Paper

High genetic diversity and blaNDM-1 prevalence among Acinetobacter baumannii in Nigerian hospitals

Dalsgaard, Anders, Aboderin, Oladipo, Yaovi Mahuton Gildas Hounmanou, Argimón, Silvia, Egwuenu, Abiodun, Ogunleye, Veronica O, Oduyebo, Oyin, Okwor, Tochi J, Underwood, Anthony, Oshun, Phillip O, Odih, Erkison Ewomazino, Ihekweazu, Chikwe, Okeke, Iruka N, Aanensen, David M, Oaikhena, Anderson O, Akpunonu, Vitus Nnaemeka, Fadeyi, Abayomi

2023

Overview

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-23 genes 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-1 prevalence 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.

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: Acinetobacter baumannii / Antimicrobial agents / Antimicrobial resistance / Carbapenemase / Genetic diversity / Genomics / Hospitals / Immunocompromised hosts / Phylogeny / Surveillance / Transposons