Antimicrobial resistance in commensal Escherichia coli isolated from poultry along a gradient of intensification of poultry production in the Northern Zone of Tanzania

Maganga, Ruth (2019) Antimicrobial resistance in commensal Escherichia coli isolated from poultry along a gradient of intensification of poultry production in the Northern Zone of Tanzania. MSc(R) thesis, University of Glasgow.

Abstract

Antimicrobial resistance is a threat to human and animal health. There is widespread, unregulated use of antimicrobials in Tanzania in poultry production, which may impose selective pressure on gastrointestinal commensals. The indiscriminate use of antimicrobials in health care and agriculture has exerted selective pressure among commensal bacteria such as Escherichia coli enabling them to acquire fitness against antimicrobials. Extensive research has been conducted in human and animal pathogens, but few studies have investigated antimicrobial resistance in enteric commensals. When enteric commensals share the same niche with pathogens, there is potential for lateral gene transfer between commensals and pathogens. One of the aims of the present study was to determine the prevalence of antimicrobial resistant commensal coliforms across four poultry farm types in Arusha and Moshi, Northern Zone, Tanzania. The second was to determine prevalence of AMR in commensal E. coli isolates using different thresholds for interpret resistance, and to examine the impact of methodology and thresholds on apparent AMR prevalence. Samples were collected from Moshi and Arusha urban districts. Ten wards were randomly chosen in each district, with random selection of one representative farm in each ward per production system (extensive, semi- intensive, indigenous intensive and broiler intensive). In each farm, cloacal swabs were collected from 10 chickens. Resistance against four antimicrobial compounds was explored, selected based on common use (tetracycline) or importance to human health based on the World Health Organization’s list of Critically Important Antimicrobials (ciprofloxacin, ceftazidime and imipenem). The breakpoint plate method was used in screening for presence of resistant coliforms in cloacal samples in Tanzania whilst confirmatory testing was conducted in Glasgow on a subset of plate weeps. Chromogenic agar was used in identification of individual E. coli isolates whilst uidA PCR was used for confirmation of the species. To analyse the susceptibility of individual isolates, disc diffusion testing was used. Inhibition zone diameters were interpreted using clinical breakpoints (CB), ecological cutoffs (ECOFFS) (provided by the European i Committee on Antimicrobial Susceptibility Testing (EUCAST) and normalised resistance interpretation based wild type cut-offs (COWT). No correlation was found between prevalence data generated in Tanzania and Glasgow. Resistance to each of the four compounds was seen at least once in every farm. There was no consistent pattern revealing a clear association between intensification of poultry production and prevalence of resistance. Tetraycline resistance was consistently higher across farm types compared to other antimicrobials based on both disc diffusion method and the breakpoint plate method. According to the CB and COWT interpretation, the prevalence of AMR was low for ceftazidime and imipenem (< 4%), intermediate for ciprofloxacin, and high for tetracycline (> 67%). Relatively high prevalence was observed based on ECOFFS, e.g. 45.8% for ceftazidime and 64.4% for imipenem. These results suggest that interpretation of resistance can be impacted by the type of threshold used. Our study reveals that healthy poultry are reservoirs of resistant E. coli. Thus, there may be a risk of transmission of resistant bacteria in and out of the farms, for example, through contaminated water, use of poultry manure in crop production, or through the food chain. Control strategies need to be developed, including further studies to determine factors that may be contributing to the AMR problem in poultry farms.

• Item Type: Thesis (MSc(R))
• Qualification Level: Masters
• Additional Information: Professor Mmbaga Blandina is a director of Kilimanjaro Clinical Research Institute in Tanzania where part of the research work was carried out.
• Keywords: Antimicrobial resistance, antimicrobials, selective pressure, breakpoint, susceptibility, prevalence, normalised resistance interpretation
• Colleges/Schools: College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
• Funder's Name: Biotechnology and Biological Sciences Research Council (BBSRC)
• Supervisor's Name: Zadoks, Professor Ruth, Matthews, Professor Louise and Blandina, Professor Mmbaga
• Date of Award: 2019
• Depositing User: Miss Ruth Maganga
• Unique ID: glathesis:2019-75028
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 02 Oct 2019 16:13
• Last Modified: 01 Aug 2022 10:25
• Thesis DOI: 10.5525/gla.thesis.75028
• URI: https://theses.gla.ac.uk/id/eprint/75028