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

Katja Hrovat; Katja Molan; Katja Seme; Jerneja Ambrožič Avguštin

doi:10.1186/s12941-023-00664-1

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

Ann Clin Microbiol Antimicrob. 2024 Jan 13;23(1):6. doi: 10.1186/s12941-023-00664-1.

Authors

Katja Hrovat¹, Katja Molan², Katja Seme³, Jerneja Ambrožič Avguštin⁴

Affiliations

¹ Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
² Department of Microbiology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
³ Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
⁴ Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia. Jerneja.Ambrozic@bf.uni-lj.si.

Abstract

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.

Keywords: Antibiotic resistance; Escherichia coli; Extended-spectrum β-lactamase; Lower respiratory tract; ST131; Virulence factors.

MeSH terms

Anti-Bacterial Agents / pharmacology
Drug Resistance, Multiple, Bacterial / genetics
Escherichia coli Infections* / epidemiology
Escherichia coli Infections* / microbiology
Escherichia coli*
Humans
Respiratory System
Slovenia / epidemiology
Virulence Factors / genetics
beta-Lactamases / genetics

Substances

Anti-Bacterial Agents
Virulence Factors
beta-Lactamases

Grants and funding

P1-0198/Slovenian Research Agency