Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes

ABSTRACT The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.

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Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes

10.1101/714626 ◽

2019 ◽

Cited By ~ 1

Author(s):

Chrystine Zou Yi Yan ◽

Christopher M. Austin ◽

Qasim Ayub ◽

Sadequr Rahman ◽

Han Ming Gan

Keyword(s):

Vibrio Parahaemolyticus ◽

Illumina Miseq ◽

Pacific White Shrimp ◽

White Shrimp ◽

Phylogenomic Analysis ◽

Genomic Characterization ◽

Genomic Resource ◽

Acute Hepatopancreatic Necrosis Disease ◽

Genomic Regions

AbstractThe Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVpand pirBVpgenes which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVpgenes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.

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Water microbiome dynamics of Pacific white shrimp Penaeus vannamei infected with Vibrio parahaemolyticus strains responsible for acute hepatopancreatic necrosis disease

Aquaculture ◽

10.1016/j.aquaculture.2021.737871 ◽

2022 ◽

pp. 737871

Author(s):

K.G. Aguilar-Rendón ◽

S.A. Soto-Rodriguez ◽

B. Gomez-Gil ◽

R. Lozano-Olvera ◽

B. Yáñez-Rivera

Keyword(s):

Vibrio Parahaemolyticus ◽

Pacific White Shrimp ◽

White Shrimp ◽

Penaeus Vannamei ◽

Acute Hepatopancreatic Necrosis Disease

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Complete Genome Sequence of a Deletion Mutant of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei)

Genome Announcements ◽

10.1128/genomea.00544-18 ◽

2018 ◽

Vol 6 (25) ◽

Cited By ~ 1

Author(s):

Siddhartha Kanrar ◽

Arun K. Dhar

Keyword(s):

Genome Sequence ◽

Vibrio Parahaemolyticus ◽

Deletion Mutant ◽

Pacific White Shrimp ◽

White Shrimp ◽

Penaeus Vannamei ◽

Content Type ◽

A Genome ◽

Acute Hepatopancreatic Necrosis Disease ◽

Experimental Challenge

ABSTRACT Vibrio parahaemolyticus carrying the toxin genes pirA and pirB causes acute hepatopancreatic necrosis disease in shrimp. A genome sequence of V. parahaemolyticus strain R13 was determined that showed deletions of the entire pirA gene and the 5ʹ end of the pirB gene and does not cause the disease in experimental challenge.

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Biases during DNA extraction affect characterization of the microbiota associated with larvae of the Pacific white shrimp,Litopenaeus vannamei

PeerJ ◽

10.7717/peerj.5257 ◽

2018 ◽

Vol 6 ◽

pp. e5257 ◽

Cited By ~ 11

Author(s):

Ming Xue ◽

Liyou Wu ◽

Yaoyao He ◽

Huafang Liang ◽

Chongqing Wen

Keyword(s):

Dna Extraction ◽

Litopenaeus Vannamei ◽

Penaeid Shrimp ◽

Illumina Miseq ◽

Pacific White Shrimp ◽

White Shrimp ◽

Dna Recovery ◽

The Pacific ◽

Α Diversity

For in-depth characterization of the microbiota associated with shrimp larvae, careful selection of DNA isolation procedure is paramount for avoiding biases introduced in community profiling. Four E.Z.N.A.™ DNA extraction kits, i.e., Bacterial, Mollusc, Stool, and Tissue DNA Kits, abbreviated as Ba, Mo, St, and Ti, respectively, were initially evaluated with zoea 2 (Z2) larvae of the Pacific white shrimp (Litopenaeus vannamei) by 16S amplicon sequencing on a Illumina MiSeq platform. Further characterization of additional larval samples, specifically nauplii 5 (N5), mysis 1 (M1), and postlarvae 1 (P1), was performed with Ba and St kits to examine the changing microbiota profile during shrimp hatchery period. The results from the Z2 samples showed that DNA yields from the four kits varied significantly (P< 0.05), whereas no significant differences were detected in the α-diversity metrics of the microbiota. By contrast, the St kit, with the lowest DNA yield and quality, successfully recovered DNA from Gram-positive and gut-associated bacterial groups, whereas the Ba kit, which showed maximal microbiota similarity with the Mo kit, manifested the best reproducibility. Notably, significant differences were observed in relative abundances of most dominant taxa when comparing results from the Ba and St kits on Z2, M1, and P1 samples. In addition, the bacterial community identified shifted markedly with larval development regardless of the DNA extraction kits. The DNA recovery biases arising from the larval microbiota could be due to different protocols for cell lysis and purification. Therefore, combined application of different DNA extraction methods may facilitate identification of some biologically important groups owing to their complementary effects. This approach should receive adequate attention for a thorough understanding of the larvae-associated microbiota of the penaeid shrimp.

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