Center for Communicable Disease Dynamics
The Center for Communicable Disease Dynamics works to improve methods for infectious disease modeling and statistical analysis, quantify disease and intervention impact, engage with policymakers to enhance decision-making, and train the next generation of scientists.
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A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation.
Bacterial populations that colonize a host can play important roles in host health, including serving as a reservoir that transmits to other hosts and from which invasive strains emerge, thus emphasizing the importance of understanding rates of acquisition and clearance of colonizing populations. Studies of colonization dynamics have been based...
A Benchtop Automated Sputum-to-Genotype System Using a Lab-on-a-Film Assembly for Detection of Multidrug-Resistant Mycobacterium tuberculosis
Automated genotyping of drug-resistant Mycobacterium tuberculosis (MTB) directly from sputum is challenging for three primary reasons. First, the sample matrix, sputum, is highly viscous and heterogeneous, posing a challenge for sample processing. Second, acid-fast MTB bacilli are difficult to lyse. And third, there are hundreds of MTB mutations that confer...
A FLOT1 host regulatory allele is associated with a recently expanded Mtb clade in patients with tuberculosis
The outcome of infectious diseases may depend on the interaction between human and pathogen genomic variations. We explore this relationship in tuberculosis (TB) by conducting a genome-to-genome (g2g) study of paired genomes from humans and the infectious agent Mycobacterium tuberculosis (Mtb) in 1,556 Peruvian TB patients.
A Genomic Perspective on the Near-term Impact of Doxycycline Post-exposure Prophylaxis on Neisseria gonorrhoeae Antimicrobial Resistance.
Pre-existing tetracycline resistance in Neisseria gonorrhoeae limits the effectiveness of post-exposure prophylaxis (PEP) with doxycycline against gonorrhea, and selection for tetracycline resistance may influence prevalence of multi-drug resistant strains. Using genomic and antimicrobial susceptibility data from N. gonorrhoeae, we assessed the near-term impact of doxycycline PEP on N. gonorrhoeae resistance....
A genomic perspective on the near-term impact of doxycycline post-exposure prophylaxis on Neisseria gonorrhoeae antimicrobial resistance.
Post-exposure prophylaxis with doxycycline (doxyPEP) is being introduced to prevent bacterial sexually transmitted infections (STIs). Pre-existing tetracycline resistance in limits doxyPEP effectiveness against gonorrhea, and selection for tetracycline resistant lineages may influence prevalence of resistance to other antimicrobials via selection for multi-drug resistant strains. Using genomic and antimicrobial susceptibility data...
A prospective real-time transfer learning approach to estimate Influenza hospitalizations with limited data
Accurate, real-time forecasts of influenza hospitalizations would facilitate prospective resource allocation and public health preparedness. State-of-the-art machine learning methods are a promising approach to produce such forecasts, but they require extensive historical data to be properly trained. Unfortunately, historically observed data of influenza hospitalizations, for the 50 states in the...
A public health intervention package for increasing tuberculosis notifications from private practitioners in Bandung, Indonesia (INSTEP2): A cluster-randomised controlled trial protocol
A significant proportion of tuberculosis (TB) patients globally make their initial visit for medical care to either an informal provider or a private practitioner, and many are not formally notified. Involvement of private practitioners (PPs) in a public–private mix for TB (TB-PPM) provides an opportunity for improving TB control. However,...
A sex-specific evolutionary interaction between ADCY9 and CETP
Pharmacogenomic studies have revealed associations between rs1967309 in the adenylyl cyclase type 9 (ADCY9) gene and clinical responses to the cholesteryl ester transfer protein (CETP) modulator dalcetrapib, however, the mechanism behind this interaction is still unknown. Here, we characterized selective signals at the locus associated with the pharmacogenomic response in...
A simple model of how varying exposure at gatherings impacts the emergence of variants and their detection.
Understanding how epidemics spread within societies is key for establishing adequate infection control responses. Dynamical models provide a means to translate surveillance data into predictions of future disease spread, yet many epidemic models do not capture empirically observed features of socialization. Here, we utilize a connection between sampling processes and...
A standardised differential privacy framework for epidemiological modelling with mobile phone data
During the COVID-19 pandemic, the use of mobile phone data for monitoring human mobility patterns has become increasingly common, both to study the impact of travel restrictions on population movement and epidemiological modelling. Despite the importance of these data, the use of location information to guide public policy can raise...