The Use of Recombined Ribosomal RNA Operon (rrn) Type-Specific Flanking Genes to Investigate rrn Differences Between Vibrio parahaemolyticus Environmental and Clinical Strains

Abstract

In order to interrogate the published genomes of clinical and environmental isolates of Vibrio parahaemolyticus an exploratory study was performed on the ribosomal RNA (rrn) type-specific conservation of the genes directly flanking the rrn operons of each rrn type. WGS was sourced from databases where available or performed de novo and resulted in 124 rrn operon sets for 5 environmental and 7 clinical isolates. Analyses showed that the number of operons varied between clinical (11–12 operons) and environmental (9–10) isolates. Recombination of operons was evident when using flanking gene homology (p<0.0001) as a criterion for identifying native structural arrangements. This was confirmed by and correlated with (p<0.0001) Mauve whole genome analysis, demonstrating considerable genome plasticity in environmental and clinical isolates. In environmental isolates, rrn types rrnD and rrnI had 23S and 16S ITS regions deleted. In comparison clinical isolates had the equivalent operons rrnEF and rrnGH arranged in tandem with no ORF between rrnE and rrnF or rrnG and rrnH. This suggested that operon components 16S, ITS and 23S respectively have been duplicated in the environmental isolates to produce 2 operons in tandem in the clinical isolates. These exploratory findings suggest that genome plasticity and recombination account for significant differences between environmental and clinical strains of V. parahaemolyticus. This information can be used to develop new typing methods that would be useful for studying the evolution of new pathogenic strains. Additionally, these types of analyses are useful for studying large genomic rrn operon recombination events over the entire genomes of V. parahaemolyticus strains.