Browsing by Author "Gupta, Sunetra"
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- EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networksPublication . Pinotti, Francesco; Lourenço, José; Gupta, Sunetra; Gupta, Suman Das; Henning, Joerg; Blake, Damer; Tomley, Fiona; Barnett, Tony; Pfeiffer, Dirk; Hoque, Md Ahasanul; Fournié, GuillaumeThe rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPIdemic NEtwork Simulation in poultry Transportation systems): an agent-based modelling framework designed to simulate pathogen transmission within realistic poultry production and distribution networks. We provide example applications to broiler production in Bangladesh, but the modular structure of the model allows for easy parameterization to suit specific countries and system configurations. Moreover, the framework enables the replication of a wide range of ecoepidemiological scenarios by incorporating diverse pathogen life-history traits, modes of transmission and interactions between multiple strains and/or pathogens. EPINEST was developed in the context of an interdisciplinary multi-centre study conducted in Bangladesh, India, Vietnam and Sri Lanka, and will facilitate the investigation of the spreading patterns of various health hazards such as avian influenza, Campylobacter, Salmonella and antimicrobial resistance in these countries. Furthermore, this modelling framework holds potential for broader application in veterinary epidemiology and One Health research, extending its relevance beyond poultry to encompass other livestock species and disease systems.
- Modelling the transmission dynamics of H9N2 avian influenza viruses in a live bird marketPublication . Pinotti, Francesco; Kohnle, Lisa; Lourenço, José; Gupta, Sunetra; Hoque, Md Ahasanul; Mahmud, Rashed; Biswas, Paritosh; Pfeiffer, Dirk; Fournié, GuillaumeH9N2 avian influenza viruses (AIVs) are a major concern for the poultry sector and human health in countries where this subtype is endemic. By fitting a model simulating H9N2 AIV transmission to data from a field experiment, we characterise the epidemiology of the virus in a live bird market in Bangladesh. Many supplied birds arrive already exposed to H9N2 AIVs, resulting in many broiler chickens entering the market as infected, and many indigenous backyard chickens entering with pre-existing immunity. Most susceptible chickens become infected within one day spent at the market, owing to high levels of viral transmission within market and short latent periods, as brief as 5.3 hours. Although H9N2 AIV transmission can be substantially reduced under moderate levels of cleaning and disinfection, effective risk mitigation also requires a range of additional interventions targeting markets and other nodes along the poultry production and distribution network.
- Shifting patterns of dengue three years after Zika virus emergence in BrazilPublication . Pinotti, Francesco; Giovanetti, Marta; Lima, Maricelia Maia de; Cerqueira, Erenilde Marques de; Alcantara, Luiz C. J.; Gupta, Sunetra; Recker, Mario; Lourenço, JoséIn 2015, the Zika virus (ZIKV) emerged in Brazil, leading to widespread outbreaks in Latin America. Following this, many countries in these regions reported a significant drop in the circulation of dengue virus (DENV), which resurged in 2018-2019. We examine age-specific incidence data to investigate changes in DENV epidemiology before and after the emergence of ZIKV. We observe that incidence of DENV was concentrated in younger individuals during resurgence compared to 2013-2015. This trend was more pronounced in Brazilian states that had experienced larger ZIKV outbreaks. Using a mathematical model, we show that ZIKV-induced cross-protection alone, often invoked to explain DENV decline across Latin America, cannot explain the observed age-shift without also assuming some form of disease enhancement. Our results suggest that a sudden accumulation of population-level immunity to ZIKV could suppress DENV and reduce the mean age of DENV incidence via both protective and disease-enhancing interactions.
- The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban MalawiPublication . Obolski, Uri; Swarthout, Todd D.; Kalizang’oma, Akuzike; Mwalukomo, Thandie S.; Chan, Jia Mun; Weight, Caroline M.; Brown, Comfort; Cave, Rory; Cornick, Jen; Kamng’ona, Arox Wadson; Msefula, Jacquline; Ercoli, Giuseppe; Brown, Jeremy S.; Lourenço, José; Maiden, Martin C.; French, Neil; Gupta, Sunetra; Heyderman, Robert S.Streptococcus pneumoniae causes substantial mortality among children under 5-years-old worldwide. Polysaccharide conjugate vaccines (PCVs) are highly effective at reducing vaccine serotype disease, but emergence of non-vaccine serotypes and persistent nasopharyngeal carriage threaten this success. We investigated the hypothesis that following vaccine, adapted pneumococcal genotypes emerge with the potential for vaccine escape. We genome sequenced 2804 penumococcal isolates, collected 4-8 years after introduction of PCV13 in Blantyre, Malawi. We developed a pipeline to cluster the pneumococcal population based on metabolic core genes into “Metabolic genotypes” (MTs). We show that S. pneumoniae population genetics are characterised by emergence of MTs with distinct virulence and antimicrobial resistance (AMR) profiles. Preliminary in vitro and murine experiments revealed that representative isolates from emerging MTs differed in growth, haemolytic, epithelial infection, and murine colonisation characteristics. Our results suggest that in the context of PCV13 introduction, pneumococcal population dynamics had shifted, a phenomenon that could further undermine vaccine control and promote spread of AMR.