Publications – Center for Communicable Disease Dynamics

Whole-Genome Sequencing to Predict Antimicrobial Susceptibility Profiles in Neisseria gonorrhoeae.

Author(s): Bristow CC, Mortimer TD, Morris S, Grad YH, Soge OO, Wakatake E, Pascual R, Murphy SM, Fryling KE, Adamson PC, Dillon JA, Parmar NR, Le HHL, Van Le H, Ovalles Ureña RM, Mitchev N, Mlisana K, Wi T, Dickson SP, Klausner JDJournal: J Infect DisPMID: 36735316 April 2023

Neisseria gonorrhoeae is a major public health problem due to increasing incidence and antimicrobial resistance. Genetic markers of reduced susceptibility…

A genomic perspective on the near-term impact of doxycycline post-exposure prophylaxis on Neisseria gonorrhoeae antimicrobial resistance.

Author(s): Mortimer TD, Grad YHJournal: medRxivPMID: 36993406 March 2023

Post-exposure prophylaxis with doxycycline (doxyPEP) is being introduced to prevent bacterial sexually transmitted infections (STIs). Pre-existing tetracycline resistance in limits…

Neisseria gonorrhoeae diagnostic escape from a gyrA-based test for ciprofloxacin susceptibility and the effect on zoliflodacin resistance: a bacterial genetics and experimental evolution study.

Author(s): Rubin DH, Mortimer TD, Grad YHJournal: Lancet MicrobePMID: 36868257 February 2023

The aetiological bacterial agent of gonorrhoea, Neisseria gonorrhoeae, has become resistant to each of the first-line antibiotics used to treat…

Resistance-minimizing strategies for introducing a novel antibiotic for gonorrhea treatment: a mathematical modeling study.

Author(s): Reichert E, Yaesoubi R, Rönn MM, Gift TL, Salomon JA, Grad YHJournal: medRxivPMID: 36824857 February 2023

Gonorrhea is a highly prevalent sexually transmitted infection and an urgent public health concern due to increasing antibiotic resistance. Only…

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 JAJournal: Health Care Manag SciPMID: 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 YHJournal: Nat MicrobiolPMID: 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 YHJournal: Ann N Y Acad SciPMID: 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 YHJournal: 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 HHJournal: Virus EvolPMID: 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 YHJournal: ElifePMID: 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…