Abstract
Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salmonella Typhi, was found to encode a flagellar operon that can mediate phase variation, which results in the rare z66 flagella phenotype. The identification and tracking of homologs of pBSSB1 is limited because it falls outside the normal replicon typing schemes for plasmids. Here we report the generation of nine new pBSSB1-family sequences using Illumina and Nanopore sequence data. Homologs of pBSSB1 were identified in 154 genomes representing 25 distinct serotypes from 67,758 Salmonella public genomes. Pangenome analysis of pBSSB1-family contigs was performed using roary and we identified three core genes amenable to a minimal pMLST scheme. Population structure analysis based on the newly developed pMLST scheme identified three major lineages representing 35 sequence types, and the distribution of these sequence types was found to span multiple serovars across the globe. This in silico pMLST scheme has shown utility in tracking and subtyping pBSSB1-family plasmids and it has been incorporated into the plasmid MLST database under the name “pBSSB1-family”.
Highlights
Serotyping is the current standard for classification of Salmonella isolates according to the reaction of antisera against the surface lipopolysaccharide layer (LPS) (O antigen) and flagellar (H antigens) [1,2,3]
In order to facilitate tracking of different lineages of the pBSSB1-family plasmid backbone, we developed a minimal Plasmid Multi-locus sequence typing (pMLST) scheme based on its plasmid sequences
Given that pBSSB1 homologues were found in less than 0.3% of samples it is suggestive that it is not common within Salmonella of clinical relevance. This is the first documentation of plasmids similar to pBSSB1 outside of Indonesian Salmonella Typhi and provides evidence for global distribution
Summary
Serotyping is the current standard for classification of Salmonella isolates according to the reaction of antisera against the surface lipopolysaccharide layer (LPS) (O antigen) and flagellar (H antigens) [1,2,3]. Based on the combination of antigens and biochemical characteristics an isolate is categorized into a serotype according to the White-Kauffman Le Minor (WKL) scheme [1,2,3]. The rfb locus is important in determining the LPS layer phenotype but there is a complex genetic basis for O antigen phenotypes [4,5]. Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid. Canada’s Genomics R&D Initiative Phase VI Shared Priority Project Management Plan on Antimicrobial Resistance
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