High genetic diversity andbla_NDM-1prevalence amongAcinetobacter baumanniiin Nigerian hospitals

Abstract

Background: Acinetobacter baumannii cause difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. Objective: This study aimed to characterise the diversity and genetic mechanisms of carbapenem resistance among A. baumanniistrains isolated from hospitals in southwestern Nigeria. Methods: We sequenced the genomes of all A. baumannii isolates submitted to Nigeria's antimicrobial resistance surveillance reference laboratory between 2016 – 2020 on an Illumina platform and performed in silico genomic characterisation. Selected strains were sequenced using the Oxford Nanopore technology to characterise the genetic context of carbapenem resistance genes. Results: The 86 A. baumannii isolates 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%) and blaNDM-1(27.9%) were the most common carbapenem resistance genes detected. All blaOXA-23genes were carried on Tn2006 or Tn2006-like transposons. Our findings suggest that the mobilisation of a 10kb Tn125 composite transposon is the primary means of blaNDM-dissemination. Conclusion: Our findings highlight an increase in blaNDM-1prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings.