Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand

Parichart Boueroy; Peechanika Chopjitt; Rujirat Hatrongjit; Masatomo Morita; Yo Sugawara; Yukihiro Akeda; Tetsuya Iida; Shigeyuki Hamada; Anusak Kerdsin

doi:10.7717/peerj.16401

Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand

PeerJ. 2023 Nov 8:11:e16401. doi: 10.7717/peerj.16401. eCollection 2023.

Authors

Affiliations

¹ Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand.
² Faculty of Science and Engineering, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand.
³ Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
⁴ Japan-Thailand Research Collaboration Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
⁵ Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
⁶ Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.

Abstract

Background: Escherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern.

Objectives: To characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS.

Methods: Antimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short- and long-read platforms.

Results: ST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6')-Ib (57.28%) was found and the coexistence of aac(6')-Ib and bla_CTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that bla_NDM-5 or bla_NDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as bla_OXA-1, bla_CTX-M-15, bla_TEM-1B, and aac(6')-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the bla_NDM-5 gene.

Conclusions: This study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism.

Keywords: Carbapenem resistance; Escherichia coli; Fluoroquinolone resistance; Urine; Virulence factors.

MeSH terms

Anti-Bacterial Agents / pharmacology
Carbapenem-Resistant Enterobacteriaceae*
Carbapenems / pharmacology
Escherichia coli / genetics
Escherichia coli Infections* / drug therapy
Fluoroquinolones / pharmacology
Humans
Thailand / epidemiology
beta-Lactamases / genetics

Substances

Fluoroquinolones
Anti-Bacterial Agents
Carbapenems
beta-Lactamases

Grants and funding

This work was financially supported by the Office of the Ministry of Higher Education, Science, Research and Innovation; and the Thailand Science Research and Innovation through the Kasetsart University Reinventing University Program 2021. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.