Browsing by Author "Johnson, Paul"

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Classification and characterisation of livestock production systems in northern Tanzania.
(PLOS ONE, 2020-12-30) de Glanville, William; Davis, Alicia; Allan, Kathryn; Buza, Joram; Claxton, John; Crump, John; Halliday, Jo E B; Johnson, Paul; Kibona, Tito; Mmbaga, Blandina; Swai, Emmanuel; Uzzell, Christopher; Yoder, Jonathan; Sharp, Jo; Cleaveland, Sarah
Livestock keepers in sub-Saharan Africa face a range of pressures, including climate change, land loss, restrictive policies, and population increase. Widespread adaptation in response can lead to the emergence of new, non-traditional typologies of livestock production. We sought to characterise livestock production systems in two administrative regions in northern Tanzania, an area undergoing rapid social, economic, and environmental change. Questionnaire and spatial data were collected from 404 livestock-keeping households in 21 villages in Arusha and Manyara Regions in 2016. Multiple factor analysis and hierarchical cluster analysis were used to classify households into livestock production systems based on household-level characteristics. Adversity-based indicators of vulnerability, including reports of hunger, illness, and livestock, land and crop losses were compared between production systems. Three distinct clusters emerged through this process. The ethnic, environmental and livestock management characteristics of households in each cluster broadly mapped onto traditional definitions of 'pastoral', 'agro-pastoral' and 'smallholder' livestock production in the study area, suggesting that this quantitative classification system is complementary to more qualitative classification methods. Our approach allowed us to demonstrate a diversity in typologies of livestock production at small spatial scales, with almost half of study villages comprising more than one production system. We also found indicators of change within livestock production systems, most notably the adoption of crop agriculture in the majority of pastoral households. System-level heterogeneities in vulnerability were evident, with agro-pastoral households most likely to report hunger and pastoral households most likely to report illness in people and livestock, and livestock losses. We demonstrate that livestock production systems can provide context for assessing household vulnerability in northern Tanzania. Policy initiatives to improve household and community well-being should recognise the continuing diversity of traditional livestock production systems in northern Tanzania, including the diversity that can exist at small spatial scales.
Integrating contact tracing and whole- genome sequencing to track the elimination of dog-mediated rabies: An observational and genomic study
(eLife Sciences Publications Ltd, 2023-05-25) Lushasi, Kennedy; Brunker, Kirstyn; Rajeev, Malavika; Ferguson, Elaine; Jaswant, Gurdeep; Baker, Laurie; Biek, Roman; Changalucha, Joel; Cleaveland, Sarah; Czupryna, Anna; Fooks, Anthony; Govella, Nicodemus; Haydon, Daniel; Johnson, Paul; Kazwala, Rudovick; Lembo, Tiziana; Masoud, Msanif; Maziku, Matthew; Mbunda, Eberhard; Mchau, Geofrey; Mohamed, Ally; Mpolya, Emmanuel; Ngeleja, Chanasa; Ng'habi, Kija; Nonga, Hezron; Omar, Kassim; Rysava, Kristyna; Sambo, Maganga; Sikana, Lwitiko; Steenson, Rachel; Hampson, Katie
Background: Dog-mediated rabies is endemic across Africa causing thousands of human deaths annually. A One Health approach to rabies is advocated, comprising emergency post-exposure vaccination of bite victims and mass dog vaccination to break the transmission cycle. However, the impacts and cost-effectiveness of these components are difficult to disentangle. Methods: We combined contact tracing with whole-genome sequencing to track rabies transmission in the animal reservoir and spillover risk to humans from 2010 to 2020, investigating how the components of a One Health approach reduced the disease burden and eliminated rabies from Pemba Island, Tanzania. With the resulting high-resolution spatiotemporal and genomic data, we inferred transmission chains and estimated case detection. Using a decision tree model, we quantified the public health burden and evaluated the impact and cost-effectiveness of interventions over a 10-year time horizon. Results: We resolved five transmission chains co-circulating on Pemba from 2010 that were all eliminated by May 2014. During this period, rabid dogs, human rabies exposures and deaths all progressively declined following initiation and improved implementation of annual islandwide dog vaccination. We identified two introductions to Pemba in late 2016 that seeded re-emergence after dog vaccination had lapsed. The ensuing outbreak was eliminated in October 2018 through reinstated islandwide dog vaccination. While post-exposure vaccines were projected to be highly cost-effective ($256 per death averted), only dog vaccination interrupts transmission. A combined One Health approach of routine annual dog vaccination together with free post-exposure vaccines for bite victims, rapidly eliminates rabies, is highly cost-effective ($1657 per death averted) and by maintaining rabies freedom prevents over 30 families from suffering traumatic rabid dog bites annually on Pemba island. Conclusions: A One Health approach underpinned by dog vaccination is an efficient, cost-effective, equitable, and feasible approach to rabies elimination, but needs scaling up across connected populations to sustain the benefits of elimination, as seen on Pemba, and for similar progress to be achieved elsewhere.
Integrating contact tracing and wholegenome sequencing to track the elimination of dog-mediated rabies: An observational and genomic study
(eLife, 2023-05-23) Lushasi, Kennedy; Brunker, Kirstyn; Rajeev, Malavika; Ferguson, Elaine; Jaswant, Gurdeep; Baker, Laurie; Biek, Roman; Changalucha, Joel; Cleaveland, Sarah; Czupryna, Anna; Fooks, Anthony; Govella, Nicodemus; Haydon, Daniel; Johnson, Paul; Kazwala, Rudovick; Lembo, Tiziana; Marston, Denise; Masoud, Msanif; Maziku, Matthew; Mbunda, Eberhard; Mchau, Geofrey; Mohamed, Ally; Mpolya, Emmanuel; Ngeleja, Chanasa; Ng'habi, Kija; Nonga, Hezron; Omar, Kassim; Rysava, Kristyna; Sambo, Maganga; Sikana, Lwitiko; Steenson, Rachel; Hampson, Katie
Background: Dog-mediated rabies is endemic across Africa causing thousands of human deaths annually. A One Health approach to rabies is advocated, comprising emergency post-exposure vaccination of bite victims and mass dog vaccination to break the transmission cycle. However, the impacts and cost-effectiveness of these components are difficult to disentangle. Methods: We combined contact tracing with whole-genome sequencing to track rabies transmission in the animal reservoir and spillover risk to humans from 2010 to 2020, investigating how the components of a One Health approach reduced the disease burden and eliminated rabies from Pemba Island, Tanzania. With the resulting high-resolution spatiotemporal and genomic data, we inferred transmission chains and estimated case detection. Using a decision tree model, we quantified the public health burden and evaluated the impact and cost-effectiveness of interventions over a 10-year time horizon. Results: We resolved five transmission chains co-circulating on Pemba from 2010 that were all eliminated by May 2014. During this period, rabid dogs, human rabies exposures and deaths all progressively declined following initiation and improved implementation of annual islandwide dog vaccination. We identified two introductions to Pemba in late 2016 that seeded re-emergence after dog vaccination had lapsed. The ensuing outbreak was eliminated in October 2018 through reinstated islandwide dog vaccination. While post-exposure vaccines were projected to be highly cost-effective ($256 per death averted), only dog vaccination interrupts transmission. A combined One Health approach of routine annual dog vaccination together with free post-exposure vaccines for bite victims, rapidly eliminates rabies, is highly cost-effective ($1657 per death averted) and by maintaining rabies freedom prevents over 30 families from suffering traumatic rabid dog bites annually on Pemba island. Conclusions: A One Health approach underpinned by dog vaccination is an efficient, cost-effective, equitable, and feasible approach to rabies elimination, but needs scaling up across connected populations to sustain the benefits of elimination, as seen on Pemba, and for similar progress to be achieved elsewhere.
Inter-epidemic Rift Valley fever virus infection incidence and risks for zoonotic spillover in northern Tanzania
(PLOS, 2022-10-28) Ngonzi, Amos; Glanville, William; Nyarobi, James; Kibona, Tito; Halliday, Jo; Thomas, Kate; Allan, Kathryn; Johnson, Paul; Davis, Alicia; Lankester, Felix; Claxton, John; Rosta, Melinda; Carter, Ryan; Jong, Rosanne; Rubach, Matthew; Crump, John; Mmbaga, Blandina; Nyasebwa, Obed; Swai, Emanuel; Willett, Brian; Cleaveland, Sarah
Rift Valley fever virus (RVFV) is a mosquito-borne pathogen that has caused epidemics involving people and animals across Africa and the Arabian Peninsula. A number of studies have found evidence for the circulation of RVFV among livestock between these epidemics but the population-level incidence of infection during this inter-epidemic period (IEP) is rarely reported. General force of infection (FOI) models were applied to age-adjusted cross-sectional serological data to reconstruct the annual FOI and population-level incidence of RVFV infection among cattle, goats, and sheep in northern Tanzania from 2009 through 2015, a period without reported Rift Valley fever (RVF) cases in people or animals. To evaluate the potential for zoonotic RVFV spillover during this period, the relationship between village-level livestock RVFV FOI and human RVFV seropositivity was quantified using multi-level logistic regression. The predicted average annual incidence was 72 (95% Credible Interval [CrI] 63, 81) RVFV infections per 10,000 animals and 96 (95% CrI 81, 113), 79 (95% CrI 62, 98), and 39 (95% CrI 28, 52) per 10,000 cattle, sheep, and goats, respectively. There was variation in transmission intensity between study villages, with the highest estimated village-level FOI 2.49% (95% CrI 1.89, 3.23) and the lowest 0.12% (95% CrI 0.02, 0.43). The human RVFV seroprevalence was 8.2% (95% Confidence Interval 6.2, 10.9). Human seropositivity was strongly associated with the village-level FOI in livestock, with the odds of seropositivity in an individual person increasing by around 1.2 times (95% CrI 1.1, 1.3) for each additional annual RVFV seroconversion per 1,000 animals. A history of raw milk consumption was also positively associated with human seropositivity. RVFV has circulated at apparently low levels among livestock in northern Tanzania in the period since the last reported epidemic. Although our data do not allow us to confirm human RVFV infections during the IEP, a strong association between human seropositivity and the FOI in cattle, goats, and sheep supports the hypothesis that RVFV circulation among livestock during the IEP poses a risk for undetected zoonotic spillover in northern Tanzania. We provide further evidence for the likely role of raw milk consumption in RVFV transmission from animals to people.
Livestock production losses attributable to brucellosis in northern and central Tanzania: Application of an epidemiological-economic modelling framework
(Public Library of Science, 2025-02-14) Mendes, Ângelo; Haydon, Daniel; Glanville, William; Bodenham, Rebecca; Lukambagire, AbdulHamid; Johnson, Paul; Shirima, Gabriel; Cleaveland, Sarah; McIntosh, Emma; Hanley, Nick; Halliday, Jo
Malignant catarrhal fever (MCF), caused by alcelaphine herpesvirus-1 (AIHV-1) transmitted from wildebeest, is a lethal cattle disease with significant impacts on East African pastoralists. Development of a live attenuated MCF vaccine has prompted research into its use in communities at risk. This study reports results from the first utilisation of the MCF vaccine in locally-owned cattle under field conditions. The study involved a primary two-dose course vaccination of 1634 cattle, followed a year later, by boost vaccination of 385 of these cattle. It aimed to: (a) evaluate the antibody response to a two-dose AlHV-1 primary vaccination course, including initial response, antibody levels after one year, and clinical events post-vaccination; (b) assess how factors like age, reproductive status, body condition, and breed influence the initial response; and (c) compare antibody responses to single- and two-dose booster protocols one year after primary vaccination. Analyses were carried out using linear mixed-effects models and paired t-tests. Clinical incidents were reported in 11/1634 cattle vaccinated during the primary course and in 0/385 cattle during the boost regimens. The primary vaccination resulted in a 9-fold increase in comparison to pre-vaccination antibody levels and the response was consistent across animals of different ages, reproductive statuses and body conditions. While antibody levels declined 11 months after primary vaccination, they remained high, and a single-dose booster vaccination was sufficient to elicit a strong immune response, with only marginal increases after a second booster. The study provides evidence of high immunogenicity and low incidences of clinical events of the vaccine in cattle across individual host factors and immunologically vulnerable groups, under prevailing environmental conditions. It also indicates the utility of a single-dose booster regimen. These findings will support progress towards commercial production and larger-scale adoption which could generate important benefits for the livelihoods, and sustainability of pastoral livestock systems.
Participation in mass dog vaccination campaigns in Tanzania: Benefits of community engagement
(Frontiers, 2022-10-13) Duamor, Christian; Lankester, Felix; Mpolya, Emmanuel; Ferguson, Elaine; Johnson, Paul; Wyke, Sally; Cleaveland, Sarah; Hampson, Katie; Kreppel, Katharina
Background: Canine rabies causes about 59,000 human deaths each year globally but the disease can be eliminated by sustaining sufficient dog vaccination coverage over several consecutive years. A challenge to achieving high coverage is low participation of dog owners in vaccination campaigns. We explored whether and how previously identified contributory factors to low participation can be addressed through community engagement activities. Methods: We engaged communities in two wards in Tanzania on dog behavior and handling, safe ways of interacting with dogs, and their perceptions of dog vaccination. We shared and elicited information from them through village meetings, video screenings, posters and leaflets and involved the leadership of one of the wards in planning and implementing a dog vaccination exercise to explore the feasibility of their participation. We assessed the impact of engagement activities with household surveys, meeting reports, observations and focus group discussions. We used a generalized linear mixed-effects model to identify predictors of knowledge and perceptions and compared knowledge amongst respondents before and after engagement activities. Qualitative data was analyzed inductively to explore perceptions of dog handling and vaccination and feasibility, opportunities and barriers to community leadership participation in organizing mass dog vaccination. Main findings: Knowledge of dog behavior, dog handling, and safe ways of interacting with dogs was positively associated with age (p < 0.0001), dog ownership (p = 0.0203), training (p = 0.0010) and previous experience of a dog bite (p = 0.0002); and was negatively associated with being afraid of dogs (p = 0.0061) and participation in a recent dog vaccination campaign (p = 0.0077). Knowledge was low before and significantly improved after engagement activities. The majority (92%) of respondents believed dog vaccination has no negative effects on dogs. Respondents perceived lack of bonding with their dog as a limitation to the ability to restrain a dog for vaccination. The community performed most roles assigned to them in the dog vaccination exercise, but barriers such as lack of motivation for volunteering exist. Conclusion: Engaging communities regularly on dog vaccination can improve their knowledge of dog behavior and dog handling techniques, and may help improve owner participation in dog vaccination campaigns.