African Journal of
Microbiology Research

  • Abbreviation: Afr. J. Microbiol. Res.
  • Language: English
  • ISSN: 1996-0808
  • DOI: 10.5897/AJMR
  • Start Year: 2007
  • Published Articles: 4998

Full Length Research Paper

Phylogenetic analysis of multidrug resistant E. coli isolates from the urinary tract in Bushenyi district, Uganda using the new Clermont phylotyping method

Martin Odoki
  • Martin Odoki
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Adamu Almustapha Aliero
  • Adamu Almustapha Aliero
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Julius Tibyangye
  • Julius Tibyangye
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Sarah Kemuma Onkoba
  • Sarah Kemuma Onkoba
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Bashir Alkali
  • Bashir Alkali
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Josephat Nyabayo Maniga
  • Josephat Nyabayo Maniga
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Emmanuel Eilu
  • Emmanuel Eilu
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Eddie Wampande
  • Eddie Wampande
  • Department of Biochemistry, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P. O. Box 71 Bushenyi, Uganda.
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Charles Drago Kato
  • Charles Drago Kato
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Ezera Agwu
  • Ezera Agwu
  • Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P.O. Box 71 Bushenyi, Uganda.
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Joel Bazira
  • Joel Bazira
  • Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda.
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  •  Received: 07 October 2019
  •  Accepted: 13 January 2020
  •  Published: 29 February 2020

Abstract

Due to the increasing rates of multidrug resistance (MDR) among the Enterobacteriaceae that cause urinary tract infections (UTIs), selection of antimicrobial agents for empirical therapy is becoming a major challenge. This study determines the antimicrobial resistance profiles, multidrug resistance profiles, multiple antibiotic resistance indices (MARI), factors associated with MDR UTIs and the phylogenetic groups of MDR Escherichia coli strains isolated from the urinary tract among patients attending hospitals in Bushenyi District, Uganda. In this cross-sectional study, a total of 86 bacterial uropathogens isolated from 267 study participants suspected to have UTIs were subjected to antimicrobial susceptibility tests using the Kirby Bauer Disk diffusion method. Data for the factors associated with MDR was obtained by the use of questionnaires. Phylogenetic groups of the MDR E. coli were determined using the new Clermont method for phylotyping E. coli. Descriptive and multiple logistic regression statistical tools were used to determine phylogenetic groups, and assess for statistically significant relationship between MDR UTIs and factors suspected to be associated with MDR UTIs respectively. The isolates assigned as group B2 9/12 (75.0%), B1 2/5 (40.0%) and A 2/7 (28.6%) by using the old Clermont method could not be phylotyped using the new Clermont method and were grouped as non-typeable strains of E. coli. Our study demonstrates high prevalence of the non-typeable strains of MDR E. coli, we therefore recommend the use of modern DNA sequencing-based approaches which is the gold standard for genotyping bacteria, that this current study could not afford.

 

Key words: Phylogenetic analysis, bacterial urinary tract infections, factors associated with, multidrug resistance, Bushenyi District, Uganda.