Alyson Singleton

All Publications

• Highway paving dramatically increased dengue transmission in the Amazon. medRxiv : the preprint server for health sciences Singleton, A. L., Lescano, A. G., MacDonald, A. J., Mandle, L., Sipin, T. J., Martel, K. S., Munayco, C. V., Carrera, E. D., Choque, G. A., Bautista, A. S., Luby, S. P., Mordecai, E. A. 2024

  Abstract

  Human mobility drives the spread of many infectious diseases, yet the health impacts of changes in mobility due to new infrastructure development are poorly understood and currently not accounted for in impact assessments. We take a novel quasi-experimental approach to identifying the link between mobility and infectious disease, leveraging historical road upgrades as a proxy for regional human mobility changes. We analyzed how highway paving altered transmission of dengue-a high-burden mosquito-borne disease-via changes in human movement in the Madre de Dios region of Peru. The paving of the Interoceanic Highway through a formerly isolated region of the Amazon in 2009 provided a unique opportunity to quantify the causal impact of road paving on disease transmission. To uncover this relationship, we compared dengue incidence data from healthcare facilities in Madre de Dios near to versus far from the newly paved highway before and after paving, while controlling for observable and unobservable confounding variables (a difference-in-differences causal inference approach). We found that the paving of the highway caused at least an additional 9,826 (95% CI: 8,562-10,684) dengue cases since paving, accounting for 45.2% (95% CI: 39.4%-49.2%) of all dengue cases recorded in the region post highway paving (2009-2022). Our findings demonstrate the impact that infrastructure can have on dengue transmission, likely via its effects on human mobility. As a result, we advocate for future road construction plans in tropical regions to account for potential increases in dengue transmission during impact assessments.

  View details for DOI 10.1101/2024.11.15.24317406

  View details for PubMedID 39606351

  View details for PubMedCentralID PMC11601761

• Mapping schistosomiasis risk landscapes and implications for disease control: A case study for low endemic areas in the Middle Paranapanema river basin, São Paulo, Brazil. PLoS neglected tropical diseases Ferreira da Silva, V. A., Kampel, M., Silva Dos Anjos, R., Gardini Sanches Palasio, R., Escada, M. I., Tuan, R., Singleton, A., Glidden, C. K., Chamberlin, A., De Leo, G. A., Pinter Dos Santos, A., Vieira Monteiro, A. M. 2024; 18 (11): e0012582

  Abstract

  Schistosomiasis, a chronic parasitic disease, remains a public health issue in tropical and subtropical regions, especially in low and moderate-income countries lacking assured access to safe water and proper sanitation. A national prevalence survey carried out by the Brazilian Ministry of Health from 2011 to 2015 found a decrease in human infection rates to 1%, with 19 out of 26 states still classified as endemic areas. There is a risk of schistosomiasis reemerging as a public health concern in low-endemic regions. This study proposes an integrated landscape-based approach to aid surveillance and control strategies for schistosomiasis in low-endemic areas.In the Middle Paranapanema river basin, specific landscapes linked to schistosomiasis were identified using a comprehensive methodology. This approach merged remote sensing, environmental, socioeconomic, epidemiological, and malacological data. A team of experts identified ten distinct landscape categories associated with varying levels of schistosomiasis transmission potential. These categories were used to train a supervised classification machine learning algorithm, resulting in a 92.5% overall accuracy and a 6.5% classification error. Evaluation revealed that 74.6% of collected snails from water collections in five key municipalities within the basin belonged to landscape types with higher potential for S. mansoni infection. Landscape connectivity metrics were also analysed.This study highlights the role of integrated landscape-based analyses in informing strategies for eliminating schistosomiasis. The methodology has produced new schistosomiasis risk maps covering the entire basin. The region's low endemicity can be partly explained by the limited connectivity among grouped landscape-units more prone to triggering schistosomiasis transmission. Nevertheless, changes in social, economic, and environmental landscapes, especially those linked to the rising pace of incomplete urbanization processes in the region, have the potential to increase risk of schistosomiasis transmission. This study will help target interventions to bring the region closer to schistosomiasis elimination.

  View details for DOI 10.1371/journal.pntd.0012582

  View details for PubMedID 39495810

• Climate and urbanization drive changes in the habitat suitability of Schistosoma mansoni competent snails in Brazil. Nature communications Glidden, C. K., Singleton, A. L., Chamberlin, A., Tuan, R., Palasio, R. G., Caldeira, R. L., Monteiro, A. M., Lwiza, K. M., Liu, P., Silva, V., Athni, T. S., Sokolow, S. H., Mordecai, E. A., De Leo, G. A. 2024; 15 (1): 4838

  Abstract

  Schistosomiasis is a neglected tropical disease caused by Schistosoma parasites. Schistosoma are obligate parasites of freshwater Biomphalaria and Bulinus snails, thus controlling snail populations is critical to reducing transmission risk. As snails are sensitive to environmental conditions, we expect their distribution is significantly impacted by global change. Here, we used machine learning, remote sensing, and 30 years of snail occurrence records to map the historical and current distribution of forward-transmitting Biomphalaria hosts throughout Brazil. We identified key features influencing the distribution of suitable habitat and determined how Biomphalaria habitat has changed with climate and urbanization over the last three decades. Our models show that climate change has driven broad shifts in snail host range, whereas expansion of urban and peri-urban areas has driven localized increases in habitat suitability. Elucidating change in Biomphalaria distribution-while accounting for non-linearities that are difficult to detect from local case studies-can help inform schistosomiasis control strategies.

  View details for DOI 10.1038/s41467-024-48335-9

  View details for PubMedID 38898012

  View details for PubMedCentralID PMC11186836

• Estimates of SARS-CoV-2 Hospitalization and Fatality Rates in the Prevaccination Period, United States. Emerging infectious diseases Griffin, I., King, J., Lyons, B. C., Singleton, A. L., Deng, X., Bruce, B. B., Griffin, P. M. 2024; 30 (6): 1144-1153

  Abstract

  Few precise estimates of hospitalization and fatality rates from COVID-19 exist for naive populations, especially within demographic subgroups. We estimated rates among persons with SARS-CoV-2 infection in the United States during May 1-December 1, 2020, before vaccines became available. Both rates generally increased with age; fatality rates were highest for persons >85 years of age (24%) and lowest for children 1-14 years of age (0.01%). Age-adjusted case hospitalization rates were highest for African American or Black, not Hispanic persons (14%), and case-fatality rates were highest for Asian or Pacific Islander, not Hispanic persons (4.4%). Eighteen percent of hospitalized patients and 44.2% of those admitted to an intensive care unit died. Male patients had higher hospitalization (6.2% vs. 5.2%) and fatality rates (1.9% vs. 1.5%) than female patients. These findings highlight the importance of collecting surveillance data to devise appropriate control measures for persons in underserved racial/ethnic groups and older adults.

  View details for DOI 10.3201/eid3006.231285

  View details for PubMedID 38781926

  View details for PubMedCentralID PMC11138987

• Species distribution modeling for disease ecology: A multi-scale case study for schistosomiasis host snails in Brazil. PLOS global public health Singleton, A. L., Glidden, C. K., Chamberlin, A. J., Tuan, R., Palasio, R. G., Pinter, A., Caldeira, R. L., Mendonca, C. L., Carvalho, O. S., Monteiro, M. V., Athni, T. S., Sokolow, S. H., Mordecai, E. A., De Leo, G. A. 2024; 4 (8): e0002224

  Abstract

  Species distribution models (SDMs) are increasingly popular tools for profiling disease risk in ecology, particularly for infectious diseases of public health importance that include an obligate non-human host in their transmission cycle. SDMs can create high-resolution maps of host distribution across geographical scales, reflecting baseline risk of disease. However, as SDM computational methods have rapidly expanded, there are many outstanding methodological questions. Here we address key questions about SDM application, using schistosomiasis risk in Brazil as a case study. Schistosomiasis is transmitted to humans through contact with the free-living infectious stage of Schistosoma spp. parasites released from freshwater snails, the parasite's obligate intermediate hosts. In this study, we compared snail SDM performance across machine learning (ML) approaches (MaxEnt, Random Forest, and Boosted Regression Trees), geographic extents (national, regional, and state), types of presence data (expert-collected and publicly-available), and snail species (Biomphalaria glabrata, B. straminea, and B. tenagophila). We used high-resolution (1km) climate, hydrology, land-use/land-cover (LULC), and soil property data to describe the snails' ecological niche and evaluated models on multiple criteria. Although all ML approaches produced comparable spatially cross-validated performance metrics, their suitability maps showed major qualitative differences that required validation based on local expert knowledge. Additionally, our findings revealed varying importance of LULC and bioclimatic variables for different snail species at different spatial scales. Finally, we found that models using publicly-available data predicted snail distribution with comparable AUC values to models using expert-collected data. This work serves as an instructional guide to SDM methods that can be applied to a range of vector-borne and zoonotic diseases. In addition, it advances our understanding of the relevant environment and bioclimatic determinants of schistosomiasis risk in Brazil.

  View details for DOI 10.1371/journal.pgph.0002224

  View details for PubMedID 39093879

• Minority-group incubators and majority-group reservoirs support the diffusion of climate change adaptations. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Turner, M. A., Singleton, A. L., Harris, M. J., Harryman, I., Lopez, C. A., Arthur, R. F., Muraida, C., Jones, J. H. 2023; 378 (1889): 20220401

  Abstract

  Successful climate change adaptation depends on the spread and maintenance of adaptive behaviours. Current theory suggests that the heterogeneity of metapopulation structure can help adaptations diffuse throughout a population. In this paper, we develop an agent-based model of the spread of adaptations in populations with minority-majority metapopulation structure, where subpopulations learn more or less frequently from their own group compared to the other group. In our simulations, minority-majority-structured populations with moderate degrees of in-group preference better spread and maintained an adaptation compared to populations with more equal-sized groups and weak homophily. Minority groups act as incubators for an adaptation, while majority groups act as reservoirs for an adaptation once it has spread widely. This means that adaptations diffuse throughout populations better when minority groups start out knowing an adaptation, as Indigenous populations often do, while cohesion among majority groups further promotes adaptation diffusion. Our work advances the goal of this theme issue by developing new theoretical insights and demonstrating the utility of cultural evolutionary theory and methods as important tools in the nascent science of culture that climate change adaptation needs. This article is part of the theme issue 'Climate change adaptation needs a science of culture'.

  View details for DOI 10.1098/rstb.2022.0401

  View details for PubMedID 37718602

• Survey of incidence, lifetime prevalence, and treatment of self-reported vulvovaginal candidiasis, United States, 2020. BMC women's health Benedict, K., Singleton, A. L., Jackson, B. R., Molinari, N. A. 2022; 22 (1): 147

  Abstract

  Vulvovaginal candidiasis (VVC) is a common gynecologic problem in the United States but estimates of its true incidence and prevalence are lacking. We estimated self-reported incidence and lifetime prevalence of healthcare provider-diagnosed VVC and recurrent VVC (RVVC), assessed treatment types, and evaluated demographic and health-related risk factors associated with VVC.An online survey sent to 4548 U.S. adults; data were weighted to be representative of the population. We conducted descriptive and bivariate analyses to examine demographic characteristics and health related factors associated with having VVC in the past year, lifetime prevalence of VVC, and over-the-counter (OTC) and prescription antifungal treatment use. We conducted multivariate analyses to assess features associated with 1) having VVC in the past year, 2) number of VVC episodes in the past year, and 3) lifetime prevalence of VVC.Among the subset of 1869 women respondents, 98 (5.2%) had VVC in the past year; of those, 5 (4.7%) had RVVC. Total, 991 (53%) women reported healthcare provider-diagnosed VVC in their lifetime. Overall, 72% of women with VVC in the past year reported prescription antifungal treatment use, 40% reported OTC antifungal treatment use, and 16% reported both. In multivariate analyses, odds of having VVC in the past year were highest for women with less than a high school education (aOR = 6.30, CI: 1.84-21.65), with a child/children under 18 years old (aOR = 3.14, CI: 1.58-6.25), with diabetes (aOR = 2.93, CI: 1.32-6.47), who were part of a couple (aOR = 2.86, CI: 1.42-5.78), and with more visits to a healthcare provider for any reason (aOR = 2.72, CI: 1.84-4.01). Similar factors were associated with increasing number of VVC episodes in the past year and with lifetime prevalence of VVC.VVC remains a common infection in the United States. Our analysis supports known clinical risk factors for VVC and suggests that antifungal treatment use is high, underscoring the need to ensure appropriate diagnosis and treatment.

  View details for DOI 10.1186/s12905-022-01741-x

  View details for PubMedID 35538480

  View details for PubMedCentralID PMC9092842

• Network structure and rapid HIV transmission among people who inject drugs: A simulation-based analysis EPIDEMICS Singleton, A. L., Marshall, B. L., Bessey, S., Harrison, M. T., Galvani, A. P., Yedinak, J. L., Jacka, B. P., Goodreau, S. M., Goedel, W. C. 2021; 34: 100426

  Abstract

  As HIV incidence among people who inject drugs grows in the context of an escalating drug overdose epidemic in North America, investigating how network structure may affect vulnerability to rapid HIV transmission is necessary for preventing outbreaks. We compared the characteristics of the observed contact tracing network from the 2015 outbreak in rural Indiana with 1000 networks generated by an agent-based network model with approximately the same number of individuals (n = 420) and ties between them (n = 913). We introduced an initial HIV infection into the simulated networks and compared the subsequent epidemic behavior (e.g., cumulative HIV infections over 5 years). The model was able to produce networks with largely comparable characteristics and total numbers of incident HIV infections. Although the model was unable to produce networks with comparable cohesiveness (where the observed network had a transitivity value 35.7 standard deviations from the mean of the simulated networks), the structural variability of the simulated networks allowed for investigation into their potential facilitation of HIV transmission. These findings emphasize the need for continued development of injection network simulation studies in tandem with empirical data collection to further investigate how network characteristics played a role in this and future outbreaks.

  View details for DOI 10.1016/j.epidem.2020.100426

  View details for Web of Science ID 000632640900003

  View details for PubMedID 33341667

  View details for PubMedCentralID PMC7940592

• Added Benefits of Pre-Exposure Prophylaxis Use on HIV Incidence with Minimal Changes in Efficiency in the Context of High Treatment Engagement Among Men Who Have Sex with Men AIDS PATIENT CARE AND STDS Singleton, A. L., Marshall, B. L., Zang, X., Nunn, A. S., Goedel, W. C. 2020; 34 (12): 506-515

  Abstract

  Although there is ongoing debate over the need for substantial increases in pre-exposure prophylaxis (PrEP) use when antiretroviral treatment confers the dual benefits of reducing HIV-related morbidity and mortality and the risk of HIV transmission, no studies to date have quantified the potential added benefits of PrEP use and changes in its efficiency in the context of high treatment engagement across multiple US subpopulations. We used a previously published agent-based model to simulate HIV transmission in a dynamic network of Black/African American and White men who have sex with men (MSM) in Atlanta, Georgia (2015-2024) to understand how reductions in HIV incidence attributable to varying levels of PrEP use change when United Nations Joint Programme on HIV/AIDS (UNAIDS) "90-90-90" goals for HIV treatment are achieved and maintained. Even at achievement of "90-90-90" goals, 75% PrEP coverage further reduced incidence by 67.9% and 74.2% to 1.53 [simulation interval (SI): 1.39-1.70] and 0.355 (SI: 0.316-0.391) per 100 person-years for Black/African American and White MSM, respectively, compared with the same scenario with no PrEP use. Increasing PrEP coverage from 15% to 75% under "90-90-90" goals only increased the number of person-years of PrEP use per infection averted by 8.1% and 10.5% to 26.7 (SI: 25.6-28.0) and 73.3 (SI: 70.6-75.7) among Black/African American MSM and White MSM, respectively. Even with high treatment engagement, substantial expansion of PrEP use contributes to meaningful decreases in HIV incidence among MSM with minimal changes in efficiency.

  View details for DOI 10.1089/apc.2020.0151

  View details for Web of Science ID 000592966300001

  View details for PubMedID 33216618

  View details for PubMedCentralID PMC7757534

• Potential effectiveness of long-acting injectable pre-exposure prophylaxis for HIV prevention in men who have sex with men: a modelling study LANCET HIV Marshall, B. L., Goedel, W. C., King, M. F., Singleton, A., Durham, D. P., Chan, P. A., Townsend, J. P., Galvani, A. P. 2018; 5 (9): E498-E505

  Abstract

  Oral pre-exposure prophylaxis (PrEP) prevents HIV infection in men who have sex with men (MSM); however, adherence is an ongoing concern. Long-acting injectable PrEP is being tested in phase 3 trials and could address challenges associated with adherence. We examined the potential effectiveness of long-acting injectable PrEP compared with oral PrEP in MSM.We used an agent-based model to simulate HIV transmission in a dynamic network of 11 245 MSM in Atlanta, GA, USA. We used raw data from studies in macaque models and pharmacokinetic data from safety trials to estimate the time-varying efficacy of long-acting injectable PrEP. The effect of long-acting injectable PrEP on the cumulative number of new HIV infections over 10 years (2015-24) was compared with no PrEP and daily oral PrEP across a range of coverage levels. Sensitivity analyses were done with varying maximum efficacy and drug half-life values.In the absence of PrEP, the model predicted 2374 new HIV infections (95% simulation interval [SI] 2345-2412) between 2015 and 2024. The cumulative number of new HIV infections was reduced in all scenarios in which MSM received long-acting injectable PrEP compared with oral PrEP. At a coverage level of 35%, compared with no PrEP, long-acting injectable PrEP led to a 44% reduction in new HIV infections (1044 new infections averted [95% SI 1018-1077]) versus 33% (792 infections averted [763-821]) for oral PrEP. The relative benefit of long-acting injectable PrEP was sensitive to the assumed efficacy of injections received every 8 weeks, discontinuation rates, and terminal drug half-life.Long-acting injectable PrEP has the potential to produce larger reductions in HIV transmission in MSM than oral PrEP. However, the real-world, population-level impact of this approach will depend on uptake of this prevention method and its effectiveness, as well as retention of patients in clinical care.National Institute on Drug Abuse and National Institute of Mental Health.

  View details for DOI 10.1016/S2352-3018(18)30097-3

  View details for Web of Science ID 000443740400012

  View details for PubMedID 29908917

  View details for PubMedCentralID PMC6138558