Genomic Characterization of Clinical Acinetobacter baumannii Isolates Obtained from COVID-19 Patients in Russia.

Andrey Shelenkov,Lyudmila Petrova,Vasiliy Akimkin,Mikhail Zamyatin,Irina Gaidukova,Yulia Mikhaylova

doi:10.3390/antibiotics11030346

Abstract

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.

Highlights

The coronavirus disease 2019 (COVID-19) pandemic affected virtually all fields of medicine, and the treatment of healthcare-associated infections is not an exception
Antibiotics panel included the following drugs: ciprofloxacin, gentamicin, imipenem, levofloxacin, netilmicin and trimethoprim/sulfomethoxazole. This is a short version of a panel that was used in intensive care units (ICU) reserved for COVID-19 patients due to limited resources’ availability and other technical issues caused by the first wave of pandemic
We presented a comprehensive genomic analysis of four multidrug-resistant A. baumannii isolates obtained from the patients of a dedicated COVID-19 ICU

Summary

Introduction

The coronavirus disease 2019 (COVID-19) pandemic affected virtually all fields of medicine, and the treatment of healthcare-associated infections is not an exception. The too-frequent and inappropriate use of antibiotics is a major concern; for example, recent meta-analysis has shown that more than 70% of hospitalized COVID-19 patients received antibiotics, while only about 9% demonstrated superimposed bacterial or fungal coinfections [1]. According to another investigation, in 96% of cases the antibiotic treat-ment was prescribed before a bacterial infection was confirmed [2]. In 96% of cases the antibiotic treat-ment was prescribed before a bacterial infection was confirmed [2] The effects of such overuse are currently hard to estimate due to limited data available [3], but the worldwide increase in resistance is a very likely scenario. An important step in this direction seems to be the monitoring of the bacterial coinfections of COVID-19 patients admitted to dedicated intensive care units (ICU) and a comparison of such infections with those found pre-COVID-19, especially, on the level of genomic resistance determinants for particular pathogens

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