Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase

Alaa Abouelfetouh; Jennifer Mattock; Dann Turner; Erica Li; Benjamin A Evans

doi:10.1099/mgen.0.000752

Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase

Microb Genom. 2022 Feb;8(2):000752. doi: 10.1099/mgen.0.000752.

Authors

Alaa Abouelfetouh¹, Jennifer Mattock², Dann Turner³, Erica Li², Benjamin A Evans²

Affiliations

¹ Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt.
² Norwich Medical School, University of East Anglia, Norwich, UK.
³ Department of Applied Sciences, University of the West of England, Bristol, UK.

Abstract

Carbapenem-resistant Acinetobacter baumannii are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here, we characterize carbapenem-resistant A. baumannii from Alexandria, Egypt, and place it in a regional context. Fifty-four carbapenem-resistant isolates from Alexandria Main University Hospital (AMUH), Alexandria, Egypt, collected between 2010 and 2015 were genome sequenced using Illumina technology. Genomes were de novo assembled and annotated. Genomes for 36 isolates from the Middle East region were downloaded from GenBank. The core-gene compliment was determined using Roary, and analyses of recombination were performed in Gubbins. Multilocus sequence typing (MLST) sequence type (ST) and antibiotic-resistance genes were identified. The majority of Egyptian isolates belonged to one of three major clades, corresponding to Pasteur MLST clonal complex (CC^PAS) 1, CC^PAS2 and ST^PAS158. Strains belonging to ST^PAS158 have been reported almost exclusively from North Africa, the Middle East and Pakistan, and may represent a region-specific lineage. All isolates carried an oxa23 gene, six carried bla_NDM-1 and one carried bla_NDM-2. The oxa23 gene was located on a variety of different mobile elements, with Tn2006 predominant in CC^PAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 13 CC^PAS1 strains, the oxa23 gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CC^PAS1 clone from the USA military. The carbapenem-resistant A. baumannii population in AMUH is very diverse, and indicates an endemic circulating population, including a region-specific lineage. A major mechanism for oxa23 dissemination in CC^PAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population.

Keywords: Egypt; MLST; antibiotic resistance; phiOXA; transposon; whole-genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acinetobacter Infections / epidemiology
Acinetobacter Infections / microbiology
Acinetobacter baumannii / drug effects*
Acinetobacter baumannii / genetics*
Africa, Northern
Anti-Bacterial Agents / pharmacology
Bacterial Proteins / genetics*
Bacteriophages / genetics*
Carbapenems
Drug Resistance, Multiple, Bacterial / drug effects
Drug Resistance, Multiple, Bacterial / genetics*
Genome, Bacterial
Humans
Microbial Sensitivity Tests
Middle East
Molecular Epidemiology
Multilocus Sequence Typing
Whole Genome Sequencing
beta-Lactamases / genetics

Substances

Anti-Bacterial Agents
Bacterial Proteins
Carbapenems
beta-Lactamases
carbapenemase