Abstract
BackgroundWithin 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.ResultsIn 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi: 10.1186/1471-2164-15-427) contains supplementary material, which is available to authorized users.
Highlights
Within the last decade, Salmonella enterica subsp. enterica serovar Cerro
Genomic characteristics associated with the emergence or reemergence of pathogens in livestock operations can be subdivided into two categories; (i) genomic features that increase the adaptation to a host, or facilitate the jump to a new host species, or (ii) genomic features that provide increased adaptation to environmental factors in the livestock environment, such as antibiotic resistance
Cerro FSL R8-0235 has a genome size of approximately 4.7 Mbp, contains six prophage regions and represents multi locus sequence typing (MLST) sequence type ST367 After exclusion of contigs fewer than 200 bp, the total length of the S
Summary
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. Cerro isolated from cattle and farms represent one pulsed field electrophoresis (PFGE) type, indicating that a single clonal lineage is involved in this emergence [7]. Cerro has distinct genomic characteristics that explain its association with cattle and limited association with human disease
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