Pan-resistome characterization of uropathogenic Escherichia coli and Klebsiella pneumoniae strains circulating in Uganda and Kenya isolated from 2017-2018

Abstract

Background: Urinary tract infection (UTI) develops after a pathogen adhered 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 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. Methods: 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 comparitive analysis their pangenome contents. Results: 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 2,862 and 3,464 genes comprised the core genome of E. coli and K. pneumoniae population, respectively. Among these are 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. Accessory genomes of both species collection were detected several β-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 3 or more antibiotic classes. Conclusions: Our findings illustrate the abundant 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.

Antimicrobial resistance and virulence characteristics of Klebsiella pneumoniae isolates in Kenya

“…For library preparation, the extracted DNA was end-repaired using the NEBNext® UltraII End Repair/dA-Tailing kit using the manufacturer's instructions. LSK 109 ligation kit, EXP-NBD 104 (1-12), and EXP-NBD 114 (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24) Native Barcoding kits were used to barcode each DNA sample and adapters added. The DNA library was loaded onto a FLO-MIN106 R9.…”

“…In Kenya, several studies have indicated an emergence of the clonal spread of MDR KP and horizontal transfer of AMR genes (6,(12)(13)(14)(15). Increased use of 3rd generation cephalosporins in the early 2000s has increased extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales, the most prevalent of which in Kenya are CTX-M-15 and SHV (10,12,16,17).…”

“…Although some studies in Kenya have identified KP lineages ST11, ST15, and ST17, associated with hospital outbreaks (6,13), and the high-risk MDR ST147 (24), few studies have examined virulence genes in Kenyan KP isolates (13).…”

Protocol for an interdisciplinary cross-sectional study investigating the social, biological and community-level drivers of antimicrobial resistance (AMR): Holistic Approach to Unravel Antibacterial Resistance in East Africa (HATUA)

“…Urine samples were analysed using culture and antibiotic sensitivity testing (C&AST), and a total of 150 bacterial isolates (n=91 from Kenya and n=59 from Uganda) were genomically characterised, which confirmed a high prevalence of uropathogenic strains Escherichia coli and Klebsiella pneumoniae , and revealed high levels of multidrug resistance mainly disseminated via clonal and horizontal transfers (the full results are reported here 28 ). This exploratory pilot study illustrated the feasibility of collecting linked microbiological, genomic and socioeconomic data, and highlighted important operational fieldwork issues regarding linkage and follow-up to the homestead.…”

Protocol for an interdisciplinary cross-sectional study investigating the social, biological and community-level drivers of antimicrobial resistance (AMR): Holistic Approach to Unravelling Antibiotic Resistance in East Africa (HATUA)

“…HATUA pilot activities in 2017-18 in Uganda demonstrated the feasibility of the holistic approach by conducting a study of microbiological and genomic features of urinary pathogens collected from clinic patients, combined with quantitative socio-demographic data. Genomic characterisation of the strains (predominantly E. coli and K. pneumoniae ) revealed high levels of resistance mainly disseminated via clonal and horizontal transfer [28]. We also conducted in-depth interviews with patients and healthcare providers, and focus group discussions with community members in Mbarara district, Uganda to explore behaviours and attitudes to AB use.…”