Recombining population structure of the Enterobacteriaceae Plesiomonas shigelloides revealed by multilocus sequence typing

Unité Biodiversité des Bactéries Pathogènes Emergentes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France; Department of Crop Systems, Forestry and Environmental Sciences, University of Basilicata, Potenza (Italy); Slovak Medical University, Faculty of Public Health, 83303 Bratislava, Limbova 12, Slovak Republic; Department of Biomedical Sciences and Veterinary Public Health, Faculty of Veterinary Medicine and Animal Science, SLU, Box 7036, 750 07 Uppsala, Sweden

^* To whom correspondence should be addressed. Email: sbrisse{at}pasteur.fr.

	Abstract

Plesiomonas shigelloides is an emerging pathogen that is widespread in the aquatic environment and responsible for intestinal diseases and extra-intestinal infections in humans and other animals. Virtually nothing is known about its genetic diversity, population structure and evolution, which severely limits epidemiological control. We addressed these questions by developing a multilocus sequence typing (MLST) system based on five genes (fusA, leuS, pyrG, recG and rpoB) and analyzing 77 epidemiologically unrelated strains from several countries and ecological sources. The phylogenetic position of P. shigelloides within family Enterobacteriaceae was precisely defined by phylogenetic analysis of the same gene portions in other family members. Within P. shigelloides, high levels of nucleotide diversity (average of 1.49% nucleotide differences between strains) and genotypic diversity (64 distinct sequence types, Simpson's index 99.7%) were evidenced, with no salient internal phylogenetic structure. We estimated that homologous recombination in housekeeping genes affects P. shigelloides alleles and nucleotides 7 times and 77 times more frequently than mutation, respectively. These ratios are similar to those observed in the naturally transformable and highly recombining species Streptococcus pneumoniae. In contrast, recombination within Salmonella enterica, Escherichia coli and Yersinia enterocolitica was much less frequent. P. shigelloides thus stands out among Enterobacteriaceae. Its high rate of recombination results in lack of association between genomic background and O and H antigenic factors, as observed for the 51 serotypes found in our sample. Given its robustness and discriminatory power, we recommend MLST as a reference method for population biology and epidemiological tracking of P. shigelloides strains.