A5019907250- COVID-19 epidemiological studies
- Gut microbiota and health
- Antibiotic Resistance in Bacteria
- COVID-19 Pandemic Impacts
- Antibiotic Use and Resistance
- Evolution and Genetic Dynamics
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Evolutionary Game Theory and Cooperation
- Influenza Virus Research Studies
- Ultrasonics and Acoustic Wave Propagation
- SARS-CoV-2 and COVID-19 Research
- Non-Destructive Testing Techniques
- COVID-19 impact on air quality
- Data-Driven Disease Surveillance
- Clostridium difficile and Clostridium perfringens research
- COVID-19 Clinical Research Studies
- Antibiotics Pharmacokinetics and Efficacy
- Genomics and Phylogenetic Studies
- Thermography and Photoacoustic Techniques
- Climate change impacts on agriculture
- Pharmaceutical and Antibiotic Environmental Impacts
- Microbial Community Ecology and Physiology
- Assisted Reproductive Technology and Twin Pregnancy
- Viral Infections and Outbreaks Research
European Centre for Disease Prevention and Control
2023-2024
Harvard University
2019-2023
Center for Disease Dynamics, Economics & Policy
2020-2021
Boston University
2021
University of Oxford
2014-2020
Massachusetts Department of Public Health
2020
Harvard University Press
2020
Mahidol Oxford Tropical Medicine Research Unit
2017
TU Dortmund University
1988-1989
Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using to assess effectiveness interventions inform policy. However, estimation from available data presents several challenges, with critical implications interpretation course pandemic. The purpose this document summarize these illustrate them examples synthetic data, and,...
Abstract As of February 13, 2020, there have been 59,863 laboratory-confirmed cases COVID-19 infections in mainland China, including 1,367 deaths. A key public health priority during the emergence a novel pathogen is estimating clinical severity. Here we estimated symptomatic case-fatality risk (sCFR; probability dying from infection after developing symptoms) Wuhan using and published information. We that sCFR was 0.5% (0.1%-1.3%), (0.2%-1.1%) 2.7% (1.5%-4.7%) for those aged 15-44, 45-64...
Microbes produce many compounds that are costly to a focal cell but promote the survival and reproduction of neighboring cells. This observation has led suggestion microbial strains species will commonly cooperate by exchanging compounds. Here, we examine this idea with an ecoevolutionary model where microbes make multiple secretions, which can be exchanged among genotypes. We show cooperation between genotypes only evolves under specific demographic regimes characterized intermediate...
Microbes have the potential to be highly cooperative organisms. The archetype of microbial cooperation is often considered secretion siderophores, molecules scavenging iron, where threatened by "cheater" genotypes that use siderophores without making them. Here, we show this view neglects a key piece biology: are imported specific receptors constrain their competing strains. We study effect specificity in an ecoevolutionary model, which vary siderophore sharing among strains, and compare...
Horizontal gene transfer is central to microbial evolution, because it enables genetic regions spread horizontally through diverse communities. However, how exerts such a strong effect not understood. Here we develop an eco-evolutionary model and show transfer, even when rare, can transform the evolution ecology of microbes. We recapitulate existing models, which suggest that asexual reproduction will overpower horizontal greatly limit its effects. then allowing immigration completely...
Abstract Risk of COVID-19 infection in Wuhan has been estimated using imported case counts international travelers, often under the assumption that all cases travelers are ascertained. Recent work indicates variation among countries detection capacity for cases. Singapore historically had very strong epidemiological surveillance and contact-tracing shown epidemic evidence a high sensitivity detection. We therefore used Bayesian modeling approach to estimate relative other compared...
Abstract Background Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many approaches inferring taxonomic composition AMR gene content complex community samples from shotgun metagenomic data, but there has been little work establishing optimum sequencing depth, data processing analysis methods these samples. In this study we cultured...
Abstract Estimation of the effective reproductive number, R t , is important for detecting changes in disease transmission over time. During COVID-19 pandemic, policymakers and public health officials are using to assess effectiveness interventions inform policy. However, estimation from available data presents several challenges, with critical implications interpretation course pandemic. The purpose this document summarize these illustrate them examples synthetic data, and, where possible,...
Cases from the ongoing outbreak of atypical pneumonia caused by 2019 novel coronavirus (2019-nCoV) exported mainland China can lead to self-sustained outbreaks in other populations. Internationally imported cases are currently being reported several different locations. Early detection is critical for containment virus. Based on air travel volume estimates Wuhan international destinations and using a generalized linear regression model we identify locations which may potentially have...
Bacteria inhibit and kill one another with a diverse array of compounds, including bacteriocins antibiotics. These attacks are highly regulated, but we lack clear understanding the evolutionary logic underlying this regulation. Here, combine detailed dynamic model bacterial competition game theory to study rules warfare. We large range possible combat strategies based upon molecular biology regulatory networks. Our predicts that regulated strategies, which use quorum sensing or stress...
The incidence of coronavirus disease 2019 (COVID-19) in Wuhan, China, has been estimated using imported case counts international travellers, generally under the assumptions that all cases travellers have ascertained and infection prevalence residents is same. However, findings indicate variation among locations capacity for detection cases. Singapore had very strong epidemiological surveillance contact tracing during previous infectious outbreaks consistently shown high sensitivity...
Abstract Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection exported from mainland China could lead to self-sustained outbreaks in other countries. By February 2020, several countries were reporting imported SARS-CoV-2 cases. To contain the virus, early detection cases is critical. We used air travel volume estimates Wuhan, China, international destinations and a generalized linear regression model identify locations that have undetected Our can be adjusted...
Abstract Early in the COVID-19 pandemic, predictions of international outbreaks were largely based on imported cases from Wuhan, China, potentially missing imports other cities. We provide a method, combining daily prevalence and flight passenger volume, to estimate importations 18 Chinese cities 43 destinations, including 26 Africa. Global case China early January came primarily but inferred source shifted mid-February, especially for African destinations. that 10.4 (6.2 – 27.1) these which...
Collaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during outbreaks. In the process collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step. We compared this to directly simulated trajectories. aimed explore information on key quantities; ensemble uncertainty; performance against data, investigating potential continuously from...
Antibiotic-induced perturbation of the human gut flora is expected to play an important role in mediating relationship between antibiotic use and population prevalence resistance bacteria, but little known about how antibiotics affect within-host dynamics. Here we develop a data-driven model dynamics extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae. We blaCTX-M (the most widespread ESBL gene family) 16S rRNA (a proxy for bacterial load) abundance data from 833 rectal...
Antimicrobial resistance (AMR) in
In response to the coronavirus disease (COVID-19) pandemic, public health scientists have produced a large and rapidly expanding body of literature that aims answer critical questions, such as proportion population in geographic area has been infected; transmissibility virus factors associated with high infectiousness or susceptibility infection; which groups are most at risk infection, morbidity mortality; degree antibodies confer protection re-infection. Observational studies subject...
Abstract Early in the COVID-19 pandemic, when cases were predominantly reported city of Wuhan, China, local outbreaks Europe, North America, and Asia largely predicted from imported on flights potentially missing imports other key source cities. Here, we account for importations Wuhan cities combining prevalence estimates 18 Chinese with flight passenger volume to predict each day between early December 2019 late February 2020 number exported China. We that main global case importation...