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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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Phylogeny and compatibility: plasmid classification in the genomics era

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Insights from 20 years of bacterial genome sequencing

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Infection control in the new age of genomic epidemiology

inferredcites →https://doi.org/10.1016/j.fsi.2015.11.008openalex-snapshot

Pathogenesis of acute hepatopancreatic necrosis disease (AHPND) in shrimp

inferredcites →https://doi.org/10.1016/j.jgar.2016.03.001openalex-snapshot

Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients

inferredcites →https://doi.org/10.1016/j.jip.2018.02.005openalex-snapshot

A Vibrio owensii strain as the causative agent of AHPND in cultured shrimp, Litopenaeus vannamei

inferredcites →https://doi.org/10.1016/j.margen.2015.05.010openalex-snapshot

Draft genome sequence of Strain ATCC 17802T, the type strain of Vibrio parahaemolyticus

inferredcites →https://doi.org/10.1016/j.micpath.2017.10.028openalex-snapshot

The spread of Vibrio parahaemolyticus in tissues of the Pacific white shrimp Litopenaeus vannamei analyzed by PCR and histopathology

inferredcites →https://doi.org/10.1038/s41598-017-09923-6openalex-snapshot

Microbiome Dynamics in a Shrimp Grow-out Pond with Possible Outbreak of Acute Hepatopancreatic Necrosis Disease

inferredcites →https://doi.org/10.1038/s41598-017-11805-wopenalex-snapshot

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions

inferredcites →https://doi.org/10.1038/srep14449openalex-snapshot

A novel adhesive factor contributing to the virulence of Vibrio parahaemolyticus

inferredcites →https://doi.org/10.1038/srep42177openalex-snapshot

Shrimp AHPND-causing plasmids encoding the PirAB toxins as mediated by pirAB-Tn903 are prevalent in various Vibrio species

inferredcites →https://doi.org/10.1073/pnas.1517100112openalex-snapshot

Correction for Lee et al., The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin

inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btq683openalex-snapshot

Scaffolding pre-assembled contigs using SSPACE

inferredcites →https://doi.org/10.1093/bioinformatics/btr039openalex-snapshot

Easyfig: a genome comparison visualizer

inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot

QUAST: quality assessment tool for genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btv421openalex-snapshot

Roary: rapid large-scale prokaryote pan genome analysis

inferredcites →https://doi.org/10.1093/bioinformatics/btv681openalex-snapshot

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

inferredcites →https://doi.org/10.1093/mollus/66.4.573openalex-snapshot

An improved method for DNA isolation from mucopolysaccharide-rich molluscan tissues

inferredcites →https://doi.org/10.1093/nar/gkx1321openalex-snapshot

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

inferredcites →https://doi.org/10.1099/00221287-136-4-717openalex-snapshot

Transposon-induced non-motile mutants of Vibrio cholerae

inferredcites →https://doi.org/10.1099/mic.0.059550-0openalex-snapshot

Cloning and functional analysis of the genes coding for 4-aminobenzenesulfonate 3,4-dioxygenase from Hydrogenophaga sp. PBC

inferredcites →https://doi.org/10.1111/1751-7915.12877openalex-snapshot

The aquaculture microbiome at the centre of business creation

inferredcites →https://doi.org/10.1111/cmi.12849openalex-snapshot

The Rho signalling pathway mediates the pathogenicity of AHPND‐causing V. parahaemolyticus in shrimp

inferredcites →https://doi.org/10.1111/j.1365-2958.2010.07445.xopenalex-snapshot

Surface sensing in Vibrio parahaemolyticus triggers a programme of gene expression that promotes colonization and virulence

inferredcites →https://doi.org/10.1111/j.1574-6968.2011.02245.xopenalex-snapshot

Identification of genes involved in the 4-aminobenzenesulfonate degradation pathway of Hydrogenophaga sp. PBC via transposon mutagenesis

inferredcites →https://doi.org/10.1111/jam.13256openalex-snapshot

Virulence of acute hepatopancreatic necrosis disease PirAB-like relies on secreted proteins not on gene copy number

inferredcites →https://doi.org/10.1128/aem.00680-17openalex-snapshot

A Natural Vibrio parahaemolyticus Δ pirA Vp pirB Vp+ Mutant Kills Shrimp but Produces neither Pir Vp Toxins nor Acute Hepatopancreatic Necrosis Disease Lesions

inferredcites →https://doi.org/10.1128/aem.00737-17openalex-snapshot

Acute Hepatopancreatic Necrosis Disease-Causing Vibrio parahaemolyticus Strains Maintain an Antibacterial Type VI Secretion System with Versatile Effector Repertoires

inferredcites →https://doi.org/10.1128/aem.02789-07openalex-snapshot

Assessing Genetic Heterogeneity within Bacterial Species Isolated from Gastrointestinal and Environmental Samples: How Many Isolates Does It Take?

inferredcites →https://doi.org/10.1128/genomea.00023-16openalex-snapshot

First High-Quality Draft Genome Sequence of Pasteurella multocida Sequence Type 128 Isolated from Infected Bone

inferredcites →https://doi.org/10.1128/genomea.00132-12openalex-snapshot

Draft Genome Sequence of Vibrio parahaemolyticus SNUVpS-1 Isolated from Korean Seafood

inferredcites →https://doi.org/10.1128/genomea.00221-14openalex-snapshot

Draft Genome Sequences of Six Strains of Vibrio parahaemolyticus Isolated from Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease Shrimp in Thailand

inferredcites →https://doi.org/10.1128/genomea.00302-17openalex-snapshot

New Sequence Types of Vibrio parahaemolyticus Isolated from a Malaysian Aquaculture Pond, as Revealed by Whole-Genome Sequencing

inferredcites →https://doi.org/10.1128/genomea.00731-15openalex-snapshot

Draft Genome Sequence of Vibrio parahaemolyticus VH3, Isolated from an Aquaculture Environment in Greece

inferredcites →https://doi.org/10.1128/genomea.00768-17openalex-snapshot

Whole-Genome Sequences of Two Carbapenem-Resistant Klebsiella quasipneumoniae Strains Isolated from a Tertiary Hospital in Johor, Malaysia

inferredcites →https://doi.org/10.1128/genomea.00800-14openalex-snapshot

High-Quality Draft Genomes of Two Vibrio parahaemolyticus Strains Aid in Understanding Acute Hepatopancreatic Necrosis Disease of Cultured Shrimps in Mexico

inferredcites →https://doi.org/10.1128/genomea.00978-15openalex-snapshot

Draft Genome Sequence of Non-Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease Strain KC13.17.5, Isolated from Diseased Shrimp in Vietnam

inferredcites →https://doi.org/10.1128/jb.01416-12openalex-snapshot

Genome Sequence and Comparative Pathogenomics Analysis of a Salmonella enterica Serovar Typhi Strain Associated with a Typhoid Carrier in Malaysia

inferredcites →https://doi.org/10.1128/jb.01608-12openalex-snapshot

Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium

inferredcites →https://doi.org/10.1128/jb.01832-12openalex-snapshot

Genome Sequence and Comparative Genomics Analysis of a Vibrio cholerae O1 Strain Isolated from a Cholera Patient in Malaysia

inferredcites →https://doi.org/10.1128/jb.153.1.408-415.1983openalex-snapshot

Characterization of the mgl operon of Escherichia coli by transposon mutagenesis and molecular cloning

inferredcites →https://doi.org/10.1128/jcm.03617-13openalex-snapshot

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

inferredcites →https://doi.org/10.1128/jcm.06094-11openalex-snapshot

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

inferredcites →https://doi.org/10.1128/mra.00829-18openalex-snapshot

Draft Genome Sequence of a Vibrio parahaemolyticus Strain, KS17.S5-1, with Multiple Antibiotic Resistance Genes, Which Causes Acute Hepatopancreatic Necrosis Disease in Penaeus monodon in the West Coast of Peninsular Malaysia

inferredcites →https://doi.org/10.1128/mra.01053-18openalex-snapshot

Draft Genome Sequence of the Shrimp Pathogen Vibrio parahaemolyticus ST17.P5-S1, Isolated in Peninsular Malaysia

inferredcites →https://doi.org/10.1139/cjm-44-4-351openalex-snapshot

Bacterial fitness and plasmid loss: the importance of culture conditions and plasmid size

inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot

BLAST+: architecture and applications

inferredcites →https://doi.org/10.1186/1471-2164-12-402openalex-snapshot

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

inferredcites →https://doi.org/10.1186/gb-2012-13-6-r56openalex-snapshot

Toward almost closed genomes with GapFiller

inferredcites →https://doi.org/10.1186/s13073-014-0090-6openalex-snapshot

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1371/journal.pone.0131080openalex-snapshot

Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps

inferredcites →https://doi.org/10.1371/journal.pone.0135783openalex-snapshot

Interaction of Vibrio spp. with the Inner Surface of the Digestive Tract of Penaeus monodon

inferredcites →https://doi.org/10.14737/journal.aavs/2015/3.2s.64.72openalex-snapshot

Early Mortality Syndrome (EMS) as new Emerging Threat in Shrimp Industry

inferredcites →https://doi.org/10.3354/dao02621openalex-snapshot

Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp

inferredcites →https://doi.org/10.3354/dao02830openalex-snapshot

Photorhabdus insect-related (Pir) toxin-like genes in a plasmid of Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (AHPND) of shrimp

inferredcites →https://doi.org/10.3389/fmicb.2017.02354openalex-snapshot

Delineating the Origins of Vibrio parahaemolyticus Isolated from Outbreaks of Acute Hepatopancreatic Necrosis Disease in Asia by the Use of Whole Genome Sequencing

inferredcites →https://doi.org/10.7717/peerj.5826openalex-snapshot

Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.12688/f1000research.21570.1openalex-snapshot

Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease

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