Increasing fluroquinolone susceptibility and genetic diversity of ESBL-producing E. coli from the lower respiratory tract during the COVID-19 pandemic

Hrovat, Katja (author), Seme, Katja (author), Ambrožič, Jerneja (author)

Lower respiratory tract infections (LRTIs) are the fourth leading cause of death worldwide, among which Escherichia coli (E. coli) pneumonia is considered a rare phenomenon. Treatment options for LRTIs have become limited, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-EC), which are usually resistant to other groups of antimicrobials as well. The aim of our study was to compare the phenotypic resistance profiles and genotypes of ESBL-EC isolates associated with LRTIs before (pre-COVID-19) and during (COVID-19) the COVID-19 pandemic. All isolates were screened for antimicrobial resistance genes (ARGs) and virulence-associated genes (VAGs) and assigned to phylogenetic groups, sequence types and clonal groups by PCR. During the pandemic, a significantly lower proportion of ciprofloxacin-, levofloxacin- and trimethoprim-sulfamethoxazole-resistant ESBL-EC isolates was retrieved from lower respiratory tract (LRT) samples. PCR-based genotypization revealed greater clonal diversity and a significantly lower proportion of isolates with bla$_{TEM}$, aac(6′)-Ib-cr and qacE∆1 genes. In addition, a higher proportion of isolates with the integrase gene int1 and virulence genes sat and tsh was confirmed. The lower prevalence of fluoroquinolone resistance and greater genetic diversity of ESBL-EC isolated during the COVID-19 period may have been due to the introduction of new bacterial strains into the hospital environment, along with changes in clinical establishment guidelines and practices.

• Language: English
• Keywords: antimicrobial resistance, Escherichia coli, extended-spectrum β-lactamases, lower respiratory tract, COVID-19
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty; MF - Faculty of Medicine
• Publication status: Published
• Publication version: Version of Record
• Year: 2024
• Number of pages: 14 str.
• Numbering: Vol. 13, iss. 9, art. 797
• PID: 20.500.12556/RUL-169393
• UDC: 615
• ISSN on article: 2079-6382
• DOI: 10.3390/antibiotics13090797
• COBISS.SI-ID: 205359875
• Publication date in RUL: 27.05.2025

Record is a part of a journal

• Title: Antibiotics
• Shortened title: Antibiotics
• Publisher: MDPI
• ISSN: 2079-6382
• COBISS.SI-ID: 522975769

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: odpornost proti protimikrobnim učinkovinam, Escherichia coli, β-laktamaze z razširjenim spektrom delovanja, spodnji dihalni trakt, COVID-19

Projects

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P1-0198
• Name: Molekularno-biološke raziskave mikroorganizmov

• Funder: ARIS - Slovenian Research and Innovation Agency
• Funding programme: Young researchers