Reservoirs, transmission and Antibiotic Resistance profiles of extended spectrum beta lactamase-producing Escherichia coli at the human-animal-environment interface among farming communities in Wakiso District, Central Uganda

Abstract

Background: The emergence of Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) has raised considerable global Public Health concern due to antimicrobial resistance (AMR). Therefore, this study aimed at understanding reservoirs, transmission dynamics and antibiotic resistance of the ESBL-Ec at the human-animals-environment interface among selected farming households in Wakiso district, central Uganda. Materials and methods: The study utilized a mixed-methods cross-sectional approach to comprehensively investigate Extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) at the human-animal-environment interface in Wakiso district, central Uganda. The research encompassed various methodologies including field epidemiology, qualitative methods such as Focus Group Discussions (FGDs) and Key Informant Interviews (KIIs), biological sample collection and respective laboratory-based techniques. The investigation consisted of five distinct sub-studies: Sub-study 1: A cross-sectional survey using a semi-structured questionnaire was conducted in Wakiso district between June and September 2021. A total of 652 households were viited to conduct the survey. Statistical analyses were employed to determine associations between demographic factors, antibiotic knowledge, and antimicrobial resistance awareness. Sub-study 2: Epidemiological data and 988 samples were collected from 104 households, encompassing human (fecal and urine), animal (fecal), and environmental samples. ESBL-Ec presence was confirmed using double-disk synergy tests, and prevalence ratios were computed. Sub-study 3: Susceptibility profiles of 100 ESBL-Ec isolates from humans, animals, and the environment were tested against 11 antibiotics. Analysis followed Clinical and Laboratory Standards Institute (CLSI) guidelines. Sub-study 4: Whole genome sequencing was conducted on 12 ESBL-Ec isolates using the MiSeq platform (Illumina), allowing for genetic relatedness comparison among isolates from different sources. Sub-study 5: A qualitative survey involving FGDs and Key Informant Interviews KIIs within Wakiso district was conducted. Data was analysed in NVivo 12 through thematic network analysis. This combination of approaches collectively aimed at unravelling the reservoirs, transmission dynamics and antibiotic resistance profiles of ESBL-Ec within the studied communities Results: Sub-study 1: Subsistence farming, higher educational level and younger age were found to be associated with belonging to a class of better knowledge. Sub-study 2: The overall prevalence of ESBL-Ec at the human-animal-environment interface was approximately 25.0% (95% CI: 22.7-28.3). The ESBL-Ec prevalence was 45.4%, 35.4% and 5.8% among humans, animals and environment respectively. Having visitors, utilizing veterinary services and using animal waste for gardening were positively associated with household ESBL-Ec contamination. However, covering the drinking water container with a lid was associated with absence of ESBL-Ec in a household. Sub-study 3: Most of the isolates (98%) were resistant to more than two antibiotic classes. Multi-drug resistance was mostly reported among households keeping goats under intensive husbandry practices. Seven percent of the isolates exhibited carbapenem resistance while 22% showed aminoglycoside resistance. Sub-study 4: The most abundant 100.0% (12/12) ESBL gene was blaEC, followed by blaTEM-1 among 91.7% (11/12) of the isolates. About 83.3% (10/12) of the isolates had the blaCTX-M-15 gene. blaCTX-M-55, bla-OXA-1 and blaCTX-M-27 were only present in 8.3% (1/12). The common phylogroups obtained from the ESBL-Ec samples were A, B2, F, B1 and D. Overall, all IncY and IncFIB (AP001918) plasmid replicons were shared among ESBL-Ec isolates from humans, animals, and environment. Within households, some human samples never had plasmids while animals and environment could only share resistance genes through plasmid IncFIB (AP001918). Sub-study 5: Cultural norms underlying animal production and close interactions between humans and animals were reported as key drivers for AMR spillover and amplification. Laxity in policy implementation, unskilled human resource, and weak surveillance systems for AMR were reported to be the underlying gaps in its management. Conclusion: Our study results provide baseline information on the wider dissemination and multi-drug resistance nature of ESBL-Ec at the human-animal-environment interface. Such abundance of the ESBL-Ec could potentially indicate un-detected transmission of AMR at this interface. Indeed, our study reveals certain plasmids for transmission of ESBL-Ec among HAE, even though these were more common between humans and environment than it is for animals. Culture-driven solutions, diagnosis before treatment, more sensitization of community health workers, and improved regulation of drug use as well as multi-sectoral collaborations may create a suitable environment for the implementation of One Health approaches in the management of AMR.