Polyclonal spread of blaCTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia

Tsegaye Sewunet; Daniel Asrat; Yimtubezinash Woldeamanuel; Sofia Ny; Fredrik Westerlund; Abraham Aseffa; Christian G Giske

doi:10.1016/j.jgar.2021.09.017

Polyclonal spread of bla_CTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia

J Glob Antimicrob Resist. 2022 Jun:29:405-412. doi: 10.1016/j.jgar.2021.09.017. Epub 2021 Nov 12.

Authors

Tsegaye Sewunet¹, Daniel Asrat², Yimtubezinash Woldeamanuel², Sofia Ny³, Fredrik Westerlund⁴, Abraham Aseffa⁵, Christian G Giske⁶

Affiliations

¹ Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia; School of Laboratory Sciences, Jimma University, Jimma, Ethiopia; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden. Electronic address: tsegaye.sewunet@ki.se.
² Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia.
³ Public Health Agency of Sweden, Sweden.
⁴ Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
⁵ Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
⁶ Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Clinical Microbiology, Sweden.

PMID: 34775133
DOI: 10.1016/j.jgar.2021.09.017

Abstract

Objectives: The burden of antimicrobial resistance and spread of epidemic clones are rarely reported from low-income countries. We aimed to investigate the genome-based epidemiology of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) at a tertiary hospital in Jimma, Ethiopia.

Methods: Bacteria were isolated from clinical specimens at Jimma Medical Center and subjected to species identification (MALDI-TOF), antimicrobial susceptibility testing (disk diffusion) and whole-genome sequencing (Illumina, HiSeq2500). Genomic data analysis was performed using EnteroBase and Center for Genomic Epidemiology bioinformatics pipelines. A maximum likelihood tree was generated using FastTree/2.1.8 based on single nucleotide polymorphisms (SNPs) in shared genomic regions to identify transmission clusters.

Results: Escherichia coli isolates (n = 261) were collected from 1087 single non-duplicate clinical specimens over a 5-month period in 2016. The prevalence of ESBL-EC was 54.8% (143/261), 96% of which were resistant to multiple antibiotic classes. The bla_CTX-M-15 ESBL gene was present in 88.4.% of isolates (122/138). Genes conferring resistance to aminoglycosides and ciprofloxacin [aac(6')-Ib-cr, 62.3% (86/138)], phenicols [catB3, 56.5% (78/138)], sulfonamides [sul1, 68.1% (94/138), trimethoprim [dfrA17, 58.0% (80/138)] and macrolides [mph(A), 67.4% (93/138) were detected. The most prevalent sequence types were ST410 (23%), ST648 (17%), ST131 (10%) and ST167 (7%). Isolates of the same sequence type collected from different units of the hospital were highly similar in the SNP analysis.

Conclusion: A high prevalence of ESBLs and dissemination of bla_CTX-M-15 through multiple high-risk E. coli clones was detected. Nosocomial spread of multidrug-resistant ESBL-EC within the hospital puts vulnerable patients at risk of difficult-to-treat infections.

Keywords: Antimicrobial resistance; ESBL; Escherichia coli; Extended-spectrum β-lactamase; Nosocomial transmission; β-Lactam.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology
Clone Cells
Escherichia coli Infections* / microbiology
Escherichia coli*
Ethiopia / epidemiology
Humans
Tertiary Care Centers
beta-Lactamases / genetics

Substances

Anti-Bacterial Agents
beta-Lactamases