CGIAR Antimicrobial Resistance Hub documents

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Antibiotic ecotoxicity and resistance risks in resource-constrained chicken and pig farming environments
(Journal Article, 2024-12-30) Gudda, Fredrick; Muloi, Dishon; Nganga, Fredrick; Nolari, Cynthia; Gao, Y.; Moodley, Arshnee
Antimicrobial resistance (AMR) data from agroecosystems in low- and middle-income countries is limited. We surveyed chicken (n = 52) and pig (n = 47) farms in Kenya to understand AMR in animal-environment pathways. Using LC-MS/MS, we validated the methods for analyzing eight common antibiotics and quantified the associated risks. Chicken compost (25.8%, n = 97/376) had the highest antibiotics prevalence, followed by pig manure-fertilized soils (23.1%, n = 83/360). The average antibiotic concentration was 63.4 µg/kg, which is below the environmentally relevant threshold (100 µg/kg), except for trimethoprim (221.4 µg/kg) among antibiotics and pig manure-fertilized soils (129.3 µg/kg) across sample types. Similarly, the average AMR risk quotient (RQ) was low (RQ < 0.1), except for trimethoprim and sulfamethoxazole (RQ ≥ 1). Ecotoxicity and AMR risks increased with flock size and the number of antibiotics used by pigs. Continuous environmental monitoring and large-scale studies on antibiotic contamination are crucial for evidence-based pollution control and the effective mitigation of environmental AMR.
Intersections between climate change and antimicrobial resistance: a systematic scoping review
(Journal Article, 2024-12-11) Bavel, B. van; Berrang-Ford, L.; Moon, K.; Gudda, Fredrick; Thornton, A.J.; Robinson, R.F.S.; King, R.
Climate change and antimicrobial resistance (AMR) present crucial challenges for the health and wellbeing of people, animals, plants, and ecosystems worldwide, yet the two are largely treated as separate and unrelated challenges. The aim of this systematic scoping Review is to understand the nature of the growing evidence base linking AMR and climate change and to identify knowledge gaps and areas for further research. We conducted a systematic search of the peer-reviewed literature in Scopus, Web of Science, and PubMed on 27 June, 2022. Our search strategy identified and screened 1687 unique results. Data were extracted and analysed from 574 records meeting our inclusion criteria. 222 (39%) of these reviewed articles discussed harmful synergies in which both climate change and AMR exist independently and can interact synergistically, resulting in negative outcomes. Just over a quarter (n=163; 28%) of the literature contained general or broad references to AMR and climate change, whereas a fifth (n=111; 19%) of articles referred to climate change influencing the emergence and evolution of AMR. 12% of articles (n=70) presented positive synergies between approaches aimed at addressing climate change and interventions targeting the management and control of AMR. The remaining literature focused on the shared drivers of AMR and climate change, the trade-offs between climate actions that have unanticipated negative outcomes for AMR (or vice versa), and, finally, the pathways through which AMR can negatively influence climate change. Our findings indicate multiple intersections through which climate change and AMR can and do connect. Research in this area is still nascent, disciplinarily isolated, and only beginning to converge, with few documents primarily focused on the equal intersection of both topics. Greater empirical and evidence-based attention is needed to investigate knowledge gaps related to specific climate change hazards and antimicrobial resistant fungi, helminths, protists, and viruses.
Prudent use and antimicrobial prescription practices in Ethiopian veterinary clinics located in different agroecological areas
(Journal Article, 2024-11-29) Tufa, T.B.; Amenu, Kebede; Fasil, N.; Regassa, F.; Beyene, T.J.; Revie, C.W.; Hogeveen, H.; Stegeman, J.A.
Background: Understanding antimicrobial prescribing (AMP) practices and their prudent use in livestock can support the implementation of stewardship programs in veterinary medicine. Empiric therapy using antimicrobials is widely practiced in resource-poor settings, including Ethiopia. This could significantly contribute to the global burden of antimicrobial resistance (AMR) and the potential accumulation of residues in food. This study assessed AMP practices in Ethiopian veterinary clinics located in different agroecological zones (AEZs) as well as adherence to antimicrobial stewardship principles (ASPs). Methods: Data were collected from case book records from four district veterinary clinics located in different AEZs in Ethiopia from 2015 to 2019. To identify factors associated with non-prudent AMP practices (i.e., the use of antimicrobials without therapeutic effects or benefits to the animal), data from registered clinical veterinary cases were selected using a systematic random sampling method. This led to the inclusion of approximately one-third of all records, including animal characteristics, disease symptoms and diagnosis, and details about the prescribed drugs. Descriptive statistics were used to report the proportions of drugs prescribed and adherence to the ASPs. The Chi-square test was used to establish an association between the drugs prescribed and the disease diagnoses and the districts. The factors associated with cases receiving antimicrobials and non-prudent AMP practices were also assessed using a multivariable logistic regression analysis. Results: In total, 12,438 clinical case records were considered. Approximately 97% of these cases received treatment without laboratory confirmation, and 15,243 drugs were prescribed. Among these prescriptions, 75% were for antimicrobials, with oxytetracycline (29%) and a combined formulation of penicillin-dihydrostreptomycin (19%) being the most often prescribed drugs. Overall, 19% of the cases were treated non-prudently with antimicrobials, with high incidences at Holeta (32%) and Sekoru (19%) (p < 0.001). Most cases, including viruses and other non-pathogens (100%), toxicants (97%), unknown causes (94%), fungi (70%), nutritional (64%), risk of bacterial infection (42%), and endo-ectoparasites (24%), were treated non-prudently. Cases receiving antimicrobials and non-prudent AMP were associated with Holeta and Sekoru study clinics, major clinical signs of bloat and loss of body condition, and illness due to viral infections (p < 0.05). Conversely, species of animals and cases diagnosed with multiple etiologic agents and respiratory diseases were negatively associated with prudent AMP practices (p < 0.05). Conclusions: Much of the prescription practice observed in this study did not adhere to the ASPs; there were significant discrepancies between the prescribed drugs and disease diagnoses. Prescribing antimicrobials for unrelated diagnoses may contribute to an increase in AMR. The study thus underlines the need for mechanisms to improve accurate disease diagnosis and prescriber adherence to prudent AMP in countries with limited resources.
Understanding the veterinary antibiotic flow in Malawi: Complexities, gaps and needs
(Journal Article, 2024-11-20) Mhone, Amos L.; Muloi, Dishon M.; Moodley, Arshnee
Introduction: Veterinary antibiotics are essential for maintaining animal health and welfare, however, small-scale farmers in Malawi face challenges in accessing them due to limited availability, affordability, and long distances to rural drug retailers. Methods: This study mapped the veterinary antibiotic distribution chain, examined the governance structure of the chain, and analyzed access and usage practices among stakeholders in Malawi. Data were collected through focus group discussions (n = 15), key informant interviews (n = 6) and individual interviews (n = 189). Results: The key stakeholders identified included regulators, local pharmaceutical manufacturers, wholesalers, veterinary clinics, veterinary retail shops, animal health practitioners, and farmers. The distribution of veterinary antibiotics was characterized by both formal and informal pathways for importing and distributing veterinary medicines. Additionally, there were issues with antibiotic mishandling such as improper storage on open shelves in direct sunlight and disposal in pit latrines. There was a marked lack of proper antibiotic dispensation training among veterinary medicine shop attendants, and in terms of regulation, there were gaps in coordination and overlapping mandates among regulatory authorities hindering effective regulation. Discussion: Regulatory agencies need to strengthen oversight of veterinary antibiotics, conduct trainings on antibiotic stewardship with various stakeholders, and enhance public-private partnerships to better manage the informal pathways for importing and distributing veterinary medicines. This multi-sectoral approach aims to ensure responsible use and improve the pharmacovigilance of veterinary antibiotics.
A cross-sectional survey on antibiotic use practices in semi-intensive chicken production systems in Thai Nguyen, Vietnam
(Poster, 2024-10-16) Yen Luu-Thi-Hai; Huyen Nguyen-Xuan; Sinh Dang-Xuan; Unger, Fred; Muloi, Dishon; Vinh Le-Dac; Nga Tran-Thi-Thuy; Hung Nguyen-Viet; Moodley, Arshnee
Enhancing public health: Five key takeaways on zoonotic disease and antimicrobial resistance surveillance
(Brief, 2024-09-30) Bett, Bernard K.; Fèvre, Eric M.; Ha Thi Thanh Nguyen; Sinh Dang-Xuan; Obuta, Amos; Mateo-Sagasta, Javier; Patel, Ekta
The need for integrated and efficient surveillance systems is important given the increasing risks of zoonotic diseases and antimicrobial resistance. These systems must account for the complex interactions at the interfaces of the environment, livestock, wildlife, humans, as well as disease dynamics, including the cross-species and regional movement of pathogens. Effective surveillance requires strong collaboration between governments, research institutions, and communities to ensure timely and accurate monitoring and response can be implemented. By employing scientific tools and approaches — such as risk mapping, watershed pollution monitoring and modelling, monitoring interfaces of the wildlife-livestock ecosystem for pathogens and resistant genes, screening at risk humans and animals as well as genomic surveillance — CGIAR aims to improve disease prevention and control, safeguarding both public health and biodiversity in vulnerable regions. This knowledge brief highlights five key takeaway messages on the integrated surveillance approach.
Five key takeaways on the irrational use of antimicrobials in livestock and aquaculture systems in low- and middle-income countries
(Brief, 2024-09-30) Moodley, Arshnee; Muloi, Dishon M.; Hoffmann, Vivian; Murphy, Mike; Rheman, Shafiq; Hossain, Sabrina; Verner-Jeffreys, David; Khor, Laura; Delamare-Deboutteville, Jerome; Patel, Ekta
This brief is important for policymakers, researchers, animal health service providers, and agricultural stakeholders in low- and middle-income countries. Crucial insights are provided into drivers of antimicrobial misuse in livestock and aquaculture, providing evidence-based recommendations for improving antimicrobial use practices. By understanding the gaps in diagnostic services, regulatory frameworks, and farmers’ education, stakeholders can design targeted interventions to promote responsible antimicrobial use. Strengthening regulatory frameworks in these areas will help mitigate antimicrobial resistance, protect animal and human health, and ensure that the animal and aquatic food sector can move toward more sustainable, antibiotic-free production systems in low- and middle-income countries.
The antimicrobial resistance landscape of slaughterhouses in western Kenya: A microbiological case study
(Journal Article, 2024-12) Hamilton, Katie A.; Njoroge, Sam M.; Momanyi, Kelvin; Murungi, Maurice K.; Odinga, Christian O.; Bor, Nicholas; Ogendo, Allan; Odaba, Josiah; Ogola, Joseph G.; Fèvre, Eric M.; Falzon, Laura C.
Slaughterhouses may be hotspots for the transmission of antimicrobial resistant (AMR) pathogens. To obtain information on the AMR landscape in Kenyan slaughterhouses, we collected swabs of the environment, animal carcasses, and workers. Bacterial isolates were identified in 101/193 (52.3 %) samples, and most showed resistance to streptomycin (68.7 %), ampicillin (48.7 %), and tetracycline (42.5 %). Multi drug resistance was exhibited by 35/80 isolates (43.8 %; 95 % CI: 33.2–54.9 %), while Extended Spectrum Beta Lactamase was expressed in 5/80 isolates (6.3 %; 95 % CI: 2.6–14.3 %). These findings illustrate the presence of resistant bacteria throughout the slaughterhouse environment, posing a risk to workers and meat consumers and highlighting the need for an integrated surveillance system along the food chain.
1–10–100: Unifying goals to mobilize global action on antimicrobial resistance
(Journal Article, 2024-08-27) Katwyk, S.R.V.; Poirier, M.J.P.; Chandy, S.J.; Faure, K.; Fisher, C.; Lhermie, G.; Moodley, Arshnee; Sarkar, S.; Masika, S.; Strong, K.; Weldon, I.; Hoffman, S.J.
The Bellagio Group for Accelerating AMR Action met in April 2024 to develop the ambitious but achievable 1–10-100 unifying goals to galvanize global policy change and investments for antimicrobial resistance mitigation: 1 Health; 10 million lives saved; and 100% sustainable access to effective antimicrobials. High profile political goals such as the Paris Agreement’s objective to keep global warming well below 2° Celsius compared to pre-industrial levels, UNAIDS’ 90–90-90 goal, and the Sustainable Development Goals challenge global norms, direct attention towards relevant activities, and serve an energizing function to motivate action over an extended period of time. The 1–10-100 unifying goals propose to unite the world through a One Health approach to safeguard human health, animal welfare, agrifood systems, and the environment from the emergence and spread of drug-resistant microbes and infections; save over 10 million lives by 2040 through concerted efforts to prevent and appropriately treat infections while preserving the vital systems and services that depend on sustained antimicrobial effectiveness; and commit to ensuring that antimicrobials are available and affordable for all, used prudently, and secured for the future through innovation. Compared to existing technical targets, these unifying goals offer advantages of focusing on prevention, encouraging multisectoral action and collaboration, promoting health equity, recognizing the need for innovation, and integrating with Sustainable Development Goals. By committing to 1 Health, 10 million lives saved, and 100% sustainable access to effective antimicrobials, we can protect lives and livelihoods today and safeguard options for tomorrow.
Rapport du troisième atelier de modélisation des impacts socio-économiques de la résistance aux antimicrobiens (RAM): cas d’étude du Sénégal
(Report, 2024-04-30) Faye, Ardiouma; Dione, Michel M.
Selecting Efficient Farm-level Antimicrobial Stewardship Interventions from a One Health perspective (SEFASI) meeting report
Campylobacter jejuni and Campylobacter coli infection, determinants and antimicrobial resistance patterns among under-five children with diarrhea in Amhara National Regional State, Northwest Ethiopia
(Journal Article, 2024-07-03) Worku, M.; Tessema, B.; Ferede, G.; Ochieng, Linnet; Leliso, S.A.; Mutua, Florence; Moodley, Arshnee; Grace, Delia; Gelaw, B.
Background: Children with under-five year age disproportionally affected with foodborne illness. Campylobacteriosis is the most common foodborne disease next to Norovirus infection. Macrolides are commonly prescribed as the first line of treatment for Campylobacter gastroenteritis, with fluoroquinolone and tetracycline as secondary options. However, resistance to these alternatives has been reported in various regions worldwide. Objective:To determine the prevalence, associated risk-factors and antimicrobial resistance of Campylobacter jejuni and C. coli among under-five children with diarrhea. Methods: Institution-based cross-sectional study was conducted from November, 2022 to April 2023. The study sites were selected using a random sampling technique, while the study subjects were included using a convenient sampling technique. The data were collected using a structured questionnaire. Stool samples were inoculated onto modified charcoal cefoperazone deoxycholate agar and incubated for 48 hours. The suspected colonies were analyzed using matrix-assisted laser desorption ionization-time of flight mass spectrometry to confirm the species. Antimicrobial susceptibility testing was performed using a disc diffusion technique. All potential covariates (independent variables) were analyzed one by one using bivariate logistic regression model to identify candidate variables with P value < 0.25. Multivariable logistic analysis was used to identify potential associated factors using the candidate variables. A p value ≤ 0.05 at a 95% confidence interval was statistically significant. Result: Among the 428 samples, 7.0% (CI: 4.5–9.3) were confirmed Campylobacter species. The prevalence of C. jejuni and C. coli among under-five children was 5.1% (CI: 3.0–7.0) and 1.9% (CI: 0.7–3.3), respectively. C. jejuni (73.3%) was dominant over C. coli (26.7%). The resident, contact with domestic animals, and parents/guardians education level were significantly associated with campylobacteriosis among under-five children. One-third of the Campylobacter isolates (33.3%, 10/30) were resistant to ciprofloxacin and tetracycline whereas 10.0% (3/30) were resistant to erythromycin. Furthermore, 3.3% (1/30) of the Campylobacter were found to be multidrug-resistant. Conclusion: The prevalence of Campylobacter species was 7.0%. The resistance rate of Campylobacter species of ciprofloxacin and tetracycline-resistance strains was 33.3%. Peri-urban residence, contact with domestic animals, and low parental educational statuses were significantly associated factors with increased risk of Campylobacter infection. Continuous surveillance on antimicrobial resistance and health education of personal and environmental hygiene should be implemented in the community.
Patterns and drivers of antibiotic use in small-scale broiler production systems in Lilongwe District, Malawi
(Journal Article, 2024-09) Ngunguni, S.M.; Moodley, Arshnee; Msefula, C.; Mkakosya, R.; Muloi, Dishon M.
Reducing the inappropriate use of antibiotics in food animals is a global priority to address antimicrobial resistance (AMR). We investigated practices and factors associated with antibiotic use in small-scale commercial broiler farms in Lilongwe district, Malawi. We used structured questionnaires to collect data on recent antibiotic use practices among 128 broiler farmers, who kept between 50 and 1 000 birds, from December 2022 to March 2023. Logistic regression analysis was used to identify risk factors associated with antibiotic use. Over half (53.1 %, n=68) of the farms reported using antibiotics at least once in the previous production cycle. Overall, 11 different types of antibiotics were used either for treatment and/or preventive purposes, with oxytetracycline (88.2 %), erythromycin (29.4 %), and enrofloxacin (26.5 %) reported as the frequently used. One-third of all antibiotic formulations contained multiple active antibiotic ingredients, with 12 % containing four antibiotics. Covariates associated with an increased likelihood of antibiotic use include disease incidence (OR=13.8, 95 % CI 5.27–42.50, p<0.001) and entry of wild birds into poultry houses (OR=3.56, 95 % CI =1.44–9.61, p=0.008). Our study highlights inappropriate usage of antibiotics, largely associated with reduced biosecurity and disease incidence. These findings underscore the need to strengthen veterinary services, reinforce regulations on antibiotic access and use, and farmer education programs promoting proper husbandry, biosecurity, and responsible antibiotic use.
Brief communication: Carrier rate, antimicrobial resistance and molecular typing of Staphylococcus aureus and Staphylococcus pseudintermedius in healthy dogs from Morogoro, Tanzania
(Journal Article, 2024-10) Katakweba, A.A.S.; Iversen, C.M.; Tsaxra, J.B.; Muhairwa, A.P.; Moodley, Arshnee; Olsen, J.E.
Background: Staphylococcus pseudintermedius and S. aureus are important pathogens in dogs. This study established carrier rates, strain diversity and antimicrobial resistance of these bacteria among healthy dogs in Tanzania. Results: Based on cultures of mouth and perineal swabs, 11.3% and 50.3% of 151 healthy dogs were carriers of S. aureus and S. pseudintermedius, respectively. Only four dogs (3%) carried meticillin-resistant S. aureus (MRSA), while none of the S. pseudintermedius strains were meticillin-resistant. 12 of 19 S. aureus strains tested were resistant to penicillin G, and resistance to enrofloxacin and tetracycline was also commonly detected. The most common resistances in 103 S. pseudintermedius strains tested were to penicillin G (28.2%) and tetracycline (22.3%). S. pseudintermedius strains showed 65 different random amplified polymorphic DNA (RAPD) fingerprints, and S. aureus strains belonged to eight different spa types, including two novel types (t18988 and t18989). MRSA strains carried SCCmec type V. Conclusions and Clinical Relevance: Healthy dogs in Tanzania were carriers of MRSA at low frequency, and half of the dogs carried S. pseudintermedius with high strain diversity.
Scaling antimicrobial resistance surveillance nationally: The case of the Fleming Fund in Kenya
(Journal Article, 2024-06-13) Kasudi, Mitchelle R.; Muloi, Dishon M.; Murungi, Maurice K.; Azegele, A.; Ndanyi, R.; Gunturu, R.; Ombajo, L.; Tanui, E.; Onsare, R.S.; Omuse, G.; Kariuki, S.; Fèvre, Eric M.
Rising levels of antimicrobial resistance (AMR) in both humans and animals have reached alarming levels and are being recognized as a serious incremental threat to global food security, animal health and public health. The One Health approach recognizes the interconnectedness of human, animal and environmental health, and that AMR can be spread between different species and environments. The Fleming Fund, a UK Overseas Development Aid program managed by the UK’s Department of Health and Social Care, aims to improve AMR and antimicrobial use (AMU) surveillance data in Africa and Asia by generating, sharing, and using data to improve antimicrobial use and encourage investment in AMR research and development. The Fund awarded grants to several countries, including Kenya, to support national efforts in strengthening their capacity to collect, manage and use data on antimicrobial use and resistance. Six institutions, including the International Livestock Research Institute, University of Nairobi, the Aga Khan University, the Kenya Medical Research Institute, PATH and Washington State University, formed the Fleming Fund consortium in Kenya. Across animal and human health sectors, this consortium supported activities that address the gaps in the surveillance of AMR and its causes including antimicrobial stewardship training, development and dissemination of standard operating procedures for both active and passive AMR surveillance, capacity building of field and laboratory personnel and infrastructure work among other activities. The wide range of data acquired through this program will impact evidence-based policies and programs, enabling consumers and stakeholders to make informed decisions that preserve the effectiveness of antibiotics.
Editorial: Antimicrobial resistance in food-producing environments: a One Health approach
(Journal Article, 2024-06-19) Agga, G.E.; Amenu, Kebede
The One Health High-Level Expert panel comprised of the United Nations Food and Agriculture Organization (FAO), the United Nations Environment Program (UNEP), the World Health Organization (WHO), and the World Organization for Animal Health (WOAH; founded as OIE) defines One Health as “an integrated, unifying approach that aims to sustainably balance and optimize the health of people, animals and ecosystems. It recognizes that the health of humans, domestic and wild animals, plants, and the wider environment (including ecosystems) are closely linked and interdependent. The approach mobilizes multiple sectors, disciplines and communities at varying levels of society to work together to foster well-being and tackle threats to health and ecosystems, while addressing the collective need for clean water, energy and air, safe and nutritious food, taking action on climate change, and contributing to sustainable development.” (Mettenleiter et al., 2023). There is nothing more fitting than antimicrobial resistance (AMR) to the principles of One Health, which provides a framework for an interdisciplinary approach to dealing with this global challenge (FAO, 2016; Robinson et al., 2016; Lancet, 2023).
Understanding veterinary drug shop workers' knowledge and practices to identify drivers of antibiotic use in Vietnamese livestock farms
(Journal Article, 2024-07-01) Nohrborg, S.; Thinh Nguyen-Thi; Huyen Nguyen Xuan; Yen Luu Thi Hai; Lindahl, Johanna F.; Boqvist, S.; Järhult, J.D.; Magnusson, Ulf
Background: Antimicrobial resistance (AMR) is a One Health issue and a major threat to animal and human health. Antibiotic use (ABU) drives AMR development, and several hotspots for ABU, and AMR, in livestock have been identified in Southeast Asia, including Vietnam. There are often multiple drivers of ABU at farms, and to identify all of them there is a need to look beyond farm level. Objectives: The overall aim of this study was to identify routines and/or competencies, related to antibiotic sales, among veterinary drug shop workers that may be improved in order to decrease the medically non-rational use of antibiotics in livestock production. Methods : A questionnaire-based survey was conducted at 50 veterinary drug shops in northern Vietnam. Results: Results showed high education and knowledge levels. According to the respondents, antibiotic treatment advice was almost always provided to the farmers, and the recommended treatment was most commonly based on recommendations for the specific disease. However, farmers had almost never had their animals properly diagnosed. Antibiotics were the most sold drug category, penicillins being the most common. Several broad-spectrum antibiotics were also quite frequently sold. Further, >50% of respondents recommended antibiotics for disease prevention. Conclusions: Even though education and knowledge levels might be high, several challenges can prevent drug shop workers from contributing to more prudent ABU at farms, for example, lack of proper diagnosis, commercial interests and individual farmer motives, often in combination with poor compliance to regulations.
FarmUSE: Assessment of antimicrobial use in poultry farms
(Report, 2024-06-06) Muloi, Dishon M.; Ibayi, Eugine L.; Murphy, Mike; Njaramba, Jane; Nielsen, S.S.; Hoffmann, Vivian; Moodley, Arshnee
Antimicrobial use in livestock systems is thought to be a key driver for the development of antimicrobial resistance (AMR). Therefore, efforts to reduce antimicrobial use are seen as a key intervention to controlling AMR. Understanding the patterns of antimicrobial use in different production systems is essential. Antimicrobials are commonly used in poultry production for disease treatment, prevention and, to an extent, growth promotion. In low- and middle-income countries, surveillance of antimicrobial use in animals is hampered by the lack of standardised data collection tools and reporting systems across different countries and regions. To address this gap, these tools were developed and adapted to poultry broiler production systems to support the collection of comprehensive data related to demographics, production and antibiotic usage data. The tools are designed for both retrospective and prospective data gathering.
Antimicrobial use and antimicrobial resistance in Escherichia coli in semi-intensive and free-range poultry farms in Uganda
(Journal Article, 2024-06) Mbatidde, Irene; Ndoboli, Dickson; Ayebare, Dreck; Muloi, Dishon; Roesel, Kristina; Ochieng, Linnet; Dione, Michel M.; Tenhagen, B.-A.; Biryomumaisho, S.; Wampande, E.; Wieland, Barbara; Olsen, J.E.; Moodley, Arshnee
Livestock associated antimicrobial resistance (AMR) can reduce productivity and cause economic losses, threatening the livelihoods of poor farming communities in low-income settings. We investigated the practices and risk factors for increased antibiotic use, and AMR in Escherichia coli including resistance to human critically important antibiotics like cefotaxime and colistin in semi-intensive and free-range poultry farms in Uganda. Samples and farm management data were collected from 402 poultry farms in two districts between October 2021 to March 2022. Samples were processed to isolate E. coli and to quantify cefotaxime (CTX) and colistin (COL) resistant coliforms. The identification of presumptive E. coli isolated on MacConkey agar without antibiotics, was confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and subjected to antimicrobial susceptibility testing by disk diffusion using EUCAST guidelines. Our models indicated that antibiotic use was associated with production intensity, and type of feed used. Moreover, semi-intensive farmers had better knowledge on antibiotic use compared to farmers in the free-range system. In semi-intensive farms, 52% harbored COL^R and 57% CTX^R coliforms. In free-range farms, 54% had COL^R and 67% CTX^R coliforms. Resistance to tetracycline, ampicillin and enrofloxacin were more frequent in semi-intensive farms compared to the free-range farms. Multi-drug resistant E. coli were identified in both poultry production systems despite different management and antibiotic use practices. There was no significant relationship between antibiotic use and resistance for the six antibiotics tested.
Antibiotic prescribing practices in community and clinical settings during the COVID-19 pandemic in Nairobi, Kenya
(Journal Article, 2024-04-25) Gacheri, June; Hamilton, Katie A.; Munywoki, Peterkin; Wakahiu, Sinaida; Kiambi, Karen; Fèvre, Eric M.; Oluka, M.N.; Guantai, E.M.; Moodley, Arshnee; Muloi, Dishon M.
The COVID-19 pandemic has significantly impacted healthcare systems, including antibiotic use practices. We present data on patterns of antibiotic dispensing and use in community and hospital settings respectively in Nairobi, Kenya during the pandemic. We conducted interviews with 243 pharmacies in Nairobi using a standardised questionnaire from November to December 2021. The data collected included demographic characteristics, antibiotic customers, types of antibiotics sold, and antibiotic prescribing practices. Additionally, we retrospectively reviewed health records for 992 and 738 patients admitted in COVID-19 and general wards at two large inpatient hospitals between April 2020 and May 2021, and January 2019 to October 2021, respectively. Demographic, utilisation of laboratory services, treatment, clinical, and outcome data were collected using a modified Global WHO Point Prevalence Surveys (Global-PPS) tool. Almost all pharmacies (91.4%) served customers suspected of having COVID-19 with a mean weekly number of 15.6 customers. All pharmacies dispensed antibiotics, mainly azithromycin and beta lactams to suspected COVID-19 infected customers. 83.4% of hospitalised COVID-19 patients received at least one antibiotic at some point during their hospitalisation, which was significantly higher than the 53.8% in general ward patients (p<0.001). Similarly, the average number of antibiotics administered to COVID-19 patients was higher than that of patients in the general ward (1.74 vs 0.9). Azithromycin and ceftriaxone were the most commonly used antibiotics in COVID-19 patients compared to ceftriaxone and metronidazole in the general wards. Only 2% of antibiotic prescriptions for COVID-19 patients were supported by microbiological investigations, which was consistent with the proportion of 6.8% among the general ward population. Antibiotics were commonly prescribed to customers and patients suspected of having COVID-19 either in community pharmacies or in hospital, without a prescription or laboratory diagnosis. These findings emphasize the crucial role of antibiotic stewardship, particularly in community pharmacies, in the context of COVID-19.
ILRI research on antimicrobial use and resistance in smallholder livestock system
(Presentation, 2024-02-29) Unger, Fred; Sinh Dang-Xuan; Hung Nguyen-Viet; Muloi, Dishon; Moodley, Arshnee

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