Stephen M Kissler's research while affiliated with University of Colorado Boulder and other places
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Publications (66)
Background
To allow time for production, seasonal influenza vaccine target strains must be chosen up to 8 months before the start of the influenza season. Antigenic drift during these months can lead to mismatch between the circulating and vaccine strains, negatively impacting vaccine effectiveness (VE). mRNA vaccines can be produced more quickly t...
Background
Rapid identification of new SARS-CoV-2 variants is a critical component of the public health response to the COVID-19 pandemic. However, we lack a quantitative framework to assess the expected performance of sampling strategies in varying epidemic contexts.
Methods
To address this gap, we used a multi-patch stochastic model of SARS-CoV-...
Background
Pharyngitis caused by group A Streptococcus (GAS) drives many outpatient pharyngitis visits and antibiotic prescriptions in the US and can have serious post-infection immunological sequelae. Like many other upper respiratory infections, GAS pharyngitis burden is usually highest in the winter. However, compared to other common illnesses s...
Background
An estimated 65% of the US population had at least two SARS-CoV-2 infections by November 2022, but the impact of prior infection on disease course in subsequent infections has been debated. Population-level studies can yield conflicting results due to biases that arise from differences in differences in infection history, vaccination sta...
Background
Group A Streptococcus (GAS) causes an estimated 5.2 million outpatient visits for pharyngitis annually in the United States (U.S.) with incidence peaking in winter, but the annual spatiotemporal pattern of GAS pharyngitis across the U.S. is poorly characterized.
Methods
We used outpatient claims data from individuals with private medical...
Receipt of antibiotics per capita vary dramatically across regions in the United States, but the relative importance in prescribing practices versus per capita visit rates in driving this variation remain unclear. Quantifying their relative importance can aid in reducing antibiotic use. Using US medical claims data from 2015-2018 covering over 15 m...
The impact of a prior SARS-CoV-2 infection on the progression of subsequent infections has been unclear. Using a convenience sample of 94,812 longitudinal RT-qPCR measurements from anterior nares and oropharyngeal swabs, we identified 71 individuals with two well-sampled SARS-CoV-2 infections between March 11th, 2020, and July 28th, 2022. We compar...
Public health surveillance for pathogens presents an optimization problem: we require enough sampling to identify intervention-triggering shifts in pathogen epidemiology, such as new introductions or sudden increases in prevalence, but not so much that costs due to surveillance itself outweigh those from pathogen-associated illness. To determine th...
Rapid identification of new SARS-CoV-2 variants is a critical component of the public health response to the COVID-19 pandemic. However, we lack a quantitative framework to assess the expected performance of sampling strategies in varying epidemic contexts. To address this gap, we used a multi-patch stochastic model of SARS-CoV-2 spread in New York...
Drug addiction, a phenomenon where cancer cells paradoxically depend on continuous drug treatment for survival, has uncovered cell signaling mechanisms and cancer codependencies. Here we discover mutations that confer drug addiction to inhibitors of the transcriptional repressor polycomb repressive complex 2 (PRC2) in diffuse large B-cell lymphoma....
The impact of a prior SARS-CoV-2 infection on the progression of subsequent infections has been unclear. Using a convenience sample of 94,812 longitudinal RT-qPCR measurements from anterior nares and oropharyngeal swabs, we compared the SARS-CoV-2 viral kinetics of first vs. second infections, adjusting for viral variant, vaccination status, and ag...
SARS-CoV-2 antibody titers may serve as a correlate for immunity and could inform optimal booster timing. The relationship between antibody titer and protection from infection was evaluated in 2,323 vaccinated individuals from the National Basketball Association who had antibody levels measured from 9/12/2021 to 12/31/2021. Cox-proportional hazards...
Background: The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear.
Methods: We characterized 1,280 infections from the National Basketball Association occupational health cohort identified between June 2020 and January 2022 using serial RT-qPCR testing. Logistic regression and semi-mechanistic...
Mathematical models help predict and manage the course of pandemics
Background:
In the United States, children under age 5 receive high volumes of antibiotics, which may contribute to antibiotic resistance. It has been unclear what role preventable illnesses and chronic comorbidities play in prompting antibiotic prescriptions.
Methods:
We conducted an observational study with a cohort of 124,759 children under a...
Social gatherings can be an important locus of transmission for many pathogens including SARS-CoV-2. During an outbreak, restricting the size of these gatherings is one of several non-pharmaceutical interventions available to policy-makers to reduce transmission. Often these restrictions take the form of prohibitions on gatherings above a certain s...
Drug addiction, a phenomenon where cancer cells paradoxically depend on continuous drug treatment for survival, has uncovered cell signaling mechanisms and cancer co-dependencies. Here, we discover mutations that confer drug addiction to inhibitors of the transcriptional repressor Polycomb Repressive Complex 2 (PRC2) in diffuse large B-cell lymphom...
A consensus methodology for the pharmacometric assessment of candidate SARS-CoV-2 antiviral drugs would be useful for comparing trial results and improving trial design. The time to viral clearance, assessed by serial qPCR of nasopharyngeal swab samples, has been the most widely reported measure of virological response in clinical trials, but it ha...
A key issue distinguishing prominent evolutionary models of human life history is whether prolonged childhood evolved to facilitate learning in a skill- and strength-intensive foraging niche requiring high levels of cooperation. Considering the diversity of environments humans inhabit, children’s activities should also reflect local social and ecol...
Cancer mutations in Polycomb Repressive Complex 2 (PRC2) drive aberrant epigenetic states. Although therapies inhibiting the PRC2 enzymatic component EZH2 are FDA-approved, oncogene-specific dependencies remain to be discovered. Here, we identify mutations that confer both resistance and drug addiction to PRC2 inhibitors in EZH2-mutant lymphoma, re...
Understanding how antibiotic use drives resistance is crucial for guiding effective strategies to limit the spread of resistance, but the use–resistance relationship across pathogens and antibiotics remains unclear. We applied sinusoidal models to evaluate the seasonal use–resistance relationship across 3 species ( Staphylococcus aureus , Escherich...
Background. The Omicron SARS-CoV-2 variant is responsible for a major wave of COVID-19, with record case counts reflecting high transmissibility and escape from prior immunity. Defining the time course of Omicron viral proliferation and clearance is crucial to inform isolation protocols aiming to minimize disease spread.
Methods. We obtained longit...
Social gatherings can be an important locus of transmission for many pathogens including SARS-CoV-2. During an outbreak, restricting the size of these gatherings is one of several non-pharmaceutical interventions available to policy-makers to reduce transmission. Often these restrictions take the form of prohibitions on gatherings above a certain s...
Antibiotic prescribing rates vary by patient race/ethnicity, with whites more likely to receive antibiotics and broader-spectrum antibiotics. However, the drivers of this disparity, and to what extent it represents antibiotic overuse or underprescribing of appropriate antibiotic treatment, remains unclear. Here, we investigate how antibiotic prescr...
Objectives. To inform efforts to reduce pediatric antibiotic use, we measured cumulative pediatric prescriptions for antibiotics and non-antibiotics and how this varies across geography and patient subgroups.
Design. Observational study.
Setting. United States, 2008-2018.
Participants. 207,814 children under age 5 born in the United States between...
Understanding how socioecology affects contemporary children’s learning and work opportunities can help researchers better model the selection pressures which have shaped the evolution of human life history and social organization. Here, we compiled a global time allocation dataset for children and adolescents from hunter-gatherer and mixed-subsist...
In 2020, life expectancy in the United States decreased by an estimated 1.5 years. Due to mortality displacement during the COVID-19 pandemic, life expectancy could soon rebound to above its pre-pandemic baseline. We estimated the size and duration of this artificial rise in life expectancy through 2030. We found that this rebound could persist for...
This paper offers projections of future transmission dynamics for SARS-CoV-2 in an SEIRS model with demographics and waning immunity. In a stylized optimal control setting calibrated to the United States, we show that the disease is endemic in steady state and that its dynamics are characterized by damped oscillations. The magnitude of the oscillat...
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quan...
Background: The impact of variable infection risk by race and ethnicity on the dynamics of SARS CoV-2 spread is largely unknown.
Methods: Here, we fit structured compartmental models to seroprevalence data from New York State and analyze how herd immunity thresholds (HITs), final sizes, and epidemic risk changes across groups.
Results: A simple mod...
Background
Reducing geographic disparities in antibiotic prescribing is a central public health priority to combat antibiotic resistance, but the drivers of this variation have been unclear.
Methods
We measured how variation in outpatient visit rates (‘observed disease’) and antibiotic prescribing rates per visit (‘prescribing practices’) each con...
We estimated the fraction of antibiotic prescribing in the US attributable to gonorrhea. Gonorrhea contributes to an outsized proportion of antibiotic prescriptions in young adults, males, and in the southern and western US. A gonococcal vaccine could substantially reduce antibiotic prescribing in these populations.
Establishing how many people have been infected by SARS-CoV-2 remains an urgent priority for controlling the COVID-19 pandemic. Serological tests that identify past infection can be used to estimate cumulative incidence, but the relative accuracy and robustness of various sampling strategies has been unclear. We developed a flexible framework that...
We present human mobility data for the United Kingdom collected from the "BBC Pandemic", a public science project linked to the BBC Four television documentary of the same name. Mobile phone GPS trajectories submitted by users and collected over a 24 hour period were aggregated to construct anonymised origin-destination flux matrices at the local a...
Background
The alpha and delta SARS-CoV-2 variants have been responsible for major recent waves of COVID-19 despite increasing vaccination rates. The reasons for the increased transmissibility of these variants and for the reduced transmissibility of vaccine breakthrough infections are unclear.
Methods
We quantified the course of viral proliferati...
Vaccine prioritization
There is likely to be high demand for the limited supplies of vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), so how should vaccine distribution be prioritized? Bubar et al. modeled across countries how uncertainty about a vaccine's characteristics affects prioritization strategies for reducing d...
There is no agreed methodology for pharmacometric assessment of candidate antiviral drugs in COVID-19. The most widely used measure of virological response in clinical trials so far is the time to viral clearance assessed by qPCR of viral nucleic acid in eluates from serial nasopharyngeal swabs. We posited that the rate of viral clearance would hav...
Background
Antibiotic use is an important driver of antibiotic resistance. Previous studies have shown that this relationship is detectable on a seasonal timescale, where seasonally cycling antibiotic prescribing corresponds with cycling levels of resistance. Here, we evaluated the seasonal relationship between antibiotic use and resistance across...
Background
Understanding how antibiotic use drives resistance is crucial for guiding effective strategies to limit the spread of resistance, but the use-resistance relationship across pathogens and antibiotics remains unclear.
Methods
We applied sinusoidal models to evaluate the seasonal use-resistance relationship across 3 species ( Staphylococcu...
We estimated the fraction of antibiotic prescribing in the US attributable to gonorrhea. Gonorrhea contributes to an outsized proportion of antibiotic prescriptions in young adults, males, and in the southern and western US. A gonococcal vaccine could substantially reduce antibiotic prescribing in these populations.
Background
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening.
Methods
We used prospecti...
SARS-CoV-2-related mortality and hospitalizations differ substantially between New York City neighborhoods. Mitigation efforts require knowing the extent to which these disparities reflect differences in prevalence and understanding the associated drivers. Here, we report the prevalence of SARS-CoV-2 in New York City boroughs inferred using tests a...
When a vaccine for COVID-19 becomes available, limited initial supply will raise the question of how to prioritize the available doses and thus underscores the need for transparent, evidence-based strategies that relate knowledge of, and uncertainty in, disease transmission, risk, vaccine efficacy, and existing population immunity. Here, we employ...
Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require survei...
Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require survei...
BACKGROUND: The isolation of symptomatic cases and tracing of contacts has been used as an early COVID-19 containment measure in many countries, with additional physical distancing measures also introduced as outbreaks have grown. To maintain control of infection while also reducing disruption to populations, there is a need to understand what comb...
Background
The isolation of symptomatic cases and tracing of contacts has been used as an early COVID-19 containment measure in many countries, with additional physical distancing measures also introduced as outbreaks have grown. To maintain control of infection while also reducing disruption to populations, there is a need to understand what combi...
Case isolation and contact tracing can contribute to the control of COVID-19 outbreaks. However, it remains unclear how real-world networks could influence the effectiveness and efficiency of such approaches. To address this issue, we simulated control strategies for SARS-CoV-2 in a real-world social network generated from high resolution GPS data....
Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require survei...
Importance. Reducing geographic disparities in antibiotic prescribing is a central public health priority to combat antibiotic resistance, but the drivers of this variation have been unclear. Objective. To measure how differences in outpatient visit rates per 1,000 individuals ('observed disease') and in antibiotic prescribing rates per outpatient...
Background
Isolation of symptomatic cases and tracing of contacts has been used as an early COVID-19 containment measure in many countries, with additional physical distancing measures also introduced as outbreaks have grown. To maintain control of infection while also reducing disruption to populations, there is a need to understand what combinati...
Establishing how many people have already been infected by SARS-CoV-2 is an urgent priority for controlling the COVID-19 pandemic. Patchy virological testing has hampered interpretation of confirmed case counts, and unknown rates of asymptomatic and mild infections make it challenging to develop evidence-based public health policies. Serological te...
What happens next?
Four months into the severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) outbreak, we still do not know enough about postrecovery immune protection and environmental and seasonal influences on transmission to predict transmission dynamics accurately. However, we do know that humans are seasonally afflicted by other, less...
The SARS-CoV-2 pandemic is straining healthcare resources worldwide, prompting social distancing measures to reduce transmission intensity. The amount of social distancing needed to curb the SARS-CoV-2 epidemic in the context of seasonally varying transmission remains unclear. Using a mathematical model, we assessed that one-time interventions will...
Existing methods to infer the relative roles of age groups in epidemic transmission can normally only accommodate a few age classes, and/or require data that are highly specific for the disease being studied. Here, symbolic transfer entropy (STE), a measure developed to identify asymmetric transfer of information between stochastic processes, is pr...
Background:
The mechanisms driving the recent decline in outpatient antibiotic prescribing are unknown. We estimated the extent to which reductions in the number of antibiotic prescriptions filled per outpatient visit (stewardship) and reductions in the monthly rate of outpatient visits (observed disease) for infectious disease conditions each con...
There is an urgent need to project how transmission of the novel betacoronavirus SARS-CoV-2 will unfold in coming years. These dynamics will depend on seasonality, the duration of immunity, and the strength of cross-immunity to/from the other human coronaviruses. Using data from the United States, we measured how these factors affect transmission o...
Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate and ineffective antibiotic use. However, because such assays infer resistance phenotypes based on the presence or absence of known genetic markers, their utility will wane in response to the emergence of novel resistance...
Importance: The mechanisms driving the recent decline in outpatient antibiotic prescribing are unknown.
Objective: To estimate the extent to which reductions in the number of antibiotic prescriptions filled per outpatient visit (stewardship) and reductions in the monthly rate of outpatient visits (observed disease) for infectious disease conditions...
The sensitivity of genotype-based diagnostics that predict antimicrobial susceptibility is limited by the extent to which they detect genes and alleles that lead to resistance. As novel resistance variants are expected to emerge, such sensitivity is expected to decline unless the new variants are detected and incorporated into the diagnostic. Here,...
A bstract
Existing methods to infer the relative roles of age groups in epidemic transmission can normally only accommodate a few age classes, and/or require data that are highly specific for the disease being studied. Here, symbolic transfer entropy (STE), a measure developed to identify asymmetric transfer of information between stochastic proces...
Teaching is cross-culturally widespread but few studies have considered children as teachers as well as learners. This is surprising, since forager children spend much of their time playing and foraging in child-only groups, and thus, have access to many potential child teachers. Using the Social Relations Model, we examined the prevalence of child...
Diagnostics that minimize the time to selection of an appropriate antibiotic treatment represent an important strategy in addressing the challenge of antimicrobial resistance (AMR). Among this class of diagnostics, the use of pathogen genotype to predict AMR phenotype has been facilitated by advances in rapid sequencing platforms. A longstanding ob...
The nexus of mobile technology, mass media, and public engagement is opening new opportunities for research into the human behaviours relevant to the spread of disease. On 22 March 2018, the British Broadcasting Corporation (BBC) released the documentary "Contagion! The BBC Four Pandemic" to describe the science behind pandemic preparedness in the...
Citations
... Importantly, Tazemetostat, which inhibits the EZH2 catalytic subunit of PRC2, was recently approved to treat epithelioid sarcomas with loss of SWI/SNF complex member SMARCB1 20 . Furthermore, diffuse large B-cell lymphoma growth can be blocked by inhibition of SETD2 in the case of EZH2 hypermorphic mutationmediated drug addiction to PRC2 inhibitors 21 . These findings suggest that disease-associated defective chromatin crosstalk could represent targets of synthetic lethality for successful therapeutic intervention. ...
... athletes also reported faster viral clearance by RT-PCR in individuals with recurrent COVID-19 compared with primary infections (4.9 vs 7.2 days, respectively) [30]. A cohort study in Alaska reported that individuals with previous COVID-19 infections were less likely to have a positive RADT result by day 5 compared to those with primary COVID-19 [25]. ...
... The time period of each phase is drawn can be found in Table S1. For each infected individual, PATAT randomly draws a withinhost viral load trajectory over the duration of infection, which impacts the sensitivity of Ag-RDTs 40 , based on known distributions for Omicron BA.1 41 . Similar viral load trajectories were drawn for both asymptomatic and symptomatic infected individuals 42 using a stochastic model modified from the one previously developed by Quilty et al. 43 A baseline Ct value (Ct baseline ) of 40 is established upon exposure. ...
... Several studies found changes in bacterial and fungal (most commonly Candida species) infection epidemiology, particularly among hospitalized patients [5,10,11]. Additionally, social distancing and the restrictions imposed by governments to quell the spread of SARS-CoV-2 may have affected the spread of other pathogens as they depend on close contact for spread [12]. While epidemiological changes in hospitalized patients have been described, only a few studies investigated epidemiological changes in bacterial and fungal infections on a larger scale or in terms of community spread during the pandemic. ...
... Until now there has been no standardized method for assessing in vivo antiviral effects. Time to viral clearance is an insensitive measure which is highly dependent on baseline viral loads [20]. The PLATCOV study is a platform randomized trial aiming to provide a standardized assessment in vivo of candidate antiviral drugs by measuring rates of viral clearance [21]. ...
... Developmentally-related differences in sleep efficiency might reflect bio-psychosocial changes associated with pubertal stages. In this sense, it is possible that, compared to pre/early pubertal participants, more mature individuals experienced more sleep arousal episodes due to changes in homeostatic mechanisms regulating sleep pressure (expressed as a less robust build-up and decay of sleep pressure), the quality and quantity of social bonds out of the household, social responsibilities (such as farming or house work), freedom to set one's own bedtimes, and shifts in cognitive-emotional states due to ongoing development and maturation of the dopaminergic reward system and prefrontal cortex [8,18,22,62,63]. A decreased sleep efficiency might serve a protective function for the social group, enabling more mature individuals, better prepared than younger individuals to physically respond to nocturnal environmental threats, to monitor the surroundings at night. ...
... The lower relative increases in excess mortality among more frail groups and those with more comorbidities have important implications and suggest that forward mortality displacement might be less of a phenomenon during the post-pandemic period than had been proposed. 29 Although the analysis of the CCI summary score indicated that those with more comorbidities had higher excess mortality on the absolute scale and lower excess mortality on the relative scale, there were some important clinical subgroups that did not follow this pattern. Notably, patients with dementia had the highest excess mortality on both absolute and relative scales, which was previously identified as an important risk group in other healthcare systems, such as that in the UK. 30 Interestingly, patients with metastatic cancer, who are likely to be at greater risk of SARS-CoV-2 infection or severe COVID-19, 31 appeared to have no excess mortality during the first 2 years of the pandemic. ...
... Instead, the increases re ect changes in the local sewage used as the background feed. Macrolide prescription rates in outpatient settings have been shown to have winter/early-spring peaks (35) suggesting this may have been a byproduct of community antibiotic usage. Therefore, we next addressed the potential consequences of changing antibiotic levels on (1) shifts in the abundance of bacteria harboring the resistance genes, and (2), the potential for HGT of contaminantassociated resistance genes. ...
... To validate our hypothesis that isolation may be a selection pressure to further drive the evolution of viral phenotypes, we additionally used the longitudinal viral load of SARS-CoV-2 from the BA.1 subvariant in 49 infected patients 41 (Table S1), and similarly analyzed those data together with the same data for the Delta variant (see METHODS in detail). The individual viral loads for the Delta variant (red) and BA.1 subvariant (green) are described in Fig. S8, and the estimated population parameters are shown in Table S5. ...
... Furthermore, the degree to which potential superspreader events could be important -not just for the initial seeding of Omicron, but for its continued spread -is not captured here. For example, it is possible that the spread of Omicron in other types of communities may be slower if the structure of the social network differs 40 , resulting in fewer opportunities for clustered transmission. Additionally, our work is limited by a few differences between MA and IHEs. ...