A megaplasmid family responsible for dissemination of multidrug resistance inPseudomonas

Abstract

Multidrug resistance (MDR) represents a global threat to health. Although plasmids can play an important role in the dissemination of MDR, they have not been commonly linked to the emergence of antimicrobial resistance in the pathogen Pseudomonas aeruginosa . We used whole genome sequencing to characterize a collection of P. aeruginosa clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicated that 1) these large plasmids comprise a family present in different members of the Pseudomonas genus and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the pangenome of the megaplasmid family is highly flexible and diverse, comprising a substantial core genome (average of 48% of plasmid genes), but with individual members carrying large numbers of unique genes. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.

Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes

“…Recent analysis of P. aeruginosa isolates recovered from patients at a hospital in Thailand also showed that the same closely related family of megaplasmids encode multidrug resistance elements, are highly recombinogenic and mediate extensive gene transfer, and have likely been carrying resistance genes dating back to the late 1970s [67].…”

Current Knowledge and Future Directions in Developing Strategies to Combat Pseudomonas aeruginosa Infection

“…These recent advancements have also facilitated the examination of Pa megaplasmids and pangenomes [4][5][6][7][8][9].…”

Epidemic Territorial Spread of IncP-2-Type VIM-2 Carbapenemase-Encoding Megaplasmids in Nosocomial Pseudomonas aeruginosa Populations

“…S3). This indicated that pJB37 and pPUVs shared also some accessory genome regions (addressed below), the variety of which, usually larger mosaic assemblies of genes and mobile elements, were identified in pBT2436-like molecules by Cazares et al and others (16,20,23,27). Interestingly, pJB37 was the only "non-Polish" pBT2436-like plasmid with the bla VIM-2 MBL gene (15); however, dissimilar integrons (In58 versus In461) and their mobile context (described below) proved separate recent evolution of these closely related molecules, comprising independent bla VIM-2 acquisitions.…”

“…They matched 27 sequenced IncP-2-type plasmids (as of 24 June 2020), of which 22 with the highest BLAST score were chosen for the analysis (Table S3). These megaplasmids (;370 to 580 kb) had been identified in clinical, environmental, or industrial pseudomonal strains identified worldwide, and conferred resistance/tolerance to various stress factors, like antibiotics, heavy metals, or organic solvents (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). Fifteen of these were analyzed recently by Cazares et al as "pBT2436-like megaplasmids" (16).…”

“…These megaplasmids (;370 to 580 kb) had been identified in clinical, environmental, or industrial pseudomonal strains identified worldwide, and conferred resistance/tolerance to various stress factors, like antibiotics, heavy metals, or organic solvents (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27). Fifteen of these were analyzed recently by Cazares et al as "pBT2436-like megaplasmids" (16). A noncontinuous core genome was discerned in these (;200 kb; 42 to 57% of a molecule), with genes/operons or regions providing plasmid backbone-associated functions ( 16), all of which were found also in pPUVs (described below).…”