Title: Comparative genomics reveals the source and mechanisms of a Salmonella Kentucky epidemic on a dairy farm Authors
Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: March 29, 2013
Publication Date: April 18, 2013
Citation: Haley, B.J., Allard, M., Brown, E., Hovingh, E., Karns, J.S., Van Kessel, J.S. 2013. Comparative genomics reveals the source and mechanisms of a Salmonella Kentucky epidemic on a dairy farm. BARC Poster Day. Technical Abstract: Salmonella enterica subsp. enterica serovar Kentucky, frequently isolated from poultry in the United States, is also commonly isolated from the feces of dairy cows and is an infrequent pathogen of humans. Using enrichments in tetrathionate broth followed by isolation on XLT4 agar, this serotype was sporadically isolated from environmental samples and fecal grab samples from dairy cows during routine sampling of a dairy farm in central Pennsylvania from 2004 to 2006. From 2006 to 2010 an asymptomatic S. Kentucky epidemic occurred during which the majority of cows (n ˜ 100 ± 10 at each sampling period) were infected. To further investigate the epidemiology and molecular mechanisms of the onset and stasis of the epidemic, two S. Kentucky genomes were sequenced using 454 Roche technology; one from a farm isolate that was collected prior to the epidemic (2004) and one from an epidemic isolate (2010). Comparative genomic analysis demonstrated significant polymorphisms between the two strains. PCR primers targeting unique and strain-specific insertions/deletions were developed and screening of the archived isolates identified the index case of the asymptomatic epidemic as a heifer that was raised off-site and transported onto the study farm in 2006. Deeper investigation of the two isolates revealed 10 indels in open reading frames (ORFs) and 102 non-synonymous substitutions in protein-coding genes in the genomic DNA and putative plasmid DNA. Of these 102 amino acid polymorphisms, two have been identified as involved in S. enterica colonization of the bovine intestine. Further, an extra virulence repressor (haemolysin expression modulating protein) was identified on a ca. 70 kb IncI1 plasmid. We hypothesize that the virulence factors, namely Salmonella pathogenicity islands 1 and 2 (SPI1 and 2) are repressed in a manner that does not induce an immune response in the host, thereby allowing cells of this strain to colonize the cattle for long periods in a commensal relationship. This analysis demonstrates that intraserovar diversity accounts for the epidemiology and mechanisms of Salmonella dynamics and shows the utility of next generation genome sequencing in outbreak source detection.