Pan-Resistome Characterization of Uropathogenic Escherichia coli and Klebsiella pneumoniae Strains Circulating in Uganda and Kenya, Isolated from 2017–2018

Antibiotics

John Kiiru¹  Hellen Onyango²  Benon Asiimwe³  Stella Neema⁴  Joel Bazira⁵  Matthew T. G. Holden⁶  Kerry Pettigrew⁶  Wilber Sabiiti⁶  Derek J. Sloan⁶  Arun Gonzales Decano⁶ 

[1] Centre of Microbiology Research, Kenya Medical Research Institute, Off Raila Odinga Way, Nairobi P.O. Box 54840 00200, Kenya;Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62 000, Kenya;Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala P.O. Box 7062, Uganda;Department of Sociology and Anthropology, Makerere University, Kampala P.O. Box 7062, Uganda;Faculty of Medicine, Mbarara University of Science and Technology, Mbarara P.O. Box 410, Uganda;School of Medicine, University of St Andrews, St Andrews KY16 8BQ, UK;

关键词: antimicrobial resistance;    pangenome;    lmic;    public health;   

DOI  :  10.3390/antibiotics10121547

来源: DOAJ

【 摘 要 】

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 β-lactamase genes, bla_CTX-M, bla_TEM and bla_OXA, or bla_NDM. 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.

【 授权许可】

Unknown