Phenotypic and molecular characterisations of carbapenem-resistant strains isolated in Madagascar.

Background: The present study aimed to perform a deep phenotypic and genotypic analysis of 15 clinical carbapenem-resistant (CRAb) strains isolated in Madagascar between 2008 and 2016 from diverse sources.

Methods: CRAb isolates collected from the Clinical Biology Centre of the Institut Pasteur of Madagascar, from the neonatal unit of Antananarivo military hospital, and from intensive care units of Mahajanga Androva and Antananarivo Joseph Ravoahangy Andrianavalona (HJRA) hospitals were subjected to susceptibility testing. Whole-genome sequencing allowed us to assess the presence of antibiotic-resistance determinants, insertion sequences, integrons, genomic islands and potential virulence factors in all strains. The structure of the porin gene and deduced protein (CarO) were also CRAb isolates.

Results: All isolates were found to be multidrug-resistant strains. Antibiotic-resistance genes against six classes of antimicrobial agents were described. The four carbapenem-resistance genes: , , , and genes were detected in 100, 53.3, 13.3, and 6.6% of the isolates, respectively. Additionally, an IS located upstream of and genes was observed in 53.3 and 66.7% of isolates, respectively. Further, Tn and Tn were found associated to the IS- structure. An 8051-bp mobilizable plasmid harbouring the gene was isolated in two strains. In addition, 46.7% of isolates were positive for class 1 integrons. Overall, five sequences types (STs), with predominantly ST2, were detected. Several virulence genes were found in the CRAb isolates, among which .

Conclusions: This study revealed the presence of high-level carbapenem resistance in with the first description of OXA-24 and OXA-58 carbapenemases in Madagascar. This highlights the importance of better monitoring and controlling CRAb in Madagascan hospitals to avoid their spread.