Whole genome-based characterization of extended-spectrum β-lactamase-producing Enterobacter cloacae from orthopedic patients and environment of a tertiary referral hospital in Tanzania

Benson R. Kidenya; Gerald Mboowa; Ivan Sserwadda; Stephen Kanyerezi; Esther Nakafu; Inyasi Lawrence Akaro; Baraka Mkinze; Moses L. Joloba; Jeremiah Seni

New Microbes and New Infections (Dec 2024)

Whole genome-based characterization of extended-spectrum β-lactamase-producing Enterobacter cloacae from orthopedic patients and environment of a tertiary referral hospital in Tanzania

Benson R. Kidenya,
Gerald Mboowa,
Ivan Sserwadda,
Stephen Kanyerezi,
Esther Nakafu,
Inyasi Lawrence Akaro,
Baraka Mkinze,
Moses L. Joloba,
Jeremiah Seni

Affiliations

Benson R. Kidenya: Department of Biochemistry and Molecular Biology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania; Corresponding author.
Gerald Mboowa: Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P. O Box 7072, Kampala, Uganda; African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O Box 22418, Kampala, Uganda; Africa Centres for Disease Control and Prevention, African Union Commission, Roosevelt Street, P.O. Box 3243, W21 K19, Addis Ababa, Ethiopia
Ivan Sserwadda: Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P. O Box 7072, Kampala, Uganda; African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O Box 22418, Kampala, Uganda; Department of Biochemistry and Bioinformatics, School of Pure and Applied Sciences, Pwani University, P.O Box 195-80108, Kilifi, Kenya
Stephen Kanyerezi: Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P. O Box 7072, Kampala, Uganda; Africa Centres for Disease Control and Prevention, African Union Commission, Roosevelt Street, P.O. Box 3243, W21 K19, Addis Ababa, Ethiopia
Esther Nakafu: College of Veterinary Medicine, Animal Resources and Bio-security (COVAB), Makerere University, P. O Box 7062, Kampala, Uganda
Inyasi Lawrence Akaro: Department of Orthopedic Surgery, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
Baraka Mkinze: Department of Orthopedic Surgery, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania
Moses L. Joloba: Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P. O Box 7072, Kampala, Uganda
Jeremiah Seni: Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza, Tanzania

Journal volume & issue: Vol. 62
p. 101486

Abstract

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Objectives: We investigated the genomic epidemiology of extended-spectrum β-lactamase-producing Enterobacter cloacae (ESBL-Ec) isolates from patients and hospital environment to better understand their distribution to help devising effective strategies for infection prevention and control. Methods: We screened ESBL-Ec at Bugando Medical Center (BMC) in Mwanza, Tanzania. Rectal swabs from orthopedic patients on admission and swabs from the neighboring inanimate environment were collected. Following microbial culture, DNA was extracted from pure ESBL-Ec, and whole-genome sequencing was done. Sequence typing (ST), plasmid replicons, drug resistance, and virulence genes were deciphered using the Rapid Microbial Analysis Pipeline (rMAP). Results: We obtained 209 ESBL isolates, of which 15 (7.2 %) were ESBL-Ec [8 (53.3 %) from patients and 7 (46.7 %) from the environment]. Seven isolates were novel and eight were diverse, each with a unique ST. All isolates harbored two to five β-lactamase genes, with the predominance of blaCTX-M-15 (15/15), blaOXA-1 (14/15), blaTEM (14/15) and blaACT (12/15). The most common non β-lactam drug resistance genes were aac(3)-IIa (14/15), aac(6′)-Ib-cr (14/15), fosA (14/15), and qnrB1 (12/15), aph(3″)-Ib (10/15) and aph(6)-Id (10/15). Eleven different types of plasmid replicons were identified in 14/15 of the isolates, harboring one to five plasmids, with the most common plasmids being IncFII (11/15) and IncFIB (10/15). All isolates harbored the outer membrane protein (ompA), and curli protein (csg) was in 14/15 isolates. Conclusion: Admitted orthopedic patients and the hospital environment act as a reservoir of ESBL-Ec with diverse STs and endowed with drug resistance and arsenals of virulence genes, calling for their routine screening on admission for mitigation of potential subsequent infections.

Published in New Microbes and New Infections

ISSN: 2052-2975 (Online)
Publisher: Elsevier
Country of publisher: United Kingdom
LCC subjects: Medicine: Internal medicine: Infectious and parasitic diseases
Website: https://www.sciencedirect.com/journal/new-microbes-and-new-infections

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