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Phylogenomic Analysis Supports Two Possible Origins for Latin American Strains of Vibrio parahaemolyticus Associated with Acute Hepatopancreatic Necrosis Disease (AHPND)

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Abstract

Acute hepatopancreatic necrosis disease (AHPND) is a severe disease affecting recently stocked cultured shrimps. The disease is mainly caused by V. parahaemolyticus that harbors the pVA1 plasmid; this plasmid contains the pirA and pirB genes, which encode a delta-endotoxin. AHPND originated in China in 2009 and has since spread to several other Asian countries and recently to Latin America (2013). Many Asian strains have been sequenced, and their sequences are publicly accessible in scientific databases, but only four strains from Latin America have been reported. In this study, we analyzed nine pVA1-harboring V. parahaemolyticus sequences from strains isolated in Mexico along with the 38 previously available pVA1-harboring V. parahaemolyticus sequences and the reference strain RIMD 2210633. The studied sequences were clustered into three phylogenetic clades (Latin American, Malaysian, and Cosmopolitan) through pangenomic and phylogenomic analysis. The nucleotide sequence alignment of the pVA1 plasmids harbored by the Asian and Latin American strains confirmed that the main structural difference in the plasmid between the Asian and Latin American strains is the absence of the Tn3 transposon in the Asian strains; in addition, some deletions in the pirAB region were found in two of the Latin American strains. Our study represents the most robust and inclusive phylogenomic analysis of pVA1-harboring V. parahaemolyticus conducted to date and provides insight into the epidemiology of AHPND. In addition, this study highlights that disease diagnosis through the detection of the pirA and pirB genes is an inadequate approach due to the instability of these genes.

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Acknowledgments

We thank the CONACyT for the scholarship granted to Jean Pierre González-Gómez. The authors would like to thank Karen Enciso-Ibarra, Julissa Enciso-Ibarra, Abraham Guerrero, Francis Marrujo, Carmen Bolán-Mejía, Rodolfo Lozano, Manuel Olea-Castillo, and Berenice González-Torres for the technical support.

Funding

This work was supported by the Consejo Nacional de Ciencia y Tecnología (CONACyT) of Mexico through a scholarship granted to Jean Pierre González-Gómez [No. 818472].

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BGG and CC conceived and designed the project; JPG and BGG performed bioinformatic analyses; JPG wrote the paper; SS contributed materials; and SS, BGG, CC, OL, and NC modified the manuscript and supervised the research. All authors read and approved the final manuscript.

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Correspondence to Cristóbal Chaidez or Bruno Gomez-Gil.

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González-Gómez, J.P., Soto-Rodriguez, S., López-Cuevas, O. et al. Phylogenomic Analysis Supports Two Possible Origins for Latin American Strains of Vibrio parahaemolyticus Associated with Acute Hepatopancreatic Necrosis Disease (AHPND). Curr Microbiol 77, 3851–3860 (2020). https://doi.org/10.1007/s00284-020-02214-w

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