Diversity of International High-Risk Clones of Acinetobacter baumannii Revealed in a Russian Multidisciplinary Medical Center during 2017–2019

Abstract

Acinetobacter baumannii is a dangerous bacterial pathogen possessing the ability to persist on various surfaces, especially in clinical settings, and to rapidly acquire the resistance to a broad spectrum of antibiotics. Thus, the epidemiological surveillance of A. baumannii within a particular hospital, region, and across the world is an important healthcare task that currently usually includes performing whole-genome sequencing (WGS) of representative isolates. During the past years, the dissemination of A. baumannii across the world was mainly driven by the strains belonging to two major groups called the global clones or international clones (ICs) of high risk (IC1 and IC2). However, currently nine ICs are already considered. Although some clones were previously thought to spread in particular regions of the world, in recent years this is usually not the case. In this study, we determined five ICs, as well as three isolates not belonging to the major ICs, in one multidisciplinary medical center within the period 2017–2019. We performed WGS using both short- and long-read sequencing technologies of nine representative clinical A. baumannii isolates, which allowed us to determine the antibiotic resistance and virulence genomic determinants, reveal the CRISPR/Cas systems, and obtain the plasmid structures. The phenotypic and genotypic antibiotic resistance profiles are compared, and the possible ways of isolate and resistance spreading are discussed. We believe that the data obtained will provide a better understanding of the spreading and resistance acquisition of the ICs of A. baumannii and further stress the necessity for continuous genomic epidemiology surveillance of this problem-causing bacterial species.

Whole-genome analysis of carbapenem-resistant Acinetobacter baumannii from clinical isolates in Southern Thailand

“…ST2 is the most predominant type and the most widespread in many parts of the world, especially Thailand [55] , [56] , [57] . The prevalences of other STs such as ST164, ST374, ST16, ST215, ST25 (IC7), ST129 (IC2), and ST1 (IC1) are different in each region [55] , [56] , [58] , [59] , [60] . Hamidian and Nigro (2019) reported the level ST of 3575 CRAB isolates showing ST2 as the most prevalent ST, followed most prominently by ST1 (IC1), ST76, SLV2 (a single-locus variant of ST2), ST25 (IC7), ST10, and then others with lower prevalences [56] .…”

Fresh produce as a potential vehicle for transmission of Acinetobacter baumannii

“…ST40 strains have been isolated from clinical and food sources, while isolates belonging to ST602 have been previously isolated from environmental and upper respiratory tract samples. The PubMLST database contains data about only one ST724 strain isolated from blood, whereas hundreds of ST2 isolates have been isolated from clinical, animal and environmental sources (Brahmi et al 2016;Khurshid et al 2020;Shelenkov et al 2021).…”

Long-Read Whole Genome Sequencing Elucidates the Mechanisms of Amikacin Resistance in Multidrug-Resistant Klebsiella pneumoniae Isolates Obtained from COVID-19 Patients

“…During recent years, the increasing use of long-read sequencing greatly facilitated the investigations of outbreaks and exploration of possible resistance transmission routes [ 37 , 38 , 39 ], and several bioinformatics protocols were developed for these purposes [ 15 , 17 , 40 ]. Another possible application of this powerful technology is the investigation of bacterial clone diversity within a particular hospital department or some other healthcare facility [ 41 , 42 , 43 ].…”