Dataset Information

Draft Genome Sequence of a bla NDM-1- and bla PME-1-Harboring Pseudomonas aeruginosa Clinical Isolate from Pakistan.

ABSTRACT: We performed Illumina whole-genome sequencing on a carbapenem-resistant Pseudomonas aeruginosa strain isolated from a cystic fibrosis patient with chronic airway colonization. The draft genome comprises 6,770,411?bp, including the carbapenemase bla NDM-1 and the extended-spectrum beta-lactamase bla PME-1 This isolate harbors 3 prophages, 14 antibiotic resistance genes, and 257 virulence genes.

SUBMITTER: Irum S

PROVIDER: S-EPMC6486239 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Draft Genome Sequence of a bla NDM-1- and bla PME-1-Harboring Pseudomonas aeruginosa Clinical Isolate from Pakistan.

Irum Sidra S Potter Robert F RF Kamran Rubina R Mustafa Zeeshan Z Wallace Meghan A MA Burnham C A CA Dantas Gautam G Andleeb Saadia S

Microbiology resource announcements 20190425 17

We performed Illumina whole-genome sequencing on a carbapenem-resistant Pseudomonas aeruginosa strain isolated from a cystic fibrosis patient with chronic airway colonization. The draft genome comprises 6,770,411 bp, including the carbapenemase bla NDM-1 and the extended-spectrum beta-lactamase bla PME-1 This isolate harbors 3 prophages, 14 antibiotic resistance genes, and 257 virulence genes. ...[more]

PMID: 31023810

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Project description:Pseudomonas aeruginosa ST308 clone has been reported to carry carbapenemase genes such as blaIMP and blaVIM but has been rarely associated with blaNDM-1. A total of 199 P. aeruginosa ST308 clinical and environmental isolates obtained between April 2019 and November 2020 from a tertiary-care hospital in Singapore were characterized using whole-genome sequencing. In addition, 71 blaNDM-1-positive ST308 whole-genome sequences from two other local tertiary-care hospitals in Singapore and 83 global blaNDM-1-negative ST308 whole-genome sequences in public databases were included to assess phylogenetic relationships and perform genome analyses. Phylogenetic analysis and divergent time estimation revealed that blaNDM-1-positive P. aeruginosa ST308 was introduced into Singapore in 2005 (95 % highest posterior density: 2001 to 2008). Core genome, resistome, and analyses of all local blaNDM-1-positive ST308 isolates showed chromosomal integration of multiple antibiotic resistance genes (ARGs) [aac(3)-Id, aac(6')-Il, aadA6, aadA11, dfrB5, msr(E), floR, sul2, and qnrVC1], which was absent in global blaNDM-1-negative ST308 sequences. Most ARGs and virulence genes were conserved across isolates originating from the three different local hospitals. Close genetic relatedness of the blaNDM-1-positive ST308 clinical and environmental isolates suggests cocirculation between the hospital environment and human hosts with the hospital environment as a potential reservoir. Core genome single nucleotide polymorphism analyses revealed possible clonal transmission of blaNDM-1-positive ST308 isolates between the three hospitals over 7 years. Bloodstream isolates accounted for six of 95 (6.3%) clinical isolates. This study reports the introduction of a pathogenic blaNDM-1-positive P. aeruginosa ST308 more than a decade ago in Singapore and warrants surveillance for wider dissemination. IMPORTANCE P. aeruginosa is a Gram-negative opportunistic pathogen ubiquitously found in the environment and a major cause of nosocomial infections. While the P. aeruginosa ST308 clone has been known to bear blaIMP and blaVIM among global isolates, reports of blaNDM-1-positive P. aeruginosa ST308 are rare. The local blaNDM-1-positive P. aeruginosa ST308 isolates detected in this study appear to be unique to this region, with evidence of chromosomal acquisition of multiple ARGs compared to global blaNDM-1-negative P. aeruginosa ST308 isolates. Surveillance in Singapore and beyond for dissemination is essential to determine whether existing measures are sufficient to control the spread of this ST308 clone.

Dataset Information

Draft Genome Sequence of a bla NDM-1- and bla PME-1-Harboring Pseudomonas aeruginosa Clinical Isolate from Pakistan.

Publications

Draft Genome Sequence of a <i>bla</i> <sub>NDM-1</sub>- and <i>bla</i> <sub>PME-1</sub>-Harboring Pseudomonas aeruginosa Clinical Isolate from Pakistan.

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