Pan-Resistome Characterization of Uropathogenic Escherichia coli and Klebsiella pneumoniae Strains Circulating in Uganda and Kenya, Isolated from 2017–2018
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Date
2021
Journal Title
Journal ISSN
Volume Title
Publisher
Antibiotics
Abstract
Urinary tract infection (UTI) develops after a pathogen adheres to the inner lining of
the urinary tract. Cases of UTIs are predominantly caused by several Gram-negative bacteria and
account for high morbidity in the clinical and community settings. Of greater concern are the strains
carrying antimicrobial resistance (AMR)-conferring genes. The gravity of a UTI is also determined by
a spectrum of other virulence factors. This study represents a pilot project to investigate the burden
of AMR among uropathogens in East Africa. We examined bacterial samples isolated in 2017–2018
from in- and out-patients in Kenya (KY) and Uganda (UG) that presented with clinical symptoms of
UTI. We reconstructed the evolutionary history of the strains, investigated their population structure,
and performed comparative analysis their pangenome contents. We found 55 Escherichia coli and 19
Klebsiella pneumoniae strains confirmed uropathogenic following screening for the prevalence of UTI
virulence genes including fimH, iutA, feoA/B/C, mrkD, and foc. We identified 18 different sequence
types in E. coli population while all K. pneumoniae strains belong to ST11. The most prevalent E. coli
sequence types were ST131 (26%), ST335/1193 (10%), and ST10 (6%). Diverse plasmid types were
observed in both collections such as Incompatibility (IncF/IncH/IncQ1/IncX4) and Col groups.
Pangenome analysis of each set revealed a total of 2862 and 3464 genes comprised the core genome
of E. coli and K. pneumoniae population, respectively. Among these are acquired AMR determinants
including fluoroquinolone resistance-conferring genes aac(3)-Ib-cr and other significant genes: aad,
tet, sul1, sul2, and cat, which are associated with aminoglycoside, tetracycline, sulfonamide, and
chloramphenicol resistance, respectively. Accessory genomes of both species collections were detected
several -lactamase genes, blaCTX-M, blaTEM and blaOXA, or blaNDM. Overall, 93% are multi-drug
resistant in the E. coli collection while 100% of the K. pneumoniae strains contained genes that are
associated with resistance to three or more antibiotic classes. Our findings illustrate the abundant
acquired resistome and virulome repertoire in uropathogenic E. coli and K. pneumoniae, which are
mainly disseminated via clonal and horizontal transfer, circulating in the East African region. We
further demonstrate here that routine genomic surveillance is necessary for high-resolution bacterial
epidemiology of these important AMR pathogens.
Description
Keywords
Antimicrobial resistance, Pangenome, lmic, Public health
Citation
Decano, A.G.; Pettigrew, K.; Sabiiti,W.; Sloan, D.J.; Neema, S.; Bazira, J.; Kiiru, J.; Onyango, H.; Asiimwe, B.; Holden, M.T.G. Pan-Resistome Characterization of Uropathogenic Escherichia coli and Klebsiella pneumoniae Strains Circulating in Uganda and Kenya, Isolated from 2017–2018. Antibiotics 2021, 10, 1547. https://doi.org/ 10.3390/antibiotics10121547