Abstract
BackgroundSalmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. In order to understand the genetic basis of these similarities, a comparative genomic approach was used to define the pan-, core, accessory, and unique coding sequences of a representative population of Salmonella and Citrobacter strains.ResultsAnalysis of the genomic content of 58 S. enterica strains and 37 Citrobacter strains revealed the presence of 31,130 and 1540 coding sequences within the pan- and core genome of this population. Amino acid sequences unique to either Salmonella (n = 1112) or Citrobacter (n = 195) were identified and revealed potential niche-specific adaptations. Phylogenetic network analysis of the protein families encoded by the pan-genome indicated that genetic exchange between Salmonella and Citrobacter may have led to the acquisition of similar traits and also diversification within the genera.ConclusionsCore genome analysis suggests that the Salmonella enterica and Citrobacter populations investigated here share a common evolutionary history. Comparative analysis of the core and pan-genomes was able to define the genetic features that distinguish Salmonella from Citrobacter and highlight niche specific adaptations.
Highlights
Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs
Characterization of Citrobacter strains falsely identified as Salmonella During routine testing of lettuce samples, an industrial producer isolated five presumptive strains testing positive for Salmonella using a commercially available rapid identification method
A consensus tree based on sequence variations of the amino acid sequences encoded by the Salmonella-Citrobacter core genes was able to resolve the two bacterial species into two distinct clades and provided sufficient delineation to infer the taxonomic affiliation of the Citrobacter strains
Summary
Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. In order to understand the genetic basis of these similarities, a comparative genomic approach was used to define the pan-, core, accessory, and unique coding sequences of a representative population of Salmonella and Citrobacter strains. Salmonella enterica subspecies enterica is one of the leading causes of foodborne illnesses in the world. The majority of human infections are attributed to S. enterica, which comprises 6 subspecies with over 2500 serological variants (serovars) that are characterized by distinct antigenic profiles [5, 6].
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