18 results found
O'Reilly KM, Grassly N, Verity R, 2018, Population sensitivity of acute flaccid paralysis and environmental surveillance for serotype 1 poliovirus in Pakistan: an observational study, BMC Infectious Diseases, Vol: 18, ISSN: 1471-2334
BackgroundTo support poliomyelitis eradication in Pakistan, environmental surveillance (ES) of wastewater has been expanded alongside surveillance for acute flaccid paralysis (AFP). ES is a relatively new method of surveillance, and the population sensitivity of detecting poliovirus within endemic settings requires estimation.MethodsData for wild serotype 1 poliovirus from AFP and ES from January 2011 to September 2015 from 14 districts in Pakistan were analysed using a multi-state model framework. This framework was used to estimate the sensitivity of poliovirus detection from each surveillance source and parameters such as the duration of infection within a community.ResultsThe location and timing of poliomyelitis cases showed spatial and temporal variability. The sensitivity of AFP surveillance to detect serotype 1 poliovirus infection in a district and its neighbours per month was on average 30.0% (95% CI 24.8–35.8) and increased with the incidence of poliomyelitis cases. The average population sensitivity of a single environmental sample was 59.4% (95% CI 55.4–63.0), with significant variation in site-specific estimates (median varied from 33.3–79.2%). The combined population sensitivity of environmental and AFP surveillance in a given month was on average 98.1% (95% CI 97.2–98.7), assuming four samples per month for each site.ConclusionsES can be a highly sensitive supplement to AFP surveillance in areas with converging sewage systems. As ES for poliovirus is expanded, it will be important to identify factors associated with variation in site sensitivity, leading to improved site selection and surveillance system performance.
Imran H, Raja D, Grassly N, et al., 2018, Routine immunization in Pakistan: comparison of multiple data sources and identification of factors associated with vaccination, International Health, Vol: 10, Pages: 84-91, ISSN: 1876-3405
BackgroundWithin Pakistan, estimates of vaccination coverage with the pentavalent vaccine, oral polio vaccine (OPV) and measles vaccine (MV) in 2011 were reported to be 74%, 75% and 53%, respectively. These national estimates may mask regional variation. The reasons for this variation have not been explored.MethodsData from the Multiple Indicator Cluster Surveys (MICS) for Balochistan and Punjab (2010–2011) are analysed to examine factors associated with receiving three or more doses of the pentavalent vaccine and one or more MVs using regression modelling. Pentavalent and OPV estimates from the MICS were compared to vaccine dose histories from surveillance for acute flaccid paralysis (AFP; poliomyelitis) to ascertain agreement.ResultsAdjusted coverage of children 12–23 months of age were estimated to be 16.0%, 75.5% and 34.2% in Balochistan and 58.0%, 87.7% and 72.6% in Punjab for the pentavalent vaccine, OPV and MV, respectively. Maternal education, healthcare utilization and wealth were associated with receiving the pentavalent vaccine and the MV. There was a strong correlation of district estimates of vaccination coverage between AFP and MICS data, but AFP estimates of pentavalent coverage in Punjab were biased toward higher values.ConclusionsNational estimates mask variation and estimates from individual surveys should be considered alongside other estimates. The development of strategies targeted towards poorly educated parents within low-wealth quintiles that may not typically access healthcare could improve vaccination rates.
Molodecky NAL, Blake IM, O'reilly KM, et al., 2017, Risk-factors and short-term projections for serotype-1 poliomyelitis incidence in Pakistan: a spatio-temporal analysis, Plos Medicine, Vol: 14, ISSN: 1549-1676
BackgroundPakistan currently provides a substantial challenge to global polio eradication, having contributed to 73% of reported poliomyelitis in 2015 and 54% in 2016. A better understanding of the risk factors and movement patterns that contribute to poliovirus transmission across Pakistan would support evidence-based planning for mass vaccination campaigns.Methods and findingsWe fit mixed-effects logistic regression models to routine surveillance data recording the presence of poliomyelitis associated with wild-type 1 poliovirus in districts of Pakistan over 6-month intervals between 2010 to 2016. To accurately capture the force of infection (FOI) between districts, we compared 6 models of population movement (adjacency, gravity, radiation, radiation based on population density, radiation based on travel times, and mobile-phone based). We used the best-fitting model (based on the Akaike Information Criterion [AIC]) to produce 6-month forecasts of poliomyelitis incidence. The odds of observing poliomyelitis decreased with improved routine or supplementary (campaign) immunisation coverage (multivariable odds ratio [OR] = 0.75, 95% confidence interval [CI] 0.67–0.84; and OR = 0.75, 95% CI 0.66–0.85, respectively, for each 10% increase in coverage) and increased with a higher rate of reporting non-polio acute flaccid paralysis (AFP) (OR = 1.13, 95% CI 1.02–1.26 for a 1-unit increase in non-polio AFP per 100,000 persons aged <15 years). Estimated movement of poliovirus-infected individuals was associated with the incidence of poliomyelitis, with the radiation model of movement providing the best fit to the data. Six-month forecasts of poliomyelitis incidence by district for 2013–2016 showed good predictive ability (area under the curve range: 0.76–0.98). However, although the best-fitting movement model (radiation) was a significant determinant of poliomyelitis incidence, it did not improve the predictive ability of the multivariable mo
O'Reilly KM, Lamoureux C, Molodecky NA, et al., 2017, An assessment of the geographical risks of wild and vaccine-derived poliomyelitis outbreaks in Africa and Asia, BMC Infectious Diseases, Vol: 17, ISSN: 1471-2334
BackgroundThe international spread of wild poliomyelitis outbreaks continues to threaten eradication of poliomyelitis and in 2014 a public health emergency of international concern was declared. Here we describe a risk scoring system that has been used to assess country-level risks of wild poliomyelitis outbreaks, to inform prioritisation of mass vaccination planning, and describe the change in risk from 2014 to 2016. The methods were also used to assess the risk of emergence of vaccine-derived poliomyelitis outbreaks.MethodsPotential explanatory variables were tested against the reported outbreaks of wild poliomyelitis since 2003 using multivariable regression analysis. The regression analysis was translated to a risk score and used to classify countries as Low, Medium, Medium High and High risk, based on the predictive ability of the score.ResultsIndicators of population immunity, population displacement and diarrhoeal disease were associated with an increased risk of both wild and vaccine-derived outbreaks. High migration from countries with wild cases was associated with wild outbreaks. High birth numbers were associated with an increased risk of vaccine-derived outbreaks.ConclusionsUse of the scoring system is a transparent and rapid approach to assess country risk of wild and vaccine-derived poliomyelitis outbreaks. Since 2008 there has been a steep reduction in the number of wild poliomyelitis outbreaks and the reduction in countries classified as High and Medium High risk has reflected this. The risk of vaccine-derived poliomyelitis outbreaks has varied geographically. These findings highlight that many countries remain susceptible to poliomyelitis outbreaks and maintenance or improvement in routine immunisation is vital.
Pons-Salort M, Molodecky NA, O'Reilly KM, et al., 2016, Population immunity against serotype-2 poliomyelitis Leading up to the global withdrawal of the oral poliovirus vaccine: spatio-temporal modelling of surveillance data, Plos Medicine, Vol: 13, ISSN: 1549-1676
BackgroundGlobal withdrawal of serotype-2 oral poliovirus vaccine (OPV2) took place in April 2016. This marked a milestone in global polio eradication and was a public health intervention of unprecedented scale, affecting 155 countries. Achieving high levels of serotype-2 population immunity before OPV2 withdrawal was critical to avoid subsequent outbreaks of serotype-2 vaccine-derived polioviruses (VDPV2s).Methods and FindingsIn August 2015, we estimated vaccine-induced population immunity against serotype-2 poliomyelitis for 1 January 2004–30 June 2015 and produced forecasts for April 2016 by district in Nigeria and Pakistan. Population immunity was estimated from the vaccination histories of children <36 mo old identified with non-polio acute flaccid paralysis (AFP) reported through polio surveillance, information on immunisation activities with different oral poliovirus vaccine (OPV) formulations, and serotype-specific estimates of the efficacy of these OPVs against poliomyelitis. District immunity estimates were spatio-temporally smoothed using a Bayesian hierarchical framework. Coverage estimates for immunisation activities were also obtained, allowing for heterogeneity within and among districts. Forward projections of immunity, based on these estimates and planned immunisation activities, were produced through to April 2016 using a cohort model.Estimated population immunity was negatively correlated with the probability of VDPV2 poliomyelitis being reported in a district. In Nigeria and Pakistan, declines in immunity during 2008–2009 and 2012–2013, respectively, were associated with outbreaks of VDPV2. Immunity has since improved in both countries as a result of increased use of trivalent OPV, and projections generally indicated sustained or improved immunity in April 2016, such that the majority of districts (99% [95% uncertainty interval 97%–100%] in Nigeria and 84% [95% uncertainty interval 77%–91%] in Pakistan) had >70
O'Reilly KM, cori A, Durry E, et al., 2015, A new method to estimate the coverage of mass vaccination campaigns against poliomyelitis from surveillance data., American Journal of Epidemiology, Vol: 182, Pages: 961-970, ISSN: 1476-6256
Mass vaccination campaigns with the oral poliovirus vaccine targeting children aged <5 years are a critical component of the global poliomyelitis eradication effort. Monitoring the coverage of these campaigns is essential to allow corrective action, but current approaches are limited by their cross-sectional nature, nonrandom sampling, reporting biases, and accessibility issues. We describe a new Bayesian framework using data augmentation and Markov chain Monte Carlo methods to estimate variation in vaccination coverage from children's vaccination histories investigated during surveillance for acute flaccid paralysis. We tested the method using simulated data with at least 200 cases and were able to detect undervaccinated groups if they exceeded 10% of all children and temporal changes in coverage of ±10% with greater than 90% sensitivity. Application of the method to data from Pakistan for 2010–2011 identified undervaccinated groups within the Balochistan/Federally Administered Tribal Areas and Khyber Pakhtunkhwa regions, as well as temporal changes in coverage. The sizes of these groups are consistent with the multiple challenges faced by the program in these regions as a result of conflict and insecurity. Application of this new method to routinely collected data can be a useful tool for identifying poorly performing areas and assisting in eradication efforts.
De Maio N, Wu C, O'Reilly K, et al., 2015, New routes to phylogeography: A Bayesian structured coalescent approximation, PLOS Genetics, Vol: 11, ISSN: 1553-7390
Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications of phylogeography are broad, and in the context of pathogens include the reconstruction of transmission histories and the origin and emergence of outbreaks. Phylogeographic inference based on bottom-up population genetics models is computationally expensive, and as a result faster alternatives based on the evolution of discrete traits have become popular. In this paper, we show that inference of migration rates and root locations based on discrete trait models is extremely unreliable and sensitive to biased sampling. To address this problem, we introduce BASTA (BAyesian STructured coalescent Approximation), a new approach implemented in BEAST2 that combines the accuracy of methods based on the structured coalescent with the computational efficiency required to handle more than just few populations. We illustrate the potentially severe implications of poor model choice for phylogeographic analyses by investigating the zoonotic transmission of Ebola virus. Whereas the structured coalescent analysis correctly infers that successive human Ebola outbreaks have been seeded by a large unsampled non-human reservoir population, the discrete trait analysis implausibly concludes that undetected human-to-human transmission has allowed the virus to persist over the past four decades. As genomics takes on an increasingly prominent role informing the control and prevention of infectious diseases, it will be vital that phylogeographic inference provides robust insights into transmission history.
Parker EP, Molodecky NA, Pons-Salort M, et al., 2015, Impact of inactivated poliovirus vaccine on mucosal immunity: implications for the polio eradication endgame., Expert Review of Vaccines, Vol: 14, Pages: 1113-1123, ISSN: 1744-8395
The polio eradication endgame aims to bring transmission of all polioviruses to a halt. To achieve this aim, it is essential to block viral replication in individuals via induction of a robust mucosal immune response. Although it has long been recognized that inactivated poliovirus vaccine (IPV) is incapable of inducing a strong mucosal response on its own, it has recently become clear that IPV may boost immunity in the intestinal mucosa among individuals previously immunized with oral poliovirus vaccine. Indeed, mucosal protection appears to be stronger following a booster dose of IPV than oral poliovirus vaccine, especially in older children. Here, we review the available evidence regarding the impact of IPV on mucosal immunity, and consider the implications of this evidence for the polio eradication endgame. We conclude that the implementation of IPV in both routine and supplementary immunization activities has the potential to play a key role in halting poliovirus transmission, and thereby hasten the eradication of polio.
Metcalf CJE, Tatem A, Bjornstad ON, et al., 2014, Transport networks and inequities in vaccination: remoteness shapes measles vaccine coverage and prospects for elimination across Africa, Epidemiology and Infection, Vol: 143, Pages: 1457-1466, ISSN: 1469-4409
Measles vaccination is estimated to have averted 13·8 million deaths between 2000 and 2012.Persisting heterogeneity in coverage is a major contributor to continued measles mortality, and abarrier to measles elimination and introduction of rubella-containing vaccine. Our objective is toidentify determinants of inequities in coverage, and how vaccine delivery must change to achieveelimination goals, which is a focus of the WHO Decade of Vaccines. We combined estimates oftravel time to the nearest urban centre (550 000 people) with vaccination data from DemographicHealth Surveys to assess how remoteness affects coverage in 26 African countries. Building on astatistical mapping of coverage against age and geographical isolation, we quantified howmodifying the rate and age range of vaccine delivery affects national coverage. Our scenarioanalysis considers increasing the rate of delivery of routine vaccination, increasing the target agerange of routine vaccination, and enhanced delivery to remote areas. Geographical isolation plays akey role in defining vaccine inequity, with greater inequity in countries with lower measles vaccinecoverage. Eliminating geographical inequities alone will not achieve thresholds for herd immunity,indicating that changes in delivery rate or age range of routine vaccination will be required. Measlesvaccine coverage remains far below targets for herd immunity in many countries on the Africancontinent and is likely to be inadequate for achieving rubella elimination. The impact of strategiessuch as increasing the upper age range eligible for routine vaccination should be considered.
O'Reilly KM, 2012, Polio vaccination in Pakistan Reply, LANCET, Vol: 380, Pages: 1645-1646, ISSN: 0140-6736
O'Reilly KM, Durry E, ul Islam O, et al., 2012, The effect of mass immunisation campaigns and new oral poliovirus vaccines on the incidence of poliomyelitis in Pakistan and Afghanistan, 2001-11: a retrospective analysis, LANCET, Vol: 380, Pages: 491-498, ISSN: 0140-6736
O'Reilly KM, Chauvin C, Aylward RB, et al., 2011, A statistical model of the international spread of wild poliovirus in Africa used to predict and prevent outbreaks, PLoS Med, Vol: 8, Pages: 1-10, ISSN: 1549-1676
BACKGROUND: Outbreaks of poliomyelitis in African countries that were previously free of wild-type poliovirus cost the Global Polio Eradication Initiative US$850 million during 2003-2009, and have limited the ability of the program to focus on endemic countries. A quantitative understanding of the factors that predict the distribution and timing of outbreaks will enable their prevention and facilitate the completion of global eradication. METHODS AND FINDINGS: Children with poliomyelitis in Africa from 1 January 2003 to 31 December 2010 were identified through routine surveillance of cases of acute flaccid paralysis, and separate outbreaks associated with importation of wild-type poliovirus were defined using the genetic relatedness of these viruses in the VP1/2A region. Potential explanatory variables were examined for their association with the number, size, and duration of poliomyelitis outbreaks in 6-mo periods using multivariable regression analysis. The predictive ability of 6-mo-ahead forecasts of poliomyelitis outbreaks in each country based on the regression model was assessed. A total of 142 genetically distinct outbreaks of poliomyelitis were recorded in 25 African countries, resulting in 1-228 cases (median of two cases). The estimated number of people arriving from infected countries and <5-y childhood mortality were independently associated with the number of outbreaks. Immunisation coverage based on the reported vaccination history of children with non-polio acute flaccid paralysis was associated with the duration and size of each outbreak, as well as the number of outbreaks. Six-month-ahead forecasts of the number of outbreaks in a country or region changed over time and had a predictive ability of 82%. CONCLUSIONS: Outbreaks of poliomyelitis resulted primarily from continued transmission in Nigeria and the poor immunisation status of populations in neighbouring countries. From 1 January 2010 to 30 June 2011, reduced transmission in Nigeria and in
O'Reilly KM, Low JC, Denwood MJ, et al., 2010, Associations between the Presence of Virulence Determinants and the Epidemiology and Ecology of Zoonotic Escherichia coli, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 76, Pages: 8110-8116, ISSN: 0099-2240
O'Reilly KM, Medley GF, Green LE, 2010, The control of Corynebacterium pseudotuberculosis infection in sheep flocks: A mathematical model of the impact of vaccination, serological testing, clinical examination and lancing of abscesses, PREVENTIVE VETERINARY MEDICINE, Vol: 95, Pages: 115-126, ISSN: 0167-5877
O'Reilly KM, Green LE, Malone FE, et al., 2008, Parameter estimation and simulations of a mathematical model of Corynebacterium pseudotuberculosis transmission in sheep, PREVENTIVE VETERINARY MEDICINE, Vol: 83, Pages: 242-259, ISSN: 0167-5877
O'Reilly KM, Harris MJ, Mendl M, et al., 2006, Factors associated with preweaning mortality on commercial pig farms in England and Wales, VETERINARY RECORD, Vol: 159, Pages: 193-196, ISSN: 0042-4900
O'Reilly KM, Green MJ, Peeler EJ, et al., 2006, Investigation of risk factors for clinical mastitis in British dairy herds with bulk milk somatic cell counts less than 150,000 cells/ml, VETERINARY RECORD, Vol: 158, Pages: 649-653, ISSN: 0042-4900
Malone FE, Fee SA, Kamp EM, et al., 2006, A serological investigation of caseous lymphadenitis in four flocks of sheep, Irish Veterinary Journal, Vol: 59, Pages: 19-21, ISSN: 1393-3817
A double antibody sandwich ELISA developed by ID-DLO, Lelystad to detect Corynebacterium pseudotuberculosis infection was used on 329 sheep from four pedigree Suffolk flocks in which clinical cases of caseous lymphadenitis (CLA) had occurred. At subsequent necropsy, typical CLA lesions were seen in 133 sheep, and the diagnosis was confirmed on culture. Lesions were most commonly seen in lungs (n = 46), parotid lymph nodes (n = 44), prescapular lymph nodes (n = 38) and mediastinal lymph nodes (n = 31). The sensitivity of the ELISA test for detecting culture-positive sheep was 0.88, while the specificity of the test was 0.55. The antibody ELISA detected 87.5 per cent of sheep that had CLA lesions restricted to internal organs only. It was concluded that the ELISA test has a valuable role in detecting sheep with both clinical and subclinical CLA.
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