Publications

Generating simple classification rules to predict local surges in COVID-19 hospitalizations.

Author(s): Yaesoubi R, You S, Xi Q, Menzies NA, Tuite A, Grad YH, Salomon JA|Journal: Health Care Manag Sci|PMID: 36692583| January 2023

Low rates of vaccination, emergence of novel variants of SARS-CoV-2, and increasing transmission relating to seasonal changes and relaxation of…

CanB is a metabolic mediator of antibiotic resistance in Neisseria gonorrhoeae.

Author(s): Rubin DHF, Ma KC, Westervelt KA, Hullahalli K, Waldor MK, Grad YH|Journal: Nat Microbiol|PMID: 36604513| January 2023

The evolution of the obligate human pathogen Neisseria gonorrhoeae has been shaped by selective pressures from diverse host niche environments…

Machine learning models for Neisseria gonorrhoeae antimicrobial susceptibility tests.

Author(s): Martin SL, Mortimer TD, Grad YH|Journal: Ann N Y Acad Sci|PMID: 36573759| December 2022

Neisseria gonorrhoeae is an urgent public health threat due to the emergence of antibiotic resistance. As most isolates in the…

Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data

Author(s): Helekal D, Keeling M, Grad YH|Journal: bioRxiv| December 2022

Increasing levels of antibiotic resistance in many bacterial pathogen populations is a major threat to public health. Resistance to an…

Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales.

Author(s): Li NK, Corander J, Grad YH, Chang HH|Journal: Virus Evol|PMID: 36601300| November 2022

Incomplete selection makes it challenging to infer selection on genes at short time scales, especially for microorganisms, due to stronger…

Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: a retrospective cohort study

Author(s): Hay JA, Kissler SM, Fauver JR, Mack C, Tai CG, Samant RM, Connolly S, Anderson DJ, Khullar G, MacKay M, Patel M, Kelly S, Manhertz A, Eiter I, Salgado D, Baker T, Howard B, Dudley JT, Mason CE, Nair M, Huang Y, DiFiori J, Ho DD, Grubaugh N, Grad YH|Journal: Elife|PMID: 36383192| November 2022

The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear. We characterized 1,280 infections…

Recent O-antigen diversification masks highly pathogenic STEC O104:H4

Author(s): Lang C, Fruth A, Campbell IW, Jenkins C, Smith P, Strockbine N, Weill FX, Nübel U, Grad YH, Waldor MK, Flieger A|Journal: bioRxiv| October 2022

Shiga toxin-producing E. coli (STEC) can give rise to a range of clinical outcomes from diarrhea to the life-threatening systemic…

Impact of respiratory infection and chronic comorbidities on early pediatric antibiotic dispensing in the United States.

Author(s): Kissler SM, Wang B, Mehrotra A, Barnett M, Grad YH|Journal: Clin Infect Dis|PMID: 36196577| October 2022

In the United States, children under age 5 receive high volumes of antibiotics, which may contribute to antibiotic resistance. It…

Optimizing prevalence estimates for a novel pathogen by reducing uncertainty in test characteristics.

Author(s): Larremore DB, Fosdick BK, Zhang S, Grad YH|Journal: Epidemics|PMID: 36191537| September 2022

Emergence of a novel pathogen drives the urgent need for diagnostic tests that can aid in defining disease prevalence. The…

Neisseria gonorrhoeae diagnostic escape from a gyrA-based test for ciprofloxacin susceptibility can lead to increased zoliflodacin resistance

Author(s): Rubin DHF, Mortimer TD, Grad YH|Journal: bioRxiv| August 2022

The etiologic agent of gonorrhea, Neisseria gonorrhoeae, has become resistant to each of the first line antibiotics used to treat…