Antimicrobial Resistance and Genomic Characterization of Six New Sequence Types in Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates from Pakistan

Abstract

Pseudomonas aeruginosa (P. aeruginosa) is a major bacterial pathogen associated with a variety of infections with high mortality rates. Most of the clinical P. aeruginosa isolates belong to a limited number of genetic subgroups characterized by multiple housekeeping genes’ sequences (usually 5–7) through the Multi-Locus Sequence Typing (MLST) scheme. The emergence and dissemination of novel multidrug-resistant (MDR) sequence types (ST) in P. aeruginosa pose serious clinical concerns. We performed whole-genome sequencing on a cohort (n = 160) of MDR P. aeruginosa isolates collected from a tertiary care hospital lab in Pakistan and found six isolates belonging to six unique MLST allelic profiles. The genomes were submitted to the PubMLST database and new ST numbers (ST3493, ST3494, ST3472, ST3489, ST3491, and ST3492) were assigned to the respective allele combinations. MLST and core-genome-based phylogenetic analysis confirmed the divergence of these isolates and positioned them in separate branches. Analysis of the resistome of the new STs isolates revealed the presence of genes blaOXA-50, blaPAO, blaPDC, blaVIM-2, aph(3′)-IIb, aac(6′)-II, aac(3)-Id, fosA, catB7, dfrB2, crpP, merP and a number of missense and frame-shift mutations in chromosomal genes conferring resistance to various antipseudomonal antibiotics. The exoS, exoT, pvdE, rhlI, rhlR, lasA, lasB, lasI, and lasR genes were the most prevalent virulence-related genes among the new ST isolates. The different genotypic features revealed the adaptation of these new clones to a variety of infections by various mutations in genes affecting antimicrobial resistance, quorum sensing and biofilm formation. Close monitoring of these antibiotic-resistant pathogens and surveillance mechanisms needs to be adopted to reduce their spread to the healthcare facilities of Pakistan. We believe that these strains can be used as reference strains for future comparative analysis of isolates belonging to the same STs.

Genomic Surveillance of Clinical Pseudomonas aeruginosa Isolates Reveals an Additive Effect of Carbapenemase Production on Carbapenem Resistance

“…Most isolates came from medical intensive care units (40/142, 28%), followed by outpatient clinics (33/142, 23%), emergency rooms (25/142, 18%), and medical wards (24/142, 17%) (Table S1). A subset of 6 isolates has been previously analyzed for genomic content ( 17 ). However, for internal consistency, the work described here results from de novo analyses and phenotyping done with the full sample set.…”

“…Seven new STs were discovered in this cohort (ST3472, ST3489, ST3491, ST3492, ST3494, ST3656, and ST3657) whose allelic profiles have been uploaded to the PubMLST database ( 22 ). A separate investigation reported the genomic context surrounding those new STs ( 17 ).…”

“…Assemblies and sequencing reads associated with this report are available from NCBI under BioProject accession code PRJNA800087 . The 6 genomes that were previously reported resulted from an independent de novo assembly and are, therefore, available as independent accession IDs ( 17 ).…”

Molecular Analysis of Carbapenem and Aminoglycoside Resistance Genes in Carbapenem-Resistant Pseudomonas aeruginosa Clinical Strains: A Challenge for Tertiary Care Hospitals

“…On the other hand, the detection of bla KPC among CRPA was reported infrequently in Pakistan [94]; however, an increasing trend in the global dissemination of bla KPC -harboring P. aeruginosa has been observed [22,28,[102][103][104][105][106][107][108]. To the best of our knowledge, the aminoglycoside resistance genes among carbapenemase-producing CRPA were not detected previously from Pakistan; however, one report described the presence of aph(3 ′ )-IIb and aac(6 ′ )-II among P. aeruginosa isolates [109]. It has been reported that AMEencoding gene aac(6 ′ )-II is significantly associated with GEN resistance in P. aeruginosa [110].…”

“…We identified 13 different STs coharboring carbapenem and aminoglycoside resistance genes, including ST235, ST277, ST234, ST170, ST381, ST175, ST1455, ST1963, ST313, ST207, ST664, ST357 and ST348. Previous studies from Pakistan described ST3493, ST3494, ST3472, ST3489, ST3491, ST3492 and ST664 among P. aeruginosa isolates [93,109]. However, global data showed a diverse range of STs [40,102,125,126].…”