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 (CCPAS) 1, CCPAS2 and STPAS158. Strains belonging to STPAS158 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 CCPAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 13 CCPAS1 strains, the oxa23 gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CCPAS1 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 CCPAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population.
Highlights
The bacterium Acinetobacter baumannii is a major opportunistic hospital-acquired pathogen that is listed by the World Health Organization (WHO) as in critical need of new treatment options due to its multidrug-resistant nature [1]
A significant number of bacteria belonged to a subgroup that have only been sporadically reported from North Africa, the Middle East and Pakistan, providing evidence that there may be a specific subgroup of A. baumannii from this geographic region
Analysis of the antibiotic susceptibilities of the Egyptian isolates showed that, as expected due to the isolates being selected for their carbapenem resistance, they were all resistant to imipenem and meropenem (Table 1)
Summary
The bacterium Acinetobacter baumannii is a major opportunistic hospital-acquired pathogen that is listed by the World Health Organization (WHO) as in critical need of new treatment options due to its multidrug-resistant nature [1]. The frequency of carbapenem-resistant A. baumannii has been steadily increasing over the last two decades, leaving very few treatment options available to combat this pathogen [2]. In countries in the Middle East and North Africa high levels of carbapenem-resistant A. baumannii are reported, with frequencies of 70% of isolates or greater being common [8]. Despite these very high rates of resistance, there are relatively few studies investigating the molecular epidemiology of the antibiotic-resistant strains. Carbapenem resistance in A. baumannii is usually the result of the expression of an OXA-type βlactamase, or occasionally metallo-β-lactamases such as the IMP, VIM and NDM groups [9]. The acquired OXA-type β-lactamases in A. baumannii are encoded by genes belonging to five main groups – oxa (or blaOXA-23-like), oxa (or blaOXA-40-like), oxa (or blaOXA-58-like), oxa134
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