Genomic Characterization of Clinical Acinetobacter baumannii Isolates Obtained from COVID-19 Patients in Russia.
Andrey A ShelenkovYulia V MikhaylovaLyudmila PetrovaIrina GaidukovaMikhail ZamyatinVasiliy AkimkinPublished in: Antibiotics (Basel, Switzerland) (2022)
The coronavirus disease 2019 (COVID-19) pandemic has already affected all realms of public healthcare and, in particular, has led to increasing use of various antibiotics to treat possible bacterial coinfections even in cases for which such infections were not confirmed clinically. This could lead to an increase in the fraction and severity of multidrug-resistant bacterial isolates in healthcare facilities, especially in intensive care units (ICU). However, detailed epidemiological investigations, possibly including whole genome sequencing (WGS), are required to confirm the increase in antibiotic resistance and changes, if any, in the population and clonal structures of bacterial pathogens. In this study, we performed a comprehensive genomic and phenotypic characterization of selected multidrug-resistant A. baumannii isolates obtained from the patients of a dedicated COVID-19 ICU in Moscow, Russia. Hybrid short- and long-read sequencing allowed us to obtain complete profiles of genomic antimicrobial resistance and virulence determinants, as well as to reveal the plasmid structure. We demonstrated the genomic similarity in terms of cgMLST profiles of the isolates studied with a clone previously identified in the same facility. We believe that the data provided will contribute to better understanding the changes imposed by the COVID-19 pandemic on the population structure and the antimicrobial resistance of bacterial pathogens in healthcare facilities.
Keyphrases
- antimicrobial resistance
- multidrug resistant
- healthcare
- acinetobacter baumannii
- coronavirus disease
- intensive care unit
- gram negative
- drug resistant
- copy number
- genetic diversity
- sars cov
- end stage renal disease
- klebsiella pneumoniae
- pseudomonas aeruginosa
- mechanical ventilation
- escherichia coli
- ejection fraction
- chronic kidney disease
- genome wide
- peritoneal dialysis
- dna methylation
- big data
- gene expression
- electronic health record
- patient reported outcomes
- prognostic factors
- cystic fibrosis
- adverse drug