Genomic characterization of an extensively drug-resistant high-risk Pseudomonas aeruginosa ST1971 harbouring tmexCD2-toprJ2 from a Vietnamese patient with urinary tract infection
Abstract
Objective: This study characterizes the complete genome of an extensively drug-resistant (XDR) P. aeruginosa high-risk clone, ST1971, identified for the first time in Vietnam.
Methods: A carbapenem- and colistin-resistant P. aeruginosa strain 71 was isolated from an 86-year-old patient with urinary tract infection at a hospital in Hanoi. Antimicrobial susceptibility testing followed CLSI guidelines. Whole-genome sequencing was performed using Illumina NovaSeq and Oxford Nanopore MinION platforms, with hybrid assembly and comprehensive genomic annotation using Bakta, COGclassifier, CARD-RGI, AMRFinderPlus, VFDB, and MobileElementFinder. Comparative genomic analysis was conducted against global ST1971 genomes.
Results: The 6,589,538 bp complete genome of strain 71 contains 19 mobile genetic elements, six prophages, and three CRISPR arrays. Average nucleotide identity (ANI) analysis delineated six distinct ST1971 clusters, while core-genome single-nucleotide polymorphism (SNP) analysis identified 34-57 SNP differences between strain 71 and ST1971 isolates originating from China. Strain 71 exhibited an XDR phenotype, with resistance to all tested antibiotics, including imipenem (16 mg/L), meropenem (32 mg/L), colistin (32 mg/L), levofloxacin (>128 mg/L) and tigecycline (16 mg/L). The genome carries 18 antimicrobial resistance genes including blaPDC-142, blaPME-1, and blaOXA-395 (carbapenem resistance), and colistin-associated mutations in cprS, pmrB, parR and parS gene. A…
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