High genetic diversity andblaNDM-1prevalence amongAcinetobacter baumanniiin Nigerian hospitals

Abstract

AbstractBackgroundAcinetobacter baumanniicause difficult-to-treat infections mostly among immunocompromised patients. Clinically relevantA. baumanniilineages and their carbapenem resistance mechanisms are sparsely described in Nigeria.ObjectiveThis study aimed to characterise the diversity and genetic mechanisms of carbapenem resistance amongA. baumanniistrains isolated from hospitals in southwestern Nigeria.MethodsWe sequenced the genomes of allA. baumanniiisolates submitted to Nigeria’s antimicrobial resistance surveillance reference laboratory between 2016 – 2020 on an Illumina platform and performedin silicogenomic characterisation. Selected strains were sequenced using the Oxford Nanopore technology to characterise the genetic context of carbapenem resistance genes.ResultsThe 86A. baumanniiisolates were phylogenetically diverse and belonged to 35 distinct sequence types (STs), 16 of which were novel. Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. Majority (n=54) of the isolates were carbapenem-resistant, particularly the IC7 (100%) and IC9 (>91.7%) strains.blaOXA-23(34.9%) andblaNDM-1(27.9%) were the most common carbapenem resistance genes detected. AllblaOXA-23genes were carried on Tn2006or Tn2006-like transposons. Our findings suggest that the mobilisation of a 10kb Tn125composite transposon is the primary means ofblaNDM-1dissemination.ConclusionOur findings highlight an increase inblaNDM-1prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverseA. baumanniilineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings.ImportanceAcinetobacter baumannii are increasingly clinically relevant due to their propensity to harbour genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterised the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.