Colin J. Worby

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The prospect of using whole genome sequence data to investigate bacterial disease outbreaks has been keenly anticipated in many quarters, and the large-scale collection and sequencing of isolates from cases is becoming increasingly feasible. While sequence data can provide many important insights into disease spread and pathogen adaptation, it remains(More)
Whole-genome sequencing of pathogens has recently been used to investigate disease outbreaks and is likely to play a growing role in real-time epidemiological studies. Methods to analyze high-resolution genomic data in this context are still lacking, and inferring transmission dynamics from such data typically requires many assumptions. While recent studies(More)
Infection control for hospital pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) often takes the form of a package of interventions, including the use of patient isolation and decolonization treatment. Such interventions, though widely used, have generated controversy because of their significant resource implications and the lack of(More)
Genome sequencing is an increasingly common component of infectious disease outbreak investigations. However, the relationship between pathogen transmission and observed genetic data is complex, and dependent on several uncertain factors. As such, simulation of pathogen dynamics is an important tool for interpreting observed genomic data in an infectious(More)
CC-BY-NC 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not. Abstract Sequencing pathogen samples during a communicable disease outbreak is becoming an increasingly common procedure in epidemiological investigations. Identifying who infected whom sheds(More)
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of control measures. We considered disease outbreaks in a setting with dense genomic sampling, and formulated stochastic(More)
OBJECTIVES The objectives of this study were to estimate the relative transmissibility of mupirocin-resistant (MupR) and mupirocin-susceptible (MupS) MRSA strains and evaluate the long-term impact of MupR on MRSA control policies. METHODS Parameters describing MupR and MupS strains were estimated using Markov chain Monte Carlo methods applied to data from(More)
There is limited information on the roles of different age groups during pertussis outbreaks. Little is known about vaccine effectiveness against pertussis infection (both clinically apparent and subclinical), which is different from effectiveness against reportable pertussis disease, with the former influencing the impact of vaccination on pertussis(More)
The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Abstract The prospect of using whole genome sequence data to investigate bacterial disease outbreaks has been keenly anticipated in many quarters, and the large-scale collection and sequencing of isolates from cases is becoming(More)
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common healthcare-associated pathogens. To examine the role of inter-hospital patient sharing on MRSA transmission, a previous study collected 2,214 samples from 30 hospitals in Orange County, California and showed by spa typing that genetic differentiation decreased significantly with(More)