Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes
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Date
2020
Journal Title
Journal ISSN
Volume Title
Publisher
PLoS ONE
Abstract
The crisis of antimicrobial resistance is already here with us, affecting both humans and animals
alike and very soon, small cuts and surgeries will become life threatening. This study
aimed at determine the whole genome sequences of multi-drug resistant Escherichia coli
isolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence
and resistant genes.
Methods
This was a laboratory based cross sectional study. Bacterial isolates analyzed in this study
were 42 multidrug resistant E. coli isolated from stool samples from both humans (n = 30)
and cattle (n = 12) in pastoralist communities collected between January 2018-March 2019.
Most of the isolates (41/42) were resistant to three or more antibiotics (multi-drug resistant)
and 21/42 isolates were ESBL producers; 13/30 from human and 8/12 from cattle. Whole
Genome Sequencing (WGS) was carried out at the facilities of Kenya Medical Research
Institute-Wellcome trust, Kilifi, to determine the phylogenomic changes, virulence and resistant
genes.
Results
At household level, the genomes from both human and animals clustered away from one
another except for one instance where two human isolates from the same household clustered
together. However, 67% of the E. coli isolated from cattle were closely related to those found in humans. The E. coli isolates were assigned to eight different phylogroups: A, B1,
B2, Cladel, D, E, F and G, with a majority being assigned to phylogroup A; while most of
the animal isolates were assigned to phylogroup B1. The carriage of multiple AMR genes
was higher from the E. coli population from humans than those from cattle. Among these
were Beta-lactamase; blaOXA-1: Class D beta-lactamases; blaTEM-1, blaTEM-235:
Beta-lactamase; catA1: chloramphenicol acetyl transferase; cmlA1: chloramphenicol
efflux transporter; dfrA1, dfrA12, dfrA14, dfrA15, dfrA17, dfrA5, dfrA7, dfrA8: macrolide
phosphotransferase; oqxB11: RND efflux pump conferring resistance to fluoroquinolone;
qacL, qacEdelta1: quinolone efflux pump; qnrS1: quinolone resistance gene; sul1, sul2,
sul3: sulfonamide resistant; tet(A), tet(B): tetracycline efflux pump. A high variation of virulence
genes was registered among the E. coli genomes from humans than those of cattle
origin.
Conclusion
From the analysis of the core genome and phenotypic resistance, this study has demonstrated
that the E. coli of human origin and those of cattle origin may have a common ancestry.
Limited sharing of virulence genes presents a challenge to the notion that AMR in
humans is as a result of antibiotic use in the farm and distorts the picture of the directionality
of transmission of AMR at a human-animal interface and presents a task of exploring alternative
routes of transmission of AMR.
Description
Keywords
Genome sequence, Multi-drug resistant Escherichia coli, Pastoralist Community, Phylogenomic changes, Virulence, Resistant genes
Citation
Iramiot JS, Kajumbula H, Bazira J, de Villiers EP, Asiimwe BB (2020) Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes. PLoS ONE 15(5): e0231852. https://doi.org/10.1371/journal.pone.0231852