierarchical clustering (HierCC) based on their pairwise patristic differences in allelic contents, exclusive of missing data [15,16]. HierCC allows the ready identification and extraction of clusters of genomes at multiple hierarchical levels without requiring ad hoc phylogenetic trees [14][15][16].…”

“…Epidemiological investigations based on HC5 or HC10 clusters have identified single source, time-delimited food-borne outbreaks or human transmission chains of Salmonella [17], Escherichia [18] or Shigella [19]. HierCC can also identify groups of genetically related strains independently of epidemiological investigations [14,15].…”

“…corn soy blend), rivers and lakes (Salinas river x 2; Salinas lake x 1) and humans (13 strains) in diverse states of the U.S. Other strains isolated in the early 2000s from global sources had been sequenced as part of the UoWUCC 10K genomes project [14], including several from humans ) are indicated on lines from nodes A1, C1 and D1 to 3. NCTC12023 Colindale.…”

“…We recently sequenced 10,000 Salmonella genomes [14], including multiple serovar Typhimurium strains from diverse geographical and environmental sources. A number of those genomes closely resembled that of ATCC14028s, but were not obviously linked to laboratory contamination.…”

AT Homopolymer Strings as a Motif for Self-Recognition and Repair of Genomes in <em>Salmonella enterica</em> Subspecies I

“…It would also account for an inherent mechanism of self-recognition, which would facilitate preferential, but not exclusive, DNA exchange within a Genus species. The pan-genome of S. enterica subspecies 1 has a mosaic structure between serotypes, with frequent inversions, deletions, and insertions occurring between serotypes; however, the chromosomal arrangement of many Salmonella lineages is comparatively stable [25,32,38,39]. AT 8+mers being important to the processes of DNA replication, repair and acquisition by repair mechanisms and homologous recombination would account for i) the stability of some serotypes with conserved genome features that are persistent, e. g. serovar Typhimurium [1], ii) the occasional emergence of a new serotype that happens to undergo clonal expansion in an environment favorable for growth, e. g. serovar Tennessee in peanut butter [40,41], iii) the rare emergence of a hybrid strain following a major recombination event that results in rapid proliferation of a serotype with new biological properties, e. g. serovar Enteritidis and its ability to contaminate and survive in the internal contents of eggs [42], and iv) the periodic emergence and disappearance of serotypes that are not optimized for the survival in the environment in which they are generated.…”