Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam

Cuong T Le; Erin P Price; Derek S Sarovich; Thu T A Nguyen; Daniel Powell; Hung Vu-Khac; D İpek Kurtböke; Wayne Knibb; Shih-Chu Chen; Mohammad Katouli

doi:10.1099/mgen.0.000845

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Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam

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Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam

Cuong T Le, Erin P Price, Derek S Sarovich, Thu T A Nguyen, Daniel Powell, Hung Vu-Khac, D İpek Kurtböke, Wayne Knibb, Shih-Chu Chen and Mohammad Katouli

Microbial Genomics, Vol.8(7), pp.1-16

2022

DOI: https://doi.org/10.1099/mgen.0.000845

PMCID: PMC9455698

PMID: 35786440

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Abstract

Nocardia seriolae

trachinotus

nocardiosis

genomics

aquaculture

permit fish

fish infection

infectious disease

fish mortality

Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.

Details

Title: Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam
Authors: Cuong T Le (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Erin P Price (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Derek S Sarovich (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Thu T A Nguyen (Author) - Nha Trang University
Daniel Powell (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Hung Vu-Khac (Author)
D İpek Kurtböke (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Wayne Knibb (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Shih-Chu Chen (Author) - National Pingtung University of Science and Technology
Mohammad Katouli (Corresponding Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Publication details: Microbial Genomics, Vol.8(7), pp.1-16
Publisher: The Microbiology Society
Date published: 2022
DOI: 10.1099/mgen.0.000845
ISSN: 2057-5858
PMID: 35786440; PMC9455698
Copyright note: © 2022 The Authors This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; Office of Research; School of Health and Sport Sciences - Legacy; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99654998802621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Genetics & Heredity; Microbiology

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