Genomic diversity and molecular epidemiology of a multidrug resistantPseudomonas aeruginosaDMC30b isolated from hospitalized burn patient in Bangladesh

Abstract

ObjectivesPseudomonas aeruginosa is a key opportunistic pathogen causing a wide range of community- and hospital-acquired infections in immunocompromised or catheterized patients. Here, we report the complete genome sequence of a multidrug resistant (MDR) P. aeruginosa DMC30b in order to elucidate the genetic diversity, molecular epidemiology, and underlying mechanisms for antimicrobial resistance and virulence.MethodsP. aeruginosa DMC30b was isolated from septic wound swab of a severe burn patient. Whole-genome sequencing (WGS) was performed under Ion Torrent platform. The genome was annotated using the SPAdes v. 3.12.01 in an integrated Genome Analysis Platform (IonGAP) for Ion Torrent sequence data. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). In-silico predictions of antimicrobial resistance genes (ARGs), virulence factor genes (VFGs) and metabolic functional potentials were performed using different curated bioinformatics tools.ResultsP. aeruginosa DMC30b was classified as MDR and belongs to sequence type 244 (ST244). The complete genome size is 6,994,756 bp with a coverage of 76.76x, G+C content of 65.7% and a BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 100. The genome of P. aeruginosa DMC30b harboured two plasmids (e,g., IncP-6 plasmid p10265-KPC; 78,007 bp and ColRNAI_pkOIISD1; 9,359 bp), 35 resistomes (ARGs) conferring resistance to 18 different antibiotics (including four beta-lactam classes), and 214 VFGs. It was identified as the 167th ST244 strain among ∼ 5,800 whole-genome sequences of P. aeruginosa available in the NCBI database.ConclusionP. aeruginosa DMC30b belongs to ST244 and was identified as the 167th such isolate to be submitted to NCBI, and the first complete ST244 genome from Bangladesh. The complete genome data with high genetic diversity and underlying mechanisms for antimicrobial resistance and virulence of P. aeruginosa DMC30b (ST244) will aid in understanding the evolution and phylogeny of such high-risk clones and provide a solid basis for further research on MDR or extensively drug resistant strains.

Informing plasmid compatibility with bacterial hosts using protein-protein interaction data

“…This identified P. aeruginosa, A. aromaticum EbN1 and 21 other common animal and plant pathogens as more likely to have PPIs with ³1 of these blaOXA-48-positive plasmids, particularly with the pKP112 and pOXA-48 isoforms, suggesting those plasmids could become common in these species. Consistent with these predictions, blaOXA-48-positive human clinical isolates from Bangladesh [88] and Sudan [89] have been found in P. aeruginosa, even though previous in vitro experiments suggested incompatibility [34]. This is concerning because blaOXA-48 is the most common AMR gene in CPE and is prevalent in Pseudomonas based on carbapenemase gene rates in England from 2020 -22 [15].…”