Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States

Abstract

Background: Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar.

Results: In addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here "NY bovine clade"), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone.Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche.

Conclusions: Our results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hosts.

Figure 1

Tip-dated phylogeny of the 27  S. Cerro isolates sequenced in this study with stepwise deletion of a D-alanine transporter encoding gene cluster mapped onto the phylogeny. Values on the branches represent posterior probabilities. Genes adjacent to the D-alanine transporter encoding gene cluster are represented as black arrows, genes in the cluster are represented as red arrows. Numbers in the arrows refer to STM gene tags as used in the genome sequence of S. Typhimurium LT2. Labels on the tips indicate isolate accession numbers, isolate date (month/year) and source.

Figure 2

Alignment of sopA in S. Cerro and selected other Salmonella serovars showing premature stop codon in Cerro and sopA polymorphisms in other Salmonella strains and serovars. Numbers above the alignment indicate the amino acid residues as found in sopA in S. Typhimurium LT2. sopA for S. Adelaide FSL A4-669 is in frame, while sopA for S. Typhi CT18 and S. Paratyphi A AKU 12601 show a four and three bp deletion in this region in this region, respectively. S. Cerro has a one bp insertion (underlined), leading to a frame shift and premature stop.

Figure 3

Caco-2 invasion efficiencies among Salmonella serovars Cerro, Kentucky, Newport, and Typhimurium. Cells were inoculated at a MOI of 10 and the invasion assays were performed at 37°C and 5% CO_2. Invasion efficiency was calculated as [CFU recovered/CFU infected] × 100. Data represent the mean of at least three biological replicates, and the error bars represent the standard deviation. The invasion efficiencies for each serovar were analyzed using one-way analysis of variance (ANOVA) and Tukey’s post hoc test, after the data was log-transformed to satisfy ANOVA assumptions of normality. Isolate sources are abbreviated as AC, Animal Clinical; ANC, Animal Non-clinical; E, Environmental; H, Human.