Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries

Abstract

Background: Salmonella 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. Results: Analysis 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. Conclusions: Core 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.

Comparative Genomic Characterization of Multidrug-resistant Citrobacter Spp. Strains in Fennec Fox Imported to China

“…The previous investigation highlighted the challenges associated with species designation of Citrobacter by core genome analysis, particularly in regards to Citrobacter freundii, which did not constitute a discrete phylogenetic group. [42] As we noted in our data, C. cronae and C. braakii strains were clustered into the same clade, which suggests further accurate taxonomic inquiry is needed to clarify the lineage of Citrobacter members.…”

Tailoring the Host Range of Ackermannviridae Bacteriophages through Chimeric Tailspike Proteins

“…Citrobacter, a close genetic relative of Salmonella, is ubiquitous in many food-related environments and has been previously noted as a source of false positives impeding accurate Salmonella detection [ 58 , 59 ]. When used as a luciferase reporter for Salmonella detection, signal production from SPTD1.NL appeared specific for Salmonella with the sole exception of C. sedlakii [ 10 ].…”

Citrobacter braakii Yield False-Positive Identification as Salmonella, a Note of Caution

“…Bacteria belonging to the Citrobacter genus are closely related to Salmonella; thus, some similarities in cell surface antigens and biochemical properties occur between them. Pilar et al proved that approximately one-third of Citrobacter and Salmonella genes are composed of core genes, confirming their close relationships [10]. This surprisingly high genotypic similarity can be explained by their common evolutionary history and genetic exchange [11].…”