Novel Resistance Regions Carrying TnaphA6, blaVIM-2, and blaPER-1, Embedded in an ISPa40-Derived Transposon from Two Multi-Resistant Pseudomonas aeruginosa Clinical Isolates

Abstract

Antibiotic resistance is an alarming problem throughout the world and carbapenem-resistant Pseudomonas aeruginosa has been cataloged as critical in the World Health Organization list of microorganisms in urgent need for the development of new antimicrobials. In this work, we describe two novel resistance regions responsible for conferring a multidrug resistance phenotype to two clinical isolates of P. aeruginosa (Pa873 and Pa6415) obtained from patients hospitalized in the ICU of University Hospital of Uruguay. Bacterial identification and antibiotic susceptibility tests were performed using MALDI-TOF and the Vitek 2 system, respectively. WGS was performed for both isolates using Oxford Nanopore Technologies and Illumina and processed by means of hybrid assembly. Both isolates were resistant to ceftazidime, cefepime, piperacillin–tazobactam, aztreonam, and imipenem. Strain Pa6415 also showed resistance to ciprofloxacin. Both strains displayed MICs below the susceptibility breakpoint for CAZ-AVI plus 4 mg/L of aztreonam as well as cefiderocol. Both resistance regions are flanked by the left and right inverted repeats of ISPa40 in two small regions spanning 39.3 and 35.6 kb, for Pa6415 and Pa873, respectively. The resistance region of Pa6415 includes TnaphA6, and the new Tn7516 consists of IRi, In899, qacEΔ1-sul1-ISCR1, qnrVC6-ISCR1-blaPER-1-qacEΔ1-sul1, araJ-like, IS481-like tnpA, ISPa17, and IRR. On the other hand, the resistance region of Pa873 includes Tnaph6 and the new Tn7517 (IRi, In899, qacEΔ1-sul1, ISCR1–blaPER-1–qacEΔ1-sul1, araJ-like, IS481-like tnpA, ISPa17, and IRR). It is necessary to monitor the emergence of genetic structures that threaten to invalidate the available therapeutic resources.

Outbreak of Pseudomonas aeruginosa High-Risk Clone ST309 Serotype O11 Featuring blaPER-1 and qnrVC6

“…Similar configurations were identified in the database, differing only in the gene cassettes carried by the class one integrons. These variations included either aminoglycoside, chloramphenicol, or β-lactam resistance genes such as aac(6 ′ )-Ib4, aadA4, catB3, bla OXA-1 , bla IMP-45 , or bla VIM-2 , the latter reported recently by our group in a clinical P. aeruginosa obtained from the same setting [17]. Upstream of the class one integron, most platforms were associated with different Tn3-family elements, typically featuring a resolvase gene and a complete or truncated transposase gene.…”

“…Moreover, the expression of PER-1 may also explain the resistance to ceftolozane/tazobactam and ceftazidime/avibactam [20,21]. Interestingly, although bla PER-1 is most frequently detected in P. aeruginosa isolates from Europe and the Middle East, to our knowledge, it has only been reported from Uruguay and Chile in the Americas [17,22,23].…”

“…Five isolates (HCPa01, HCPa02, HCPa10, HCPa12, and HCPa16) belonging to different pulse type variants were subjected to whole genome sequencing (WGS) using short-read genome sequencing, and one of them (HCPa10) was also subjected to long-read genome sequencing, as previously described [17].…”

“…Previously, P. aeruginosa clinical isolates carrying the carbapenemase-coding gene bla VIM-2 in class one integrons were reported from different settings in Uruguay [16]. Subsequently, its co-occurrence with bla PER-1 was described, associated with novel resistance regions and transposition units [17]. In this study, we describe an outbreak caused by multidrug-resistant P. aeruginosa in an Intensive Care Unit (ICU), and characterize the molecular and microbiological features of the clone involved.…”

Genomic Characterization of IMP-Producing Pseudomonas aeruginosa in Bulgaria Reveals the Emergence of IMP-100, a Novel Plasmid-Mediated Variant Coexisting with a Chromosomal VIM-4

“…Similar structures have been reported in most pMOS94-like plasmids where ISPa17 preceded carbapenemase carrying Tn402 integrons [ 63 ]. Recently it was hypothesized that the ISPa17 transposase might be capable of the mobilization of adjacent Tn402 integrons resulting in distinct transposon elements [ 68 ]. The Tn7700 transposon had 5bp direct repeats (AAAAC) located up to 26bp apart from each IR, which although unexpected might be suggestive of past transposition events.…”