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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Publisher
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