High rate of multi-drug resistant Escherichia coli isolated from patients with urinary tract infections in Ifakara-Tanzania: implications for empirical antibiotic treatment guidelines and stewardship programs

Abstract

Background: Antimicrobial resistance (AMR) in Sub-Saharan Africa is a significant health threat, with limited data guide treatment. This study investigates multi-drug resistant Escherichia coli in urinary tract infections (UTIs) in rural Tanzania to guide empirical treatment strategies.

Methods: A cross-sectional prospective study of adults with UTIs was conducted at St. Francis Regional Referral Hospital in Ifakara, Tanzania, from September 2021 to August 2023. Urine culture isolates underwent routine diagnostics in Tanzania and E. coli isolates underwent whole-genome sequencing in Switzerland.

Results: Of 1055 patients, 248 (23.5%) had positive urine cultures, with E. coli as predominant pathogen (n = 87; 55.7%). Extended-spectrum beta-lactamase-producing E. coli (ESBL-E) was identified in 20 (23.0%) isolates, primarily sequence type ST167 carrying CTX-M-27. All ESBL-E cases (20/20, 100.0%) and half of non-ESBL-E cases (29/58, 50.0%) received empiric antibiotics to which the isolates were documented as resistant. ESBL-E showed higher resistance to cotrimoxazole (100.0%) and ciprofloxacin (90.0%) latter recommended for complicated UTIs in Tanzania's Standard Treatment Guidelines (STG) compared to non-ESBL-E. All ESBL-E isolates were susceptible to nitrofurantoin, as recommended by STG for uncomplicated UTIs, and fosfomycin showed potential alternative for complicated cases.

Conclusion: Nearly one-quarter of E. coli isolates causing UTIs were ESBL-E, predominantly ST167 harboring bla_CTX-M-27. Notably, nitrofurantoin remained effective for uncomplicated UTIs, similarly, fosfomycin emerged as a viable alternative. However, ciprofloxacin, despite being recommended in local guidelines for complicated UTIs, showed no efficacy. The genetic similarity between human and environmental isolates underscores the critical need for a One Health approach to tackle antimicrobial resistance (AMR) in the region.

Keywords: Multi-drug resistant Escherichia coli; Rural-Tanzania; Treatment guidelines; Urinary tract infections.

Fig. 1

Map showing the location of St. Francis Regional Referral Hospital (SFRRH), Ifakara-Tanzania

Fig. 2

Flow chart of bacteria identification, resistance and antibiotic treatment

Fig. 3

Phylogenetic tree based on SNPs showing the clonal relationship among our ESBL E. coli isolated from UTI patients (blue rectangle) and ESBL E. coli from the aquatic environment of Lake Victoria-Tanzania (red square)

Fig. 4

STs of Non-ESBL and ESBL E. coli Clones

Fig. 5

SNP-based phylogenetic tree of 97 E. coli (20 ESBL-E. coli, 67 Non-ESBL E. coli and 10 E. coli isolates from Lake Victoria [20]. From centre to periphery, the different layers correspond to the isolate name, cohorts, the phylogroup, the fimH allele, the serotype, the sequence type (according to the Achtman scheme), the quinolone resistance gene. In the layer dedicated to ST type, ST167 ESBL E. coli from our study closely related to those of fish are annotated with a star