About

Josh Colston is an Assistant Professor of Medicine in the fields of Infectious Diseases and International Health at the School of Medicine. He is an epidemiologist and spatial demographer whose research interests include childhood undernutrition and infectious diseases, focusing on their socio-economic and environmental determinants in low-resource settings. He provides analytical expertise to numerous research projects funded by organizations such as NASA, NIH, CDC, WHO, and the Gates Foundation, primarily under the supervision of his longtime mentor Dr. Margaret Kosek. His research involves characterizing environmental drivers of enteric diseases, emerging febrile illnesses, and COVID-19 through the use of earth observation (satellite), household survey, and surveillance data. Additionally, he has taken on the role of instructor for the undergraduate Introduction to Epidemiology course (PHS 3104) in the Department of Public Health Sciences.

Research topics

• Medicine
• Environmental health
• Geography
• Biology
• Environmental science

Selected publications

• Prevalence and Risk Factors of Respiratory Tract Infections Following Medically-Attended-Diarrhea in Children Aged 6-35 Months: Enterics for Global Health (EFGH)- <i>Shigella</i> Surveillance Study, 2022-2024

  medRxiv · 2026-04-20

  articleOpen access

  Abstract 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 &lt;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 &lt;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.

  PublisherDOI

• Updated Estimates of the Global, Regional and National Burden, and Etiology of Diarrheal Diseases Transmissible via Food: A Systematic Review and Meta-Analytical Modelling Study for the World Health Organization

  medRxiv · 2026-01-27 · 2 citations

  articleOpen access1st author

  Abstract 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.

  PublisherOA PDFDOI

• Genomic epidemiology of a 2023–2024 Oropouche virus disease outbreak in Iquitos, Peru: descriptive analysis of a case control study for acute febrile illness

  The Lancet Regional Health - Americas · 2026-02-19

  articleOpen access

  Background: Oropouche virus (OROV) is an emerging vector-borne pathogen endemic to the Americas, which causes acute febrile illness (AFI) in humans. Starting in late 2023, surges in OROV infections were reported across Latin America, including an outbreak in Iquitos, a city in the Eastern Peruvian Amazon, where RIVERA, an ongoing AFI surveillance program detected and characterized incident OROV cases. Methods: AFI cases presenting to health facilities were screened for OROV using PCR. OROV-positive subjects were compared to AFI OROV negative cases to describe the principal features of clinical disease. Genomes from OROV strains were sequenced and compared using phylogenetic analysis with those from extant samples isolated from other locations in the Americas. Findings: In early 2024, an 8.6% OROV-positivity rate (29 detections in 339 samples) in RIVERA subjects was recorded, a more than 20-fold increase compared with pre-outbreak levels. Illness was characterized by fever, arthralgia, myalgia and dysuria. Genome sequences from strains in this outbreak were phylogenetically distinct from those from a concurrent one in Brazil, but resembled strains from Colombia and Ecuador. The last common ancestor of outbreak strains from Peru and Brazil was 226 years prior to sampling, and that of Peru and Ecuador and Colombia approximately 10 and 8 years prior to sampling, respectively. Interpretation: Genomic analysis suggests that the current outbreak in South America is multifocal in origin and not the result of geographic spread from Brazil. An existing AFI surveillance program successfully documented the emergence and characterized the symptom profile of this emerging arboviral disease. Funding: CDC/HHS U01GH002270; NIH D43TW010913, K43TW012298, K01AI168493, 5T32AI007046-48.

  PublisherDOI

• Updating global estimates of pathogen-attributable diarrhoeal disease burden: a methodology and integrated protocol for a broad-scope systematic review of a syndrome with diverse infectious aetiologies

  BMJ Open · 2025-04-01 · 2 citations

  reviewOpen access1st authorCorresponding

  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.

  PublisherDOI

• Frequency and correlates of non-receipt of age-appropriate vaccination among children aged 6-35 months with medically attended diarrhea: Findings from the Enterics for Global Health (EFGH) <i>Shigella</i> study, 2022-2024

  medRxiv · 2025-12-06

  articleOpen access

  Abstract Background Complete childhood immunization protects children from long-term health complications and disabilities caused by vaccine-preventable diseases. Enterics for Global Health (EFGH)- Shigella surveillance was a two-year study measuring incidence rates and consequences of Shigella among children aged 6-35 months in seven sites located in Asia, Latin America and Africa. Here, we estimated the prevalence and factors associated with non-receipt of age-appropriate vaccination among children enrolled in the EFGH- Shigella study. Methods In this nested cross-sectional study, we analysed data from 7,932 children aged 6-35 months presenting with medically attended diarrhea (MAD). Vaccines recommended per each country’s national immunization schedule were extracted from medical records and risk factors were collected by caregiver interview and physical exam. We defined age-appropriate vaccines as receipt of the early childhood vaccinations within one month of the recommended age, according to the national immunization schedule, on the immunization card. Poison regression was used to identify independent factors associated with non-receipt of age-appropriate vaccination accounting for all covariates. Results Over half of enrolled children (51.7%) did not receive all age-appropriate vaccines most commonly in The Gambia (75.2%) and least frequently in Bangladesh (22.3%). Children 12-35 months of age were more likely not have all age appropriate vaccines compared to children 6-11 months (aPR: 1.47, 95%CI 1.39 to 1.54), children who came from households with ≥3 children aged &lt;5 years (aPR:1.07;1.01-1.13), had mothers with low education (aPR:1.18; 1.12-1.25), and were wasted (Moderately: aPR: 1.06; 1.00-1.13; Severely: aPR : 1.14, 1.04-1.25) were more likely to miss all age-appropriate vaccines compared to their counterparts who did not. Conclusion Non-receipt of age-appropriate vaccination was largely age dependent, driven by mother’s education and severe wasting highlighting the need to design effective strategies that incorporate site complexities to improve timely vaccination targeting vulnerable groups.

  PublisherOA PDFDOI

• Mapping the Prevalence of Household-Scale Livestock Ownership by Animal Taxon in Low- and Middle-Income Countries: An INLA Prediction Model

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access1st authorCorresponding
  PublisherDOI

• Mapping the prevalence of household-scale livestock ownership by animal taxon in low- and middle-income countries: an INLA prediction model

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access1st authorCorresponding
  PublisherDOI

• Comparison of ARIMA and FB-Prophet time series models for the prediction of national and regional malaria incidence in Uganda

  Malaria Journal · 2025-09-24

  articleOpen access

  BACKGROUND: Within sub-Saharan Africa, Uganda carries the third largest burden of malaria with 5% of global cases. Due to the stochastic nature of malaria incidence, resource allocation of preventive measures, rapid diagnostic tests, and chemotherapeutics is a significant challenge. To better identify areas at risk and address the challenge of resource allocation, this study aimed to: (1) characterize national and regional malaria incidence in Uganda, and (2) compare the performance of time series models in predicting malaria incidence at national and regional levels. METHODS: Aggregated data from District Health Information Software 2 (DHIS2), was used to assess national and regional malaria incidence in Uganda from 2020 through 2023. Auto-regressive moving average (ARIMA) models of national and regional malaria incidence were then created. The same data was applied to FB-Prophet, an open source generalized additive time series model. Training and validation datasets were created for each model, which ran for 41 and 6 months, respectively. Model performance was then evaluated via key performance indicators including mean average error (MAE), root mean square error (RMSE), and mean average percentage error (MAPE). RESULTS: The incidence of malaria within Uganda increased from 200.5 cases per 1000 persons annually in 2021 to 265.4 cases per 1000 persons annually in 2022. The northern regions of West Nile and Acholi, along with Busoga region in the east, experienced the highest burden and incidence of malaria. The mean regional MAE, MAPE, and RMSE was 0.007, 31.2, and 0.01, respectively for ARIMA, and 0.01, 47.8, and 0.01, respectively for FB-Prophet. The ARIMA model outperformed the FB-Prophet model at the national level and in 14 of 15 regions. CONCLUSIONS: Time series models accurately predicted malaria incidence on a national and regional scale in Uganda. Both the ARIMA and FB-Prophet models have the potential to guide malaria resource allocation and response efforts among other malaria control interventions deployed in Uganda and possibly in other malaria endemic settings.

  PublisherOA PDFDOI

• The Enterics for Global Health (EFGH) <i>Shigella</i> Surveillance Study in Peru

  Open Forum Infectious Diseases · 2024-03-01 · 8 citations

  articleOpen access

  Abstract Background The Enterics for Global Health (EFGH) Peru site will enroll subjects in a periurban area of the low Amazon rainforest. The political department of Loreto lags behind most of Peru in access to improved sources of water and sanitation, per capita income, children born &amp;lt;2.5 kg, and infant and child mortality. Chronic undernutrition as manifested by linear growth shortfalls is common, but wasting and acute malnutrition are not. Methods The recruitment of children seeking care for acute diarrheal disease takes place at a geographic cluster of government-based primary care centers in an area where most residents are beneficiaries of free primary healthcare. Results Rates of diarrheal disease, dysentery, and Shigella are known to be high in the region, with some of the highest rates of disease documented in the literature and little evidence in improvement over the last 2 decades. This study will update estimates of shigellosis by measuring the prevalence of Shigella by polymerase chain reaction and culture in children seeking care and deriving population-based estimates by measuring healthcare seeking at the community level. Conclusions Immunization has been offered universally against rotavirus in the region since 2009, and in a context where adequate water and sanitation are unlikely to obtain high standards in the near future, control of principal enteropathogens through immunization may be the most feasible way to decrease the high burden of disease in the area in the near future.

  PublisherDOI

• The Planetary Child Health &amp;amp; Enterics Observatory (Plan-EO): a protocol for an interdisciplinary research initiative and web-based dashboard for mapping enteric infectious diseases and their risk factors and interventions in LMICs

  Research Square · 2024-01-10

  preprintOpen access1st authorCorresponding
  PublisherOA PDFDOI

Frequent coauthors

• Margaret Kosek

  University of Virginia

  62 shared

• Pablo Peñataro Yori

  University of Virginia

  39 shared

• Francesca Schiaffino

  University of Virginia

  29 shared

• Maribel Paredes Olórtegui

  Prisma

  29 shared

• Eric R. Houpt

  University of Virginia

  27 shared

• Benjamin F. Zaitchik

  Planetary Science Institute

  23 shared

• Hamada S. Badr

  Johns Hopkins University

  18 shared

• Jasie Hearn

  University of Virginia

  16 shared

Education

• PhD in Global Disease Epidemiology and Control, International Health

  Johns Hopkins Bloomberg School of Public Health

  2018

• Master of Science in Demography and Health, Department of Population Health

  London School of Hygiene and Tropical Medicine

  2008