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Entezami M, Mustaqqim F, Morris E, Lim ESH, Prada JM, Paramasivam SJ. Effect of Human Activity and Presence on the Behavior of Long-Tailed Macaques ( Macaca fascicularis) in an Urban Tourism Site in Kuala Selangor, Malaysia. Animals (Basel) 2024; 14:1173. [PMID: 38672321 PMCID: PMC11047574 DOI: 10.3390/ani14081173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The increasing overlap of resources between human and long-tailed macaque (Macaca fascicularis) (LTM) populations have escalated human-primate conflict. In Malaysia, LTMs are labeled as a 'pest' species due to the macaques' opportunistic nature. This study investigates the activity budget of LTMs in an urban tourism site and how human activities influence it. Observational data were collected from LTMs daily for a period of four months. The observed behaviors were compared across differing levels of human interaction, between different times of day, and between high, medium, and low human traffic zones. LTMs exhibited varying ecological behavior patterns when observed across zones of differing human traffic, e.g., higher inactivity when human presence is high. More concerning is the impact on these animals' welfare and group dynamics as the increase in interactions with humans takes place; we noted increased inactivity and reduced intra-group interaction. This study highlights the connection that LTMs make between human activity and sources of anthropogenic food. Only through understanding LTM interaction can the cause for human-primate conflict be better understood, and thus, more sustainable mitigation strategies can be generated.
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Affiliation(s)
- Mahbod Entezami
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Daphne Jackson Road, Guildford GU2 7AL, UK; (M.E.); (E.M.); (J.M.P.)
| | - Fiqri Mustaqqim
- School of Postgraduate Studies, Perdana University, Serdang 43400, Malaysia
| | - Elizabeth Morris
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Daphne Jackson Road, Guildford GU2 7AL, UK; (M.E.); (E.M.); (J.M.P.)
| | - Erin Swee Hua Lim
- Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates;
- Centre for Research Excellence, Perdana University, Serdang 43400, Malaysia
| | - Joaquín M. Prada
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Daphne Jackson Road, Guildford GU2 7AL, UK; (M.E.); (E.M.); (J.M.P.)
| | - Sharmini Julita Paramasivam
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Daphne Jackson Road, Guildford GU2 7AL, UK; (M.E.); (E.M.); (J.M.P.)
- Animal Neighbours Project, School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford GU2 7AL, UK
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Galvis JA, Corzo CA, Prada JM, Machado G. Modeling between-farm transmission dynamics of porcine epidemic diarrhea virus: Characterizing the dominant transmission routes. Prev Vet Med 2022; 208:105759. [PMID: 36155353 DOI: 10.1016/j.prevetmed.2022.105759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 10/31/2022]
Abstract
The role of transportation vehicles, pig movement between farms, proximity to infected premises, and feed deliveries has not been fully considered in the dissemination dynamics of porcine epidemic diarrhea virus (PEDV). This has limited efforts for disease prevention, control and elimination restricting the development of risk-based resource allocation to the most relevant modes of PEDV dissemination. Here, we modeled nine pathways of between-farm transmission represented by a contact network of pig movements between sites, farm-to-farm proximity (local transmission), four distinct contact networks of transportation vehicles (trucks that transport pigs from farm-to-farm and farm-to-markets, as well as trucks transporting feed and staff), the volume of animal by-products in feed diets (e.g., fat and meat-and-bone-meal) to reproduce PEDV transmission dynamics. The model was calibrated in space and time with weekly PEDV outbreaks. We investigated the model performance to identify outbreak locations and the contribution of each route in the dissemination of PEDV. The model estimated that 42.7% of the infections in sow farms were related to vehicles transporting feed, 34.5% of infected nurseries were associated with vehicles transporting pigs between farms, and for both farm types, local transmission or pig movements were the next most relevant transmission routes. On the other hand, finishers were most often (31.4%) infected via local transmission, followed by the vehicles transporting feed and pigs between farms. Feed ingredients did not significantly improve model calibration metrics, sensitivity, and specificity; therefore, it was considered to have a negligible contribution in the dissemination of PEDV. The proposed modeling framework provides an evaluation of PEDV transmission dynamics, ranking the most important routes of PEDV dissemination and granting the swine industry valuable information to focus efforts and resources on the most important transmission routes.
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Affiliation(s)
- Jason A Galvis
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Cesar A Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Joaquín M Prada
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
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3
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Widdicombe J, Basáñez MG, Entezami M, Jackson D, Larrieu E, Prada JM. The economic evaluation of Cystic echinococcosis control strategies focused on zoonotic hosts: A scoping review. PLoS Negl Trop Dis 2022; 16:e0010568. [PMID: 35797271 PMCID: PMC9262177 DOI: 10.1371/journal.pntd.0010568] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/07/2022] [Indexed: 12/29/2022] Open
Abstract
Background Cystic echinococcosis (CE) is a zoonotic neglected tropical disease (zNTD) which imposes considerable financial burden to endemic countries. The 2021–2030 World Health Organization’s roadmap on NTDs has proposed that intensified control be achieved in hyperendemic areas of 17 countries by 2030. Successful interventions for disease control, and the scale-up of programmes applying such interventions, rely on understanding the associated costs and relative return for investment. We conducted a scoping review of existing peer-reviewed literature on economic evaluations of CE control strategies focused on Echinococcus granulosus zoonotic hosts. Methodology/Principal findings Database searches of Scopus, PubMed, Web of Science, CABI Direct and JSTOR were conducted and comprehensively reviewed in March 2022, using predefined search criteria with no date, field or language restrictions. A total of 100 papers were initially identified and assessed for eligibility against strict inclusion and exclusion criteria, following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines. Bibliography review of included manuscripts was used to identify additional literature. Full review of the final manuscript selection (n = 9) was performed and cost data for control interventions were extracted. Conclusions/Significance There are very little published data pertaining to the cost and cost effectiveness of CE control interventions targeting its zoonotic hosts. Data given for costs are often incomplete, thus we were unable to perform an economic analysis and cost effectiveness study, highlighting a pressing need for this information. There is much scope for future work in this area. More detailed information and disaggregated costings need to be collected and made available. This would increase the accuracy of any cost-effective analyses to be performed and allow for a greater understanding of the opportunity cost of healthcare decisions and resource allocation by stakeholders and policy makers for effective and cost-effective CE control. Cystic echinococcosis (CE) is a zoonotic neglected tropical disease which predominantly affects poor pastoral communities globally. The parasite cycles between farm dogs and livestock, and is associated with livestock farming and feeding of infected offal to dogs. Although no noticeable clinical signs are seen in livestock, some production losses, such as reduced milk yield and live weight gain may be observed, and offal condemnation at slaughter is common. The disease can also affect people, due to accidental ingestion of parasite eggs on contaminated food and contact with dogs. Human morbidity and mortality occur due to cyst formation in body organs, exerting a substantial health and financial burden to the health sector of affected countries. Control interventions to reduce CE transmission include sheep vaccination and dog deworming. Long-term control programmes are often expensive, and the true costs of such programmes poorly documented. This scoping review aims to examine published literature on the costs of CE control in zoonotic hosts and report detailed costs of individual elements of a control programme, thereby furthering our understanding of the true economic cost of CE control.
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Affiliation(s)
- Jo Widdicombe
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- * E-mail:
| | - María-Gloria Basáñez
- MRC Centre for Global Infectious Disease Analysis and London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Mahbod Entezami
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Daniel Jackson
- Surrey Health Economics Centre, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Edmundo Larrieu
- Universidad Nacional de Rio Negro, Choele Choel, Rio Negro, Argentina
| | - Joaquín M. Prada
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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Deza-Cruz I, Prada JM, Del Rio Vilas V. An analysis of the accuracy of COVID-19 country transmission classification. Sci Rep 2022; 12:9604. [PMID: 35688930 PMCID: PMC9186008 DOI: 10.1038/s41598-022-13494-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
Accurate epidemiological classification guidelines are essential to ensure implementation of adequate public health and social measures. Here, we investigate two frameworks, published in March 2020 and November 2020 by the World Health Organization (WHO) to categorise transmission risks of COVID-19 infection, and assess how well the countries’ self-reported classification tracked their underlying epidemiological situation. We used three modelling approaches: an ordinal longitudinal model, a proportional odds model and a machine learning One-Rule classification algorithm. We applied these models to 202 countries’ daily transmission classification and epidemiological data, and study classification accuracy over time for the period April 2020 to June 2021, when WHO stopped publishing country classifications. Overall, the first published WHO classification, purely qualitative, lacked accuracy. The incidence rate within the previous 14 days was the best predictor with an average accuracy throughout the period of study of 61.5%. However, when each week was assessed independently, the models returned predictive accuracies above 50% only in the first weeks of April 2020. In contrast, the second classification, quantitative in nature, increased significantly the accuracy of transmission labels, with values as high as 94%.
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Affiliation(s)
- I Deza-Cruz
- Faculty of Health and Medical Sciences, University of Surrey, 30 Priestley Road, Surrey Research Park, Guildford, GU2 7YH, Surrey, UK.
| | - J M Prada
- Faculty of Health and Medical Sciences, University of Surrey, 30 Priestley Road, Surrey Research Park, Guildford, GU2 7YH, Surrey, UK
| | - V Del Rio Vilas
- World Health Organization, Regional Office for South-East Asia, World Health House, Indraprastha Estate, Mahatama Gandhi Marg, New Delhi, 110 002, India
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Janoušková E, Clark J, Kajero O, Alonso S, Lamberton PHL, Betson M, Prada JM. Public Health Policy Pillars for the Sustainable Elimination of Zoonotic Schistosomiasis. Front Trop Dis 2022. [DOI: 10.3389/fitd.2022.826501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Schistosomiasis is a parasitic disease acquired through contact with contaminated freshwater. The definitive hosts are terrestrial mammals, including humans, with some Schistosoma species crossing the animal-human boundary through zoonotic transmission. An estimated 12 million people live at risk of zoonotic schistosomiasis caused by Schistosoma japonicum and Schistosoma mekongi, largely in the World Health Organization’s Western Pacific Region and in Indonesia. Mathematical models have played a vital role in our understanding of the biology, transmission, and impact of intervention strategies, however, these have mostly focused on non-zoonotic Schistosoma species. Whilst these non-zoonotic-based models capture some aspects of zoonotic schistosomiasis transmission dynamics, the commonly-used frameworks are yet to adequately capture the complex epi-ecology of multi-host zoonotic transmission. However, overcoming these knowledge gaps goes beyond transmission dynamics modelling. To improve model utility and enhance zoonotic schistosomiasis control programmes, we highlight three pillars that we believe are vital to sustainable interventions at the implementation (community) and policy-level, and discuss the pillars in the context of a One-Health approach, recognising the interconnection between humans, animals and their shared environment. These pillars are: (1) human and animal epi-ecological understanding; (2) economic considerations (such as treatment costs and animal losses); and (3) sociological understanding, including inter- and intra-human and animal interactions. These pillars must be built on a strong foundation of trust, support and commitment of stakeholders and involved institutions.
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Andrade-Mogrovejo DA, Gonzales-Gustavson E, Ho-Palma AC, Prada JM, Bonnet G, Pizzitutti F, Gomez-Puerta LA, Arroyo G, O’Neal SE, Garcia HH, Guitian J, Gonzalez A. Development of a dose-response model for porcine cysticercosis. PLoS One 2022; 17:e0264898. [PMID: 35286329 PMCID: PMC8920259 DOI: 10.1371/journal.pone.0264898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/21/2022] [Indexed: 01/11/2023] Open
Abstract
Taenia solium is an important cause of acquired epilepsy worldwide and remains endemic in Asia, Africa, and Latin America. Transmission of this parasite is still poorly understood despite the design of infection experiments to improve our knowledge of the disease, with estimates for critical epidemiological parameters, such as the probability of human-to-pig infection after exposure to eggs, still lacking. In this paper, a systematic review was carried out and eight pig infection experiments were analyzed to describe the probability of developing cysts. These experiments included different pathways of inoculation: with ingestion of proglottids, eggs, and beetles that ingested eggs, and direct injection of activated oncospheres into the carotid artery. In these experiments, different infective doses were used, and the numbers of viable and degenerated cysts in the body and brain of each pig were registered. Five alternative dose-response models (exponential, logistic, log-logistic, and exact and approximate beta-Poisson) were assessed for their accuracy in describing the observed probabilities of cyst development as a function of the inoculation dose. Dose-response models were developed separately for the presence of three types of cysts (any, viable only, and cysts in the brain) and considered for each of the four inoculation methods ("Proglottids", "Eggs", "Beetles" and "Carotid"). The exact beta-Poisson model best fit the data for the three types of cysts and all relevant exposure pathways. However, observations for some exposure pathways were too scarce to reliably define a dose-response curve with any model. A wide enough range of doses and sufficient sample sizes was only found for the "Eggs" pathway and a merged "Oral" pathway combining the "Proglottids", "Eggs" and "Beetles" pathways. Estimated parameter values from this model suggest that a low infective dose is sufficient to result in a 50% probability for the development of any cyst or for viable cyst infections. Although this is a preliminary model reliant on a limited dataset, the parameters described in this manuscript should contribute to the design of future experimental infections related to T. solium transmission, as well as the parameterization of simulation models of transmission aimed at informing control.
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Affiliation(s)
- Daniel A. Andrade-Mogrovejo
- Department of Animal and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Eloy Gonzales-Gustavson
- Department of Animal and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Tropical and Highlands Veterinary Research Institute, Universidad Nacional Mayor de San Marcos, Lima, Peru
- * E-mail:
| | - Ana C. Ho-Palma
- Department of Human Medicine, School of Human Medicine, Universidad Nacional del Centro del Perú, Huancayo, Peru
| | - Joaquín M. Prada
- Department of Veterinary Epidemiology and Public Health, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Gabrielle Bonnet
- School of Public Health, Oregon Health & Science University and Portland State University, Portland, Oregon, United States of America
| | - Francesco Pizzitutti
- School of Public Health, Oregon Health & Science University and Portland State University, Portland, Oregon, United States of America
| | - Luis A. Gomez-Puerta
- Department of Animal and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Gianfranco Arroyo
- Center for Global Health Tumbes, Universidad Peruana Cayetano Heredia, San Martín de Porres, Peru
| | - Seth E. O’Neal
- School of Public Health, Oregon Health & Science University and Portland State University, Portland, Oregon, United States of America
- Center for Global Health Tumbes, Universidad Peruana Cayetano Heredia, San Martín de Porres, Peru
| | - Hector H. Garcia
- Center for Global Health Tumbes, Universidad Peruana Cayetano Heredia, San Martín de Porres, Peru
- Cysticercosis Unit, National Institute of Neurological Sciences, Lima, Peru
| | - Javier Guitian
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hertfordshire, United Kingdom
| | - Armando Gonzalez
- Department of Animal and Public Health, School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
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Prada JM, Stolk WA, Davis EL, Touloupou P, Sharma S, Muñoz J, Caja Rivera RM, Reimer LJ, Michael E, de Vlas SJ, Hollingsworth TD. Delays in lymphatic filariasis elimination programmes due to COVID-19, and possible mitigation strategies. Trans R Soc Trop Med Hyg 2021; 115:261-268. [PMID: 33515454 PMCID: PMC7928650 DOI: 10.1093/trstmh/trab004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 12/25/2022] Open
Abstract
Background In view of the current global coronavirus disease 2019 pandemic, mass drug administration interventions for neglected tropical diseases, including lymphatic filariasis (LF), have been halted. We used mathematical modelling to estimate the impact of delaying or cancelling treatment rounds and explore possible mitigation strategies. Methods We used three established LF transmission models to simulate infection trends in settings with annual treatment rounds and programme delays in 2020 of 6, 12, 18 or 24 months. We then evaluated the impact of various mitigation strategies upon resuming activities. Results The delay in achieving the elimination goals is on average similar to the number of years the treatment rounds are missed. Enhanced interventions implemented for as little as 1 y can allow catch-up on the progress lost and, if maintained throughout the programme, can lead to acceleration of up to 3 y. Conclusions In general, a short delay in the programme does not cause a major delay in achieving the goals. Impact is strongest in high-endemicity areas. Mitigation strategies such as biannual treatment or increased coverage are key to minimizing the impact of the disruption once the programme resumes and lead to potential acceleration should these enhanced strategies be maintained.
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Affiliation(s)
- Joaquín M Prada
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Wilma A Stolk
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emma L Davis
- Big Data Institute, Li Ka Shing Center for Health Information and Discovery, Headington, Oxford, UK
| | - Panayiota Touloupou
- Department of Statistics, University of Warwick, Coventry, UK.,School of Mathematics, University of Birmingham, Birmingham, UK
| | - Swarnali Sharma
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Johanna Muñoz
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rocio M Caja Rivera
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.,Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL, USA
| | - Lisa J Reimer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Edwin Michael
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.,Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL, USA
| | - Sake J de Vlas
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - T Déirdre Hollingsworth
- Big Data Institute, Li Ka Shing Center for Health Information and Discovery, Headington, Oxford, UK
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Lepper HC, Prada JM, Davis EL, Gunawardena SA, Hollingsworth TD. Complex interactions in soil-transmitted helminth co-infections from a cross-sectional study in Sri Lanka. Trans R Soc Trop Med Hyg 2019; 112:397-404. [PMID: 30053259 PMCID: PMC6092609 DOI: 10.1093/trstmh/try068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/19/2018] [Indexed: 11/14/2022] Open
Abstract
Background Co-infection with multiple soil-transmitted helminth (STH) species is common in communities with a high STH prevalence. The life histories of STH species share important characteristics, particularly in the gut, and there is the potential for interaction, but evidence on whether interactions may be facilitating or antagonistic are limited. Methods Data from a pretreatment cross-sectional survey of STH egg deposition in a tea plantation community in Sri Lanka were analysed to evaluate patterns of co-infection and changes in egg deposition. Results There were positive associations between Trichuris trichiura (whipworm) and both Necator americanus (hookworm) and Ascaris lumbricoides (roundworm), but N. americanus and Ascaris were not associated. N. americanus and Ascaris infections had lower egg depositions when they were in single infections than when they were co-infecting. There was no clear evidence of a similar effect of co-infection in Trichuris egg deposition. Conclusions Associations in prevalence and egg deposition in STH species may vary, possibly indicating that effects of co-infection are species dependent. We suggest that between-species interactions that differ by species could explain these results, but further research in different populations is needed to support this theory.
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Affiliation(s)
- Hannah C Lepper
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, Mathematics Institute and School of Life Sciences, University of Warwick, UK
| | - Joaquín M Prada
- School of Veterinary Medicine, University of Surrey, Guilford, UK
| | - Emma L Davis
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, Mathematics Institute and School of Life Sciences, University of Warwick, UK
| | | | - T Déirdre Hollingsworth
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Minetti C, Tettevi EJ, Mechan F, Prada JM, Idun B, Biritwum NK, Osei-Atweneboana MY, Reimer LJ. Elimination within reach: A cross-sectional study highlighting the factors that contribute to persistent lymphatic filariasis in eight communities in rural Ghana. PLoS Negl Trop Dis 2019; 13:e0006994. [PMID: 30608931 PMCID: PMC6342320 DOI: 10.1371/journal.pntd.0006994] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 01/22/2019] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
Background Despite the progress achieved in scaling-up mass drug administration (MDA) for lymphatic filariasis (LF) in Ghana, communities with persistent LF still exist even after 10 years of community treatment. To understand the reasons for persistence, we conducted a study to assess the status of disease elimination and understand the adherence to interventions including MDA and insecticide treated nets. Methodology and principal findings We conducted a parasitological and epidemiological cross-sectional study in adults from eight villages still under MDA in the Northern Region savannah and the coastal Western Region of the country. Prevalence of filarial antigen ranged 0 to 32.4% and in five villages the prevalence of night blood microfilaria (mf) was above 1%, ranging from 0 to 5.7%. Median mf density was 67 mf/ml (range: 10–3,560). LF antigen positivity was positively associated with male sex but negatively associated with participating in MDA the previous year. Male sex was also associated with a decreased probability of participating in MDA. A stochastic model (TRANSFIL) was used to assess the expected microfilaria prevalence under different MDA coverage scenarios using historical data on one community in the Western Region. In this example, the model simulations suggested that the slow decline in mf prevalence is what we would expect given high baseline prevalence and a high correlation between MDA adherence from year to year, despite high MDA coverage. Conclusions There is a need for an integrated quantitative and qualitative research approach to identify the variations in prevalence, associated risk factors and intervention coverage and use levels between and within regions and districts. Such knowledge will help target resources and enhance surveillance to the communities most at risk and to reach the 2020 LF elimination goals in Ghana. Lymphatic filariasis (LF) is a mosquito-borne disease and a leading cause of disability and chronic morbidity worldwide. Despite the progress achieved so far in stopping LF transmission by treating the affected communities with specific drugs over several years, areas where lymphatic filariasis persists still exist. Understanding the reasons behind this is pivotal to both reach and sustain elimination. We investigated the factors associated with filariasis persistence in various communities still under drug treatment from two regions of Ghana. We reported high variability in disease burden, adherence to drug treatment and mosquito net use between regions and communities. LF infection was associated with men and not taking the drugs, and men were also less likely to take treatment. Using mathematical modelling, we showed that slight increases in treatment coverage will accelerate elimination. Our findings highlight the reasons for LF persistence and provide guidance on how to successfully achieve elimination by refining drug treatment distribution and mosquito control interventions more tailored to individuals and communities. We also demonstrated the value of using field-collected data in mathematical models to assess the current status of disease elimination and to identify the gaps in control interventions.
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Affiliation(s)
- Corrado Minetti
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Edward J. Tettevi
- Department of Environmental Biology and Health, Council for Scientific and Industrial Research Water Research Institute, Accra, Ghana
| | - Frank Mechan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Joaquín M. Prada
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Bright Idun
- Department of Environmental Biology and Health, Council for Scientific and Industrial Research Water Research Institute, Accra, Ghana
| | | | - Mike Yaw Osei-Atweneboana
- Department of Environmental Biology and Health, Council for Scientific and Industrial Research Water Research Institute, Accra, Ghana
| | - Lisa J. Reimer
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail:
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Abstract
The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce panini (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm. panini is browser-based and integrates with the Microreact platform for rapid online visualization and exploration of both core and accessory genome evolutionary signals, together with relevant epidemiological, geographical, temporal and other metadata. Several case studies with single- and multi-clone pneumococcal populations are presented to demonstrate the ability to identify biologically important signals from gene content data. panini is available at http://panini.pathogen.watch and code at http://gitlab.com/cgps/panini.
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Affiliation(s)
- Khalil Abudahab
- 1Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Joaquín M Prada
- 2School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Zhirong Yang
- 3Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Nicholas J Croucher
- 5Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jukka Corander
- 3Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, FI-00014 Helsinki, Finland.,6Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, N-0317 Oslo, Norway
| | - David M Aanensen
- 1Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.,7Big Data Institute, Li Ka Shing Centre for Health Informatics, University of Oxford, Oxford, UK
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11
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Davis EL, Danon L, Prada JM, Gunawardena SA, Truscott JE, Vlaminck J, Anderson RM, Levecke B, Morgan ER, Hollingsworth TD. Seasonally timed treatment programs for Ascaris lumbricoides to increase impact-An investigation using mathematical models. PLoS Negl Trop Dis 2018; 12:e0006195. [PMID: 29346383 PMCID: PMC5773001 DOI: 10.1371/journal.pntd.0006195] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/27/2017] [Indexed: 11/19/2022] Open
Abstract
There is clear empirical evidence that environmental conditions can influence Ascaris spp. free-living stage development and host reinfection, but the impact of these differences on human infections, and interventions to control them, is variable. A new model framework reflecting four key stages of the A. lumbricoides life cycle, incorporating the effects of rainfall and temperature, is used to describe the level of infection in the human population alongside the environmental egg dynamics. Using data from South Korea and Nigeria, we conclude that settings with extreme fluctuations in rainfall or temperature could exhibit strong seasonal transmission patterns that may be partially masked by the longevity of A. lumbricoides infections in hosts; we go on to demonstrate how seasonally timed mass drug administration (MDA) could impact the outcomes of control strategies. For the South Korean setting the results predict a comparative decrease of 74.5% in mean worm days (the number of days the average individual spend infected with worms across a 12 month period) between the best and worst MDA timings after four years of annual treatment. The model found no significant seasonal effect on MDA in the Nigerian setting due to a narrower annual temperature range and no rainfall dependence. Our results suggest that seasonal variation in egg survival and maturation could be exploited to maximise the impact of MDA in certain settings.
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Affiliation(s)
- Emma L. Davis
- Department of Mathematics, University of Warwick, Coventry, UK
- * E-mail:
| | - Leon Danon
- Data Science Institute, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Joaquín M. Prada
- Department of Mathematics, University of Warwick, Coventry, UK
- Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | | | - James E. Truscott
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Johnny Vlaminck
- Department of Virology, Parasitology and Immunology, Ghent University, Merelbeke, Belgium
| | - Roy M. Anderson
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Bruno Levecke
- Department of Virology, Parasitology and Immunology, Ghent University, Merelbeke, Belgium
| | - Eric R Morgan
- Institute for Global Food Security, School of Biological Sciences, Queen’s University, Belfast, UK
- School of Veterinary Science, University of Bristol, Langford, UK
| | - T. Deirdre Hollingsworth
- Department of Mathematics, University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
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12
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Prada JM, Touloupou P, Adriko M, Tukahebwa EM, Lamberton PHL, Hollingsworth TD. Understanding the relationship between egg- and antigen-based diagnostics of Schistosoma mansoni infection pre- and post-treatment in Uganda. Parasit Vectors 2018; 11:21. [PMID: 29310695 PMCID: PMC5759883 DOI: 10.1186/s13071-017-2580-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/06/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Schistosomiasis is a major socio-economic and public health problem in many sub-Saharan African countries. After large mass drug administration (MDA) campaigns, prevalence of infection rapidly returns to pre-treatment levels. The traditional egg-based diagnostic for schistosome infections, Kato-Katz, is being substituted in many settings by circulating antigen recognition-based diagnostics, usually the point-of-care circulating cathodic antigen test (CCA). The relationship between these diagnostics is poorly understood, particularly after treatment in both drug-efficacy studies and routine monitoring. RESULTS We created a model of schistosome infections to better understand and quantify the relationship between these two egg- and adult worm antigen-based diagnostics. We focused particularly on the interpretation of "trace" results after CCA testing. Our analyses suggest that CCA is generally a better predictor of prevalence, particularly after treatment, and that trace CCA results are typically associated with truly infected individuals. CONCLUSIONS Even though prevalence rises to pre-treatment levels only six months after MDAs, our model suggests that the average intensity of infection is much lower, and is probably in part due to a small burden of surviving juveniles from when the treatment occurred. This work helps to better understand CCA diagnostics and the interpretation of post-treatment prevalence estimations.
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Affiliation(s)
- Joaquín M. Prada
- Department of Mathematics, University of Warwick, Coventry, UK
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | | | - Moses Adriko
- Vector Control Division, Ministry of Health, Uganda, Kampala, Uganda
| | | | - Poppy H. L. Lamberton
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
- Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow, UK
| | - T. Déirdre Hollingsworth
- Department of Mathematics, University of Warwick, Coventry, UK
- Big Data Institute, University of Oxford, Oxford, UK
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13
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Abstract
Defense against infection incurs costs as well as benefits that are expected to shape the evolution of optimal defense strategies. In particular, many theoretical studies have investigated contexts favoring constitutive versus inducible defenses. However, even when one immune strategy is theoretically optimal, it may be evolutionarily unachievable. This is because evolution proceeds via mutational changes to the protein interaction networks underlying immune responses, not by changes to an immune strategy directly. Here, we use a theoretical simulation model to examine how underlying network architectures constrain the evolution of immune strategies, and how these network architectures account for desirable immune properties such as inducibility and robustness. We focus on immune signaling because signaling molecules are common targets of parasitic interference but are rarely studied in this context. We find that in the presence of a coevolving parasite that disrupts immune signaling, hosts evolve constitutive defenses even when inducible defenses are theoretically optimal. This occurs for two reasons. First, there are relatively few network architectures that produce immunity that is both inducible and also robust against targeted disruption. Second, evolution toward these few robust inducible network architectures often requires intermediate steps that are vulnerable to targeted disruption. The few networks that are both robust and inducible consist of many parallel pathways of immune signaling with few connections among them. In the context of relevant empirical literature, we discuss whether this is indeed the most evolutionarily accessible robust inducible network architecture in nature, and when it can evolve.
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Affiliation(s)
- Edward C Schrom
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Joaquín M Prada
- Mathematics Institute, University of Warwick, Coventry, United Kingdom.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
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14
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Prada JM, Metcalf CJE, Takahashi S, Lessler J, Tatem AJ, Ferrari M. Demographics, epidemiology and the impact of vaccination campaigns in a measles-free world - Can elimination be maintained? Vaccine 2017; 35:1488-1493. [PMID: 28216186 PMCID: PMC5341736 DOI: 10.1016/j.vaccine.2017.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 12/09/2022]
Abstract
Introduction All six WHO regions currently have goals for measles elimination by 2020. Measles vaccination is delivered via routine immunization programmes, which in most sub-Saharan African countries reach children around 9 months of age, and supplementary immunization activities (SIAs), which target a wider age range at multi-annual intervals. In the absence of endemic measles circulation, the proportion of individuals susceptible to measles will gradually increase through accumulation of new unvaccinated individuals in each birth cohort, increasing the risk of an epidemic. The impact of SIAs and the financial investment they require, depend on coverage and target age range. Materials and methods We evaluated the impact of target population age range for periodic SIAs, evaluating outcomes for two different levels of coverage, using a demographic and epidemiological model adapted to reflect populations in 4 sub-Saharan African countries. Results We found that a single SIA can maintain elimination over short time-scales, even with low routine coverage. However, maintaining elimination for more than a few years is difficult, even with large (high coverage/wide age range) recurrent SIAs, due to the build-up of susceptible individuals. Across the demographic and vaccination contexts investigated, expanding SIAs to target individuals over 10 years did not significantly reduce outbreak risk. Conclusions Elimination was not maintained in the contexts we evaluated without a second opportunity for vaccination. In the absence of an expanded routine program, SIAs provide a powerful option for providing this second dose. We show that a single high coverage SIA can deliver most key benefits in terms of maintaining elimination, with follow-up campaigns potentially requiring smaller investments. This makes post-campaign evaluation of coverage increasingly relevant to correctly assess future outbreak risk.
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Affiliation(s)
- J M Prada
- Department of Ecology and Evolutionary Biology, Princeton University, USA.
| | - C J E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, USA; Office of Population Research, WWS, Princeton University, USA; Fogarty International Center, National Institutes of Health, USA
| | - S Takahashi
- Department of Ecology and Evolutionary Biology, Princeton University, USA
| | - J Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - A J Tatem
- WorldPop, Department of Geography and Environment, University of Southampton, UK; Flowminder Foundation, Stockholm, Sweden
| | - M Ferrari
- Center for Infectious Disease Dynamics, Pennsylvania State University, USA
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15
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Atlija M, Prada JM, Gutiérrez-Gil B, Rojo-Vázquez FA, Stear MJ, Arranz JJ, Martínez-Valladares M. Implementation of an extended ZINB model in the study of low levels of natural gastrointestinal nematode infections in adult sheep. BMC Vet Res 2016; 12:97. [PMID: 27283535 PMCID: PMC4901511 DOI: 10.1186/s12917-016-0723-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 06/03/2016] [Indexed: 12/18/2022] Open
Abstract
Background In this study, two traits related with resistance to gastrointestinal nematodes (GIN) were measured in 529 adult sheep: faecal egg count (FEC) and activity of immunoglobulin A in plasma (IgA). In dry years, FEC can be very low in semi-extensive systems, such as the one studied here, which makes identifying animals that are resistant or susceptible to infection a difficult task. A zero inflated negative binomial model (ZINB) model was used to calculate the extent of zero inflation for FEC; the model was extended to include information from the IgA responses. Results In this dataset, 64 % of animals had zero FEC while the ZINB model suggested that 38 % of sheep had not been recently infected with GIN. Therefore 26 % of sheep were predicted to be infected animals with egg counts that were zero or below the detection limit and likely to be relatively resistant to nematode infection. IgA activities of all animals were then used to decide which of the sheep with zero egg counts had been exposed and which sheep had not been recently exposed. Animals with zero FEC and high IgA activity were considered resistant while animals with zero FEC and low IgA activity were considered as not recently infected. For the animals considered as exposed to the infection, the correlations among the studied traits were estimated, and the influence of these traits on the discrimination between unexposed and infected animals was assessed. Conclusions The model presented here improved the detection of infected animals with zero FEC. The correlations calculated here will be useful in the development of a reliable index of GIN resistance that could be of assistance for the study of host resistance in studies based on natural infection, especially in adult sheep, and also the design of breeding programs aimed at increasing resistance to parasites. Electronic supplementary material The online version of this article (doi:10.1186/s12917-016-0723-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M Atlija
- Departamento de Producción Animal, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - J M Prada
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK. .,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08540, USA.
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain.,Instituto de Ganadería de Montaña, CSIC-ULE, 24346, Grulleros, León, Spain
| | - F A Rojo-Vázquez
- Instituto de Ganadería de Montaña, CSIC-ULE, 24346, Grulleros, León, Spain.,Departamento de Sanidad Animal, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
| | - M J Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK
| | - J J Arranz
- Departamento de Producción Animal, Universidad de León, Campus de Vegazana s/n, 24071, León, Spain
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