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

Paul G Higgins,Philipp Warnke,Ulrike Loderstädt,Ralf Matthias Hagen,Bernd Kreikemeyer,Hagen Frickmann,Andreas Podbielski

doi:10.3390/antibiotics10030291

Abstract

At the Bundeswehr Hospitals of Hamburg and Westerstede, patients repatriated from subtropical war and crisis zones of Northern Africa and the Middle East were medically treated, including microbiological assessment. Within a six-year interval, 16 Acinetobacter spp. strains, including 14 Acinetobacter baumannii (Ab) isolates with resistance against carbapenems and origins in Afghanistan (n = 4), Iraq (n = 2), Libya (n = 2), and Syria (n = 8) were collected. While clonal relationships of Libyan and Syrian strains had been assessed by superficial next generation sequencing (NGS) and “DiversiLab” repetitive elements sequence-based (rep-)PCR so far, this study provides core genome-based sequence typing and thus more detailed epidemiological information. In detail, sequencing allowed a definitive species identification and comparison with international outbreak-associated Ab strains by core genome multi locus sequence typing (cgMLST) and the identification of MLST lineages, as well as the identification of known resistance genes. The sequence analysis allowed for the confirmation of outbreak-associated clonal clusters among the Syrian and Afghan Ab isolates, indicating likely transmission events. The identified acquired carbapenem resistance genes comprised blaOXA-23, blaOXA-58, blaNDM-1, and blaGES-11, next to other intrinsic and acquired, partly mobile resistance-associated genes. Eleven out of 14 Ab isolates clustered with the previously described international clonal lineages IC1 (4 Afghan strains), IC2 (6 Syrian strains), and IC7 (1 Syrian strain). Identified Pasteur sequence types of the 14 Ab strains comprised ST2 (Syrian), ST25 (Libyan), ST32 (Iraqi), ST81 (Afghan), ST85 (Libyan), and ST1112 (Syrian), respectively. In conclusion, the study revealed a broad spectrum of resistance genes in Ab isolated from war-injured patients from Northern Africa and the Middle East, thereby broadening the scarcely available data on locally abundant clonal lineages and resistance mechanisms.

Highlights

During the last two decades, military conflicts have affected many regions of NorthernAfrica, the Middle East and neighboring countries, including Afghanistan, Iraq, Libya, and Syria
The remaining two strains were identified as A. dijkshooriniae and A. radioresistens using the Jspecies Tetra correlation search [35] and matrix-assisted laserdesorption-ionization time-of-flight mass spectrometry (MALDI TOF MS) (Table 1)
All isolates were typed based on two 7-loci multi-locus sequence typing3 o(fM14LST) schemes, i.e., the Oxford scheme and the Pasteur scheme (Table 1) [37,38]

Summary

Introduction

During the last two decades, military conflicts have affected many regions of NorthernAfrica, the Middle East and neighboring countries, including Afghanistan, Iraq, Libya, and Syria. As previously summarized [1,2], war-associated wounds are prone to colonization or infection with multidrug-resistant Gram-negative bacteria including Acinetobacter baumannii (Ab). The epidemiology of war trauma-associated infections, nosocomial transmission as well as deployment-associated colonization with A. baumannii has been best studied during the recent military interventions of US-American and British Forces in Iraq [3,4,5,6,7,8,9,10,11,12,13]. As early as in 2006, blaOXA-58-like and blaPER-like genes were identified via sequencing sequenced in Iraqi A. baumannii strains [4]. BlaOXA-40-like genes were detected in Acinetobacter strains isolated in the Iraqi Kurdistan region. There was even a decline in A. baumannii colonization in US troops during post-deployment screening from 21% to 4% between 2005 and 2009 [9]

Methods

Results

Discussion

Conclusion