Publications

Sink-traps are a major source for carbapenemase-producing Enterobacteriaceae transmission.

Author(s): Regev-Yochay G, Margalit I, Smollan G, Rapaport R, Tal I, Hanage WP, Pinas Zade N, Jaber H, Taylor BP, Che Y, Rahav G, Zimlichman E, Keller N|Journal: Infect Control Hosp Epidemiol|PMID: 38149351| March 2024

We studied the extent of carbapenemase-producing Enterobacteriaceae (CPE) sink contamination and transmission to patients in a nonoutbreak setting.

Successful treatment of SARS-CoV-2 in an immunocompromised patient with persistent infection for 245 days: A case report.

Author(s): Overbeck V, Taylor BP, Turcinovic J, Qiu X, Schaeffer B, Seitz S, Curry SR, Hanage WP, Connor JH, Kuppalli K|Journal: Heliyon|PMID: 38223743| December 2023

Immunocompromised patients receiving B-cell-depleting therapies are at increased risk of persistent SARS-CoV-2 infection, with many experiencing fatal outcomes. We report…

Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.

Author(s): Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles S|Journal: Nat Commun|PMID: 37907520| October 2023

Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts…

A simple model of how varying exposure at gatherings impacts the emergence of variants and their detection.

Author(s): Taylor BP, Hanage WP|Journal: medRxiv| October 2023

Understanding how epidemics spread within societies is key for establishing adequate infection control responses. Dynamical models provide a means to…

Enterobacteriaceae isolated from patients share antibiotic resistance conferring plasmids recently acquired from those isolated from sinks in the same treatment room

Author(s): Taylor BP, Che Y, Passarelli H, Smollan G, Cohen C, Rapaport R, Tal I, Zade NP, Jaber H, Keller N, Hanage WP, Regev-Yochay G|Journal: bioRxiv| November 2022

Identifying how and where pathogens acquire antibiotic resistance is crucial to developing effective strategies to limit its spread. Many bacterial…

Beyond consensus sequence: a quantitative scheme for inferring transmission using deep sequencing in a bacterial transmission model

Author(s): Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles S|Journal: bioRxiv| October 2022

Genomic surveillance provides a data source complementary to contact tracing to resolve putative transmission chains. However, the role of within-host…

Understanding early pandemic SARS-CoV-2 transmission in a medical center by incorporating public sequencing databases to mitigate bias.

Author(s): Turcinovic J, Schaeffer B, Taylor BP, Bouton TC, Odom-Mabey AR, Weber SE, Lodi S, Ragan EJ, Connor JH, Jacobson KR, Hanage WP|Journal: J Infect Dis|PMID: 35993116| August 2022

Throughout the SARS-CoV-2 pandemic, healthcare workers (HCWs) have faced risk of infection from within the workplace via patients and staff…

Early introduction and rise of the Omicron SARS-CoV-2 variant in highly vaccinated university populations.

Author(s): Petros BA, Turcinovic J, Welch NL, White LF, Kolaczyk ED, Bauer MR, Cleary M, Dobbins ST, Doucette-Stamm L, Gore M, Nair P, Nguyen TG, Rose S, Taylor BP, Tsang D, Wendlandt E, Hope M, Platt JT, Jacobson KR, Bouton T, Yune S, Auclair JR, Landaverde L, Klapperich CM, Hamer DH, Hanage WP, MacInnis BL, Sabeti PC, Connor JH, Springer M|Journal: Clin Infect Dis|PMID: 35616119| May 2022

The Omicron variant of SARS-CoV-2 is highly transmissible in vaccinated and unvaccinated populations. The dynamics governing its establishment and propensity…

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.

Author(s): Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Badr H, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St George K, Adams MD, Grubaugh ND|Journal: Commun Biol|PMID: 35545661| May 2022

SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat…

Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak.

Author(s): Siddle KJ, Krasilnikova LA, Moreno GK, Schaffner SF, Vostok J, Fitzgerald NA, Lemieux JE, Barkas N, Loreth C, Specht I, Tomkins-Tinch CH, Paull JS, Schaeffer B, Taylor BP, Loftness B, Johnson H, Schubert PL, Shephard HM, Doucette M, Fink T, Lang AS, Baez S, Beauchamp J, Hennigan S, Buzby E, Ash S, Brown J, Clancy S, Cofsky S, Gagne L, Hall J, Harrington R, Gionet GL, Deruff KC, Vodzak ME, Adams GC, Dobbins ST, Slack SD, Reilly SK, Anderson LM, Cipicchio MC, DeFelice MT, Grimsby JL, Anderson SE, Blumenstiel BS, Meldrim JC, Rooke HM, Vicente G, Smith NL, Messer KS, Reagan FL, Mandese ZM, Lee MD, Ray MC, Fisher ME, Ulcena MA, Nolet CM, English SE, Larkin KL, Vernest K, Chaluvadi S, Arvidson D, Melchiono M, Covell T, Harik V, Brock-Fisher T, Dunn M, Kearns A, Hanage WP, Bernard C, Philippakis A, Lennon NJ, Gabriel SB, Gallagher GR, Smole S, Madoff LC, Brown CM, Park DJ, MacInnis BL, Sabeti PC|Journal: Cell|PMID: 35051367| December 2021

An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated…