Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii isolates from Germany and Vietnam

Phenotypic and genotypic characterization of 100 clinical and non-clinical A. baumannii strains isolated between 2005 and 2018 were evaluated and compared. The strains were originated from humans, milk powder, and animals in Germany (n=89) and eleven human strains from Vietnam. Antimicrobial susceptibility testing was done using the broth microdilution method, and the minimum inhibitory concentration (MIC) was determined for 18 antibiotics. The whole-genome-sequencing (WGS) data from all isolates were mapped to intrinsic genes known to be associated with phenotypic AMR. The highest resistant frequency was observed toward chloramphenicol (100%), followed by fosfomycin (96%) and cefotaxime (95%). The lowest resistant rates were observed toward colistin (3%), trimethoprim/sulfamethoxazole (17%), tigecycline (19%), and amikacin (19%). Thirty-five percentage of tested strains displayed resistance to at least one of the carbapenems. Resistance to fluoroquinolones, aminoglycosides, tigecycline, penicillins, trimethoprim/sulfamethoxazole, and the 4th generation cephalosporins was determined only in human strains. About one-quarter of isolates (24%) were multidrug resistance (MDR) and all were of human origin. Among them, 16 isolates were extensively drug resistance (XDR) and ten from those 16 isolates showing resistance to all tested antibiotics except colistin. In-Silico detection of intrinsic AMR genes revealed the presence of 36 β-lactamases and 24 non- β-lactamases resistance genes. Two colistin resistant and ten ertapenem resistant strains have been isolated from powdered milk produced in Germany. Thirty-eight AMR genes associated with resistance to antibiotics were found in isolates recovered from milk powder. Several resistance mechanisms toward many classes of antibiotics exist in A. baumannii, including β-lactamases, multidrug efflux pumps, and aminoglycoside-modifying enzymes. The use of WGS for routine public health surveillance is a reliable method for the rapid detection of emerging AMR in isolates of A. baumannii. Milk powder poses a risk for MDR Acinetobacter strains or resistance genes in Germany.