Whole-genome sequencing of NDM-1-producing ST85 Acinetobacter baumannii isolates from Tunisia

Abstract

New Delhi metallo-β-lactamase (NDM)-producing Acinetobacter baumannii have been described in several countries worldwide, and studies have suggested that Acinetobacter spp. could play the role of intermediate progenitor of the blaNDM-1 gene between environmental progenitor and Enterobacteriaceae. In total, 246 carbapenem-resistant A. baumannii isolates from a teaching hospital in Sousse, Tunisia were investigated between 1st June 2013 and 31st December 2015 to detect metallo-ß-lactamase (MBL) production. Polymerase chain reaction (PCR), antibiotic susceptibility testing, and genetic and whole-genome sequencing tools were used to study the underlying carbapenem resistance mechanisms. PCR screening of the 246 carbapenem-resistant A. baumannii isolates revealed that 242 of 246 isolates harboured carbapenemase genes (seven of 246 positive for blaNDM-1, four of 246 positive for blaNDM-1 and blaOXA-23, 231 positive for blaOXA-23). Conjugation and electroporation experiments suggested that the blaNDM-1 gene is likely to be chromosomally located. All the NDM-1-producing A. baumannii isolates were clonally related, and belonged to ST85 according to the Pasteur Institute's multi-locus sequence typing scheme. Analysis of the immediate genetic environment of the blaNDM-1 gene revealed that the gene was located within a truncated isoform of Tn125 transposon (ΔTn125). The blaOXA-23 gene was located within transposon Tn2008. This study showed the dissemination of a single clone of NDM-1-producing A. baumannii in a Tunisian hospital. Countries in north Africa may constitute a significant reservoir for NDM-1-producing A. baumannii. The spread of the blaNDM-1 gene in A. baumannii was linked to clonal spread in this study.