Molecular characterization of multidrug resistant Acinetobacter baumannii clinical isolates from Alexandria, Egypt

Abstract

Carbapenem resistant Acinetobacter baumannii is a major global concern, especially in countries of the Middle East and North Africa, where the antibiotic resistance rates are on the rise. The aim of this study was to study the genomic characteristics and antimicrobial susceptibility profile of thirty-six multidrug resistant A. baumannii clinical isolates obtained in hospitals from Alexandria, Egypt. Antibiotic resistance rates were estimated by determination of Minimum Inhibitory Concentrations. Carbapenemase genes, other antibiotic resistance genes and virulence factors were then screened by the use of Whole Genome Sequencing. Isolates were also subjected to Multi Locus Sequence Typing (MLST) using the Pasteur Scheme and to core genome MLST to study their clonal relatedness. In addition, plasmid analysis was performed by the use of a commercial kit and S1- Pulsed Field Gel Electrophoresis, and Hybridization experiments with DIG-labeled DNA probes for blaNDM-1, blaPER-7 and blaGES-like were performed to locate these genes. The majority of isolates were resistant to β-lactams (including carbapenems), fluoroquinolones, aminoglycosides and trimethoprim; and some showed resistance to cefiderocol and minocycline. We identified 8 different blaOXA-51-like variants including blaOXA-51, blaOXA-64, blaOXA-65, blaOXA-66, blaOXA-68, blaOXA-91, blaOXA-94 and blaOXA-336; blaOXA-23, blaNDM-1, blaPER-7, blaGES-like and blaADC-like and other antibiotic resistance genes, some of these genes were within transposons or class 1 integrons. Multiple virulence factors responsible for adherence, biofilm production, type II and type VI secretion systems, exotoxins, exoenzymes, immune modulation and iron uptake were observed and 34 out of 36 isolates showed motility. Thirty-five out of 36 isolates clustered with International Clones 2, 4, 5, 7, 8 and 9; and 9 STs were identified including ST570, ST2, ST600, ST15, ST113, ST613, ST85, ST158, ST164. Plasmids ranging in size from 1.7 to 70 kb were found; blaNDM-1 and blaPER-7 genes were located in the chromosome and blaGES-like genes were simultaneously located in the chromosome and in a plasmid of 70kb. In conclusion, this study revealed a wide spectrum of antibiotic resistance genes and a variety of lineages among A. baumannii isolated in hospitals from Alexandria, and highlights the importance of investigating the molecular epidemiology to control the spread of multi-drug resistant isolates.

Plasmid content of carbapenem resistant Acinetobacter baumannii isolates belonging to five International Clones collected from hospitals of Alexandria, Egypt

“…Six carbapenem resistant Acinetobacter baumannii clinical isolates were selected from a group of 36 isolates collected in hospitals from Alexandria, Egypt. These isolates were previously characterized by the analysis of plasmid profiles obtained by conventional lysis, PCR-Based Replicon Typing to identify the replicases, and by Multi Locus Sequence Typing experiments to determine their clonal lineage ( Sánchez-Urtaza et al., 2023 ). We made the selection of these isolates based on the different replicase combinations we found and the International Clone they belonged to, choosing an isolate that represents each group: Ale9 (IC8; Aci1/2 + p2S1), Ale10 (IC2; Aci6 + Aci8/9), Ale18 (IC9; Aci6), Ale20 (IC2; Aci1/2 + Aci6), Ale21 (IC4; Aci4 + Aci8/9) and Ale26 (IC5; Aci6 + p2S1).…”

“…The isolates were sequenced by both Illumina and Oxford Nanopore methodology as previously described ( Sánchez-Urtaza et al., 2023 ). Total DNA was extracted using Qiagen DNeasy ® Blood and Tissue (Qiagen, Hilden, Germany), according to the protocol supplied by the manufacturer.…”

Healthcare-Associated Acinetobacter Infections: An Urgent Call for Action

“…So, global organizations like European Centre for Disease Prevention and Control (ECDC), and the Center for Disease Control and Prevention (CDC) have declared it as an urgent threat to public health. 3 There is an estimated incidence of 1 million cases of A. baumannii infections each year worldwide with significant mortality rates, especially in critically ill or immunocompromised patients. So, how can the infections be treated and pathogen will be targeted with high specificity?…”