Genomic characterization of an extensively drug-resistant high-risk Pseudomonas aeruginosa ST1971 harbouring tmexCD2–toprJ2 from a Vietnamese patient with urinary tract infection

• The first complete genome sequence of extensively drug-resistant Pseudomonas aeruginosa , a China-unique high-risk ST1971 clone, now identified in Hanoi, Vietnam. • P. aeruginosa carried multiple carbapenem-resistance associated genes and colistin-resistance associated mutations. • tmexCD2–toprJ2 efflux pump cluster was identified between two prophage regions. 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. 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. 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 bla PDC-142 , bla PME-1 , and bla OXA-395 (carbapenem resistance), and colistin-associated mutations in cprS, pmrB, parR and parS gene. A tmexCD2 - toprJ2 efflux cluster was located between two prophage regions, suggesting that bacteriophages may serve as potential vehicles for antibiotic resistance gene dissemination. This study provides insight into the genomic characteristics of a XDR Pseudomonas aeruginosa ST1971 isolate in Vietnam, underscoring the need for enhanced surveillance of this genotype across clinical and geographical settings.