Exploring the Genomic Traits of Non-toxigenic Vibrio parahaemolyticus Strains Isolated in Southern Chile

Abstract

<i>Vibrio parahaemolyticus</i> is the leading cause of seafood-borne gastroenteritis worldwide. As reported in other countries, after the rise and fall of the pandemic strain in Chile, other post-pandemic strains have been associated with clinical cases, including strains lacking the major toxins TDH and TRH. Since the presence or absence of <i>tdh</i> and <i>trh</i> genes has been used for diagnostic purposes and as a proxy of the virulence of <i>V. parahaemolyticus</i> isolates, the understanding of virulence in <i>V. parahaemolyticus</i> strains lacking toxins is essential to detect these strains present in water and marine products to avoid possible food-borne infection. In this study, we characterized the genome of four environmental and two clinical non-toxigenic strains (<i>tdh</i>-, <i>trh</i>-, and T3SS2-). Using whole-genome sequencing, phylogenetic, and comparative genome analysis, we identified the core and pan-genome of <i>V. parahaemolyticus</i> of strains of southern Chile. The phylogenetic tree based on the core genome showed low genetic diversity but the analysis of the pan-genome revealed that all strains harbored genomic islands carrying diverse virulence and fitness factors or prophage-like elements that encode toxins like Zot and RTX. Interestingly, the three strains carrying Zot-like toxin have a different sequence, although the alignment showed some conserved areas with the <i>zot</i> sequence found in <i>V. cholerae</i>. In addition, we identified an unexpected diversity in the genetic architecture of the T3SS1 gene cluster and the presence of the T3SS2 gene cluster in a non-pandemic environmental strain. Our study sheds light on the diversity of <i>V. parahaemolyticus</i> strains from the southern Pacific which increases our current knowledge regarding the global diversity of this organism.