Antimicrobial use, prevalence of extended spectrum beta-lactamase producing escherichia coli and economic effects on cattle and poultry in Dar es salaam Tanzania

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Date

2023

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SOKOINE UNIVERSITY OF AGRICULTURE

Abstract

Antimicrobial usage (AMU) in livestock production provides a basis for improving animal health and productivity. However, it is evident that the over-dependence of animal production on antimicrobial agents is one of the major factors driving the emergence of antimicrobial resistance (AMR) in bacteria that can be transmitted via the food chain or environment to humans. This thesis aims to assess antimicrobial use in cattle and poultry production in relation to resistance in Extended Spectrum Beta-Lactamase (ESBL) producing Escherichia coli (E. coli) and also gain insight into economic effects (cost and benefit) of antimicrobial use reduction in animal production inIlala, Kinondoni and Ubungo districts which form part of the Dar es Salaam region, Tanzania with the following objectives.(i) To conduct a systematic review on the methods and metrics used to quantify and assess MU in cattle and poultry production in Sub-Saharan Africa, (ii) To determine the quantity, quality and pattern of antimicrobial use in cattle and poultry production in Dar es Salaam, Tanzania, (iii) To assess antimicrobial consumption in food-producing animals in Dar es Salaam, Tanzania, (iv) To determine the prevalence and antimicrobial resistance pattern of ESBL producing E.coli isolates from cattle and poultry production, and (v) To estimate the economic effects (costs and benefits) of antimicrobial use reduction in cattle and poultry production. In view of these objectives, the findings of this thesis are presented in five scientific papers. Paper 1: A systematic literature review was conducted to provide an overview of methods of measuring AMU and metrics used, reviewing existing data on AMU in cattle and poultry production in order to identify gaps in Sub-Saharan Africa. The study revealed a deficit of studies on estimate of quantity and quality of antimicrobials used in food-producing animals in Sub-Saharan Africa. Paper 2: A cross-sectional study was conducted on 116 farms (51 poultry and 65 small-scale dairy cattle) in Ilala, Kinondoni and Ubungo Districts of Dar-es-Salaam region, Eastern Tanzania from 15th August to 30th September 2019 to investigate the level of antimicrobial use practice, type and quantity (amount) of antimicrobials consumed. The study revealed that 23 (19.8%) of the farms visited had records while 93 (80.2%) relied on recall, 58.6% of the livestock farmers had adequate level of practices (favorable) in accordance to antimicrobial use based on their responses, the most commonly used class of antimicrobials in poultry production were: Fluoroquinolones (25.5%), sulphonamides (21.6%), tetracycline (11.8%) while in the small-scale dairy farms, tetracycline (20.0%), beta-lactams (18.5%), sulphonamides (12.3%) were most commonly used. Quantitatively, in the poultry farms, the frequently used antimicrobial class sulphonamides (46.1%), tetracycline (19%) and Macrolides (14.2%). In the small-scale dairy farms, the use beta-lactams (36.4%), sulphonamides (22.3%), tetracycline (14.3%) were predominant. For Paper 3: a cross-sectional study, using data extraction form to collate antimicrobial use data from sales records (three consecutive years) of five established licensed veterinary pharmaceutical wholesales/outlets which were purposively selected in Ilala, Kinondoni and Ubungo. The study revealed that 178.4 tonnes of antimicrobials (by weight of active ingredients) were consumed during the 3 year study period (2016-2018), with an average of 59.5 ± 3.8 tonnes/year. The commonly sold antimicrobials were tetracycline (44.4%), sulphonamides (20.3%) and aminoglycosides (10.3%). Regarding veterinary antimicrobial use importance to human medicine, 34.4% were critically important antimicrobials; 4.1% were reserve and 51% were watch groups according to AWaRe categorization of WHO. Overall, a mean of 7.44 ± 0.81 mg/PCU (population correction unit) was consumed by food-producing animals during the three-year study period. Paper 4: A cross-sectional study was conducted in 54 of the previously visited farms where a pre-tested questionnaire on antimicrobial (antibiotics) usage was completed. A total of 121 E. coli isolates were obtained from 201 sampled small-scale dairy cattle rectal swabs. Looped rectal swab specimens from Stuart transport medium, were streaked directly onto plain MacConkey agar (Oxoid, Basingstoke, UK) and aerobically incubated at 370C for 24 hours. Presumptive E. coli colonies were Gram stained and then subjected to biochemical tests (Indole test, Methyl red test, Voges-Proskauer test and Citrate Utilisation test; IMViC test) for identification. E. coli strain ATCC 29522 was used as a reference organism. Antimicrobial susceptibility testing (AST) was performed against eight types of antimicrobials: (Tetracycline, (TE) (30 μg), Ampicillin, (AMP) (10 μg), Gentamicin, (CN) (10 μg), Ciprofloxacin,(CIP) (5 μg), Cefotaxime,(CTX) (30 μg), Nalidixic Acid, (NA) (30 μg), Trimethoprim/Sulfamethoxazole, (SXT) (1.25/23.75μg) and Chloramphenicol,(C) (30 μg)). The highest prevalence of AMR was against AMP (96.7%), CTX (95.0%), TE (50.4%) and SXT (42.1%). The 121 isolates of E. coli belong to 41 different phenotypes showing a variation of resistance. The most frequently observed phenotypes were AMP-SXT-CTX with a prevalence of 12.4%, followed by the combination AMP-CTX with 10.7% and TE-AMP-CTX and NA+TE+AMP+CTX with 8.3% each. Fifteen different phenotypes that produce Extended Spectrum Beta-Lactamases (ESBLs) were detected with a prevalence of 42.9% and 74.4% of E.coli isolates exhibited multidrug resistance (MDR). This probably confirms that antimicrobial use is unregulated and thus inappropriate use which led to the emergence and development of resistance. Paper 5: A cross-sectional study was conducted on randomly sampled broiler farms which were in production for one year in Kinondoni and Ubungo Districts in Dar es Salaam region of Tanzania from February to March 2021. A pre-tested questionnaire was used to capture data required to complete the model for the estimation of the economic effects (costs and benefits) on reduction of antimicrobial use. Data collected included: number of chicks bought and dead on the farm (mortality), observed clinical signs; signs of respiratory infections (coughing, wheezing, sneezing and nasal discharge), enteric infection (diarrhea) and lameness (locomotive signs) (morbidity). A Mclnerney model built on biological and economic parameters of disease effects on livestock production was used to analyze the data. The net costs and benefits were estimated within a partial budgeting framework in the model. The results of this study showed that antimicrobial use reduction will have an effect on mortality and morbidity and thus increase the cost of production due to changes in additional management changes (animal health management and technical management). Findings from this thesis recommend that rational AMU should be emphasized by targeting cattle and poultry production in Tanzania in general and Dar es Salaam in particular.

Description

PhD Dissertation.

Keywords

antimicrobial, effects on cattle, poultry, in livestock production, animal health

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