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ImportanceUnderstanding the role of school attendance on transmission of SARS-CoV-2 among children is of importance for responding to future epidemics. Estimating discontinuities in outcomes by age of eligibility for school attendance has been used to examine associations between school attendance and a variety of outcomes, but has yet to be applied to describe associations between school attendance and communicable disease transmission.ObjectiveTo estimate the association between eligibility for elementary school and COVID-19 incidence.Design, setting, and participantsThis case series used data on all pediatric COVID-19 cases reported to California's disease surveillance system between May 16, 2020, and December 15, 2022, among children within 24 months of the age threshold for school eligibility.ExposureBirthdate before or after the age threshold for elementary school eligibility during periods when school was remote vs in person.Main outcomes and measuresCOVID-19 cases and hospitalizations.ResultsBetween May 16, 2020, and December 15, 2022, there were 688 278 cases of COVID-19 (348 957 cases [50.7%] among boys) and 1423 hospitalizations among children who turned 5 years within 24 months of September 1 of the school year when their infection occurred. The mean (SD) age of the study sample was 5.0 (1.3) years. After adjusting for higher rates of testing in schooled populations, the estimated pooled incidence rate ratio among kindergarten-eligible individuals (eg, those born just before the age threshold for school eligibility) compared with those born just after the eligibility threshold for in-person fall 2021 semester was 1.52 (95% CI, 1.36-1.68), for in-person spring 2022 semester was 1.26 (95% CI, 1.15-1.39), and for in-person fall 2022 semester was 1.19 (95% CI, 1.03-1.38). Reported incidence rates among school-eligible children remained higher during the month-long winter 2021-2022 school break but were lower during the longer summer break that followed. The findings were unable to establish whether associations between school eligibility and COVID-19 incidence were based on in-school vs out-of-school routes (eg, classrooms vs school buses). The study lacked power to detect associations between school attendance and hospitalization. Results were robust to functional form. A simulation study was conducted to demonstrate bias associated with nonadjustment for differential case acquisition by exposure status.Conclusions and relevanceIn this case series of children in California, the magnitude of the association between school eligibility and COVID-19 incidence decreased over time and was generally lower than other published associations between out-of-school child social interactions and COVID-19 incidence. This regression discontinuity design approach could be adapted to other geographies and/or disease systems to assess associations between schooling and disease transmission.

ImportanceA SARS-CoV-2 vaccine was approved for adolescents aged 12 to 15 years on May 10, 2021, with approval for younger age groups following thereafter. The population level impact of the pediatric COVID-19 vaccination program has not yet been established.ObjectiveTo identify whether California's pediatric COVID-19 immunization program was associated with changes in pediatric COVID-19 incidence and hospitalizations.Design, setting, and participantsA case series on COVID-19 vaccination including children aged 6 months to 15 years was conducted in California. Data were obtained on COVID-19 cases in California between April 1, 2020, and February 27, 2023.ExposurePostvaccination evaluation periods spanned 141 days (June 10 to October 29, 2021) for adolescents aged 12 to 15 years, 199 days (November 29, 2021, to June 17, 2022) for children aged 5 to 11 years, and 225 days (July 17, 2022, to February 27, 2023) for those aged 6 to 59 months. During these periods, statewide vaccine coverage reached 53.5% among adolescents aged 12 to 15 years, 34.8% among children aged 5 to 11 years, and 7.9% among those aged 6 to 59 months.Main outcomes and measuresAge-stepped implementation of COVID-19 vaccination was used to compare observed county-level incidence and hospitalization rates during periods when each age group became vaccine eligible to counterfactual rates predicted from observations among other age groups. COVID-19 case and hospitalization data were obtained from the California reportable disease surveillance system.ResultsBetween April 1, 2020, and February 27, 2023, a total of 3 913 063 pediatric COVID-19 cases and 12 740 hospitalizations were reported in California. Reductions of 146 210 cases (95% prediction interval [PI], 136 056-158 948) were estimated among adolescents aged 12 to 15 years, corresponding to a 37.1% (35.5%-39.1%) reduction from counterfactual predictions. Reductions of 230 134 (200 170-265 149) cases were estimated among children aged 5 to 11 years, corresponding to a 23.7% (20.6%-27.3%) reduction from counterfactual predictions. No evidence of reductions in COVID-19 cases statewide were found among children aged 6 to 59 months (estimated averted cases, -259; 95% PI, -1938 to 1019), although low transmission during the evaluation period may have limited the ability to do so. An estimated 168 hospitalizations (95% PI, 42-324) were averted among children aged 6 to 59 months, corresponding to a 24.4% (95% PI, 6.1%-47.1%) reduction. In meta-analyses, county-level vaccination coverage was associated with averted cases for all age groups. Despite low vaccination coverage, pediatric COVID-19 immunization in California averted 376 085 (95% PI, 348 355-417 328) reported cases and 273 (95% PI, 77-605) hospitalizations among children aged 6 months to 15 years over approximately 4 to 7 months following vaccination availability.Conclusions and relevanceThe findings of this case series analysis of 3 913 063 cases suggest reduced pediatric SARS-CoV-2 transmission following immunization. These results support the use of COVID-19 vaccines to reduce COVID-19 incidence and hospitalization in pediatric populations.

Passive surveillance systems are widely used to monitor diseases occurrence over wide spatial areas due to their cost-effectiveness and integration into broadly distributed healthcare systems. However, such systems are generally associated with imperfect ascertainment of disease cases and with heterogeneous capture probabilities arising from factors such as differential access to care. Augmenting passive surveillance systems with other surveillance efforts provides a way to estimate the true number of incident cases. We develop a hierarchical modeling framework for analyzing data from multiple surveillance systems that allows for individual-level covariate-dependent heterogeneous capture probabilities, and borrows information across surveillance sites to improve estimation of the true number of incident cases. Inference is carried out via a two-stage Bayesian procedure. Simulation studies illustrated superior performance of the proposed approach with respect to bias, root mean square error, and coverage compared to a model that does not borrow information across sites. We applied the proposed model to data from three surveillance systems reporting pulmonary tuberculosis (PTB) cases in a major center of ongoing transmission in China. The analysis yielded bias-corrected estimates of PTB cases from the passive system and led to the identification of risk factors associated with PTB rates, as well as factors influencing the operating characteristics of the implemented surveillance systems.

ObjectiveThe aim of the study is to examine associations between years of firefighting service and eight chronological age-adjusted measures of blood leukocyte epigenetic age acceleration: Horvath, Hannum, SkinBloodClock, Intrinsic, Extrinsic, PhenoAge, GrimAge, and DNAm telomere length.MethodsThe study used a repeated measures analysis of data from 379 incumbent firefighters from eight career departments and 100 recruit firefighters from two of the departments, across the United States.ResultsIncumbent firefighters had on average greater epigenetic age acceleration compared with recruit firefighters, potentially due to the cumulative effect of occupational exposures. However, among incumbent firefighters, additional years of service were associated with epigenetic age deceleration, particularly for GrimAge, a strong predictor of mortality.ConclusionsLong-term studies with more specific occupational exposure classification are needed to better understand the relationship between years of service and aging biomarkers.

Gestational age (GA) is an important determinant of child health and disease risk. Two epigenetic GA clocks have been developed using DNA methylation (DNAm) patterns in cord blood. We investigate the accuracy of GA clocks and determinants of epigenetic GA acceleration (GAA), a biomarker of biological ageing. We hypothesize that prenatal and birth characteristics are associated with altered GAA, thereby disrupting foetal biological ageing. We examined 372 mother-child pairs from the Center for the Health Assessment of Mothers and Children of Salinas study of primarily Latino farmworkers in California. Chronological GA was robustly correlated with epigenetic GA (DNAm GA) estimated by the Knight (r = 0.48, p

With the aid of laboratory typing techniques, infectious disease surveillance networks have the opportunity to obtain powerful information on the emergence, circulation, and evolution of multiple genotypes, serotypes or other subtypes of pathogens, informing understanding of transmission dynamics and strategies for prevention and control. The volume of typing performed on clinical isolates is typically limited by its ability to inform clinical care, cost and logistical constraints, especially in comparison with the capacity to monitor clinical reports of disease occurrence, which remains the most widespread form of public health surveillance. Viewing clinical disease reports as arising from a latent mixture of pathogen subtypes, laboratory typing of a subset of clinical cases can provide inference on the proportion of clinical cases attributable to each subtype (i.e., the mixture components). Optimizing protocols for the selection of isolates for typing by weighting specific subpopulations, locations, time periods, or case characteristics (e.g., disease severity), may improve inference of the frequency and distribution of pathogen subtypes within and between populations. Here, we apply the Disease Surveillance Informatics Optimization and Simulation (DIOS) framework to simulate and optimize hand foot and mouth disease (HFMD) surveillance in a high-burden region of western China. We identify laboratory surveillance designs that significantly outperform the existing network: the optimal network reduced mean absolute error in estimated serotype-specific incidence rates by 14.1%; similarly, the optimal network for monitoring severe cases reduced mean absolute error in serotype-specific incidence rates by 13.3%. In both cases, the optimal network designs achieved improved inference without increasing subtyping effort. We demonstrate how the DIOS framework can be used to optimize surveillance networks by augmenting clinical diagnostic data with limited laboratory typing resources, while adapting to specific, local surveillance objectives and constraints.

School closures may reduce the size of social networks among children, potentially limiting infectious disease transmission. To estimate the impact of K-12 closures and reopening policies on children's social interactions and COVID-19 incidence in California's Bay Area, we collected data on children's social contacts and assessed implications for transmission using an individual-based model. Elementary and Hispanic children had more contacts during closures than high school and non-Hispanic children, respectively. We estimated that spring 2020 closures of elementary schools averted 2167 cases in the Bay Area (95% CI: -985, 5572), fewer than middle (5884; 95% CI: 1478, 11.550), high school (8650; 95% CI: 3054, 15 940) and workplace (15 813; 95% CI: 9963, 22 617) closures. Under assumptions of moderate community transmission, we estimated that reopening for a four-month semester without any precautions will increase symptomatic illness among high school teachers (an additional 40.7% expected to experience symptomatic infection, 95% CI: 1.9, 61.1), middle school teachers (37.2%, 95% CI: 4.6, 58.1) and elementary school teachers (4.1%, 95% CI: -1.7, 12.0). However, we found that reopening policies for elementary schools that combine universal masking with classroom cohorts could result in few within-school transmissions, while high schools may require masking plus a staggered hybrid schedule. Stronger community interventions (e.g. remote work, social distancing) decreased the risk of within-school transmission across all measures studied, with the influence of community transmission minimized as the effectiveness of the within-school measures increased.

BackgroundEnterovirus 71 (EV71) is a major causative agent of hand, foot, and mouth disease (HFMD), associated with severe manifestations of the disease. Pediatric immunization with inactivated EV71 vaccine was initiated in 2016 in the Asia-Pacific region, including China. We analyzed a time series of HFMD cases attributable to EV71, coxsackievirus A16 (CA16), and other enteroviruses in Chengdu, a major transmission center in China, to assess early impacts of immunization.MethodsReported HFMD cases were obtained from China's notifiable disease surveillance system. We compared observed postvaccination incidence rates during 2017-2018 with counterfactual predictions made from a negative binomial regression and a random forest model fitted to prevaccine years (2011-2015). We fit a change point model to the full time series to evaluate whether the trend of EV71 HFMD changed following vaccination.ResultsBetween 2011 and 2018, 279 352 HFMD cases were reported in the study region. The average incidence rate of EV71 HFMD in 2017-2018 was 60% (95% prediction interval [PI], 41%-72%) lower than predicted in the absence of immunization, corresponding to an estimated 6911 (95% PI, 3246-11 542) EV71 cases averted over 2 years. There were 52% (95% PI, 42%-60%) fewer severe HFMD cases than predicted. However, the incidence rate of non-CA16 and non-EV71 HFMD was elevated in 2018. We identified a significant decline in the trend of EV71 HFMD 4 months into the postvaccine period.ConclusionsWe provide the first real-world evidence that programmatic vaccination against EV71 is effective against childhood HFMD and present an approach to detect early vaccine impact or intended consequences from surveillance data.

Global food security is a major driver of population health, and food system collapse may have complex and long-lasting effects on health outcomes. We examined the effect of prenatal exposure to the Great Chinese Famine (1958-1962)-the largest famine in human history-on pulmonary tuberculosis (PTB) across consecutive generations in a major center of ongoing transmission in China. We analyzed >1 million PTB cases diagnosed between 2005 and 2018 in Sichuan Province using age-period-cohort analysis and mixed-effects metaregression to estimate the effect of the famine on PTB risk in the directly affected birth cohort (F1) and their likely offspring (F2). The analysis was repeated on certain sexually transmitted and blood-borne infections (STBBI) to explore potential mechanisms of the intergenerational effects. A substantial burden of active PTB in the exposed F1 cohort and their offspring was attributable to the Great Chinese Famine, with more than 12,000 famine-attributable active PTB cases (>1.23% of all cases reported between 2005 and 2018). An interquartile range increase in famine intensity resulted in a 6.53% (95% confidence interval [CI]: 1.19-12.14%) increase in the ratio of observed to expected incidence rate (incidence rate ratio, IRR) in the absence of famine in F1, and an 8.32% (95% CI: 0.59-16.6%) increase in F2 IRR. Increased risk of STBBI was also observed in F2. Prenatal and early-life exposure to malnutrition may increase the risk of active PTB in the exposed generation and their offspring, with the intergenerational effect potentially due to both within-household transmission and increases in host susceptibility.

Disease surveillance data are important for monitoring disease burden and occurrence, and for informing a wide range of efforts to improve population health. Surveillance for infectious diseases may be conducted passively, relying on reports from healthcare facilities, or actively, involving surveys of the population at risk. Passive surveillance typically provides wide spatial coverage, but is subject to biases arising from differences in care-seeking behavior, diagnostic practices, and under-reporting. Active surveillance minimizes these biases, but is typically constrained to small areas and subpopulations due to resource limitations. Methods based on linkage of individual records between passive and active surveillance datasets provide a means to estimate and correct for the biases of each system, leveraging the size and coverage of passive surveillance and the quality of data in active surveillance. We develop a spatial Bayesian hierarchical model for bias-correcting data from both systems to yield an improved estimate of disease measures after adjusting for under-ascertainment. We apply the framework to data from a passive and an active surveillance system for pulmonary tuberculosis (PTB) in Sichuan, China, and estimate the average sensitivity of the active surveillance system at 70% (95% credible interval: 62%, 78%), and the passive system at 30% (95% CI: 24%, 35%). Passive surveillance sensitivity exhibited considerable spatial variability, and was positively associated with a site's gross domestic product per capita. Bias-corrected estimates of county-level PTB prevalence in the province in 2010 identified regions in the southeast with the highest PTB burden, yielding different geographic priorities than previous reports.

Background Large-scale school closures have been implemented worldwide to curb the spread of COVID-19. However, the impact of school closures and re-opening on epidemic dynamics remains unclear. Methods We simulated COVID-19 transmission dynamics using an individual-based stochastic model, incorporating social-contact data of school-aged children during shelter-in-place orders derived from Bay Area (California) household surveys. We simulated transmission under observed conditions and counterfactual intervention scenarios between March 17-June 1, and evaluated various fall 2020 K-12 reopening strategies. Findings Between March 17-June 1, assuming children

Infectious disease surveillance systems provide vital data for guiding disease prevention and control policies, yet the formalization of methods to optimize surveillance networks has largely been overlooked. Decisions surrounding surveillance design parameters-such as the number and placement of surveillance sites, target populations, and case definitions-are often determined by expert opinion or deference to operational considerations, without formal analysis of the influence of design parameters on surveillance objectives. Here we propose a simulation framework to guide evidence-based surveillance network design to better achieve specific surveillance goals with limited resources. We define evidence-based surveillance design as an optimization problem, acknowledging the many operational constraints under which surveillance systems operate, the many dimensions of surveillance system design, the multiple and competing goals of surveillance, and the complex and dynamic nature of disease systems. We describe an analytical framework-the Disease Surveillance Informatics Optimization and Simulation (DIOS) framework-for the identification of optimal surveillance designs through mathematical representations of disease and surveillance processes, definition of objective functions, and numerical optimization. We then apply the framework to the problem of selecting candidate sites to expand an existing surveillance network under alternative objectives of: (1) improving spatial prediction of disease prevalence at unmonitored sites; or (2) estimating the observed effect of a risk factor on disease. Results of this demonstration illustrate how optimal designs are sensitive to both surveillance goals and the underlying spatial pattern of the target disease. The findings affirm the value of designing surveillance systems through quantitative and adaptive analysis of network characteristics and performance. The framework can be applied to the design of surveillance systems tailored to setting-specific disease transmission dynamics and surveillance needs, and can yield improved understanding of tradeoffs between network architectures.

BackgroundChina contributed 8.9% of all incident cases of tuberculosis globally in 2017, and understanding the spatiotemporal distribution of pulmonary tuberculosis (PTB) in major transmission foci in the country is critical to ongoing efforts to improve population health.MethodsWe estimated annual PTB notification rates and their spatiotemporal distributions in Sichuan province, a major center of ongoing transmission, from 2005 to 2017. Time series decomposition was used to obtain trend components from the monthly incidence rate time series. Spatiotemporal cluster analyses were conducted to detect spatiotemporal clusters of PTB at the county level.ResultsFrom 2005 to 2017, 976,873 cases of active PTB and 388,739 cases of smear-positive PTB were reported in Sichuan Province, China. During this period, the overall reported incidence rate of active PTB decreased steadily at a rate of decrease (3.77 cases per 100,000 per year, 95% confidence interval (CI): 3.28-4.31) that was slightly faster than the national average rate of decrease (3.14 cases per 100,000 per year, 95% CI: 2.61-3.67). Although reported PTB incidence decreased significantly in most regions of the province, incidence was observed to be increasing in some counties with high HIV incidence and ethnic minority populations. Active and smear-positive PTB case reports exhibited seasonality, peaking in March and April, with apparent links to social dynamics and climatological factors.ConclusionsWhile PTB incidence rates decreased strikingly in the study area over the past decade, improvements have not been equally distributed. Additional surveillance and control efforts should be guided by the seasonal-trend and spatiotemporal cluster analyses presented here, focusing on areas with increasing incidence rates, and updated to reflect the latest information from real-time reporting.

Mass gatherings exacerbate infectious disease risks by creating crowded, high-contact conditions and straining the capacity of local infrastructure. While mass gatherings have been extensively studied in the context of epidemic disease transmission, the role of gatherings in incidence of high-burden, endemic infections has not been previously studied. Here, we examine diarrheal incidence among 17 communities in Esmeraldas, Ecuador, in relation to recurrent gatherings characterized using ethnographic data collected during and after the epidemiologic surveillance period (2004-2007). Using distributed-lag generalized estimating equations, adjusted for seasonality, trend, and heavy rainfall events, we found significant increases in diarrhea risk in host villages, peaking 2 weeks after an event's conclusion (incidence rate ratio, 1.21; confidence interval, adjusted for false coverage rate of ≤0.05: 1.02, 1.43). Stratified analysis revealed heightened risks associated with events where crowding and travel were most likely (2-week-lag incidence rate ratio, 1.51; confidence interval, adjusted for false coverage rate of ≤0.05: 1.09, 2.10). Our findings suggest that community-scale mass gatherings might play an important role in endemic diarrheal disease transmission and could be an important focus for interventions to improve community health in low-resource settings.

BackgroundChina contributed 8.9% of all incident cases of tuberculosis globally in 2017, and understanding the spatiotemporal distribution of pulmonary tuberculosis (PTB) in major transmission foci in the country is critical to ongoing efforts to improve population health.MethodsWe estimated annual PTB notification rates and their spatiotemporal distributions in Sichuan province, a major center of ongoing transmission, from 2005 to 2017. Time series decomposition was used to obtain trend components from the monthly incidence rate time series. Spatiotemporal cluster analyses were conducted to detect spatiotemporal clusters of PTB at the county level.ResultsFrom 2005 to 2017, 976,873 cases of active PTB and 388,739 cases of smear-positive PTB were reported in Sichuan Province, China. During this period, the overall reported incidence rate of active PTB decreased steadily at a rate of decrease (3.77 cases per 100,000 per year, 95% confidence interval (CI): 3.28-4.31) that was slightly faster than the national average rate of decrease (3.14 cases per 100,000 per year, 95% CI: 2.61-3.67). Although reported PTB incidence decreased significantly in most regions of the province, incidence was observed to be increasing in some counties with high HIV incidence and ethnic minority populations. Active and smear-positive PTB case reports exhibited seasonality, peaking in March and April, with apparent links to social dynamics and climatological factors.ConclusionsWhile PTB incidence rates decreased strikingly in the study area over the past decade, improvements have not been equally distributed. Additional surveillance and control efforts should be guided by the seasonal-trend and spatiotemporal cluster analyses presented here, focusing on areas with increasing incidence rates, and updated to reflect the latest information from real-time reporting.

The relationship between rainfall, especially extreme rainfall, and increases in waterborne infectious diseases is widely reported in the literature. Most of this research, however, has not formally considered the impact of exposure measurement error contributed by the limited spatiotemporal fidelity of precipitation data. Here, we evaluate bias in effect estimates associated with exposure misclassification due to precipitation data fidelity, using extreme rainfall as an example. We accomplished this via a simulation study, followed by analysis of extreme rainfall and incident diarrheal disease in an epidemiologic study in Ecuador. We found that the limited fidelity typical of spatiotemporal rainfall data sets biases effect estimates towards the null. Use of spatial interpolations of rain-gauge data or satellite data biased estimated health effects due to extreme rainfall (occurrence) and wet conditions (accumulated totals) downwards by 35%-45%. Similar biases were evident in the Ecuadorian case study analysis, where spatial incompatibility between exposed populations and rain gauges resulted in the association between extreme rainfall and diarrheal disease incidence being approximately halved. These findings suggest that investigators should pay greater attention to limitations in using spatially heterogeneous environmental data sets to assign exposures in epidemiologic research.

Climate exerts complex influences on leptospirosis transmission, affecting human behavior, zoonotic host population dynamics, and survival of the pathogen in the environment. Here, we describe the spatiotemporal distribution of leptospirosis incidence reported to China's National Infectious Disease Surveillance System from 2004-2014 in an endemic region in western China, and employ distributed lag models at annual and sub-annual scales to analyze its association with hydroclimatic risk factors and explore evidence for the potential role of a soil reservoir in the transmission of Leptospira spp. More than 97% of the 2,934 reported leptospirosis cases occurred during the harvest season between August and October, and most commonly affected farmers (83%). Using a distributed lag Poisson regression framework, we characterized incidence rate ratios (IRRs) associated with interquartile range increases in precipitation of 3.45 (95% confidence interval 2.57-4.64) over 0-1-year lags, and 1.90 (1.18-3.06) over 0-15-week lags. Adjusting for soil moisture decreased IRRs for precipitation at both timescales (yearly adjusted IRR: 1.05, 0.74-1.49; weekly adjusted IRR: 1.36, 0.72-2.57), suggesting precipitation effects may be mediated through soil moisture. Increased soil moisture was positively associated with leptospirosis at both timescales, suggesting that the survival of pathogenic Leptospira spp. in moist soils may be a critical control on harvest-associated leptospirosis transmission in the study region. These results support the hypothesis that soils may serve as an environmental reservoir and may play a significant yet underrecognized role in leptospirosis transmission.

Rotavirus is considered a directly transmitted disease due to its high infectivity. Environmental pathways have, therefore, largely been ignored. Rotavirus, however, persists in water sources, and both its surface water concentrations and infection incidence vary with temperature. Here, we examine the potential for waterborne rotavirus transmission. We use a mechanistic model that incorporates both direct and waterborne transmission pathways, coupled with a hydrological model, and we simulate rotavirus transmission between two communities with interconnected water sources. To parameterize temperature dependency, we estimated temperature-dependent decay rates in water through a meta-analysis. Our meta-analysis suggests that rotavirus decay rates are positively associated with temperature (n = 39, P [Formula: see text] 0.001). This association is stronger at higher temperatures (over 20 °C), consistent with tropical climate conditions. Our model analysis demonstrates that water could disseminate rotavirus between the two communities for all modeled temperatures. While direct transmission was important for disease amplification within communities, waterborne transmission could also amplify transmission. In standing-water systems, the modeled increase in decay led to decreased disease, with every 1 °C increase in temperature leading to up to a 2.4% decrease in incidence. These effect sizes are consistent with prior meta-analyses, suggesting that environmental transmission through water sources may partially explain the observed associations between temperature and rotavirus incidence. Waterborne rotavirus transmission is likely most important in cooler seasons and in communities that use slow-moving or stagnant water sources. Even when indirect transmission through water cannot sustain outbreaks, it can seed outbreaks that are maintained by high direct transmission rates.

As the appreciation for the importance of the environment in infectious disease transmission has grown, so too has interest in pathogen fate and transport. Fate has been traditionally described by simple exponential decay, but there is increasing recognition that some pathogens demonstrate a biphasic pattern of decay-fast followed by slow. While many have attributed this behavior to population heterogeneity, we demonstrate that biphasic dynamics can arise through a number of plausible mechanisms. We examine the identifiability of a general model encompassing three such mechanisms: population heterogeneity, hardening off, and the existence of viable-but-not-culturable states. Although the models are not fully identifiable from longitudinal sampling studies of pathogen concentrations, we use a differential algebra approach to determine identifiable parameter combinations. Through case studies using Cryptosporidium and Escherichia coli, we show that failure to consider biphasic pathogen dynamics can lead to substantial under- or overestimation of disease risks and pathogen concentrations, depending on the context. More reliable models for environmental hazards and human health risks are possible with an improved understanding of the conditions in which biphasic die-off is expected. Understanding the mechanisms of pathogen decay will ultimately enhance our control efforts to mitigate exposure to environmental contamination.

Flooding is known to facilitate infectious disease transmission, yet quantitative research on microbiological risks associated with floods has been limited. Pathogen fate and transport models provide a framework to examine interactions between landscape characteristics, hydrology, and waterborne disease risks, but have not been widely developed for flood conditions. We critically examine capabilities of current hydrological models to represent unusual flow paths, non-uniform flow depths, and unsteady flow velocities that accompany flooding. We investigate the theoretical linkages between hydrodynamic processes and spatio-temporally variable suspension and deposition of pathogens from soils and sediments; pathogen dispersion in flow; and concentrations of constituents influencing pathogen transport and persistence. Identifying gaps in knowledge and modeling practice, we propose a research agenda to strengthen microbial fate and transport modeling applied to inland floods: 1) development of models incorporating pathogen discharges from flooded sources (e.g., latrines), effects of transported constituents on pathogen persistence, and supply-limited pathogen transport; 2) studies assessing parameter identifiability and comparing model performance under varying degrees of process representation, in a range of settings; 3) development of remotely sensed datasets to support modeling of vulnerable, data-poor regions; and 4) collaboration between modelers and field-based researchers to expand the collection of useful data in situ.