Data on whole-genome sequencing of extended-spectrum beta-lactamases producing Enterobacteriaceae isolates from Malaysia

Gan, Han Ming; Eng, Wilhelm Wei Han; Dhanoa, Amreeta

doi:10.1016/j.dib.2019.104257

Cited by 3 publications

(2 citation statements)

References 12 publications

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“…In this study, the ESBL-producing MDR Enterobacteriaceae isolates that were isolated from the retail raw milk have been increasingly reported to cause infections in healthcare settings (Wilson and T€ or€ ok 2018;Gan et al 2019;Jesumirhewe et al 2020). Moreover, the co-existence of ESBL genes on mobile genetic elements, such as plasmids, transposons and integrons, leads to the selection and continuous dissemination of MDR bacteria (Partridge et al 2018).…”

Section: Discussionmentioning

confidence: 87%

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Whole‐genome sequencing of extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacteriaceae from retail raw milk

Aslantaş¹,

Yılmaz²,

Büyükaltay

et al. 2021

Int J of Dairy Tech

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The contaminated products of food-producing animals have been proposed to lead the transmission of resistant bacteria to consumers. Extended-spectrum b-lactamase (ESBL)-producing Enterobacteriaceae, which were isolated from raw milk samples, were characterised using whole-genome sequencing in this study. Three confirmed ESBL and one plasmid-mediated AmpC b-lactamase (pAmpC)-producing isolate were obtained. All of the ESBL-producing isolates showed a multidrugresistant (MDR) phenotype, but the pAmpC-producing isolate was only resistant to b-lactams. This study showed that raw milk can contain MDR bacteria that have several resistance determinants and highlighted the necessity of efficiently and routinely screening the products of food-producing animals.

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Section: Discussionmentioning

confidence: 87%

“…In this study, the ESBL‐producing MDR Enterobacteriaceae isolates that were isolated from the retail raw milk have been increasingly reported to cause infections in healthcare settings (Wilson and Török 2018; Gan et al . 2019; Jesumirhewe et al . 2020).…”

Section: Discussionmentioning

confidence: 99%

Whole‐genome sequencing of extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacteriaceae from retail raw milk

Aslantaş¹,

Yılmaz²,

Büyükaltay

et al. 2021

Int J of Dairy Tech

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Nanopore long reads enable the first complete genome assembly of a MalaysianVibrio parahaemolyticusisolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease

Gan

Austin

2019

Preprint

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BackgroundVibrio parahaemolyticus MVP1 was isolated from a Malaysian aquaculture farm affected with shrimp acute hepatopancreatic necrosis disease (AHPND). Its genome was previously sequenced on the Illumina MiSeq platform and assembled de novo producing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood.MethodsThe genome of Vibrio parahaemolyticus MVP1 was sequenced on the Nanopore MinION device to obtain long reads that can span longer repeats and improve genome contiguity. De novo genome assembly was subsequently performed using long-read only assembler (Flye) followed by genome polishing as well as hybrid assembler (Unicycler).ResultsLong-read only assembly produced three complete circular MVP1 contigs consisting of chromosome 1, chromosome 2 and the pVa plasmid that pirABvp binary toxin genes. Polishing of the long read assembly with Illumina short reads was necessary to remove indel errors. The complete assembly of the pVa plasmid could not be achieved using Illumina reads due to the presence of identical repetitive elements flanking the binary toxin genes leading to multiple contigs. Whereas these regions were fully spanned by the Nanopore long reads resulting in a single contig. In addition, alignment of Illumina reads to the complete genome assembly indicated there is sequencing bias as read depth was lowest in low-GC genomic regions. Comparative genomic analysis revealed the presence of a gene cluster coding for additional insecticidal toxins in chromosome 2 of MVP1 that may further contribute to host pathogenesis pending functional validation. Scanning of all publicly available V. parahaemolyticus genomes revealed the presence of a single AinS-family quorum-sensing system in this species that can be targeted for future microbial management.ConclusionsWe generated the first chromosome-scale genome assembly of a Malaysian pirABVp-bearing V. parahaemolyticus isolate. Structural variations identified from comparative genomic analysis provide new insights into the genomic features of V. parahaemolyticus MVP1 that may be associated with host colonization and pathogenicity.

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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

Gan

Austin

2019

F1000Res

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Background: The genome of Vibrio parahaemolyticus MVP1, isolated from a Malaysian aquaculture farm with shrimp acute hepatopancreatic necrosis disease (AHPND), was previously sequenced using Illumina MiSeq and assembled de novo, producing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood. Methods: The genome of MVP1 was sequenced on Nanopore MinION to obtain long reads to improve genome contiguity. De novo genome assembly was performed using long-read only assembler followed by genome polishing and hybrid assembler. Results: Long-read assembly produced three complete circular MVP1 contigs: chromosome 1, chromosome 2 and the pVa plasmid encoding pirABvp binary toxin genes. Polishing of the long-read assembly with Illumina short reads was necessary to remove indel errors. Complete assembly of the pVa plasmid could not be achieved using Illumina reads due to identical repetitive elements flanking the binary toxin genes leading to multiple contigs. These regions were fully spanned by the Nanopore long-reads resulting in a single contig. Alignment of Illumina reads to the complete genome assembly indicated there is sequencing bias as read depth was lowest in low-GC genomic regions. Comparative genomic analysis revealed a gene cluster coding for additional insecticidal toxins in chromosome 2 of MVP1 that may further contribute to host pathogenesis pending functional validation. Scanning of publicly available V. parahaemolyticus genomes revealed the presence of a single AinS-family quorum-sensing system that can be targeted for future microbial management. Conclusions: We generated the first chromosome-scale genome assembly of a Malaysian pirABVp-bearing V. parahaemolyticus isolate. Structural variations identified from comparative genomic analysis provide new insights into the genomic features of V. parahaemolyticus MVP1 that may be associated with host colonization and pathogenicity.

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Data on whole-genome sequencing of extended-spectrum beta-lactamases producing Enterobacteriaceae isolates from Malaysia

Cited by 3 publications

References 12 publications

Whole‐genome sequencing of extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacteriaceae from retail raw milk

Whole‐genome sequencing of extended‐spectrum β‐lactamase (ESBL)‐producing Enterobacteriaceae from retail raw milk

Nanopore long reads enable the first complete genome assembly of a MalaysianVibrio parahaemolyticusisolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease

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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