Background: Antimicrobial resistance is a global public health concern contributing to increased morbidity and mortality particularly in low-income countries. Studies on commensal bacteria are important as they reflect the state of antimicrobial susceptibility patterns in populations. However, susceptibility data on potentially pathogenic commensal bacteria from individuals in communities are still limited. The aim of this cross-sectional study was to determine the susceptibility profiles of Escherichia coli and Klebsiella species isolated from clients attending outpatient clinics in Kampala (urban district) and two rural districts of Uganda, Kayunga and Mpigi. Factors associated with such carriage are also reported.
Results: A total of 1448 participants were recruited into the study with 985 yielding organisms of interest from stool or urine samples (one per client). Most growth occurred from stool samples (636/985, 87%), of which 620/636 (97%) grew E. coli while 16 (3%) were Klebsiella pneumoniae. Growth from urine was 349/985 (35%) of which 310/349 (89%) were E. coli while 39 (11%) K. pneumoniae. High rates of antimicrobial resistance were detected among E. coli and Klebsiella isolates combined: sulphamethoxazole/trimethoprim 70%, amoxicillin/clavulanate 36%, chloramphenicol 20%, ciprofloxacin 11%, gentamicin 11%, nitrofurantoin 4%, ceftriaxone 3%, piperacillin/tazobactam 27%, cefoxitin 22%, and cefepime 15%. Multidrug resistance was noted in 33% of the isolates. None of the isolates were resistant to imipenem. Overall, isolates from Kampala were more resistant to antimicrobials. Across the three districts combined, isolates producing beta-lactamase enzymes extended spectrum β-lactamase-(ESBL) and AmpC comprised 5.3 and 13.2%, respectively. Further, medical procedures involving inoculation were independent risk factors [aOR 50.76 (1.80, 1432.90)] while residing in a rural district and use of sulphamethoxazole/trimethoprim 3 months prior to visiting the outpatient clinics were protective against carriage of multidrug resistant isolates. Furthermore, use of gentamicin was protective against AmpC producing isolates while clients attending HIV/AIDs clinics were less likely to carry such isolates. No factor was independently associated with carriage of ESBL-producing isolates.
Conclusion: Antimicrobial resistance is prevalent among E. coli and K. pneumoniae carried in the gut of clients attending outpatient clinics in Kampala and two rural districts in Uganda. This could complicate treatment options for community-acquired infections caused by the Enterobacteriaceae.
Keywords: Antimicrobial resistance; Commensal bacteria; Escherichia coli; Kampala; Klebsiella pneumoniae; Outpatient clinic; Rural; Uganda; Urban.