Molecular Characterization of Uropathogenic Escherichia coli Isolates from Clients with Community-acquired Urinary Tract Infections Attending Outpatient Clinics in Kampala District

Abstract

Background: Community-acquired urinary tract infection (CA-UTI) commonly caused by uropathogenic Escherichia coli (UPEC) is mainly treated empirically but there is increased resistance to different common antimicrobial classes, hence multidrug resistance (MDR). The resistance spread mode, if known more would inform control measures to limit its evolution. This study aimed at determining resistance transfer pattern, virulence profiles and predominant Sequence Type (ST) of UPEC isolates from outpatients in Kampala District, Uganda. Methodology: This was a cross-sectional study to analyze UPEC isolated from outpatients with CA-UTI in Kampala District, done at the Medical Microbiology Department of Makerere University College of Health Sciences. Kirby-Bauer disc diffusion method for drug susceptibility of all sample population isolates, in-vitro conjugation on ESBL-positive isolates, polymerase chain reaction (PCR) and agarose gel electrophoresis were done. A two-locus approach with sequencing of fumC and adk alleles was performed to determine the isolates population clonal relatedness. Two (fumC and adk) phylogenetic trees were compared for any agreement. Phenotype and genotype proportions and ST relatedness were analyzed by running frequencies. Results: Out of 30, 18 (60%) of the isolates had ESBL phenotype. MDR isolates (28/30, 93%) were resistant to beta-lactam agents and at least two of commonly used non-beta-lactams (like nalidixic acid, sulphamethoxazole-trimethoprim and tetracycline), and 18/28 (64%) of these had ESBL. The most effective antimicrobials were amikacin and meropenem with none (0%), and nitrofurantoin with 1/30 (3%) of the isolates resistant. In-vitro conjugation resulted into all (5/5, 100%) of the tested donors transferring all their resistance phenotypes to transconjugants. All genotypes present in donors i.e. beta-lactamases (blaCtxmu & blaTem) and non-beta-lactamase (qnrS, sul1, sul3, tetA & cat) were transferred (7/8, 88%) to transconjugants, apart from qep. The population of CA-UPEC consisted of diverse STs – with no dominant clone spreading the observed resistance. Participants with CA-UTI and MDR E. coli (17/25, 68%) had characteristics which increase spread of antimicrobial resistance by horizontal transfer between bacteria. Conclusions: The high frequencies of ESBL and MDR phenotypes and genotypes are more likely disseminated by mainly horizontal resistance gene transfer as opposed to clonal transfer. Recommendations: Authorities should focus on minimizing spread by horizontal resistance transfer, by reducing antibiotic pressure in the environment and regulating the empirical regimen. Whole genome sequencing (not ABI) and NGS should be used in E. coli genetic analyses.