Phenotypic Characterization and Antibiograms of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated at the Human-Animal-Environment Interface Using a One Health Approach Among Households in Wakiso District, Uganda.

Background: The occurrence of extended spectrum beta-lactamase (ESBL) producing bacteria such as Escherichia coli has increasingly become recognized beyond hospital settings. Resistance to other types of antibiotics limits treatment options while the existence of such bacteria among humans, animals, and the environment is suggestive of potential zoonotic and reverse-zoonotic transmission. This study aimed to establish the antibiotic susceptibility profiles of the ESBL-producing Escherichia coli (ESBL-EC) from human, animal, and environmental isolates obtained among farming households within Wakiso district using a One Health approach. Methods: A total of 100 ESBL-EC isolates from humans 35/100 (35%), animals 56/100 (56%), and the environment 9/100 (9%) were tested for susceptibility to 11 antibiotics. This was done using the Kirby-Bauer disk diffusion method according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Data were analyzed in STATA ver. 16 and graphs were drawn in Microsoft excel ver. 10. Results: Most of the ESBL-EC isolates (98%) were resistant to more than two antibiotics. ESBL-EC isolates were most susceptible to meropenem (MEM) (88.0%), and imipenem (82.0%) followed by gentamicin (72%). ESBL-EC isolates from humans were most susceptible to meropenem (MEM) followed by imipenem (IPM)> gentamicin (CN)> ciprofloxacin (CIP). Animal samples were more susceptible to MEM, IPM, and CN but were highly resistant to cefotaxime (CTX)> cefepime (FEP)>other antibiotics. Multidrug resistance (MDR) was mostly reported among households keeping goats under intensive husbandry practices. Seven percent of the isolates exhibited carbapenem resistance while 22% showed aminoglycoside resistance. Similar resistance patterns among humans, animals, and environmental samples were also reported. Conclusion: Our study provides baseline information on non-hospital-based MDR caused by ESBL-EC using a One Health approach. ESBL-EC isolates were prevalent among apparently healthy community members, animals, and their environment. It is important to conduct more One Health approach studies to generate evidence on the drivers, resistance patterns, and transmission of ESBL-producing organisms at the human-animal-environmental interface.

Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda.

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017-2019). AST revealed 73 % (30 of 41) of isolates were resistant to one or more antibiotics and 29 % (12 of 41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24 % carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton-Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.

Prevalence of plasmid-mediated AmpC beta-lactamases in Enterobacteria isolated from urban and rural folks in Uganda.

Background: AmpC beta-lactamase-producing bacteria are associated with increased resistance to third-generation cephalosporins. Here, we describe plasmid-mediated AmpC beta-lactamase-producing enterobacteria isolated from urban and rural dwellers in Uganda. Methods: Stool and urine from 1,448 individuals attending outpatient clinics in Kampala and two rural districts in central Uganda were processed for isolation of Escherichia coli and Klebsiella. Following antibiotic susceptibility testing, cefoxitin resistant isolates, and amoxicillin/clavulanate resistant but cefoxitin susceptible isolates, were tested for AmpC beta-lactamase production using the cefoxitin-cloxacillin double-disc synergy test. Carriage of plasmid-mediated AmpC beta-lactamase-encoding genes (pAmpC) and extended spectrum beta-lactamase (ESBL) encoding genes was determined by PCR. Results: Nine hundred and thirty E. coli and 55 Klebsiella were recovered from the cultured samples, yielding 985 isolates investigated (one per participant). One hundred and twenty-nine isolates (13.1%, 129/985) were AmpC beta-lactamase producers, of which 111 were molecularly characterized for pAmpC and ESBL gene carriage. pAmpC genes were detected in 60% (67/111) of the AmpC beta-lactamase producers; pAmpC genes were also detected in 18 AmpC beta-lactamase non-producers and in 13 isolates with reduced susceptibility to third-generation cephalosporins, yielding a total of 98 isolates that carried pAmpC genes. Overall, the prevalence of pAmpC genes in cefoxitin resistant and/or amoxicillin/clavulanate resistant E. coli and Klebsiella was 59% (93/157) and 26.1% (5/23), respectively. The overall prevalence of pAmpC-positive enterobacteria was 10% (98/985); 16.4% (45/274) in Kampala, 6.2% (25/406) Kayunga, and 9.2% (28/305) Mpigi. Ciprofloxacin use was associated with carriage of pAmpC-positive bacteria while residing in a rural district was associated with protection from carriage of pAmpC-positive bacteria. Conclusion: pAmpC beta-lactamase producing enterobacteria are prevalent in urban and rural dwellers in Uganda; therefore, cefoxitn should be considered during routine susceptibility testing in this setting.

Antimicrobial susceptibility profiles of Escherichia coli and Klebsiella pneumoniae isolated from outpatients in urban and rural districts of Uganda.

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 ß-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.