Clustering of Vibrio parahaemolyticus Isolates Using MLST and Whole-Genome Phylogenetics and Protein Motif Fingerprinting.

Kelsey J Jesser,Jessica L Jones,Willy Valdivia-Granda,Rachel T Noble

doi:10.3389/fpubh.2019.00066

Abstract

Vibrio parahaemolyticus is a ubiquitous and abundant member of native microbial assemblages in coastal waters and shellfish. Though V. parahaemolyticus is predominantly environmental, some strains have infected human hosts and caused outbreaks of seafood-related gastroenteritis. In order to understand differences among clinical and environmental V. parahaemolyticus strains, we used high quality DNA sequencing data to compare the genomes of V. parahaemolyticus isolates (n = 43) from a variety of geographic locations and clinical and environmental sample matrices. We used phylogenetic trees inferred from multilocus sequence typing (MLST) and whole-genome (WG) alignments, as well as a novel classification and genome clustering approach that relies on protein motif fingerprints (MFs), to assess relationships between V. parahaemolyticus strains and identify novel molecular targets associated with virulence. Differences in strain clustering at more than one position were observed between the MLST and WG phylogenetic trees. The WG phylogeny had higher support values and strain resolution since isolates of the same sequence type could be differentiated. The MF analysis revealed groups of protein motifs that were associated with the pathogenic MLST type ST36 and a large group of clinical strains isolated from human stool. A subset of the stool and ST36-associated protein motifs were selected for further analysis and the motif sequences were found in genes with a variety of functions, including transposases, secretion system components and effectors, and hypothetical proteins. DNA sequences associated with these protein motifs are candidate targets for future molecular assays in order to improve surveys of pathogenic V. parahaemolyticus in the environment and seafood.

Highlights

Vibrio parahaemolyticus is a native member of bacterial flora in coastal ecosystems worldwide [1] and is a leading cause of illness associated with seafood [2, 3]
The objective of this research was to compare the results of multilocus sequence typing (MLST) and WG phylogenetic clustering with motif fingerprints (MFs) clustering for both clinical and environmental V. parahaemolyticus isolates
We demonstrate that the phylogenetic and MF clustering methods are complementary and describe how MF clustering can be used to identify molecular targets associated with virulent V. parahaemolyticus strains

Summary

Introduction

Vibrio parahaemolyticus is a native member of bacterial flora in coastal ecosystems worldwide [1] and is a leading cause of illness associated with seafood [2, 3]. When conditions are optimal for growth, virtually 100% of oysters have detectable concentrations of V. parahaemolyticus or other potentially pathogenic Vibrio species [5]. The prevalence of V. parahaemolyticus in densely populated coastal areas, as well as the economic value of the tourism and seafood industries, underscores the importance of accurate detection, quantification, and monitoring measures for this pathogen. Measuring the abundance of disease-causing V. parahaemolyticus is difficult because most strains isolated from environmental sources are considered nearly exclusively environmental and nonpathogenic. Ecological and genomic similarities between known virulent strains and strictly environmental strains of V. parahaemolyticus make differentiating the organisms that cause disease challenging, but is vital when considering the risk V. parahaemolyticus populations may pose to human health [12]

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