Research
My research spans methods and applications in infectious disease epidemiology, with a focus on network-based modeling. A comprehensive listing of publications is available on PubMed and Google Scholar, or see the full Publications page for a filterable list.
Below are the major research themes with representative papers (click to expand for abstracts and links).
Methods and Software for Infectious Disease Modeling
My methodological research centers on developing generalized methods and software tools for modeling infectious disease transmission dynamics, most notably EpiModel, a software platform for building and simulating mechanistic epidemic models. EpiModel specializes in network-based modeling using the statistical framework of exponential-family random graph models, a flexible and robust approach to representing dynamic contact structures. The platform is fully open source, with Github source and a supporting annual workshop, Network Modeling for Epidemics.
Representative publications
Klumb C, Morris M, Goodreau SM, Jenness SM. Improving and Extending STERGM Approximations Based on Cross-Sectional Data and Tie Durations. Journal of Computational and Graphical Statistics. 2024; 33(1): 166–180.
Abstract. Temporal exponential-family random graph models (TERGMs) are a flexible class of models for network ties that change over time. Separable TERGMs (STERGMs) are a subclass of TERGMs in which the dynamics of tie formation and dissolution can be separated within each discrete time step and may depend on different factors. The Carnegie et al. (2015) approximation improves estimation efficiency for a subclass of STERGMs, allowing them to be reliably estimated from inexpensive cross-sectional study designs. This approximation adapts to cross-sectional data by attempting to construct a STERGM with two specific properties: a cross-sectional equilibrium distribution defined by an exponential-family random graph model (ERGM) for the network structure, and geometric tie duration distributions defined by constant hazards for tie dissolution. In this paper we focus on approaches for improving the behavior of the Carnegie et al. approximation and increasing its scope of application. We begin with Carnegie et al.’s observation that the exact result is tractable when the ERGM is dyad-independent, and then show that taking the sparse limit of the exact result leads to a different approximation than the one they presented. We show that the new approximation outperforms theirs for sparse, dyad-independent models, and observe that the errors tend to increase with the strength of dependence for dyad-dependent models. We then develop theoretical results in the dyad-dependent case, showing that when the ERGM is allowed to have arbitrary dyad-dependent terms and some dyad-dependent constraints, both the old and new approximations are asymptotically exact as the size of the STERGM time step goes to zero. We note that the continuous-time limit of the discrete-time approximations has the desired cross-sectional equilibrium distribution and exponential tie duration distributions with the desired means. We show that our results extend to hypergraphs, and we propose an extension of the Carnegie et al. framework to dissolution hazards that depend on tie age.
Jenness SM, Willebrand KS, Malik AA, Lopman BA, Omer S. Dynamic Network Strategies for SARS-CoV-2 Control on a Cruise Ship. Epidemics. 2021; 37: 100488.
Abstract. SARS-CoV-2 outbreaks have occurred on several nautical vessels, driven by the high-density contact networks on these ships. Optimal strategies for prevention and control that account for realistic contact networks are needed. We developed a network-based transmission model for SARS-CoV-2 on the Diamond Princess outbreak to characterize transmission dynamics and to estimate the epidemiological impact of outbreak control and prevention measures. This model represented the dynamic multi-layer network structure of passenger-passenger, passenger-crew, and crew-crew contacts, both before and after the large-scale network lockdown imposed on the ship in response to the disease outbreak. Model scenarios evaluated variations in the timing of the network lockdown, reduction in contact intensity within the sub-networks, and diagnosis-based case isolation on outbreak prevention. We found that only extreme restrictions in contact patterns during network lockdown and idealistic clinical response scenarios could avert a major COVID-19 outbreak. Contact network changes associated with adequate outbreak prevention were the restriction of passengers to their cabins, with limited passenger-crew contacts. Clinical response strategies required for outbreak prevention may be infeasible in many cruise settings: early mass screening with an ideal PCR test (100 % sensitivity) and immediate case isolation upon diagnosis. Personal protective equipment (e.g., facemasks) had limited impact in this environment because the majority of transmissions after the ship lockdown occurred between passengers in cabins where masks were not consistently used. Public health restrictions on optional leisure activities like these should be considered until longer-term effective solutions such as a COVID-19 vaccine become widely available.
Uong S, Rosenberg ES, Luisi N, Goodreau SM, Sullivan PS, Jenness SM. Assessing the Validity of Sexual Network Degree among Men Who Have Sex with Men using Prospective Cohort Data. Epidemiology. 2020; 31(2): 229–237.
Abstract. Sexual network degree, a count of ongoing partnerships, plays a critical role in the transmission dynamics of human immunodeficiency virus and other sexually transmitted infections. Researchers often quantify degree using self-reported cross-sectional data on the day of survey, which may result in bias because of uncertainty about future sexual activity. Methods. We evaluated the bias of a cross-sectional degree measure with a prospective cohort study of men who have sex with men (MSM). At baseline, we asked men about whether recent sexual partnerships were ongoing. We confirmed the true, ongoing status of those partnerships at baseline at follow-up. With logistic regression, we estimated the partnership-level predictors of baseline measure accuracy. With Poisson regression, we estimated the longitudinally confirmed degree as a function of baseline predicted degree. Results. Across partnership types, the baseline ongoing status measure was 70% accurate, with higher negative predictive value (91%) than positive predictive value (39%). Partnership exclusivity and racial pairing were associated with higher accuracy. Baseline degree generally overestimated confirmed degree. Bias, or number of ongoing partners different than predicted at baseline, was -0.28 overall, ranging from -1.91 to -0.41 for MSM with any ongoing partnerships at baseline. Comparing MSM of the same baseline degree, the level of bias was stronger for black compared with white MSM, and for younger compared with older MSM. Conclusions. Research studies may overestimate degree when it is quantified cross-sectionally. Adjustment and structured sensitivity analyses may account for bias in studies of human immunodeficiency virus or sexually transmitted infection prevention interventions.
Jenness SM, Goodreau SM, Morris M. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks. Journal of Statistical Software. 2018; 84(8): 1-47.
Abstract. Package EpiModel provides tools for building, simulating, and analyzing mathematical models for the population dynamics of infectious disease transmission in R. Several classes of models are included, but the unique contribution of this software package is a general stochastic framework for modeling the spread of epidemics on networks. EpiModel integrates recent advances in statistical methods for network analysis (temporal exponential random graph models) that allow the epidemic modeling to be grounded in empirical data on contacts that can spread infection. This article provides an overview of both the modeling tools built into EpiModel, designed to facilitate learning for students new to modeling, and the application programming interface for extending package EpiModel, designed to facilitate the exploration of novel research questions for advanced modelers.
Empirical Network Data and Bias Analysis
Good models depend on good data. I have extensive experience developing and executing empirical studies to generate descriptive data points directly useful for model parameterization. A highlight is the ARTnet study of MSM across the United States, generating detailed sexual partnership network features used across modeling projects. Related work addresses measurement bias in survey-based network data and methods to correct it.
Representative publications
Nelson KN, Kiti MC, Shiiba M, Sacoor C, Bardají A, Macicame I, Jamisse E, Tchavana C, José A, Cavele N, Maldonado H, Jarquin C, Ajsivinac HM, Samuel P, Srinivasan R, Kazi M, Allana R, Kim SS, Prasad PV, Chen D, Liu C, Jenness SM, Ahmed N, Aguolu O, Sundaram MA, Yildirim I, Malik F, Melegaro A, Lopman BA, Omer SB. Characterizing Social Behavior Relevant for Infectious Disease Transmission in Four Low- and Middle-Income Countries, 2021–2023. Nature Communications. 2025; 16(1): 9586.
Abstract. Background: Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), a bacterium which is transmitted through the air. Close, sustained contact can lead to transmission of Mtb, but evidence also shows that transmission occurs also in community settings through more transient contact. However, social patterns that influence Mtb transmission, and locations that are most central to spread, are likely different by setting. Methods: We use data from the GlobalMix study, which characterized social behavior across four countries, to evaluate differences in age-sex patterning and locations of contact across four moderate- to high-TB burden countries. Healthy individuals self-completed a survey about their daily person-to-person interactions and locations in which they spent time. To capture the Mtb exposure profile of participants, we calculated daily exposure-hours from household contacts, close non-household contacts, and casual contacts, stratified by contact age and sex, and weighted by country-, age-, and sex-specific tuberculosis incidence estimates. Results: The most prominent shifts in the profile of exposure occur at entry to primary school (5-9 years) and early adulthood (20-29 years). Community locations varied in their relative importance as locations of transmission by country and age group, with school most important in India and Guatemala, transit more important in Pakistan, and others’ homes most important in Mozambique. Conclusions: Our findings demonstrate that locations of community transmission are likely varied across settings, underscoring the importance of interventions designed specifically for the communities in which they will be implemented.
Jenness SM, Wallrafen-Sam K, Schneider I, Kennedy S, Akiyama MJ, Spaulding AC. Dynamic Contact Networks of Residents of an Urban Jail in the Era of SARS-CoV-2. Epidemics. 2024; 47: 100772.
Abstract. Background: In custodial settings such as jails and prisons, infectious disease transmission is heightened by factors such as overcrowding and limited healthcare access. Specific features of social contact networks within these settings have not been sufficiently characterized, especially in the context of a large-scale respiratory infectious disease outbreak. The study aims to quantify contact network dynamics within the Fulton County Jail in Atlanta, Georgia. Methods: Jail roster data were utilized to construct social contact networks. Rosters included resident details, cell locations, and demographic information. This analysis involved 6702 male residents over 140,901 person days. Network statistics, including degree, mixing, and dissolution (movement within and out of the jail) rates, were assessed. We compared outcomes for two distinct periods (January 2022 and April 2022) to understand potential responses in network structures during and after the SARS-CoV-2 Omicron variant peak. Results: We found high cross-sectional network degree at both cell and block levels. While mean degree increased with age, older residents exhibited lower degree during the Omicron peak. Block-level networks demonstrated higher mean degrees than cell-level networks. Cumulative degree distributions increased from January to April, indicating heightened contacts after the outbreak. Assortative age mixing was strong, especially for younger residents. Dynamic network statistics illustrated increased degrees over time, emphasizing the potential for disease spread. Conclusions: Despite some reduction in network characteristics during the Omicron peak, the contact networks within the Fulton County Jail presented ideal conditions for infectious disease transmission. Age-specific mixing patterns suggested unintentional age segregation, potentially limiting disease spread to older residents. This study underscores the necessity for ongoing monitoring of contact networks in carceral settings and provides valuable insights for epidemic modeling and intervention strategies, including quarantine, depopulation, and vaccination, laying a foundation for understanding disease dynamics in such environments.Top of Form.
Weiss KM, Goodreau SM, Morris M, Prasad P, Ramaraju R, Sanchez T, Jenness SM. Egocentric Sexual Networks of Men Who Have Sex with Men in the United States: Results from the ARTnet Study. Epidemics. 2020; 30: 100386.
Abstract. In this paper, we present an overview and descriptive results from one of the first egocentric network studies of men who have sex with men (MSM) from across the United States: the ARTnet study. ARTnet was designed to support prevention research for human immunodeficiency virus (HIV) and other sexually transmitted infections (STIs) that are transmitted across partnership networks. ARTnet implemented a population-based egocentric network study design that sampled egos from the target population and asked them to report on the number, attributes, and timing of their sexual partnerships. Such data provide the foundation needed for parameterizing stochastic network models that are used for disease projection and intervention planning. ARTnet collected data online from 2017 to 2019, with a final sample of 4904 participants who reported on 16198 sexual partnerships. The aims of this paper were to characterize the joint distribution of three network parameters needed for modeling: degree distributions, assortative mixing, and partnership age, with heterogeneity by partnership type (main, casual and one-time), demography, and geography. Participants had an average of 1.19 currently active partnerships (“mean degree”), which was higher for casual partnerships (0.74) than main partnerships (0.45). The mean rate of one-time partnership acquisition was 0.16 per week (8.5 partners per year). Main partnerships lasted 272.5 weeks on average, while casual partnerships lasted 133.0 weeks. There was strong but heterogenous assortative mixing by race/ethnicity for all groups. The mean absolute age difference for all partnership types was 9.5 years, with main partners differing by 6.3 years compared to 10.8 years for casual partners. Our analysis suggests that MSM may be at sustained risk for HIV/STI acquisition and transmission through high network degree of sexual partnerships. The ARTnet network study provides a robust and reproducible foundation for understanding the dynamics of HIV/STI epidemiology among U.S. MSM and supporting the implementation science that seeks to address persistent challenges in HIV/STI prevention.
Uong S, Rosenberg ES, Luisi N, Goodreau SM, Sullivan PS, Jenness SM. Assessing the Validity of Sexual Network Degree among Men Who Have Sex with Men using Prospective Cohort Data. Epidemiology. 2020; 31(2): 229–237.
Abstract. Sexual network degree, a count of ongoing partnerships, plays a critical role in the transmission dynamics of human immunodeficiency virus and other sexually transmitted infections. Researchers often quantify degree using self-reported cross-sectional data on the day of survey, which may result in bias because of uncertainty about future sexual activity. Methods. We evaluated the bias of a cross-sectional degree measure with a prospective cohort study of men who have sex with men (MSM). At baseline, we asked men about whether recent sexual partnerships were ongoing. We confirmed the true, ongoing status of those partnerships at baseline at follow-up. With logistic regression, we estimated the partnership-level predictors of baseline measure accuracy. With Poisson regression, we estimated the longitudinally confirmed degree as a function of baseline predicted degree. Results. Across partnership types, the baseline ongoing status measure was 70% accurate, with higher negative predictive value (91%) than positive predictive value (39%). Partnership exclusivity and racial pairing were associated with higher accuracy. Baseline degree generally overestimated confirmed degree. Bias, or number of ongoing partners different than predicted at baseline, was -0.28 overall, ranging from -1.91 to -0.41 for MSM with any ongoing partnerships at baseline. Comparing MSM of the same baseline degree, the level of bias was stronger for black compared with white MSM, and for younger compared with older MSM. Conclusions. Research studies may overestimate degree when it is quantified cross-sectionally. Adjustment and structured sensitivity analyses may account for bias in studies of human immunodeficiency virus or sexually transmitted infection prevention interventions.
HIV Prevention Research
Applied research on HIV transmission and prevention, with a focus on how biomedical, behavioral, and structural interventions interact at the population level. Recent projects include the impact of long-acting injectable PrEP, over-the-counter PrEP (OFFSCRIPT), decision analytics for the PrEP cascade of care, and the role of HIV partner services in a modern biomedical prevention era.
Representative publications
Traeger MW, Leyden WA, Volk JE, Silverberg MJ, Horberg MA, Davis TL, Mayer KH, Krakower DS, Young JG, Jenness SM, Marcus JL. Doxycycline Postexposure Prophylaxis and Bacterial Sexually Transmitted Infections Among Individuals Using HIV Preexposure Prophylaxis. JAMA Internal Medicine. 2025; 185(3): 273–281.
Abstract. Background: Doxycycline postexposure prophylaxis (doxyPEP) is a promising strategy to prevent bacterial sexually transmitted infections. Limited data exist evaluating patient and provider experiences since doxyPEP has become widely available. We aimed to explore such factors among providers and patients during real-world implementation within one community health center. Methods: Doxycycline postexposure prophylaxis was rolled out at Fenway Health on February 2, 2023. To support rollout, electronic health record tools, 3 provider training sessions, and a community town hall were developed and implemented. All providers who participated in doxyPEP trainings were surveyed as well as patients with evidence of a doxyPEP discussion during a clinic encounter who were retrospectively identified via chart review. Results: Between rollout and September 3, 2024, there were 3770 doxyPEP prescriptions. Among 45 providers, the median score of comfort having conversations about doxyPEP increased from 78 (interquartile range, 52-100) out of 100 after the second training to 100 (interquartile range, 88-100) after the third training. Of 150 patient responses, 90 (60.0%) were from individuals prescribed doxyPEP; reasons for use included sex with a random partner (65.6%) and condomless anal intercourse (63.3%). Among 60 patients not prescribed doxyPEP, 25 (41.7%) reported they did not feel it was warranted due to low perceived risk. Eleven (18.3%) reported they felt the risks outweighed the benefits. Conclusion: Without national guidelines, the uptake of doxyPEP was robust, supported by electronic support tools and provider training sessions for clinicians, as well as community engagement efforts. Differences in risk perception were important factors in the choice to use doxyPEP.
Jenness SM, Knowlton G, Smith DK, Marcus JL, Anderson EJ, Siegler AJ, Jones J, Sullivan PS, Enns E. A Decision Analytics Model to Optimize Investment in Interventions Targeting the HIV PrEP Cascade of Care. AIDS. 2021; 35(9): 1479–89.
Abstract. Objectives: Gaps between recommended and actual levels of HIV preexposure prophylaxis (PrEP) use remain among MSM. Interventions can address these gaps but it is unknown how public health initiatives should invest prevention funds into these interventions to maximize their population impact. Design: We used a stochastic network-based HIV transmission model for MSM in the Atlanta area paired with an economic budget optimization model. Methods: The model simulated MSM participating in up to three real-world PrEP cascade interventions designed to improve initiation, adherence, or persistence. The primary outcome was infections averted over 10 years. The budget optimization model identified the investment combination under different budgets that maximized this outcome, given intervention costs from a payer perspective. Results: From the base 15% PrEP coverage level, the three interventions could increase coverage to 27%, resulting in 12.3% of infections averted over 10 years. Uptake of each intervention was interdependent: maximal use of the adherence and persistence interventions depended on new PrEP users generated by the initiation intervention. As the budget increased, optimal investment involved a mixture of the initiation and persistence interventions but not the adherence intervention. If adherence intervention costs were halved, the optimal investment was roughly equal across interventions. Conclusion: Investments into the PrEP cascade through initiatives should account for the interactions of the interventions as they are collectively deployed. Given current intervention efficacy estimates, the total population impact of each intervention may be improved with greater total budgets or reduced intervention costs.
Jenness SM, Maloney K, Smith SK, Hoover KW, Rosenberg ES, Goodreau SM, Weiss KM, Liu AY, Rao D, Sullivan PS. Addressing Gaps in HIV Preexposure Prophylaxis Care to Reduce Racial Disparities in HIV Incidence in the United States. American Journal of Epidemiology. 2019; 188(4): 743–752.
Abstract. The potential for human immunodeficiency virus (HIV) preexposure prophylaxis (PrEP) to reduce the racial disparities in HIV incidence in the United States might be limited by racial gaps in PrEP care. We used a network-based mathematical model of HIV transmission for younger black and white men who have sex with men (BMSM and WMSM) in the Atlanta, Georgia, area to evaluate how race-stratified transitions through the PrEP care continuum from initiation to adherence and retention could affect HIV incidence overall and disparities in incidence between races, using current empirical estimates of BMSM continuum parameters. Relative to a no-PrEP scenario, implementing PrEP according to observed BMSM parameters was projected to yield a 23% decline in HIV incidence (hazard ratio = 0.77) among BMSM at year 10. The racial disparity in incidence in this observed scenario was 4.95 per 100 person-years at risk (PYAR), a 19% decline from the 6.08 per 100 PYAR disparity in the no-PrEP scenario. If BMSM parameters were increased to WMSM values, incidence would decline by 47% (hazard ratio = 0.53), with an associated disparity of 3.30 per 100 PYAR (a 46% decline in the disparity). PrEP could simultaneously lower HIV incidence overall and reduce racial disparities despite current gaps in PrEP care. Interventions addressing these gaps will be needed to substantially decrease disparities.
Goodreau SM, Rosenberg ES, Jenness SM, Luisi N, Stansfield SE, Millett G, Sullivan P. Sources of Racial Disparities in HIV Prevalence in Men Who Have Sex with Men in Atlanta, GA: A Modeling Study. Lancet HIV. 2017; 4(7): e311–e320.
Abstract. In the USA, men who have sex men (MSM) are at high risk for HIV, and black MSM have a substantially higher prevalence of infection than white MSM. We created a simulation model to assess the strength of existing hypotheses and data that account for these disparities. Methods. We built a dynamic, stochastic, agent-based network model of black and white MSM aged 18-39 years in Atlanta, GA, USA, that incorporated race-specific individual and dyadic-level prevention and risk behaviours, network attributes, and care patterns. We estimated parameters from two Atlanta-based studies in this population (n=1117), supplemented by other published work. We modelled the ability for racial assortativity to generate or sustain disparities in the prevalence of HIV infection, alone or in conjunction with scenarios of observed racial patterns in behavioural, care, and susceptibility parameters. Findings. Race-assortative mixing alone could not sustain a pre-existing disparity in prevalence of HIV between black and white MSM. Differences in care cascade, stigma-related behaviours, and CCR5 genotype each contributed substantially to the disparity (explaining 10·0%, 12·7%, and 19·1% of the disparity, respectively), but nearly half (44·5%) could not be explained by the factors investigated. A scenario assessing race-specific reporting differences in risk behaviour was the only one to yield a prevalence in black MSM (44·1%) similar to that observed (43·4%). Interpretation. Racial assortativity is an inadequate explanation for observed disparities. Work to close the gap in the care cascade by race is imperative, as are efforts to increase serodiscussion and strengthen relationships among black MSM particularly. Further work is urgently needed to identify other sources of, and pathways for, this disparity, to integrate concomitant epidemics into models, and to understand reasons for racial differences in behavioural reporting.
Jenness SM, Goodreau SM, Rosenberg E, Beylerian EN, Hoover KW, Smith DK, Sullivan PS. Impact of CDC’s HIV Pre-Exposure Prophylaxis Guidelines among MSM in the United States. Journal of Infectious Diseases. 2016; 214(12): 1800–1807.
Abstract. Preexposure prophylaxis (PrEP) is effective for preventing human immunodeficiency virus (HIV) infection among men who have sex with men (MSM) within trial settings. Population impact will depend on clinical indications for PrEP initiation, coverage levels, and drug adherence. No modeling studies have estimated the impact of clinical practice guidelines for PrEP issued by the Centers for Disease Control and Prevention (CDC). Methods. Mathematical models of HIV transmission among MSM were used to estimate the percentage of infections averted (PIA) and the number needed to treat (NNT) under behavioral indications of the CDC’s PrEP guidelines. We modeled the contribution of these indications while varying treatment coverage and adherence. Results. At 40% coverage of indicated MSM over the next decade, application of CDC guidelines would avert 1162 infections per 100 000 person-years, 33.0% of expected infections. The predicted NNT for the guidelines would be 25. Increasing coverage and adherence jointly raise the PIA, but reductions to the NNT were associated with better adherence only. Conclusions. Implementation of CDC PrEP guidelines would result in strong and sustained reductions in HIV incidence among MSM in the United States. The guidelines strike a good balance between epidemiological impact (PIA) and efficiency (NNT) at plausible scale-up levels. Adherence counseling could maximize public health investment in PrEP by decreasing the NNT. Shiny Web App
STI Epidemiology and Doxy-PEP
Research on the epidemiology and prevention of bacterial sexually transmitted infections (gonorrhea, chlamydia, syphilis) among key populations. Work ranges from cost-effectiveness of doxycycline post-exposure prophylaxis (STIRRUP), to expedited partner therapy modeling, to the interaction between HIV PrEP uptake and bacterial STI incidence.
Representative publications
Traeger MW, Leyden WA, Volk JE, Silverberg MJ, Horberg MA, Davis TL, Mayer KH, Krakower DS, Young JG, Jenness SM, Marcus JL. Doxycycline Postexposure Prophylaxis and Bacterial Sexually Transmitted Infections Among Individuals Using HIV Preexposure Prophylaxis. JAMA Internal Medicine. 2025; 185(3): 273–281.
Abstract. Background: Doxycycline postexposure prophylaxis (doxyPEP) is a promising strategy to prevent bacterial sexually transmitted infections. Limited data exist evaluating patient and provider experiences since doxyPEP has become widely available. We aimed to explore such factors among providers and patients during real-world implementation within one community health center. Methods: Doxycycline postexposure prophylaxis was rolled out at Fenway Health on February 2, 2023. To support rollout, electronic health record tools, 3 provider training sessions, and a community town hall were developed and implemented. All providers who participated in doxyPEP trainings were surveyed as well as patients with evidence of a doxyPEP discussion during a clinic encounter who were retrospectively identified via chart review. Results: Between rollout and September 3, 2024, there were 3770 doxyPEP prescriptions. Among 45 providers, the median score of comfort having conversations about doxyPEP increased from 78 (interquartile range, 52-100) out of 100 after the second training to 100 (interquartile range, 88-100) after the third training. Of 150 patient responses, 90 (60.0%) were from individuals prescribed doxyPEP; reasons for use included sex with a random partner (65.6%) and condomless anal intercourse (63.3%). Among 60 patients not prescribed doxyPEP, 25 (41.7%) reported they did not feel it was warranted due to low perceived risk. Eleven (18.3%) reported they felt the risks outweighed the benefits. Conclusion: Without national guidelines, the uptake of doxyPEP was robust, supported by electronic support tools and provider training sessions for clinicians, as well as community engagement efforts. Differences in risk perception were important factors in the choice to use doxyPEP.
Chandra CL, Weiss KM, Kelley CF, Marcus JL, Jenness SM. Gaps in Screening of Sexually Transmitted Infections among Men Who Have Sex with Men during PrEP Care in the United States. Clinical Infectious Diseases. 2021; 73(7): e2261–69.
Abstract. The U.S. Centers for Disease Control and Prevention (CDC) recommends comprehensive sexually transmitted infection (STI) screening every 3-6 months for men who have sex with men (MSM) using HIV preexposure prophylaxis (PrEP). The gaps between these recommendations and clinical practice by region have not been quantified. Methods. We used survey data collected from the internet-based ARTnet study between 2017 and 2019 on STI screening among MSM across the U.S., stratified by current, prior, and never PrEP use. Poisson regression models with robust error variance were used to model factors, including residence in the Southeast, associated with consistent (“always” or “sometimes”) exposure site-specific STI screening during PrEP care. Results. Of 3259 HIV-negative MSM, 19% were currently using PrEP, 6% had used PrEP in the past, and 75% had never used PrEP. Among ever PrEP users, 87%, 78%, 57%, and 64% reported consistent screening for STIs by blood sample, urine sample or urethral swab, rectal swab, or pharyngeal swab, respectively, during PrEP care. Compared to PrEP users in all other regions, PrEP users in the Southeast were significantly less likely to be consistently screened for urogenital (adjusted prevalence ratio [aPR], 0.86; 95% confidence interval [CI], 0.76-0.98) and rectal STIs (aPR, 0.76; 95% CI, 0.62-0.93) during PrEP care. Conclusions. Substantial gaps exist between CDC recommendations for STI screening during PrEP care and current clinical practice, particularly for rectal and pharyngeal exposure sites that can harbor asymptomatic infections and for MSM in Southeast states where the STI burden is substantial.
Jenness SM, Weiss KM, Prasad P, Zlotorzynska M, Sanchez T. Bacterial STI Screening Rates by Symptomatic Status among Men Who Have Sex with Men in the United States: A Hierarchical Bayesian Analysis. Sexually Transmitted Diseases. 2019; 46(1): 25–30.
Abstract. Prevention of bacterial sexually transmitted infections (STIs) among men who have sex with men (MSM) requires timely disease detection, but this is complicated by asymptomatic infection. We estimated screening/testing rates by symptomatic status to evaluate adherence to Centers for Disease Control and Prevention STI screening guidelines. Methods. In a cross-sectional study of 2572 US MSM aged 15 to 65 years in 2017 to 2018, we measured the reported number of asymptomatic STI screens in the past 2 years versus tests prompted by disease symptoms. Using negative binominal regression within a hierarchical Bayesian framework, we estimated yearly rates of asymptomatic screening and symptomatic testing by geographic, demographic, and behavioral factors. Results. Human immunodeficiency virus (HIV) status was most strongly associated with all testing/screening frequency (incidence rate ratio [IRR], 1.72; 95% credible interval [Crl], 1.49, 1.97). The HIV-uninfected MSM had 0.14 (95% credible interval [CrI], 0.12-0.17) symptomatic tests and 0.88 (95% CrI, 0.77-1.01) asymptomatic screens per year. The HIV-infected MSM had 0.25 (95% CrI, 0.18-0.35) symptomatic tests and 1.53 (95% CrI, 1.24-1.88) asymptomatic screens per year. Rates of asymptomatic screening were higher among black compared with white MSM (IRR, 1.41; 95% CrI, 1.15-1.73), but weakly associated with number of past-year sexual partners (IRR, 1.01; 95% CrI, 1.00-1.01). Overall, 85% to 90% of diagnostic events were asymptomatic screens. Conclusions. Self-reported rates of STI screening were close to Centers for Disease Control and Prevention’s recommended overall annual screening frequency, but with gaps defined by demographics and behavioral risk. Targeted screening efforts may be indicated specifically for younger MSM and those with multiple partners. Shiny Web App
Jenness SM, Weiss KM, Goodreau SM, Rosenberg E, Gift T, Chesson H, Hoover KW, Smith DK, Liu AY, Sullivan P. Incidence of Gonorrhea and Chlamydia Following HIV Preexposure Prophylaxis among Men Who Have Sex with Men. Clinical Infectious Diseases. 2017; 65(5): 712–18.
Abstract. Preexposure prophylaxis (PrEP) is highly effective for preventing human immunodeficiency virus (HIV) infection, but risk compensation (RC) in men who have sex with men (MSM) raises concerns about increased sexually transmitted infections (STIs). The Center for Disease Control and Prevention’s (CDC’s) PrEP guidelines recommend biannual STI screening, which may reduce incidence by treating STIs that would otherwise remain undiagnosed. We investigated these two counteracting phenomena. Methods. With a network-based mathematical model of HIV, Neisseria gonorrhoeae (NG), and Chlamydia trachomatis (CT) transmission dynamics among MSM in the United States, we simulated PrEP uptake following the prescription indications and HIV/STI screening recommendations in the CDC guidelines. Scenarios varied PrEP coverage (the proportion of MSM indicated for PrEP who received it), RC (a reduction in the per-act probability of condom use), and the STI screening interval. Results. In our reference scenario (40% coverage, 40% RC), 42% of NG and 40% of CT infections would be averted over the next decade. A doubling of RC would still result in net STI prevention relative to no PrEP. STIs declined because PrEP-related STI screening resulted in a 17% and 16% absolute increase in the treatment of asymptomatic and rectal STIs, respectively. Screening and timely treatment at quarterly vs biannual intervals would reduce STI incidence an additional 50%. Conclusions. Implementation of the CDC PrEP guidelines while scaling up PrEP coverage could result in a significant decline in STI incidence among MSM. Our study highlights the design of PrEP not only as antiretroviral medication but as combination HIV/STI prevention incorporating STI screening.
Respiratory Infectious Diseases
Network-based and compartmental models for respiratory pathogens, including SARS-CoV-2, influenza, and tuberculosis. Projects have examined university campuses, cruise ships, workplaces, urban jails, and household transmission in low-resource settings. Collaborative work on drug-resistant TB transmission in KwaZulu-Natal, South Africa (CONTEXT study) integrates geospatial, genomic, and social network data to characterize the contributions of casual contact and migration to XDR-TB transmission.
Representative publications
Nelson KN, Kiti MC, Shiiba M, Sacoor C, Bardají A, Macicame I, Jamisse E, Tchavana C, José A, Cavele N, Maldonado H, Jarquin C, Ajsivinac HM, Samuel P, Srinivasan R, Kazi M, Allana R, Kim SS, Prasad PV, Chen D, Liu C, Jenness SM, Ahmed N, Aguolu O, Sundaram MA, Yildirim I, Malik F, Melegaro A, Lopman BA, Omer SB. Characterizing Social Behavior Relevant for Infectious Disease Transmission in Four Low- and Middle-Income Countries, 2021–2023. Nature Communications. 2025; 16(1): 9586.
Abstract. Background: Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), a bacterium which is transmitted through the air. Close, sustained contact can lead to transmission of Mtb, but evidence also shows that transmission occurs also in community settings through more transient contact. However, social patterns that influence Mtb transmission, and locations that are most central to spread, are likely different by setting. Methods: We use data from the GlobalMix study, which characterized social behavior across four countries, to evaluate differences in age-sex patterning and locations of contact across four moderate- to high-TB burden countries. Healthy individuals self-completed a survey about their daily person-to-person interactions and locations in which they spent time. To capture the Mtb exposure profile of participants, we calculated daily exposure-hours from household contacts, close non-household contacts, and casual contacts, stratified by contact age and sex, and weighted by country-, age-, and sex-specific tuberculosis incidence estimates. Results: The most prominent shifts in the profile of exposure occur at entry to primary school (5-9 years) and early adulthood (20-29 years). Community locations varied in their relative importance as locations of transmission by country and age group, with school most important in India and Guatemala, transit more important in Pakistan, and others’ homes most important in Mozambique. Conclusions: Our findings demonstrate that locations of community transmission are likely varied across settings, underscoring the importance of interventions designed specifically for the communities in which they will be implemented.
Jenness SM, Wallrafen-Sam K, Schneider I, Kennedy S, Akiyama MJ, Spaulding AC. Dynamic Contact Networks of Residents of an Urban Jail in the Era of SARS-CoV-2. Epidemics. 2024; 47: 100772.
Abstract. Background: In custodial settings such as jails and prisons, infectious disease transmission is heightened by factors such as overcrowding and limited healthcare access. Specific features of social contact networks within these settings have not been sufficiently characterized, especially in the context of a large-scale respiratory infectious disease outbreak. The study aims to quantify contact network dynamics within the Fulton County Jail in Atlanta, Georgia. Methods: Jail roster data were utilized to construct social contact networks. Rosters included resident details, cell locations, and demographic information. This analysis involved 6702 male residents over 140,901 person days. Network statistics, including degree, mixing, and dissolution (movement within and out of the jail) rates, were assessed. We compared outcomes for two distinct periods (January 2022 and April 2022) to understand potential responses in network structures during and after the SARS-CoV-2 Omicron variant peak. Results: We found high cross-sectional network degree at both cell and block levels. While mean degree increased with age, older residents exhibited lower degree during the Omicron peak. Block-level networks demonstrated higher mean degrees than cell-level networks. Cumulative degree distributions increased from January to April, indicating heightened contacts after the outbreak. Assortative age mixing was strong, especially for younger residents. Dynamic network statistics illustrated increased degrees over time, emphasizing the potential for disease spread. Conclusions: Despite some reduction in network characteristics during the Omicron peak, the contact networks within the Fulton County Jail presented ideal conditions for infectious disease transmission. Age-specific mixing patterns suggested unintentional age segregation, potentially limiting disease spread to older residents. This study underscores the necessity for ongoing monitoring of contact networks in carceral settings and provides valuable insights for epidemic modeling and intervention strategies, including quarantine, depopulation, and vaccination, laying a foundation for understanding disease dynamics in such environments.Top of Form.
Jenness SM, Willebrand KS, Malik AA, Lopman BA, Omer S. Dynamic Network Strategies for SARS-CoV-2 Control on a Cruise Ship. Epidemics. 2021; 37: 100488.
Abstract. SARS-CoV-2 outbreaks have occurred on several nautical vessels, driven by the high-density contact networks on these ships. Optimal strategies for prevention and control that account for realistic contact networks are needed. We developed a network-based transmission model for SARS-CoV-2 on the Diamond Princess outbreak to characterize transmission dynamics and to estimate the epidemiological impact of outbreak control and prevention measures. This model represented the dynamic multi-layer network structure of passenger-passenger, passenger-crew, and crew-crew contacts, both before and after the large-scale network lockdown imposed on the ship in response to the disease outbreak. Model scenarios evaluated variations in the timing of the network lockdown, reduction in contact intensity within the sub-networks, and diagnosis-based case isolation on outbreak prevention. We found that only extreme restrictions in contact patterns during network lockdown and idealistic clinical response scenarios could avert a major COVID-19 outbreak. Contact network changes associated with adequate outbreak prevention were the restriction of passengers to their cabins, with limited passenger-crew contacts. Clinical response strategies required for outbreak prevention may be infeasible in many cruise settings: early mass screening with an ideal PCR test (100 % sensitivity) and immediate case isolation upon diagnosis. Personal protective equipment (e.g., facemasks) had limited impact in this environment because the majority of transmissions after the ship lockdown occurred between passengers in cabins where masks were not consistently used. Public health restrictions on optional leisure activities like these should be considered until longer-term effective solutions such as a COVID-19 vaccine become widely available.
Lopman B, Liu CY, Le Guillou A, Handel A, Lash TL, Isakov AP, Jenness SM. A Model of COVID-19 Transmission and Control on University Campuses. Scientific Reports. 2021; 11(1): 5900.
Abstract. Serological testing remains a passive component of the public health response to the COVID-19 pandemic. Using a transmission model, we examine how serological testing could have enabled seropositive individuals to increase their relative levels of social interaction while offsetting transmission risks. We simulate widespread serological testing in New York City, South Florida, and Washington Puget Sound and assume seropositive individuals partially restore their social contacts. Compared to no intervention, our model suggests that widespread serological testing starting in late 2020 would have averted approximately 3300 deaths in New York City, 1400 deaths in South Florida and 11,000 deaths in Washington State by June 2021. In all sites, serological testing blunted subsequent waves of transmission. Findings demonstrate the potential benefit of widespread serological testing, had it been implemented in the pre-vaccine era, and remain relevant now amid the potential for emergence of new variants.
Nelson KN, Gandhi NR, Mathema B, Lopman BA, Brust JC, Auld SC, Ismail N, Omar SV, Brown RS, Allana S, Campbell A, Moodley P, Mlisana K, Shah NS, Jenness SM. Modeling Missing Cases and Transmission Links in Networks of Extensively Drug-Resistant Tuberculosis in KwaZulu-Natal, South Africa. American Journal of Epidemiology. 2020; 189(7): 735–745.
Abstract. Patterns of transmission of drug-resistant tuberculosis (TB) remain poorly understood, despite over half a million incident cases worldwide in 2017. Modeling TB transmission networks can provide insight into drivers of transmission, but incomplete sampling of TB cases can pose challenges for inference from individual epidemiologic and molecular data. We assessed the effect of missing cases on a transmission network inferred from Mycobacterium tuberculosis sequencing data on extensively drug-resistant TB cases in KwaZulu-Natal, South Africa, diagnosed in 2011-2014. We tested scenarios in which cases were missing at random, missing differentially by clinical characteristics, or missing differentially by transmission (i.e., cases with many links were under- or oversampled). Under the assumption that cases were missing randomly, the mean number of transmissions per case in the complete network needed to be larger than 20, far higher than expected, to reproduce the observed network. Instead, the most likely scenario involved undersampling of high-transmitting cases, and models provided evidence for super-spreading. To our knowledge, this is the first analysis to have assessed support for different mechanisms of missingness in a TB transmission study, but our results are subject to the distributional assumptions of the network models we used. Transmission studies should consider the potential biases introduced by incomplete sampling and identify host, pathogen, or environmental factors driving super-spreading.