A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia

Rebecca Weiser; Zhong Ling Yap; Ashley Otter; Brian V. Jones; Jonathan Salvage; Julian Parkhill; Eshwar Mahenthiralingam

doi:10.3390/v12060601

A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia

Viruses ◽

10.3390/v12060601 ◽

2020 ◽

Vol 12 (6) ◽

pp. 601 ◽

Cited By ~ 1

Author(s):

Rebecca Weiser ◽

Zhong Ling Yap ◽

Ashley Otter ◽

Brian V. Jones ◽

Jonathan Salvage ◽

...

Keyword(s):

Genetic Material ◽

Lytic Activity ◽

Phylogenomic Analysis ◽

Opportunistic Pathogens ◽

Burkholderia Species ◽

Burkholderia Vietnamiensis ◽

Strain Collection ◽

Search Tool ◽

Genomic Characterization

Burkholderia species have environmental, industrial and medical significance, and are important opportunistic pathogens in individuals with cystic fibrosis (CF). Using a combination of existing and newly determined genome sequences, this study investigated prophage carriage across the species B. vietnamiensis, and also isolated spontaneously inducible prophages from a reference strain, G4. Eighty-one B. vietnamiensis genomes were bioinformatically screened for prophages using PHASTER (Phage Search Tool Enhanced Release) and prophage regions were found to comprise up to 3.4% of total genetic material. Overall, 115 intact prophages were identified and there was evidence of polylysogeny in 32 strains. A novel, inducible Mu-like phage (vB_BvM-G4P1) was isolated from B. vietnamiensis G4 that had lytic activity against strains of five Burkholderia species prevalent in CF infections, including the Boston epidemic B. dolosa strain SLC6. The cognate prophage to vB_BvM-G4P1 was identified in the lysogen genome and was almost identical (>93.5% tblastx identity) to prophages found in 13 other B. vietnamiensis strains (17% of the strain collection). Phylogenomic analysis determined that the G4P1-like prophages were widely distributed across the population structure of B. vietnamiensis. This study highlights how genomic characterization of Burkholderia prophages can lead to the discovery of novel bacteriophages with potential therapeutic or biotechnological applications.

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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

FEMS Microbiology Letters ◽

10.1093/femsle/fnz211 ◽

2019 ◽

Vol 366 (17) ◽

Cited By ~ 2

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

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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Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

Foods ◽

10.3390/foods10112637 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2637

Author(s):

Jolien D’aes ◽

Marie-Alice Fraiture ◽

Bert Bogaerts ◽

Sigrid C. J. De Keersmaecker ◽

Nancy H. C. Roosens ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetically Modified ◽

Added Value ◽

Phylogenomic Analysis ◽

Whole Genome ◽

Antimicrobial Resistance Genes ◽

Long Read ◽

Genomic Characterization

Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.

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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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Genomic Characterization of an Emerging Enterobacteriaceae Species for the First Case of Human Infection in Cooperation with a Typical Pathogen

10.21203/rs.2.22057/v1 ◽

2020 ◽

Author(s):

Zhao Zhang ◽

Daixi Li ◽

xing shi ◽

Yao Zhai ◽

Yatao Guo ◽

...

Keyword(s):

Continuous Monitoring ◽

Novel Species ◽

Human Infection ◽

Klebsiella Pneumonia ◽

Opportunistic Pathogens ◽

Antibiotic Resistant ◽

First Case ◽

Infection Treatment ◽

Genomic Characterization

Abstract Opportunistic pathogens are important for clinical practice as they often cause antibiotic resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a novel species of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient of biliary tract infection. The isolate grows very slowly but confers strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumonia. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis, and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains respectively isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. As its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both wild environment and animal host, tens of genetic mobile elements, and a plasmid bearing blaCTX-M-3 gene, indicating its ability to disseminate antimicrobial resistant genes from wild to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18 which could serve as targets for novel antimicrobial strategies. These findings imply that AF18 and its species are not only infection-relevant but also potential disseminators in transferring antibiotic determinants, which highlights the need for continuous monitoring for this novel species and efforts to develop controlling strategies.

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