Biology subjects

Diggle, P.

Publications and source records attributed to Diggle, P..

4 recordsLinked to original sources

bioRxiv2021

A joint distribution framework to improve presence-only species distribution models by exploiting opportunistic surveys

{whitebullet} AimWe propose a Bayesian framework for modelling species distributions using presence-only biodiversity occurrences obtained from historical opportunistic surveys. {whitebullet}LocationGlobal applicability with two case studies in south-east Mexico. {whitebullet}MethodsThe framework defines a bivariate spatial process separable into ecological and sampling effort processes that jointly generate occurrence observations of biodiversity records. Presence-only data are conceived as incomplete observations where some presences have been filtered out. A choosing principle is used to separate out presences, missing data and absences relative to the species of interest and the sampling observations. The framework provides three modelling alternatives for accounting the spatial autocorrelation structure: independent latent variables (model I); common latent spatial random effect (model II); and correlated latent spatial random effects (model III). The framework was compared against the Maximum Entropy (MaxEnt) algorithm in two case studies: one for the prediction of pines (Class: Pinopsida), using botanical records as sampling observations and another for the prediction of Flycatchers (Family: Tyranidae), using bird sightings as sampling records. {whitebullet} [a]ResultsIn both case studies, at least one of the proposed models achieved higher predictive accuracy than MaxEnt. The model with correlated spatial effects fit best when the sampling effort was informative, while the one with a shared spatial effect was more suitable in cases with high proportion of non sampled sites. {whitebullet}Main ConclusionsOur approach provides a flexible framework for presence-only SDMs aided by a sampling effort process informed by the accumulated observations of independent and heterogeneous surveys. For the two case studies, the framework provided a model with a higher predictive accuracy than an optimised version MaxEnt.

ecology↗

bioRxiv2020

A Live Attenuated Vaccine Model Confers Cross-Protective Immunity Against Different Species of Leptospira spp.

Leptospirosis is the leading zoonotic disease in terms of morbidity and mortality worldwide with a great health and economic impact in both humans and animals. Effective prevention is urgently needed as rapid urbanization, climate change and drivers of disease transmission continue to intensify. The key challenge has been developing a widely-applicable vaccine that protects against the 13 different pathogenic species and >300 serovars that can cause leptospirosis, providing a major public health benefit and opportunity to leverage One Health approaches. Live attenuated mutants that can boost immunity and induce protection are enticing vaccine candidates and poorly explored in the field. We evaluated a recently characterized motility-deficient mutant lacking the expression of a flagellar protein, FcpA. Although the fcpA- mutant has lost its ability to penetrate mucous membranes and cause disease, a transient bacteremia prior to clearance by the host immune response was observed. In two animal models, immunization with a single dose of the fcpA- mutant was sufficient to induce robust anti-protein antibodies response that promoted protection against infection with different Leptospira spp. species. Furthermore, characterization of the immune response identified a small repertoire of biologically relevant proteins that are highly conserved among pathogenic Leptospira species and potential correlates of cross-protective immunity.

microbiology↗

bioRxiv2019

Rainfall and other meteorological factors as drivers of urban transmission of leptospirosis

BackgroundLeptospirosis is an important public health problem affecting vulnerable urban slum populations in developing country settings. However, the complex interaction of meteorological factors driving the temporal trends of leptospirosis remain incompletely understood.\n\nMethods and findingsFrom 1996 to 2010, we investigated the association between the weekly incidence of leptospirosis and climatic variables in the city of Salvador, Brazil by using a dynamic generalized linear model that accounted for time lags, overall trend and seasonal variation. Our model showed an increase of leptospirosis cases associated with rainfall, lower temperature and higher humidity. There was a lag of one-to-two weeks between weekly values for significant meteorological variables and leptospirosis incidence. Independent of the season, a weekly cumulative rainfall of 20 mm increased the risk of the leptospirosis by 10% compared to a week without rain. Finally, over the 14 year study period the incidence of leptospirosis decreased significantly by four fold (12.8 versus 3.6 per 100,000 people), independently of variations in climate.\n\nConclusionsStrategies to control leptospirosis should focus on avoiding contact with contaminated sources of Leptospira as well as on increasing awareness in the population and health professionals within the short time window after both low-level and extreme rainfall events. Increased leptospirosis incidence was restricted to one-to-two weeks after those events suggesting that infectious Leptospira survival may be limited to short time intervals.\n\nAuthor SummaryTo determine the role of meteorological variables, seasonal variation and temporal trends in the incidence of leptospirosis, we investigated the time series of leptospirosis incidence amongst residents of Salvador, Brazil, from 1996 to 2010. Exploratory and confirmatory statistical methods detected associations between meteorological factors and disease incidence. Results showed the importance of extreme meteorological conditions, particularly rainfall, as short-term predictors of leptospirosis incidence. In addition, we found a long-term decreasing trend of in disease incidence over the observation period.

epidemiology↗

bioRxiv2018

High residual prevalence of vaccine serotype Streptococcus pneumoniae carriage 4 to 6 years after introduction of 13-valent pneumococcal conjugate vaccine in Malawi: a prospective serial cross-sectional study

BackgroundThere are concerns that pneumococcal conjugate vaccines (PCV) in sub-Saharan Africa sub-optimally interrupt vaccine-serotype (VT) carriage and transmission, thus limiting vaccine-induced direct and indirect protection. We assessed carriage in vaccinated children and unvaccinated populations targeted for indirect protection, between 4 and 7 years after Malawis November 2011 introduction of PCV13 using a 3+0 schedule.\n\nMethodsWe conducted sequential prospective nasopharyngeal carriage surveys between 2015 and 2018 among healthy PCV-vaccinated and PCV-unvaccinated children, and HIV-infected adults. VT and NVT carriage risk by age was analysed by non-linear regression.\n\nResultsAmong PCV-vaccinated children, there was a 24% relative reduction in carriage, from a mean 21.1% to 16.1%; 45% reduction among older PCV-unvaccinated children, from 27.5% to 15.2%; 41.4% reduction among adults, from 15.2% to 8.9%. Using carriage data from children 3.6 to 10 years of age, VT carriage probability declined with age, with a similar prevalence half-life among PCV-vaccinated (3.34 years) and PCV-unvaccinated (3.26 years) children.\n\nConclusionCompared to high-income settings, the 3+0 schedule in Malawi has led to a sub-optimal reduction in pneumococcal carriage prevalence. This is likely due to recolonisation of vaccinated children with waning vaccine-induced immunity, resulting in insufficient indirect protection of unvaccinated populations. Rigorous evaluation of strategies to augment vaccine-induced control of carriage, including alternative schedules and catch-up campaigns is required.

epidemiology↗