Josh Michael Colston

Animal husbandry is widely practiced on the household scale in communities in low- and middle-income countries (LMICs) and, while having economic and health benefits, exposes household members to risk of zoonotic infections to an extent that is unclear. While demand for georeferenced information on infectious disease risk factors and drivers is growing, spatial variation in livestock ownership remains poorly characterized at high resolution. This study aimed to use geostatistical methods to model and map the prevalence of livestock husbandry in LMICs for three major animal taxa: poultry, swine, and ruminants. Microdata relating to ownership of livestock animal species were sourced from various population-based survey programs which together cover the majority of LMICs and categorized. These were georeferenced and spatially matched with a panel of time-fixed environmental and demographic spatial covariates, INLA models were fitted to the resulting database, and probabilities for ownership of each livestock taxon predicted based on the model parameter estimates. The results indicated widespread poultry ownership across rural Central America, the Amazon basin, tropical Africa and river basins and forests of East Asia. Swine husbandry is the least widely practiced among the three livestock taxa and concentrated in an undulating belt of higher prevalence extending from central China, through southeast Asia to Northeastern India, though such predictions in data-sparse regions (particularly Muslim-majority areas) represent regional covariate patterns rather than fine-scale measurements. To address non-stationarity in swine spatial structure, region-specific spatial kernels were implemented. Rearing of ruminant livestock appears widespread across subequatorial Africa, Central Asia, the Gobi Desert, the Himalayas, Mongolia and northern India. The models perform impressively by most standard evaluation metrics, and the patterns in their predictions align with external evidence. The distribution of this important risk factor for infectious disease transmission can be modeled using publicly available data sources to generate plausible and potentially actionable predictions over wide geographic areas and identify regions of high exposure to animal disease reservoirs. The resulting predicted prevalence estimates are made available as supplementary files in GIS-compatible format.

Cervical cancer (CC) is a leading cause of death, with women with HIV at an increased risk. Geographic disparities in CC and HIV reflect inequities in care access. The purpose of this systematic review was to evaluate integrated models for HIV and CC screening. This review was conducted following PRISMA guidelines. Full-text screening and data extraction were conducted independently. Eligible studies described integrated HIV and CC services. Of 4,280 records, 24 met inclusion criteria. Most studies ( n = 21) were conducted in sub-Saharan Africa; the remaining studies were conducted in high-income settings. Most studies integrated CC screening into HIV care ( n = 19); however, three integrated HIV screening into CC screening/treatment. Two studies implemented fully integrated HIV and CC screening in community settings. Integrated services were considered highly acceptable and feasible. Models introducing CC screening into HIV care will advance global CC elimination goals, but equitable access and HIV metrics will require creative integrative solutions.

Globally, respiratory tract infections (RTI) are the main cause of morbidity, and in Low-middle-income countries (LMICs) RTI including pneumonia are a leading cause of morbidity and mortality in children <5 years. Diarrheal illness increases RTI risk in young children through micronutrient depletion, and immune stress, yet data on post-diarrhea RTI burden in LMICs are limited. We determined the prevalence and risk factors of RTI within three months following medically-attended diarrhea (MAD) in children aged 6-35 months enrolled in seven EFGH country sites in Asia, Africa and South America. The EFGH study prospectively enrolled children aged 6-35 months with MAD in selected health facilities during a 24-month period from 2022 to 2024 and followed them for three months. RTI was defined as cough or difficulty breathing and the presence of one of the following symptoms at any scheduled or unscheduled visit during follow-up: stridor; fast-breathing; oxygen saturation <90%; or chest indrawing. The period prevalence and 95% confidence intervals of RTI were calculated, and correlates of RTI were assessed using modified-Poisson regression. From June 2022 to August 2024, 9,476 children aged 6-35 months presenting with MAD in the EFGH study sites were screened: 9,116 (96.2%) included in the current study. Nearly half were female (46.7%), and median age was 15 months. Overall, 48.5% received all age-appropriate vaccines, and 87.6% received the pneumococcal vaccine, with significant variation across countries. Nearly one-quarter of children were stunted, 17.2% wasted, and 21.9% underweight. RTI occurred in 3.8% of children during the three-month follow-up, mostly within the first month. Higher prevalence of RTI occurred among children aged 12-23 months (8.7%), those undernourished (16.1%), unvaccinated (4.0%) or living in poor sanitation settings (4.1%). While children who received all age-appropriate or pneumococcal vaccinations had a lower crude prevalence of RTI, these associations were not statistically significant after adjusting for age, sex and study site. RTI was infrequently observed in the three months following MAD presentation, with significant variability by site and with the highest prevalence in Malawi. RTI risk was highest in 12-23-month-olds and among children with undernutrition, and those living in poor sanitation conditions.

Diarrheal disease is caused by diverse species of viruses, bacteria and protozo that are transmitted from different sources, including from contaminated food. Sustaining progress in reducing diarrheal illnesses and deaths, including vaccines and food safety measures, may require interventions targeting specific pathogens. In 2015, the WHO’s published etiology-specific estimates by their Foodborne Disease Burden Epidemiology Reference Group (FERG) of the incidence and mortality of diarrheal diseases caused by 11 pathogens at global and regional scales in 2010. Since then, much new evidence has been published about the epidemiology of enteropathogens. This study aims to update estimates to the year 2021 with the addition of three pathogens (Rotavirus, Cyclospora cayetanensis , Enteroaggregative E. coli (EAEC)). For low- and middle-income countries (LMICs), we conducted a systematic review of publications that reported the prevalence of pathogens diagnosed in stool samples from asymptomatic subjects, community-detected and outpatient diarrhea cases, and those treated as inpatients. Hierarchical, mixed effects models were fitted to pathogen-specific prevalence data extracted from studies that met prespecified inclusion criteria, and population attributable fractions (PAF) were calculated from the model parameter estimates, adjusting for background asymptomatic transmission where appropriate. The PAFs were applied to previously estimated diarrhea incidence and mortality envelopes. A separate, parallel systematic review identified studies that estimated diarrhea incidence and mortality due to specific etiologies for high income countries (HICs) from surveillance data. Meta-analytical models were fitted to data extracted from these. Data from 324 studies published between 1990 and 2023 representing results from up to 540,000 samples were used in the meta-analysis. Globally the 14 pathogens were responsible for 2.2 billion diarrheal disease cases and 880,000 deaths in 2021, with the largest number of cases occurring in South-East Asia, the largest number of deaths in Sub-Saharan Africa, and Europe being the region with the lowest burden by both measures. We found the leading causes of diarrhea morbidity to be bacteria – Shigella (426.4 million cases in 2021), Campylobacter (291.4 million) and ETEC (259.7 million)) – as well as the protozoon Giardia (321.2 million), in contrast to previous studies that have ranked rotavirus and norovirus highest. Our estimates support a much higher morbidity burden for Shigella than previously estimated with an incidence rate for 2021 (5,400 per 100,000). This is due to its high PAF in outpatients aged ≥5 years. As causes of diarrhea mortality, our estimates rank rotavirus first (214,700 deaths in 2021), Shigella second (152,500), and V. cholerae (94,100) third, due to the latter’s large PAF in inpatients aged ≥5 years and high case fatality rate. Caution is urged when interpreting PAFs for pathogens that elicit prolonged residual shedding following resolution of symptoms (e.g., norovirus, Campylobacter , Giardia ). These findings, derived from rigorous systematic review and statistical methodologies and the largest database yet compiled of pathogen detection rates, will serve as inputs for the WHO’s broader estimates of hazard-specific incidence and mortality from foodborne diseases and are made available to the research and policy-making communities to inform targeted strategies for global diarrheal disease control. Funding: WHO EDTF_001; 1K01AI168493-01A1; K43TW012298; 5T32AI007046-48.

Introduction: Sustaining declines in global infectious disease burden will increasingly require efforts targeted to specific aetiological agents and common transmission pathways, particularly in this era of global change and human interconnectivity accelerating transmission and emergence of infectious pathogens. Systematic reviews and meta-analyses can be an effective and resource-efficient method for synthesising evidence regarding disease epidemiology for a wide range of pathogens and are the evidence source used by initiatives like the Planetary Child Health and Enterics Observatory (Plan-EO) and the WHO to determine the aetiology-specific epidemiology of diarrhoeal disease. Therefore, we developed this integrated systematic review methodology and protocol that aims to compile a database of published prevalence estimates for 17 diarrhoea-causing pathogens as inputs for disease burden estimation. Methods and analysis: We will seek estimates of the prevalence of each endemic enteric pathogen estimated from published population-based studies that diagnosed their presence in stool samples from both asymptomatic subjects and those experiencing diarrhoea. The pathogens include the enteric viruses adenovirus, astrovirus, norovirus, rotavirus and sapovirus, the bacteria Campylobacter , Shigella , Salmonella enterica , Vibrio cholerae and the Escherichia coli (E. coli) pathotypes enteroaggregative E. coli , enteropathogenic E. coli , enterotoxigenic E. coli and Shiga-toxin-producing E. coli and the intestinal protozoa Cryptosporidium , Cyclospora , Entamoeba histolytica and Giardia . Meta-analytical methods for analyses of the resulting database (including risk of bias analysis) will be published alongside their findings. Ethics and dissemination: This systematic review is exempt from ethics approval because the work is carried out on published documents. The database that results from this review will be made available as a supplementary file of the resulting published manuscript. It will also be made available for download from the Plan-EO website, where updated versions will be posted on a quarterly basis. PROSPERO registration number: CRD42023427998.

: Large diagnostic panels allow for pathogens with high or low likelihood of causing attributable illness to be tested simultaneously. Infectious mononucleosis (IM) due to primary infection with Epstein-Barr virus (EBV) is a common cause of acute febrile illness (AFI) in case series from high-income countries, though its contribution to AFI in tropical low-income settings is unclear. As part of a case-control study using multiplex quantitative polymerase chain reaction (qPCR) diagnostics, we set out to determine if primary EBV infection was an underrecognized cause of AFI in the Peruvian Amazon. Presence of EBV DNA in whole-blood samples was equally prevalent among febrile cases and afebrile controls (34.6% [247/714] versus 35.7% [248/695]) and was not correlated with classic IM symptoms. Given the clear lack of clinical significance of the whole-blood PCR results, additional testing was pursued to ascertain the true prevalence of IM among cases of AFI in this population. The presence of EBV DNA in plasma, a marker of active EBV-related processes, was detected in 7% (5/68). Anti–EBNA-1 IgG, a late marker of prior infection, was tested via ELISA and detected in 4/5 of the plasma-positive patients, thereby excluding an acute primary EBV infection in all but one patient. Infectious mononucleosis due to primary infection with EBV was not an important etiology of AFI in the Peruvian Amazon, despite high rates of initial test positivity.

Housing infrastructure and quality is a major determinant of infectious disease risk and other health outcomes in regions where vector borne, waterborne and neglected tropical diseases are endemic. It is important to quantify the geographical distribution of improvements to dwelling components to identify and target resources towards populations at risk. This study aimed to model the sub-national spatial variation in housing materials using covariates with quasi-global coverage and use the resulting estimates to map predicted coverage across the world’s low- and middle-income countries. Data on materials used in dwelling construction were sourced from nationally representative household surveys conducted since 2005. Materials used for construction of flooring, walls, and roofs were reclassified as improved or unimproved. Households lacking location information were georeferenced using a novel methodology. Environmental and demographic spatial covariates were extracted at those locations for use as model predictors. Integrated nested Laplace approximation models were fitted to obtain, and map predicted probabilities for each dwelling component. The dataset compiled included information from households in 283,000 clusters from 350 surveys. Low coverage of improved housing was predicted across the Sahel and southern Sahara regions of Africa, much of inland Amazonia, and areas of the Tibetan plateau. Coverage of improved roofs and walls was high in the Central Asia, East Asia and Pacific and Latin America and the Caribbean regions. Improvements in all three components, but most notably floors, was low in Sub-Saharan Africa. The strongest determinants of dwelling component quality related to urbanization and economic development, suggesting that programs should focus on supply-side interventions, providing resources for housing improvements directly to the populations that need them. These findings are made available to researchers as files that can be imported into a GIS for integration into relevant analyses to derive improved estimates of preventable health burdens attributed to housing.

Oropouche virus is an arbovirus endemic to the Americas. Periodic outbreaks have occurred since its description in 1955. In late 2023, an outbreak occurred in Peru, centered in and around Iquitos in the Eastern Peruvian Amazon. An existing acute febrile illness (AFI) surveillance program was able to document its emergence and characterize arthralgia and dysuria and the absence of diarrhea as distinctive clinical features of Oropouche virus-associated febrile illness relative to other causes of AFI. Sequencing of isolates from the outbreak demonstrated that strains from this region were distinct from those causing disease in Brazil, despite the large-scale movement of people along the Amazon corridor, but highly similar to strains from Colombia and Ecuador. Our findings suggest that the current outbreak in South America is fundamentally multifocal in origin and not the result of geographic spread from Brazil, which experienced an outbreak between 2022 and 2024.