Genomic Characteristics of an Extensive-Drug-Resistant Clinical Escherichia coli O99 H30 ST38 Recovered from Wound

Dashti, Ali A, Vali, Leila ORCID: 0009-0000-7740-3703, Shamsah, Sara, Jadaon, Mehrez and ElShazly, Sherief (2024) Genomic Characteristics of an Extensive-Drug-Resistant Clinical Escherichia coli O99 H30 ST38 Recovered from Wound. Iranian Journal of Pharmaceutical Research, 23 (1). e143910. doi:10.5812/ijpr-143910

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Text Dashti, Vali, Shamsah, Jadaon, El-Shazly (2024) Genomic characteristics of an extensive-drug-resistant clinical escherichia coli O99 H30 ST38 recovered from wound.pdf - Published Version Available under License Creative Commons Attribution 4.0. Download (2MB) | Preview

Abstract

Background: Antibiotic-resistant Escherichia coli is one of the major opportunistic pathogens that cause hospital-acquired infections worldwide. These infections include catheter-associated urinary tract infections (UTIs), ventilator-associated pneumonia, surgical wound infections, and bacteraemia. Objectives: To understand the mechanisms of resistance and prevent its spread, we studied E. coli C91 (ST38), a clinical outbreak strain that was extensively drug-resistant. The strain was isolated from an intensive care unit (ICU) in one of Kuwait's largest hospitals from a patient with UTI. Methods: This study used whole-genome sequencing (Illumina, MiSeq) to identify the strain's multi-locus sequence type, resistance genes (ResFinder), and virulence factors. This study also measured the minimum inhibitory concentrations (MIC) of a panel of antibiotics against this isolate. Results: The analysis showed that E. coli C-91 was identified as O99 H30 ST38 and was resistant to all antibiotics tested, including colistin (MIC > 32 mg/L). It also showed intermediate resistance to imipenem and meropenem (MIC = 8 mg/L). Genome analysis revealed various acquired resistance genes, including mcr-1, bla CTX-M-14, bla CTX-M-15, and bla OXA1. However, we did not detect bla NDM or bla VIM. There were also several point mutations resulting in amino acid changes in chromosomal genes: gyrA, parC, pmrB, and ampC promoter. Additionally, we detected several multidrug efflux pumps, including the multidrug efflux pump mdf(A). Eleven prophage regions were identified, and PHAGE_Entero_SfI_NC was detected to contain ISEc46 and ethidium multidrug resistance protein E (emrE), a small multidrug resistance (SMR) protein family. Finally, there was an abundance of virulence factors in this isolate, including fimbriae, biofilm, and capsule formation genes. Conclusions: This isolate has a diverse portfolio of antimicrobial resistance and virulence genes and belongs to ST38 O99 H30, posing a serious challenge to treating infected patients in clinical settings.

Item Type:	Article
Article Type:	Article
Uncontrolled Keywords:	Whole Genome Sequencing; Colistin Resistance; Virulence Factors; Antimicrobial Resistance; Insertion Sequences
Subjects:	Q Science > Q Science (General) Q Science > QR Microbiology R Medicine > R Medicine (General)
Divisions:	Schools and Research Institutes > School of Education and Science
Research Priority Areas:	Place, Environment and Community
Depositing User:	Anna Kerr
Date Deposited:	11 Jul 2024 09:06
Last Modified:	19 Jul 2024 11:15
URI:	https://eprints.glos.ac.uk/id/eprint/14215

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