Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolated from War-Injured Patients from the Eastern Ukraine

Abstract

Recently, a total of 32 carbapenem- and fluoroquinolone-resistant Acinetobacter baumannii (Ab) isolates was isolated from war-injured patients who were treated at German Bundeswehr Hospitals, and preliminarily typed by “DiversiLab” repetitive elements sequence-based (rep-) PCR. Core genome-based sequence typing was also used to provide more detailed epidemiological information. From the clusters observed by rep-PCR, selected Ab strains were subjected to Next Generation Sequencing (NGS) in order to compare them with international outbreak-associated Ab strains and to identify MLST (multi-locus sequence type) lineages, as well as to identify known resistance genes. Accordingly, NGS indicated higher diversity than rep-PCR, but also confirmed likely transmission events. The identified acquired carbapenem-resistant genes comprised blaOXA-23, blaOXA-72 and blaGES-12, as well as various other intrinsic and acquired resistance-associated genetic elements. All isolates clustered with the previously identified international clonal lineages IC1, IC2, IC6 and IC7, with corresponding Pasteur sequence types ST1, ST2, ST78 and ST25, respectively. In conclusion, the assessment confirmed a broad spectrum of resistance-associated genes in Ab isolated from war-injured patients from the Eastern Ukraine, and provided the first insights into locally abundant clonal lineages.

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolates from Northern Africa and the Middle East

“…As an interesting side-effect, cgMLST confirmed the clonal relationships as suggested by rep-PCR in the recent assessment [ 33 ], thus additionally confirming the basic reliability of this comparably cheap and easy-to-perform typing approach for local outbreak scenarios, in spite of the undeniably higher resolution of genome-based typing [ 34 , 40 , 42 ]. A comparison with other A. baumannii isolates from Ukrainian conflict zones that we have investigated did not show any clonality to those in the current study (data not shown) [ 40 ].…”

“…The latter clustering as observed with the cgMLST-typing confirmed likely transmission events between Syrian patients prior to admission at the Bundeswehr Hospitals Westerstede and Hamburg, which had already been suspected based on the results of rep-PCR and superficial sequencing [ 33 ]. Those transmission events might either have occurred in medical facilities in the patients′ home country but also, as previously discussed for Syrian and Ukrainian war-injured patients treated at German military hospitals [ 33 , 40 , 41 ], during the evacuation flights out of the patients’ crisis-struck home countries. Of note, two strains isolated from Syrian patients at the military hospital in Westerstede (“WEST”-strains) showed completely identical sequences and other isolates of this cluster, which were isolated at the Bundeswehr Hospital Hamburg (“HBG”-strains) showed only one, two, and nine allele differences, respectively ( Figure 1 ).…”

“…DNA extraction and whole genome sequencing was performed exactly as described recently [ 40 ]. In detail, MagAttract HMW DNA Kits (Qiagen, Hilden, Germany) were used to extract the genomic DNA of the isolates according to the manufacturer’s instructions for whole genome sequencing (WGS).…”

Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria

“…The ST1089 (IC9) strains were the second most common lineage in this study. These strains have been isolated from clinical samples and hospital environments, particularly from studies in Northern Africa and in the Middle East, and are frequently reported to carry blaNDM-1 and blaOXA-94 carbapenem resistance genes (32,(33)(34)(35)(36)(37)(38)(39). An ST1089 strain carrying blaNDM-1 was also isolated from raw milk in a dairy farm in Algeria (40).…”

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Strains Isolated at the German Military Field Laboratory in Mazar-e Sharif, Afghanistan

“…Additional screening PCRs [25,26] targeting common beta-lactamases were applied. In addition, whole-genome sequencing from the extracted nucleic acids of the strains was performed as previously described with minor modifications [17,27]. Briefly, sequencing libraries were prepared with the purified DNA using the Ultra II FS DNA Library Prep Kit (New England Biolabs, Frankfurt, Germany) for 250 bp paired-end sequencing runs on an Illumina MiSeq sequencer.…”