Molecular characterization of extended-spectrum β-lactamase-producing Escherichia coli isolated from lower respiratory tract samples between 2002 and 2019 in the Central Slovenia region

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

Background Antibiotic resistance is one of the most serious global health problems and threatens the effective treatment of bacterial infections. Of greatest concern are infections caused by extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC). The aim of our study was to evaluate the prevalence and molecular characteristics of ESBL-EC isolated over an 18-year pre-COVID period from lower respiratory tract (LRT) samples collected from selected Slovenian hospitals. Objectives and methods All isolates were identified by MALDI-TOF and phenotypically confirmed as ESBLs by a disk diffusion assay. Using a PCR approach, 487 non-repetitive isolates were assigned to phylogroups, sequence type groups, and clonal groups. Isolates were also screened for virulence-associated genes (VAGs) and antimicrobial resistance genes. Results The prevalence of ESBL-EC isolates from LRT in a large university hospital was low (1.4%) in 2005 and increased to 10.8% by 2019. The resistance profile of 487 non-repetitive isolates included in the study showed a high frequency of group 1 bla$_{CTX-M}$ (77.4%; n = 377), bla$_{TEM}$ (54.4%; n = 265) and aac(6’)-Ib-cr (52%; n = 253) genes and a low proportion of bla$_{SHV}$ and qnr genes. Isolates were predominantly assigned to phylogroup B2 (73.1%; n = 356), which was significantly associated with clonal group ST131. The ST131 group accounted for 67.6% (n = 329) of all isolates and had a higher number of virulence factor genes than the non-ST131 group. The virulence gene profile of ST131 was consistent with that of other extraintestinal pathogenic E. coli (ExPEC) strains and was significantly associated with ten of sixteen virulence factor genes tested. Using ERIC-PCR fingerprinting, isolates with the same ERIC-profile in samples from different patients, and at different locations and sampling dates were confirmed, indicating the presence of “hospital-adapted” strains. Conclusion Our results suggest that the ESBL-EC isolates from LRT do not represent a specific pathotype, but rather resemble other ExPEC isolates, and may be adapted to the hospital environment. To our knowledge, this is the first study of ESBL-EC isolated from LRT samples collected over a long period of time.

• Language: English
• Keywords: Escherichia coli, lower respiratory tract, extended-spectrum β-lactamase, antibiotic resistance, ST131, virulence factors
• 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: 13 str.
• Numbering: Vol. 23, art. 6
• PID: 20.500.12556/RUL-164701
• UDC: 577.18
• ISSN on article: 1476-0711
• DOI: 10.1186/s12941-023-00664-1
• COBISS.SI-ID: 180952579
• Publication date in RUL: 07.11.2024

Record is a part of a journal

• Title: Annals of clinical microbiology and antimicrobials
• Shortened title: Ann. clin. microbiol. antimicrob.
• Publisher: Springer Nature
• ISSN: 1476-0711
• COBISS.SI-ID: 2593556

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: Escherichia coli, spodnji dihalni trakt, β-laktamaze z razširjenim spektrom delovanja, odpornost proti antibiotikom, ST131

Projects

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

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