Dr Joaquin M. Prada


Lecturer in Veterinary Epidemiology
BEng, MEng, PhD, FHEA

Biography

University roles and responsibilities

  • School of Veterinary Medicine Impact Champion

    Courses I teach on

    Undergraduate

    Postgraduate taught

    My publications

    Publications

    E. Michael, S. Sharma, M.E. Smith, P. Touloupou, F. Giardina, Joaquin Prada, W.A. Stolk, D. Hollingsworth, S.J. de Vlas (2018)Quantifying the value of surveillance data for improving model predictions of lymphatic filariasis elimination, In: PLoS neglected tropical diseases12(10) NLM (Medline)

    Mathematical models are increasingly being used to evaluate strategies aiming to achieve the control or elimination of parasitic diseases. Recently, owing to growing realization that process-oriented models are useful for ecological forecasts only if the biological processes are well defined, attention has focused on data assimilation as a means to improve the predictive performance of these models.

    H.C. Lepper, Joaquin Prada, E.L. Davis, S.A. Gunawardena, T. DÃirdre Hollingsworth (2018)Complex interactions in soil-transmitted helminth co-infections from a cross-sectional study in Sri Lanka, In: Transactions of the Royal Society of Tropical Medicine and Hygiene112(8)pp. 397-404 Oxford University Press

    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. © The Author(s) 2018. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.

    Joaquin Prada, C.J.E. Metcalf, M.J. Ferrari (2018)Improving measles incidence inference using age-structured serological data, In: Epidemiology and Infection146(13)pp. 1699-1706 Cambridge University Press

    Measles is a target for elimination in all six WHO regions by 2020, and over the last decade, there has been considerable progress towards this goal. Surveillance is recognised as a cornerstone of elimination programmes, allowing early identification of outbreaks, thus enabling control and preventing re-emergence. Fever-rash surveillance is increasingly available across WHO regions, and this symptom-based reporting is broadly used for measles surveillance. However, as measles control increases, symptom-based cases are increasingly likely to reflect infection with other diseases with similar symptoms such as rubella, which affects the same populations, and can have a similar seasonality. The WHO recommends that cases from suspected measles outbreaks be laboratory-confirmed, to identify 'true' cases, corresponding to measles IgM titres exceeding a threshold indicative of infection. Although serological testing for IgM has been integrated into the fever-rash surveillance systems in many countries, the logistics of sending in every suspected case are often beyond the health system's capacity. We show how age data from serologically confirmed cases can be leveraged to infer the status of non-Tested samples, thus strengthening the information we can extract from symptom-based surveillance. Applying an age-specific confirmation model to data from three countries with divergent epidemiology across Africa, we identify the proportion of cases that need to be serologically tested to achieve target levels of accuracy in estimated infected numbers and discuss how this varies depending on the epidemiological context. Our analysis provides an approach to refining estimates of incidence leveraging all available data, which has the potential to improve allocation of resources, and thus contribute to rapid and efficient control of outbreaks. © Cambridge University Press 2018 This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

    M. Atlija, Joaquin Prada, B. Gutierrez-Gil, F.A. Rojo-Vázquez, M.J. Stear, J.J. Arranz, M. Martínez-Valladares (2016)Implementation of an extended ZINB model in the study of low levels of natural gastrointestinal nematode infections in adult sheep, In: BMC Veterinary Research12(1) BioMed Central Ltd.

    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. © 2016 The Author(s).

    E.L. Davis, L. Danon, Joaquin Prada, S.A. Gunawardena, J.E. Truscott, J. Vlaminck, R.M. Anderson, B. Levecke, E.R. Morgan, T.D. Hollingsworth (2018)Seasonally timed treatment programs for Ascaris lumbricoides to increase impact—An investigation using mathematical models, In: PLoS Neglected Tropical Diseases12(1) Public Library of Science

    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. © 2018 Davis et al.

    Joaquin Prada, C.J.E. Metcalf, S. Takahashi, J. Lessler, A.J. Tatem, M. Ferrari (2017)Demographics, epidemiology and the impact of vaccination campaigns in a measles-free world – Can elimination be maintained?, In: Vaccine35(11)pp. 1488-1493 Elsevier Ltd

    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. © 2017 The Author(s)

    W.A. Stolk, Joaquin Prada, M.E. Smith, P. Kontoroupis, A.S. De Vos, P. Touloupou, M.A. Irvine, P. Brown, S. Subramanian, M. Kloek, E. Michael, T.D. Hollingsworth, S.J. De Vlas (2018)Are alternative strategies required to accelerate the global elimination of lymphatic filariasis? Insights from mathematical models, In: Clinical Infectious Diseases66pp. S260-S266 Oxford University Press

    Background. With the 2020 target year for elimination of lymphatic filariasis (LF) approaching, there is an urgent need to assess how long mass drug administration (MDA) programs with annual ivermectin + albendazole (IA) or diethylcarbamazine + albendazole (DA) would still have to be continued, and how elimination can be accelerated. We addressed this using mathematical modeling. Methods. We used 3 structurally different mathematical models for LF transmission (EPIFIL, LYMFASIM, TRANSFIL) to simulate trends in microfilariae (mf) prevalence for a range of endemic settings, both for the current annual MDA strategy and alternative strategies, assessing the required duration to bring mf prevalence below the critical threshold of 1%. Results. Three annual MDA rounds with IA or DA and good coverage (≥65%) are sufficient to reach the threshold in settings that are currently at mf prevalence

    Jon Pey, Joaquin Prada, John E Beasley, Francisco J Planes (2019)Path finding methods accounting for stoichiometry in metabolic networks, In: Genome biology12(5) BioMed Central
    NN Jonsson, MRS Fortes, EK Piper, DM Vankan, Joaquin Prada, T Wittek (2019)Comparison of metabolic, hematological, and peripheral blood leukocyte cytokine profiles of dairy cows and heifers during the periparturient period, In: Journal of Dairy Science Elsevier
    Martha Betson, Allen Jethro I Alonte, Rico C Ancog, Angelou Marie O Aquino, Vicente Y Belizario, Jr, Anna Monica D Bordado, Jessica Clark, Ma Christina G Corales, Mary Grace Dacuma, Billy P Divina, Matthew A Dixon, Stephen A Gourley, Jasmine Renette D Jimenez, Ben P Jones, Sheina Macy P Manalo, Joaquin M Prada, Arnoud H M van Vliet, Kezia C L Whatley, Vachel Gay V Paller (2021)Zoonotic transmission of intestinal helminths in southeast Asia: Implications for control and elimination, In: Advances in Parasitology108pp. 47-131

    Intestinal helminths are extremely widespread and highly prevalent infections of humans, particularly in rural and poor urban areas of low and middle-income countries. These parasites have chronic and often insidious effects on human health and child development including abdominal problems, anaemia, stunting and wasting. Certain animals play a fundamental role in the transmission of many intestinal helminths to humans. However, the contribution of zoonotic transmission to the overall burden of human intestinal helminth infection and the relative importance of different animal reservoirs remains incomplete. Moreover, control programmes and transmission models for intestinal helminths often do not consider the role of zoonotic reservoirs of infection. Such reservoirs will become increasingly important as control is scaled up and there is a move towards interruption and even elimination of parasite transmission. With a focus on southeast Asia, and the Philippines in particular, this review summarises the major zoonotic intestinal helminths, risk factors for infection and highlights knowledge gaps related to their epidemiology and transmission. Various methodologies are discussed, including parasite genomics, mathematical modelling and socio-economic analysis, that could be employed to improve understanding of intestinal helminth spread, reservoir attribution and the burden associated with infection, as well as assess effectiveness of interventions. For sustainable control and ultimately elimination of intestinal helminths, there is a need to move beyond scheduled mass deworming and to consider animal and environmental reservoirs. A One Health approach to control of intestinal helminths is proposed, integrating interventions targeting humans, animals and the environment, including improved access to water, hygiene and sanitation. This will require coordination and collaboration across different sectors to achieve best health outcomes for all.

    Emma Taylor, Victor Del Rio Vilas, Terence Scott, Andre Coetzer, Joaquin M Prada, Gholami Alireza, Nasr A Alqadi, Atika Berry, Bassel Bazzal, Abdelaziz Barkia, Firuzjon Davlyatov, Firoozeh Farahtaj, Khaouther Harabech, Paata Imnadze, Fazia Mahiout, Mohammed Ismael Majeed, Vitalii Nedosekov, Louis Nel, Hassan Rich, Abderazak Soufi, Radovan Vodopija, Nenad Vranjes, Valentina Sanchez Picot, Daniel Horton (2021)Rabies in the Middle East, Eastern Europe, Central Asia, North Africa: Building, In: Journal of Infection and Public Health14(6)pp. 787-794 Elsevier Ltd

    The Middle East, Eastern Europe, Central Asia and North Africa Rabies Control Network (MERACON), is built upon the achievements of the Middle East and Eastern Europe Rabies Expert Bureau (MEEREB). MERACON aims to foster collaboration among Member States (MS) and develop shared regional objectives, building momentum towards dog-mediated rabies control and elimination. Here we assess the epidemiology of rabies and preparedness in twelve participating MS, using case and rabies capacity data for 2017, and compare our findings with previous published reports and a predictive burden model. Across MS, the number of reported cases of dog rabies per 100,000 dog population and the number of reported human deaths per 100,000 population as a result of dog-mediated rabies appeared weakly associated. Compared to 2014 there has been a decrease in the number of reported human cases in five of the twelve MS, three MS reported an increase, two MS continued to report zero cases, and the remaining two MS were not listed in the 2014 study and therefore no comparison could be drawn. Vaccination coverage in dogs has increased since 2014 in half (4/8) of the MS where data are available. Most importantly, it is evident that there is a need for improved data collection, sharing and reporting at both the national and international levels. With the formation of the MERACON network, MS will be able to align with international best practices, while also fostering international support with other MS and international organisations.

    Joaquin Prada, Panayiota Touloupou, Moses Adriko, Edridah M. Tukahebwa, Poppy H. L. Lamberton, T. Déirdre Hollingsworth (2018)Understanding the relationship between egg- and antigen-based diagnostics of Schistosoma mansoni infection pre- and post-treatment in Uganda, In: Parasites & Vectors11(21)pp. 1-8 BioMed Central

    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.

    Edward C Schrom, Joaquin Prada, Andrea L Graham (2017)Immune Signaling Networks: Sources of Robustness and Constrained Evolvability during Coevolution, In: Molecular Biology and Evolution35(3)pp. 676-687 Oxford University Press (OUP)

    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.

    Colette Mair, Michael Stear, Paul Johnson, Matthew Denwood, Joaquin Prada, Thorsten Stefan, Louise Matthews (2019)A Bayesian generalized random regression model for estimating heritability using overdispersed count data, In: Genetics Selection Evolution47(1) BioMed Central
    Jon Pey, Luis Tobalina, Joaquin Prada, Francisco J Planes (2019)A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype, In: BMC systems biology7(1) BioMed Central
    Khalil Abudahab, Joaquin Prada, Zhirong Yang, Stephen D Bentley, Nicholas J Croucher, Jukka Corander, David M Aanensen (2019)PANINI: Pangenome Neighbor Identification for Bacterial Populations, In: bioRxiv Cold Spring Harbor Laboratory
    Colette Mair, Louise Matthews, Joaquin Prada, Thorsten Stefan, Michael J Stear (2019)Multitrait indices to predict worm length and number in sheep with natural, mixed predominantly Teladorsagia circumcincta infection, In: Parasitology142(6)pp. 773-782 Cambridge University Press
    Joaquin Prada, Louise Matthews, Colette Mair, Thorsten Stefan, Michael J Stear (2019)The transfer of IgA from mucus to plasma and the implications for diagnosis and control of nematode infections, In: Parasitology141(7)pp. 875-879 Cambridge University Press
    Joaquin Prada, Michael J Stear, Colette Mair, Darran Singleton, Thorsten Stefan, Abigail Stear, Glenn Marion, Louise Matthews (2019)An explicit immunogenetic model of gastrointestinal nematode infection in sheep, In: Journal of The Royal Society Interface11(99) The Royal Society