Determining optimal neighborhood size for ecological studies using leave-one-out cross validation

We employed a leave-one-out cross validation to determine optimally sized neighborhood. Variations between a single point and the other points within each filter size for all the points in the study area were evaluated, and the mean squared error (MSE) for each filter was calculated. The filter with the lowest MSE was considered as the optimal neighborhood. The method is useful in determining the optimal neighborhood for both geographic and population filters

A systematic review of the epidemiology of hepatitis E virus in Africa

BACKGROUND: Hepatitis E Virus (HEV) infection is a newly recognized serious threat to global public health and Africa is suspected to be among the most severely affected regions in the world. Understanding HEV epidemiology in Africa will expedite the implementation of evidence-based control policies aimed at preventing the spread of HEV including policies for the use of available resources such as HEV vaccines. METHODS: Here we present a comprehensive review of HEV epidemiology in Africa based on published data. We searched for articles on HEV epidemiology in Africa from online databases such as PubMed, Scopus, and ISI Web of Science and critically reviewed appropriate publications to extract consistent findings, identify knowledge gaps, and suggest future studies. RESULTS: Taking a particularly high toll in pregnant women and their fetuses, HEV has infected human populations in 28 of 56 African countries. Since 1979, 17 HEV outbreaks have been reported about once every other year from Africa causing a reported 35,300 cases with 650 deaths. CONCLUSIONS: In Africa, HEV infection is not new, is widespread, and the number of reported outbreaks are likely a significant underestimate. The authors suggest that this is a continent-wide public health problem that deserves the attention of local, regional and international agencies to implement control policies that can save numerous lives, especially those of pregnant women and their fetuses

A Perspective on the Strategy for Advancing ETVAX®, An Anti-ETEC Diarrheal Disease Vaccine, into a Field Efficacy Trial in Gambian Children: Rationale, Challenges, Lessons Learned, and Future Directions.

For the first time in over 20 years, an Enterotoxigenic Escherichia coli (ETEC) vaccine candidate, ETVAX®, has advanced into a phase 2b field efficacy trial for children 6-18 months of age in a low-income country. ETVAX® is an inactivated whole cell vaccine that has gone through a series of clinical trials to provide a rationale for the design elements of the Phase 2b trial. This trial is now underway in The Gambia and will be a precursor to an upcoming pivotal phase 3 trial. To reach this point, numerous findings were brought together to define factors such as safe and immunogenic doses for children, and the possible benefit of a mucosal adjuvant, double mutant labile toxin (dmLT). Considering the promising but still underexplored potential of inactivated whole cells in oral vaccination, we present a perspective compiling key observations from past ETVAX® trials that informed The Gambian trial design. This report will update the trial's status and explore future directions for ETEC vaccine trials. Our aim is to provide not only an update on the most advanced ETEC vaccine candidate but also to offer insights beneficial for the development of other much-needed oral whole-cell vaccines against enteric and other pathogens

Burden of typhoid fever in low-income and middle-income countries: a systematic, literature-based update with risk-factor adjustment

Background No access to safe water is an important risk factor for typhoid fever, yet risk-level heterogeneity is unaccounted for in previous global burden estimates. Since WHO has recommended risk-based use of typhoid polysaccharide vaccine, we revisited the burden of typhoid fever in low-income and middle-income countries (LMICs) after adjusting for water-related risk. Methods We estimated the typhoid disease burden from studies done in LMICs based on blood-culture-confi rmed incidence rates applied to the 2010 population, after correcting for operational issues related to surveillance, limitations of diagnostic tests, and water-related risk. We derived incidence estimates, correction factors, and mortality estimates from systematic literature reviews. We did scenario analyses for risk factors, diagnostic sensitivity, and case fatality rates, accounting for the uncertainty in these estimates and we compared them with previous disease burden estimates. Findings The estimated number of typhoid fever cases in LMICs in 2010 after adjusting for water-related risk was 11·9 million (95% CI 9·9–14·7) cases with 129 000 (75 000–208 000) deaths. By comparison, the estimated riskunadjusted burden was 20·6 million (17·5–24·2) cases and 223 000 (131 000–344 000) deaths. Scenario analyses indicated that the risk-factor adjustment and updated diagnostic test correction factor derived from systematic literature reviews were the drivers of diff erences between the current estimate and past estimates. Interpretation The risk-adjusted typhoid fever burden estimate was more conservative than previous estimates. However, by distinguishing the risk diff erences, it will allow assessment of the eff ect at the population level and will facilitate cost-eff ectiveness calculations for risk-based vaccination strategies for future typhoid conjugate vaccine

Heterogeneity in enterotoxigenic Escherichia coli and shigella infections in children under 5 years of age from 11 African countries: a subnational approach quantifying risk, mortality, morbidity, and stunting.

BACKGROUND: Diarrhoea, a global cause of child mortality and morbidity, is linked to adverse consequences including childhood stunting and death from other diseases. Few studies explore how diarrhoeal mortality varies subnationally, especially by cause, which is important for targeting investments. Even fewer examine indirect effects of diarrhoeal morbidity on child mortality. We estimated the subnational distribution of mortality, morbidity, and childhood stunting attributable to enterotoxigenic Escherichia coli (ETEC) and shigella infection in children younger than 5 years from 11 eastern and central African countries. These pathogens are leading causes of diarrhoea in young children and have been linked to increased childhood stunting. METHODS: We combined proxy indicators of morbidity and mortality risk from the most recent Demographic and Health Surveys with published relative risks to estimate the potential distribution of diarrhoeal disease risk. To estimate subnational burden, we used country-specific or WHO region-specific morbidity and mortality estimates and distributed them subnationally by three indices that integrate relevant individual characteristics (ie, underweight, probability of receiving oral rehydration treatment of diarrhoea, and receiving vitamin A supplementation) and household characteristics (ie, type of drinking water and sanitation facilities). FINDINGS: Characterising ETEC and shigella subnational estimates of indirect morbidity (infection-attributable stunting) and indirect mortality (stunting-related deaths from other infectious diseases) identified high-risk areas that could be missed by traditional metrics. Burundi and Democratic Republic of the Congo had the highest ETEC-associated and shigella-associated mortality and stunting rates. Mozambique, Democratic Republic of the Congo, and Zimbabwe had the greatest subnational heterogeneity in most ETEC and shigella mortality measures. Inclusion of indirect ETEC and shigella mortality in burden estimates resulted in a 20-30% increase in total ETEC and shigella mortality rates in some subnational areas. INTERPRETATION: Understanding the indirect mortality and morbidity of diarrhoeal pathogens on a subnational level will strengthen disease control strategies and could have important implications for the relative impact and cost-effectiveness of new enteric vaccines. Because our methods rely on publicly available data, they could be employed for national planning. FUNDING: Bill & Melinda Gates Foundation

Rapid-Test Based Identification of Influenza as an Etiology of Acute Febrile Illness in Cambodia

Influenza can be manifested as an acute febrile illness, with symptoms similar to many pathogens endemic to Cambodia. The objective of this study was to evaluate the Quickvue influenza A+B rapid test to identify the etiology of acute febrile illness in Cambodia. During December 2006–May 2008, patients enrolled in a study to identify the etiology of acute febrile illnesses were tested for influenza by real-time reverse transcriptase PCR (RT-PCR) and Quickvue influenza A+B rapid test. The prevalence of influenza was 19.7% by RT-PCR. Compared with RT-PCR, the sensitivity and specificity of the rapid test were 52.1% and 92.5%, respectively. The influenza rapid test identified the etiology in 10.2% of enrollees and ≥ 35% during peak times of influenza activity. This study suggests that rapid influenza tests may be useful during peak times of influenza activity in an area where several different etiologies can present as an acute febrile illness

Replacing paper data collection forms with electronic data entry in the field: findings from a study of community-acquired bloodstream infections in Pemba Zanzibar

BackgroundEntering data on case report forms and subsequently digitizing them in electronic media is the traditional way to maintain a record keeping system in field studies. Direct data entry using an electronic device avoids this two-step process. It is gaining in popularity and has replaced the paper-based data entry system in many studies. We report our experiences with paper- and PDA-based data collection during a fever surveillance study in Pemba Island, Zanzibar, Tanzania.MethodsData were collected on a 14-page case report paper form in the first period of the study. The case report paper forms were then replaced with handheld computers (personal digital assistants or PDAs). The PDAs were used for screening and clinical data collection, including a rapid assessment of patient eligibility, real time errors, and inconsistency checking.ResultsA comparison of paper-based data collection with PDA data collection showed that direct data entry via PDA was faster and 25% cheaper. Data was more accurate (7% versus 1% erroneous data) and omission did not occur with electronic data collection. Delayed data turnaround times and late error detections in the paper-based system which made error corrections difficult were avoided using electronic data collection.ConclusionsElectronic data collection offers direct data entry at the initial point of contact. It has numerous advantages and has the potential to replace paper-based data collection in the field. The availability of information and communication technologies for direct data transfer has the potential to improve the conduct of public health research in resource-poor settings

Whom and Where Are We Not Vaccinating? Coverage after the Introduction of a New Conjugate Vaccine against Group A Meningococcus in Niger in 2010

MenAfriVac is a new conjugate vaccine against Neisseria meningitidis serogroup A developed for the African “meningitis belt”. In Niger, the first two phases of the MenAfriVac introduction campaign were conducted targeting 3,135,942 individuals aged 1 to 29 years in the regions of Tillabéri, Niamey, and Dosso, in September and December 2010. We evaluated the campaign and determined which sub-populations or areas had low levels of vaccination coverage in the regions of Tillabéri and Niamey. After Phase I, conducted in the Filingué district, we estimated coverage using a 30×15 cluster-sampling survey and nested lot quality assurance (LQA) analysis in the clustered samples to identify which subpopulations (defined by age 1–14/15–29 and sex) had unacceptable vaccination coverage (<70%). After Phase II, we used Clustered Lot Quality Assurance Sampling (CLQAS) to assess if any of eight districts in Niamey and Tillabéri had unacceptable vaccination coverage (<75%) and estimated overall coverage. Estimated vaccination coverage was 77.4% (95%CI: 84.6–70.2) as documented by vaccination cards and 85.5% (95% CI: 79.7–91.2) considering verbal history of vaccination for Phase I; 81.5% (95%CI: 86.1–77.0) by card and 93.4% (95% CI: 91.0–95.9) by verbal history for Phase II. Based on vaccination cards, in Filingué, we identified both the male and female adult (age 15–29) subpopulations as not reaching 70% coverage; and we identified three (one in Tillabéri and two in Niamey) out of eight districts as not reaching 75% coverage confirmed by card. Combined use of LQA and cluster sampling was useful to estimate vaccination coverage and to identify pockets with unacceptable levels of coverage (adult population and three districts). Although overall vaccination coverage was satisfactory, we recommend continuing vaccination in the areas or sub-populations with low coverage and reinforcing the social mobilization of the adult population