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AIM: We aimed to characterize the phenotype and genotype of 17 carbapenem-resistant Klebsiella pneumoniae (CRKP) strains isolated from 2006 to 2021 in French Polynesia and to identify potential mobile genetic elements (MGEs) associated with carbapenemase genes responsible for their dissemination. BACKGROUND: CRKP strains have emerged as a significant nosocomial pathogen worldwide, representing a global health threat. METHODS: Whole-genome sequencing using Miseq and Nanopore technologies and computational analysis of 17 CRKP strains were performed. RESULTS: All strains were resistant to ertapenem (MIC 0.5→>32 mg/L), two to imipenem (MIC >32 mg/L) and ten to meropenem (MIC 4→>8mg/L). Carbapenem resistance was mediated by class B β-lactamase (five NDM-1 and two NDM-9) and/or mutations in ompk35 (n=4) and ompk36 (n=6) genes encoding two major porin membrane channels (Fig.1). Interestingly, a novel composite transposon Tn7722 (16,246 bp) of the IS6 family, was identified on five plasmids of two incompatibility types IncF, IncR in NDM-1 isolates. This transposon also contained qnrS1, aph(3’)-VI conferring resistance to fluoroquinolones and aminoglycosides. We found other genomes of bacterial species from different continents harboring a similar Tn77220-like element in NCBI database (Fig.2). NDM-9 gene was carried on two identical ∼ 260-kb conjugative plasmids of IncHI2 type in two CRKP strains belonging to two different STs (ST34, ST307) suggesting transfer of NDM-9 by conjugation. CONCLUSION: This study highlights the potential risk of dissemination of NDM producers among CRKP isolates by MGEs in French Polynesia. Continuous genome analysis is crucial for monitoring antimicrobial resistance with real-time surveillance of CRKP.

The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.