Genomic insights into carbapenemase-producing Pseudomonas aeruginosa from Tunisia

International audience BackgroundCarbapenem-resistant Pseudomonas aeruginosa (CRPa) is considered as a priority pathogen according to WHO. In North Africa, molecular and genomic data on CRPa remain scarce, particularly regarding emerging high-risk clones that might impair lead to treatment failures due to their intrinsic and acquired resistance arsenal.MethodsA retrospective study was conducted at the University Hospital of Sahloul (Sousse, Tunisia) from 2019 to 2024. Carbapenemase production among CRPa isolates was screened using Carba NP and NG-Test Carba5 assays. Short and long read whole-genome sequencing (Illumina and Oxford Nanopore) were performed to determine sequence types, resistome, virulome, and genetic contexts of the carbapenemase genes. Phylogenetic SNP-based analyzes were performed usingPPanGGolin on the Tunisian genomes and on relevant genomes from the NCBI database.ResultsAmong 1006 P. aeruginosa clinical isolates, 108 (10.7%) were carbapenem-resistant and ten (1%) produced a carbapenemase: nine VIM-2 and one NDM-1. These enzymes were distributed across multiple sequence types (ST235, ST773, ST244, ST856, ST298), indicating polyclonal hospital dissemination. The blaVIM-2 gene was embedded within class 1 integrons (In1183- and In2142-like), while blaNDM-1 was located on a 117-kb chromosomal integrative conjugative element (ICE) identical to those circulating in Europe, supporting intercontinental spread of the ST773 high-risk clone. All isolates displayed multidrug-resistant phenotypes, with colistin remaining the only consistently active and available antibiotic in Tunisia. Genomic analysis revealed additional resistance mechanisms, including OprD disruption, AmpC deregulation, efflux pump mutations, and quinolone resistance mutations (gyrA, parC). One isolate was identified as P. paraeruginosa, lacking type III secretion system effectors but harboring the ExlA/ExlB cytotoxic system.ConclusionsThis study reports the first blaNDM-1-producing P. aeruginosa and blaVIM-2-producing P. paraeruginosa in North Africa. The findings highlight the emergence in Tunisia of globally disseminated high-risk clones such as the NDM-1-positive ST773, and underscore the urgent need for genomic surveillance and strengthened infection control in Tunisian hospital settings