Pre-prints and Publications


Oliveira Roster KI, Mittelstaedt R, Reyes J, Aatresh AV, Grad YH. Molecular surveillance to monitor the prevalence of tetracycline resistance in Neisseria gonorrhoeaemedRxiv. 2024

Lipsitch M and Grad YH. Diagnostics for Public Health — Infectious Disease Surveillance and ControlNEJM Evidence. 2024;3(5) DOI: 10.1056/EVIDra2300271

Yu Q, Olesen SW, Duvallet C, Grad YH. Assessment of sewer connectivity in the United States and its implications for equity in wastewater-based epidemiology. PLOS Global Public Health. 2024 Apr 17;4(4):e0003039. doi: 10.1371/journal.pgph.0003039. eCollection 2024.

Tai CG, Haviland MK, Kissler S, Lucia RM, Merson M, Maragakis LL, Ho DD, Anderson DJ, DiFiori J, Grubaugh ND, Grad YH*, Mack CD*. Low Antibody Levels Associated with Significantly Increased Rate of SARS-CoV-2 Infection in a Highly Vaccinated Population from the US National Basketball Association. Journal of Medical Virology. 2024. Mar;96(3):e29505. doi: 10.1002/jmv.29505. *co-senior authors

Kissler SM*, Roster KIO*, Petherbridge R, Mehrotra A, Barnett ML, Grad YH. Drivers of geographic patterns in outpatient antibiotic prescribing in the United StatesClinical Infectious Diseases. 2024 Mar 21:ciae111. doi: 10.1093/cid/ciae111.. *co-first authors

Ofori SK, Dankwa EA, Ngwakongnwi E, Amberbir A, Bekele A, Murray MB, Grad YH, Buckee CO, Hedt-Gauthier BL. Evidence-based decision making: Infectious disease modeling training for policymakers in East Africa. Annals of Global Health. 2024 Mar 22;90(1):22. doi: 10.5334/aogh.4383. eCollection 2024.

Olejarz JW, Oliveira Roster KI, Kissler SM, Lipsitch M, Grad YH. Optimal environmental testing frequency for outbreak surveillanceEpidemics. 2024 Feb 15;46:100750. doi: 10.1016/j.epidem.2024.100750

Kline MC, Kissler SM, Whittles LK, Barnett ML, Grad YH. Spatiotemporal Trends in Group A Streptococcal Pharyngitis in the United States. Clinical Infectious Diseases. 2024. ciae083,

Wilcock AD, Kissler SM, Mehrotra A, McGarry BE, Sommers BD, Grabowski DC, Grad YH, Barnett ML. Clinical Risk and Utilization of Antiviral Therapy for COVID-19 in Medicare. JAMA Health Forum. 2024;5(1):e235044.

Oliveira Roster KI and Grad YH. Estimating changes in antibiotic consumption with the introduction of doxycycline post-exposure prophylaxis in the United States. Lancet Microbe. 2024 Jan;5(1):e9..

Yaesoubi R, Xi Q, Hsu K, Gift TL, St Cyr SB, Rönn MM, Salomon JA, Grad YH. The impact of rapid drug susceptibility tests on gonorrhea burden and lifespan of antibiotic treatments: a modeling study among men who have sex with men in the United StatesAmerican Journal of Epidemiology. 2024 Jan 8;193(1):17-25. doi: 10.1093/aje/kwad175.


Lipsitch M, Bassett MT, Brownstein JS, Elliott P, Eyre D, Grabowski MK, Hay JA, Johansson M, Kissler SM, Larremore DB, Layden J, Lessler J, Lynfield R, MacCannell D, Madoff LC, Metcalf CJE, Meyers LA, Ofori SK, Quinn C, Bento AIR, Reich N, Riley S, Rosenfeld R, Samore MH, Sampath R, Slayton RB, Swerdlow DL, Truelove S, Varma JK, Grad YH. Infectious disease surveillance needs for the United States: lessons from COVID-19. arXiv. 2023.

Mack CD, Merson MH, Sims L, Maragakis LL, Davis R, Tai CG, Meisel P, Grad YH, Ho DD, Anderson DJ, LeMay C, DiFiori J. The “Bubble”: What Can Be Learned from the National Basketball Association (NBA)’s 2019-20 Season Restart in Orlando during the COVID-19 Pandemic. J Appl Lab Med. 2023 Oct 30:jfad073. doi: 10.1093/jalm/jfad073.

Ojala F, Sater MRA, Miller LG, McKinnell JA, Huang SS, Grad YH*, Marttinen P*. Bayesian modeling of the impact of antibiotic resistance on the efficiency of MRSA decolonization. PLOS Computational Biology. 2023. 19(10): e1010898. *co-senior authors

Kissler SM, Hay JA, Fauver JR, Mack C, Tai CG, Anderson DJ, Ho DD, Grubaugh ND, Grad YH. Viral kinetics of sequential SARS-CoV-2 infectionsNature Communications. 2023. 14, 6206.

Lang C, Fruth A, Campbell IW, Jenkins C, Smith P, Strockbine N, Weill FX, Nübel U, Grad YH, Waldor MK, Flieger A. O-antigen diversification masks identification of highly pathogenic STEC O104:H4-like strains. Microbiology Spectrum. 2023. e00987-23.

Helekal D, Keeling M, Grad YH, Didelot X. Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data. Journal of the Royal Society Interface. 2023. Jun;20(203):20230074.

Oliveira Roster KI, Kissler SM, Omoregie E, Wang JC, Amin HS, Di Lonardo S, Hughes S, Grad YH. Surveillance strategies for detection of new SARS-CoV-2 variants across epidemiological contexts. medRxiv. 2023.

Reichert E, Yaesoubi R, Rönn MM, Gift TL, Salomon JA, Grad YH. Resistance-minimizing strategies for introducing a novel antibiotic for gonorrhea treatment: a mathematical modeling study. Lancet Microbe. 2023.

Mortimer TD and Grad YH. A genomic perspective on the near-term impact of doxycycline post-exposure prophylaxis on Neisseria gonorrhoeae antimicrobial resistanceClinical Infectious Diseases. 2023. ciad279,

Reichert E and Grad YH. Resistance and prevalence implications of doxycycline post-exposure prophylaxis for gonorrhea prevention in men who have sex with men: a modeling studymedRxiv. 2023.

Riou J, Althouse CL, Allen H, Cole JK, Grad YH, Heijne JCM, Unemo M, Low N. Projecting the development of antimicrobial resistance in Neisseria gonorrhoeae from antimicrobial surveillance data: a mathematical modelling study. BMC Infect Dis. 2023 Apr 20;23(1):252. doi: 10.1186/s12879-023-08200-4.

Rubin DHF, Mortimer TD, Grad YH. Neisseria gonorrhoeae diagnostic escape from a gyrA-based test for ciprofloxacin susceptibility and the impact on zoliflodacin resistance: a bacterial genetics and experimental evolution study. Lancet Microbe. 2023. Feb 28:S2666-5247(22)00356-1.

Tai CG, Haviland MK, Kissler S, Lucia RM, Merson M, Maragakis LL, Ho DD, Anderson DJ, DiFiori J, Grubaugh ND, Grad YH*, Mack CD*. Low Antibody Titers Demonstrate Significantly Increased Rate of SARS-CoV-2 Infection in a Highly Vaccinated Population from the National Basketball Association. medRxiv. 2023. *co-senior authors

Bristow CC*, Mortimer TD*, Morris S, Grad YH, Soge OO, Wakatake E, Pascual R, Murphy SM, Fryling KE, Adamson PC, Dillon J, Gohil N, Le HHL, Le HV, Urena RMO, Mitchev N, Mlisana K, Wi T, Dickson SP, Klausner JD. Whole Genome Sequencing to Predict Antimicrobial Susceptibility Profiles in Neisseria gonorrhoeae. J Infect Dis. 2023. Apr 12;227(7):917-925. doi: 10.1093/infdis/jiad027. *co-first authors.

Brown TS, Martinez de Salazar Munoz P, Bhatia A, Bunda B, Williams WK, Bor D, Miller JS, Mohareb A, Naranbai V, Beltran WG, Miller TE, Thierauf J, Yang W, Kress D, Stelljes K, Johnson K, Larremore D, Lennerz J, Iafrate AJ, Balsari S, Buckee CO*, Grad YH*. Geographically skewed recruitment and COVID-19 seroprevalence estimates: A cross-sectional serosurveillance study and mathematical modeling analysis. BMJ Open. 2023. 13:e061840. doi: 10.1136/bmjopen-2022-061840 *co-senior authors

Yaesoubi R, You S, Xi Q, Menzies NA, Tuite A, Grad YH, Salomon JA. Generating simple classification rules to predict local surges in COVID-19 hospitalizations. Health Care Manag Sci. 2023 Jan 24. doi: 10.1007/s10729-023-09629-4.

Rubin DHF, Ma KC, Westervelt KA, Hullahalli K, Waldor MK, Grad YH. CanB is a metabolic mediator of antibiotic resistance in Neisseria gonorrhoeae. Nature Microbiology. 2023. Jan;8(1):28-39


Martin SL, Mortimer TD, Grad YH. Machine learning models for Neisseria gonorrhoeae antimicrobial susceptibility tests. Ann NY Acad Sci. 2022.

Li N-K, Corander J, Grad YH, Chang H-H. Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales. Virus Evolution. 2022. veac108,

Hay JA, Kissler SM, Fauver JR, Mack C, Tai CG, Radhika RM, Connelly S, Anderson DJ, Khullar G, MacKay M, Patel M, Kelly S, ManhertzA, Eiter I, Salgado D, Baker T, However B, Dudley JT, Mason CM, Ho DD, Grubaugh ND, Grad YH. Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: a retrospective cohort study. eLife. 2022. 11:e81849.

Kissler SM, Wang B, Mehrotra A, Barnett M, Grad YH. Impact of Respiratory Infection and Chronic Comorbidities on Early Pediatric Antibiotic Dispensing in the United StatesClinical Infectious Diseases. 2022. ciac811,

Larremore DB, Fosdick BK, Zhang S, Grad YH. Jointly modeling prevalence, sensitivity and specificity for optimal sample allocation. Epidemics. 2022.

Quan KA, Sater MRA, Uly C, Clifton-Koeppel R, Dickey LL, Wilson W, Patton P, Chang W, Samuelson P, Lagoudas GK, Allen T, Merchant L, Gannotta R, Bittencourt CE, Soto JC, Evans KD, Blainey PC, Murray J, Shelton D, Lee HS, Zahn M, Wolfe J, Madey K, Yim J, Gohil SK, Grad YH, Huang SS. Epidemiology and Genomics of a Slow Outbreak of MRSA in a NICU: Successful Chronic Decolonization of MRSA-Positive Health Care Personnel. Infect Control Hosp Epidemiol. 2022. 1-8. doi:10.1017/ice.2022.133

Tai CG, Maragakis LL, Connolly S, DiFiori J, Sims L, Adams E, Anderson DJ, Merson MH, Ho DH, Grad YH*, Mack CD*. Association Between COVID-19 Booster Vaccination and Omicron Infection in a Highly Vaccinated Cohort of Players and Staff in the National Basketball Association. JAMA. 2022. doi:10.1001/jama.2022.9479. *co-senior authors.

Watson JA, Kissler SM, Day NPJ, Grad YH, White NJ. Characterizing SARS-CoV-2 viral clearance kinetics to improve the design of antiviral pharmacometric studies. Antimicrob. Agents Chemother. 2022 Jul 19;66(7):e0019222. doi: 10.1128/aac.00192-22. Epub 2022 Jun 23.

Poyraz O, Sater MRA, Miller LG, McKinnell JA, Huang SS, Grad YH*, Marttinen P*. The impact of site-specific clearance on Methicillin-resistant Staphylococcus aureus decolonization. J. R. Soc. Interface. 2022. 19: 20210916.  *co-senior authors.

Kissler SM, Grad YH. Anticipating racial/ethnic mortality displacement from COVID-19. American Journal of Epidemiology. 2022.

Hadjineophytou C, Anonsen J, Svingerud T, Mortimer T, Grad YH, Scott N, Koomey M. Concerted evolution of protein substrates and oligosaccharyltransferase – targeting specificities govern O-glycoproteome diversity within a bacterial genus. mBio. 2022. e03797-21

Mortimer TD, Zhang JJ, Ma KC, Grad YH. Loci for prediction of penicillin and tetracycline susceptibility in Neisseria gonorrhoeae: a genome wide association study. Lancet Microbe. 2022.

Olesen SW, Kanjilal S, Kissler SM, Sun DS, Grad YH. Effects of racial/ethnic disparities in healthcare utilization on antibiotic use, United States, 2016/2018. medRxiv. 2022.

Sun DS, Kissler SM, Kanjilal S, Olesen SW, Lipsitch M, Grad YH. Analysis of multiple bacterial species and antibiotic classes reveals large variation in the association between seasonal antibiotic use and resistance. PLOS Biology. 2022. 20(3): e3001579. pbio.3001579

Ma KC, Hale JE, Grad YH, Alter G, Luzuriaga K, Eaton RB, Fischinger S, Kaur D, Brody R, Siddiqui SM, Leach D, Brown C, Klevens RM, Madoff L, Comeau AM. Trends in SARS-CoV-2 seroprevalence in Massachusetts estimated from newborn screening specimens. Clinical Infectious Diseases. 2022. ciac158,

Yaesoubi R, Cohen T, Hsu K, Gift TL, St Cyr SB, Salomon JA, Grad YH. Evaluating spatially adaptive guidelines for the treatment of gonorrhea to increase the effective lifespan of antibiotics. PLOS Computational Biology. 2022.


Gussin GM, Heim L, Tjoa T, McKinnell JA, Miller LG, Gillen DL, Sater MRA, Grad YH, Singh RD, Huang SS. Post-discharge decolonization of patients harboring methicillin-resistant Staphylococcus aureus (MRSA) USA300 strains: secondary analysis of the CLEAR Trial. Infection Control & Hospital Epidemiology. 2021.

Kissler SM, Fauver JR, Mack C, Tai CG, Breban MI, Watkins AE, Samant RM, Anderson DJ, Metti J, Khullar G, Baits R, MacKay M, Salgado D, Baker T, Dudley JT, Mason CE, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated persons. NEJM. 2021. Dec 23;385(26):2489-2491. doi: 10.1056/NEJMc2102507

Mack CD, Tai C, Sikka R, Grad YH, Maragakis LL, Grubaugh ND, Anderson DJ, Ho D, Merson M, Samant RM, Fauver JR, Barrett J, DiFiori J. SARS-CoV-2 Reinfection: A Case Series from a 12-Month Longitudinal Occupational Cohort. Clinical Infectious Diseases. 2021. Nov 2;73(9):e3146-e3155. doi: 10.1093/cid/ciaa1229.

Palace SG, Fryling KE, Li Y, Wentworth AJ, Traverso G, Grad YH. Identification of bile acid and fatty acid species as candidate rapidly bactericidal agents for topical treatment of gonorrhea. Journal of Antimicrobial Chemotherapy. 2021. Jul 10:dkab217. doi: 10.1093/jac/dkab217.

Kissler SM, Fauver JR, Mack C, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND*, Grad YH*. Viral dynamics of SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLOS Biology. 2021. Jul 12;19(7):e3001333. doi: 10.1371/journal.pbio.3001333. *co-senior authors.

Johnson EK, Kahn R, Grad YH, Lipsitch M, Larremore DB. Test negative designs with uncertainty, sensitivity, and specificity. medRxiv. 2021.

Ma KC, Menkir T, Kissler SM, Grad YH, Lipsitch M. Modeling the impact of racial and ethnic disparities on COVID-19 epidemic dynamicseLife. 2021. 10:e66601 DOI: 10.7554/eLife.66601.

Neprash HT, Sheridan B, Jena AB, Grad YH, Barnett ML. Within office transmission of influenza-like illness. Health Affairs. 2021. Aug;40(8):1321-1327. doi: 10.1377/hlthaff.2020.01594

Mack CD, DiFiori, J, Tai CG, Shiue KY, Grad YH, Anderson DJ, Ho DD, Sims L, LeMay C, Mancell J, Maragakis LL. SARS-CoV-2 Transmission Risk Among National Basketball Association Players, Staff, and Vendors Exposed to Individuals With Positive COVID-19 Test Results After Recovery During the 2020 Season Restart. JAMA Internal Medicine. 2021. doi:10.1001/jamainternmed.2021.2114. Accompanied by an editor’s commentary.

Kissler SM, Mitchell M, Grad YH. Reduction in antibiotic prescribing attainable with a gonococcal vaccine. Clinical Infectious Diseases. 2021. ciab276,

Cobey S, Larremore D, Grad YH, Lipsitch M. Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination. Nature Reviews Immunology. 2021.

Kissler SM, Klevens M, Barnett ML*, Grad YH*. Childhood respiratory outpatient visits correlate with socioeconomic status and drive geographic patterns in antibiotic prescribing. Journal of Infectious Diseases. 2021. jiab218, *co-senior authors. With an accompanying editorial!

Larremore DB, Fosdick BK, Bubar KM, Zhang S, Kissler SM, Metcalf CJE, Buckee CO, Grad YH. Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys. eLife. 2021. 10:e64206

Yahara K, Ma KC, Mortimer TD, Shimuta K, Nakayama S, Hirabayashi A, Suzuki M, Jinnai M, Ohya H, Kuroki T, Watanabe Y, Yasuda M, Deguchi T, Eldholm V, Harrison OB, Maiden MCJ, Grad YH, Ohnishi M. Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae. Genome Medicine. 2021. 13:51;

Sánchez-Busó L, Yeats CA, Taylor B, Goater R, Underwood A, Abudahab K, Argimon S, Ma KC, Mortimer TD, Cole MJ, Grad YH, Martin I, Raphael BH, Shafer WM, Spiteri G, Town K, Wi T, Harris SR, Unemo M, Aanensen D. A community-driven resource for genomic surveillance of Neisseria gonorrhoeae at PathogenwatchGenome Medicine. 2021. 13:61

Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. Science. 2021. 10.1126/science.abe6959. With associated commentary.



Ogbebor O, Mortimer TD, Fryling K, Zhang JJ, Bhanot N, Grad YH. Disseminated gonococcal infection complicated by prosthetic joint infection: case report and genomic and phylogenetic analysis. Open Forum Infectious Diseases. 2020.

Olesen SW, Lipsitch M, Grad YH. The role of “spillover” in antibiotic resistance. PNAS. 2020.

Vegvari C, Grad YH, White PJ, Didelot X, Whittles LK, Scangarella-Oman NE, Mitrani-Gold FS, Dumont E, Perry CR, Gilchrist K, Hossain M, Mortimer TD, Anderson RM, Gardiner D. Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea. Eurosurveillance. 2020;25(43):pii=1900210.

Ma K, Mortimer T, Duckett M, Hicks A, Wheeler N, Sánchez-Busó L, Grad YH. Increased power from conditional bacterial genome-wide association identifies Neisseria gonorrhoeae macrolide resistance mutations. Nature Communications. 2020. 11:5374 | Selected as Editors’ Highlight!

Lipsitch M, Grad YH, Sette A, Crotty S. Memory T cells and herd immunity to SARS-CoV-2. Nature Reviews Immunology. 2020.

Kissler SM, Kishore N, Prabhu M, Goffman D, Beilin Y, Landau R, Gyamfi-Bannerman C, Bateman BT, Katz D, Gal J, Bianco A, Stone J, Larremore D, Buckee CO, Grad YH. Reductions in commuting mobility correlate with geographic differences in SARS-CoV-2 prevalence in New York City. Nature Communications. 2020. 11:4674

Ashcroft MA, Chow EPF, Lee DYJ, De Petra V, Soumilas M, Tschaepe M, Zhang L, Ingle DJ, Taiaroa G, Hicks AL, Grad YH, Howden BP, Fairley CK, Williamson DA. Genomic assessment of within-host population variation in Neisseria gonorrhoeae: Implications for gonorrhoea transmission. medRxiv. 2020.

Ma KC, Mortimer TD, Grad YH. Efflux pump antibiotic binding site mutations are associated with azithromycin nonsusceptibility in clinical Neisseria gonorrhoeae isolates. mBio. 2020. 11:e01509-20.

Mortimer TD, Pathela P, Crawley A, Rakeman JL, Lin Y, Harris SR, Blank S, Schillinger JA*, Grad YH*. The distribution and spread of susceptible and resistant Neisseria gonorrhoeae across demographic groups in a major metropolitan center. Clinical Infectious Diseases. 2020. ciaa1229, *co-senior authors.

Ma KC, Mortimer TD, Hicks AL, Wheeler NE, Sánchez-Busó L, Golparian D, Taiaroa G, Rubin DHF, Wang Y, Williamson DA, Unemo M, Harris SR, Grad YH. Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae. Nature Communications. 2020. 11:4126 . 

Kahn R, Kennedy-Shaffer L, Grad YH, Robins JM, Lipsitch M. Potential biases arising from epidemic dynamics in observational seroprotection studies. American Journal of Epidemiology. 2020 Sep 1:kwaa188. doi: 10.1093/aje/kwaa188.

Larremore DB, Bubar KM, Grad YH. Implications of test characteristics and population seroprevalence on ‘immune passport’ strategies. Clinical Infectious Diseases. 2020. 

Brynildsrud OB, Osnes MN, Ma KC, Grad YH, Koomey JM, Caugant DA, Eldholm V. High-frequency phase-switching of modB methylase is associated with phenotypic ceftriaxone susceptibility in Neisseria gonorrhoeae. bioRxiv. 2020.

Hicks AL, Kissler SM, Mortimer TD, Ma KC, Taiaroa G, Ashcroft M, Williamson DA, Lipsitch M, Grad YH. Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants. eLife. 2020;9:e56367. DOI: Accompanied by a commentary

Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, Buckee CO. Modeling the comparative impact of individual quarantine vs active monitoring of contacts for the mitigation of COVID-19. Lancet Infectious Diseases. 2020 May 20:S1473-3099(20)30361-3.

Kissler SM, Tedijanto C, Goldstein E, Grad YH*, Lipsitch M*. Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period. Science. 2020 May 22;368(6493):860-868. *co-senior authors

Buckee CO, Balsari S, Chan J, Crosas M, Dominici F, Gasser U, Grad YH, Grenfell B, Halloran ME, Kraemer MUG, Lipsitch M, Metcalf CJE, Meyers LA, Perkins TA, Santillana M, Scarpino SV, Viboud C, Wesolowski A, Schroeder A. Aggregated mobility data could help fight COVID-19. Science. 23 Mar 2020: DOI: 10.1126/science.abb8021

Kissler SM, Klevens M, Barnett ML, Grad YH. Distinguishing the roles of antibiotic stewardship and reductions in outpatient visits in generating a five-year decline in antibiotic prescribing. Clinical Infectious Diseases. 2020 Mar 16. pii: ciaa269. doi: 10.1093/cid/ciaa269. 

Yaesoubi R, Cohen T, Hsu K, Gift TL, Chesson H, Salomon JA, Grad YH. Adaptive guidelines for the treatment of gonorrhea to increase the effective life span of antibiotics among men who have sex with men in the United States: A mathematical modeling study. PLOS Medicine. 2020. 17(4):e1003077.

Rubin DHF, Ross JDC, Grad YH. The frontiers of addressing antibiotic resistance in Neisseria gonorrhoeae. Translational Research. 2020 Feb 29. pii: S1931-5244(20)30031-1. doi: 10.1016/j.trsl.2020.02.002.

Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O’Grady J, Baym M, and Hanage WP. Rapid heuristic inference of antibiotic resistance and susceptibility by genomic neighbor typing. Nature Microbiology. 2020.

Palace SG, Wang Y, Rubin DHF, Welsh MA, Mortimer TD, Cole K, Eyre DW, Walker S, Grad YH. RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates. eLife. 2020;9:e51407 DOI: 10.7554/eLife.51407.

Volz EM, Wiuf C, Grad YH, Frost SDW, Dennis AM, Didelot X. Identification of hidden population structure in time-scaled phylogenies. Systematic Biology. 2020. Feb 12. pii: syaa009. doi: 10.1093/sysbio/syaa009.

Tedijanto CR, Grad YH, Lipsitch M. Potential impact of outpatient stewardship interventions on antibiotic exposures of bacterial pathogens. eLife. 2020. 2020 Feb 5;9. pii: e52307. doi: 10.7554/eLife.52307.

Wohl S, Metsky HC, Schaffner SF, Piantadosi A, Burns M, Lewnard JA, Chak B, Krasilnikova LA, Siddle KJ, Matranga CB, Bankamp B, Bennigan S, Sabina B, Byrne EH, McNall RJ, Park DJ, Gharib S, Fitzgerald S, Berriera P, Fleming S, Lett S, Rota PA, Madoff LC, MacInnis BL, Yozwiak NL, Smole S, Grad YH, Sabeti PC. Combining genomics and epidemiology to track mumps virus transmission in the United States. PLOS Biology. 2020. 18(2): e3000611.


Hadjineophytou C, Anonsen JH, Wang N, Ma KC, Viburiene R, Vik Å, Grad YH, Koomey JM. Genetic determinants of genus-wide glycan diversity in a bacterial protein glycosylation system. PLOS Genetics. 2019 Dec 23;15(12):e1008532. doi: 10.1371/journal.pgen.1008532.

Ryu S, Cowling B, Wu P, Olesen S, Fraser C, Sun DS, Lipsitch M, Grad YH. Case-based surveillance of antimicrobial resistance with full susceptibility profiles. JAC Antimicrob Resist. 2019. doi:10.1093/jacamr/dlz070

Coe KA, Lee W, Komazin-Meredeith G, Meredith TC, Grad YH, Walker S. Comparative Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus despite strain-dependent differences in essentiality of shared cell envelope genes. PLOS Pathogens. 2019 Nov 18;15(11):e1007862. doi: 10.1371/journal.ppat.1007862.

Hicks AL, Kissler SM, Lipsitch M*, Grad YH*. Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics. PLOS Biology. 2019. 17(11): e3000547. *co-senior authors.

Arnold BJ, Sohail M, Wadsworth CB, Corander J, Hanage WP, Sunyaev S, Grad YH. Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen. Molecular Biology and Evolution. 2019 Oct 7. pii: msz225. doi: 10.1093/molbev/msz225.

Abuelezam NN, Reshef YA, Novak D, Grad YH, Seage GR, Mayer K, Lipsitch M. Interaction patterns of men who have sex with men on a geosocial networking phone application in seven U.S. metropolitan areas. J Med Internet Res. 2019; 21(8):e13766 doi 10.2196/13766

Hicks AL, Wheeler N, Sanchez-Buso L, Rakeman JL, Harris SR, Grad YH. Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data. PLOS Computational Biology. 2019. 15(9): e1007349.

Williamson D, Chow E, Gorrie C, Seemann, T, Ingle D, Higgins N, Easton M, Taiaroa G, Grad YH, Kwong J, Fairley C, Chen M, Howden B. Bridging of Neisseria gonorrhoeae across diverse sexual networks in the HIV pre-exposure prophylaxis (PrEP) era: A clinical and molecular epidemiological study. Nature Communications. 2019 Sep 5;10(1):3988. doi: 10.1038/s41467-019-12053-4.

Sanchez-Buso L, Golparian D, Corander J, Grad YH, Ohnishi M, Flemming R, Parkhill J, Bentley SD, Unemo M, Harris SR. The impact of antimicrobials on gonococcal evolution. Nature Microbiology. 2019 Jul 29. doi: 10.1038/s41564-019-0501-y.

Wadsworth CB, Sater MRA, Bhattacharyya RP, Grad YH. Impact of population structure on the design of RNA-based diagnostics for antibiotic resistance in Neisseria gonorrhoeae. Antimicrob. Agents Chemother. 2019 May 28. pii: AAC.00549-19. doi: 10.1128/AAC.00549-19.

Olesen SW, MacFadden D, Grad YH. Cumulative probability of receiving an antibiotic prescription. New England Journal of Medicine. 2019; 380:1872-1873. DOI: 10.1056/NEJMc1816699.

Olesen SW and Grad YH. Deciphering the impact of bystander selection for antibiotic resistance in Neisseria gonorrhoeae. Journal of Infectious Diseases. 2019 Apr 8. pii: jiz156. doi: 10.1093/infdis/jiz156. Selected as “Editor’s Choice”!

Klevens M, Caten E, Olesen SW, DeMaria A Jr, Troppy S, Grad YH. Outpatient antibiotic prescribing in Massachusetts, 2011-2015. Open Forum Infectious Diseases. 2019.

Järvenpää M, Sater M, Lagoudas G, Blainey P, Miller L, McKinnnell J, Huang S, Grad YH*, Marttinen P*. A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation. PLoS Comput Biol 15(4): e1006534. *co-senior authors

Wang Y, Baglo Y, Ferrer-Espada R, Goh XS, Held KD, Grad YH, Gu Y, Gelfand JA, Dai T. Photo-inactivation of Neisseria gonorrhoeae: A paradigm changing approach for combating antibiotic-resistant gonococcal infection. J Infect Dis. 2019 Jan 9. doi: 10.1093/infdis/jiz018.


Olesen SW, Barnett M, MacFadden D, Brownstein JS, Hernández-Díaz S, Lipsitch M, Grad YH. The distribution of antibiotic use and its effect on antibiotic resistance. eLife. 2018. 7:e39435 DOI: 10.7554/eLife.39435. Highlighted in CIDRAP

Tedijanto C, Olesen SW, Grad YH, Lipsitch M. Estimating the proportion of bystander selection for antibiotic resistance in the US. PNAS. 2018. 201810840; DOI: 10.1073/pnas.1810840115.

Olesen SW, Torrone EA, Papp JR, Kirkcaldy RD, Lipsitch M, Grad YH. Azithromycin susceptibility in Neisseria gonorrhoeae and seasonal macrolide use. Journal of Infectious Diseases. 2018 Sep 15. doi: 10.1093/infdis/jiy551. Highlighted in CIDRAP

Olesen SW, Grad YH. Racial/ethnic disparities in antibiotic use. Emerging Infectious Diseases. 2018. DOI: 10.3201/eid2411.180762. Highlighted in CIDRAP

Hicks N, Yang J, Zhang X, Zhao B, Grad YH, Liu L, Ou X, Chang Z, Xia H, Zhou Y, Wang S, Dong J, Sun L, Zhu Y, Zhao Y, Jin Q, Fortune S. Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance. Nature Microbiology. 2018 Aug 6. doi: 10.1038/s41564-018-0218-3.

Wadsworth CB, Arnold BJ, Abdul Sater MR, Grad YH. Azithromycin resistance through interspecific acquisition of an epistasis dependent efflux pump component and transcriptional regulator in Neisseria gonorrhoeae. mBio. 2018. 9:e01419-18. Highlighted in an accompanying commentary!

Olesen SW, Barnett ML, McFadden DR, Lipsitch M, Grad YH. Trends in outpatient antibiotic prescribing practice among US older adults, 2011-2015: an observational study. BMJ. 2018 Jul 27;362:k3155. doi: 10.1136/bmj.k3155. Featured in CIDRAP article.

Mortimer TD, Grad YH. Applications of genomics to slow the spread of multidrug-resistant Neisseria gonorrhoeae. Ann NY Acad Sci. 2018 doi: 10.1111/nyas.13871
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Lewnard JA and Grad YH. Vaccine waning and mumps re-emergence in the United States. Science Translational Medicine. 2018. DOI: 10.1126/scitranslmed.aao5945 Press in NYT, CNN, Science, and Philly Inquirer among others. And highlighted in a great piece on waning vaccine immunity in Science.

Cobey S, Gouma S, Parkhouse K, Chambers BS, Ertl HC, Schmader KE, Halpin RA, Lin X, Stockwell TB, Das S, Landon E, Tesic V, Youngster I, Pinsky BA, Wentworth D, Hensley SE, Grad YH. Poor immunogenicity, not vaccine strain egg adaptation, may explain the low H3N2 influenza vaccine effectiveness in 2012-13. Clinical Infectious Diseases. 2018 Feb 20. doi: 10.1093/cid/ciy097. Press in ABC News, among others.

Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP. Weak Epistasis May Drive Adaptation in Recombining Bacteria. Genetics. 2018 Jan 12. pii: genetics.300662.2017. doi: 10.1534/genetics.117.300662.


Kanjilal S, Sater M, Thayer M, Lagoudas G, Kim S, Blainey P, Grad YH. Trends in Antibiotic Susceptibility in Staphylococcus aureus in Boston, Massachusetts, from 2000 to 2014. J Clin Micro. 2017 Nov 1. pii: JCM.01160-17.

Ma KC, Unemo M, Jeverica S, Kirkcaldy RD, Takahashi H, Ohnishi M, Grad YH. Genomic characterization of urethritis-associated Neisseria meningitidis shows that a wide range of N. meningitidis strains can cause urethritis. J Clin Micro. 2017 Dec;55(12):3374-3383.
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Tuite AR, Gift TL, Chesson HW, Hsu K, Salomon JA, Grad YH. Impact of rapid susceptibility testing and antibiotic selection strategy on the emergence and spread of antibiotic resistance in gonorrhea. J Infect Dis. 2017 Nov 27;216(9):1141-1149.

Lau JW, Kim YI, Murphy R, Newman R, Yang X, Zody M, DeVincenzo J, Grad YH. Deep sequencing of RSV from an adult challenge study and from naturally infected infants reveals heterogeneous diversification dynamics. Virology. 2017 Oct;510:289-296. Selected for Virology Highlights Blog!

Piantadosi A, Mukerji SS, Chitneni P, Cho TA, Cosimi LA, Hung DT, Goldberg MB, Sabeti PC, Kuritzkes DR, Grad YH. Metagenomic sequencing of an echovirus 30 genome from cerebrospinal fluid of a patient with aseptic meningitis and orchitis. Open Forum Infect Dis. 2017 Jul 28;4(3):ofx138.

Eyre DW, De Silva D, Cole K, Peters J, Cole MJ, Grad YH, Demczuk W, Martin I, Mulvey MR, Crook DW, Walker AS, Peto TEA, Paul J. WGS to predict antibiotic MICs for Neisseria gonorrhoeae J Antimicrob Chemother. 2017. Mar 10. doi: 10.1093/jac/dkx067

Peak C, Childs L, Grad Y, Buckee CO. A Quantitative Comparison of Non-Pharmaceutical Interventions for Containing Emerging Epidemics. Proc Natl Acad Sci. 2017. published ahead of print March 28, 2017, doi:10.1073/pnas.1616438114

Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O’Brien TF, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP. Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc Natl Acad Sci. 2017 Jan 17. pii: 201616248. doi: 10.1073/pnas.1616248114


Johnson SR, Grad Y, Abrams AJ, Pettus K, Trees DL. Use of whole-genome sequencing data to analyze 23S rRNA-mediated azithromycin resistance. Int J Antimicrob Agents. 2017 Feb;49(2):252-254. doi: 10.1016/j.ijantimicag.2016.10.023. Epub 2016 Dec 19.

Grad YH, Harris SR, Kirkcaldy RD, Green AG, Marks DS, Bentley SD, Trees D, Lipsitch M. Genomic epidemiology of gonococcal resistance to extended spectrum cephalosporins, macrolides, and fluoroquinolones in the US, 2000-2013. J Infect Dis. 2016 Nov 15;214(10):1579-1587. Epub 2016 Sep 16.

Harrison OB, Clemence M, Dillard JP, Tang CM, Trees D, Grad YH, Maiden MC. Genomic analyses of Neisseria gonorrhoeae reveal an association of the gonococcal genetic island with antimicrobial resistanceJ Infect. 2016 Dec;73(6):578-587. doi: 10.1016/j.jinf.2016.08.010. Epub 2016 Aug 26.

Chang H-H, Huber RG, Bond PJ, Grad YH, Camerini D, Mauer-Stroh S, Lipsitch M.  Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses . Bull World Health Organ. Bulletin of the World Health Organization 2017;95:517-525I. E-pub: 18 July 2016

De Silva D, Peters J, Cole K, Cole MJ, Cresswell F, Dean G, Dave J, Thomas D Rh, Foster K, Waldram A, Wilson DJ, Didelot X, Grad YH, Crook DW, Peto TEA, Walker AS, Paul J, Eyre DW. Whole-genome sequencing to determine Neisseria gonorrhoeae transmission: an observational study. Lancet Infect Dis. 2016 Nov;16(11):1295-1303. doi: 10.1016/S1473-3099(16)30157-8. Epub 2016 Jul 12.

Unemo M, Golparian D, Sánchez-Busó L, Grad Y, Jacobsson S, Ohnishi M, Lahra M, Limnios A, Sikora A, Wi T, Harris S. The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations – phenotypic, genetic and reference genome characterization. J Antimicrob Chemother. 2016 Nov;71(11):3096-3108. Epub 2016 Jul 17.

Grad YH, Fortune SM. Biodiversity and hypervirulence of Listeria monocytogenes. Nat Genet. 2016 Mar;48(3):229-30. doi: 10.1038/ng.3515.

Grad YH, Goldstein E, Lipsitch M, White P. Improving control of antibiotic resistant gonorrhea by integrating research agendas across disciplines: key questions arising from mathematical modeling. J Infect Dis. 2016 Mar 15;213(6):883-90. doi: 10.1093/infdis/jiv517. Epub 2015 Oct 30.


2015 and before

Chang H, Cohen T, Grad YH, Hanage WP, O’Brien TF, Lispitch M. Origin and proliferation of multiple drug resistance in bacterial pathogens. Microbiol Mol Biol Rev. 2015 Mar;79(1):101-16. doi: 10.1128/MMBR.00039-14.

Hollenbeck BL, Gannon S, Qian Q, and Grad YH. Genome sequence and analysis of resistance and virulence determinants in a strain of Neisseria mucosa causing native-valve endocarditis. JMM Case Reports. 2015.

Pessia A, Grad YH, Cobey S, Puranen JS, Corander J. K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets. Microbial Genomics. 2015 Jul 15;1(1):e000025. doi: 10.1099/mgen.0.000025. eCollection 2015 Jul.

Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public healthGenome Biol. 2014 Nov 18;15(11):538. doi: 10.1186/s13059-014-0538-4.

Johnson SR, Grad Y, Ganakammal SR, Burroughs M, Frace M, et al. In Vitro selection of Neisseria gonorrhoeae mutants with elevated MIC values and increased resistance to cephalosporins. Antimicrob Agents Chemother. 2014 Nov;58(11):6986-9. doi: 10.1128/AAC.03082-14. Epub 2014 Sep 8.

Watkins ER, Grad YH, Gupta S, Buckee CO. Contrasting within- and between-host immune selection shapes Neisseria Opa repertoires. Sci Rep. 2014 Oct 9;4:6554. doi: 10.1038/srep06554.

Grad YH, Newman R, Zody M, Yang X, Murphy R, et al. Within-host whole-genome deep sequencing and diversity analysis of human respiratory syncytial virus infection reveals dynamics of genomic diversity in the absence and presence of immune pressure. J Virol. 2014 Jul;88(13):7286-93.

Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR, et al. Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. Lancet Infect Dis. 2014 Mar;14(3):220-6. doi: 10.1016/S1473-3099(13)70693-5. Epub 2014 Jan 22.

Grad YH, Waldor MK. Deciphering the origins and tracking the evolution of cholera epidemics with whole-genome-based molecular epidemiology. MBio. 2013 Sep 10;4(5):e00670-13. doi: 10.1128/mBio.00670-13

Croucher NJ, Harris SR, Grad YH, Hanage WP. Bacterial genomes in epidemiology–present and future. Philos Trans R Soc Lond B Biol Sci. 2013 Feb 4;368(1614):20120202. doi: 10.1098/rstb.2012.0202. Print 2013 Mar 19.

Wei K, Vaidya A, Rohloff P, Sun YP, Grad Y. Interactive medical case. A patient with fevers and fatigue. N Engl J Med. 2013 Feb 14;368(7):e9. doi: 10.1056/NEJMimc1208059.

Grad YH, Godfrey P, Cerquiera GC, Mariani-Kurkdjian P, Gouali M, et al. Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. MBio. 2013 Jan 22;4(1):e00452-12. doi: 10.1128/mBio.00452-12.

Grad YH, Lipsitch M, Griggs AD, Haas BJ, Shea TP, et al. Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3065-70. doi: 10.1073/pnas.1121491109. Epub 2012 Feb 6.

Grad YH, Miller JC, Lipsitch M. Cholera modeling: challenges to quantitative analysis and predicting the impact of interventions. Epidemiology. 2012 Jul;23(4):523-30. doi: 10.1097/EDE.0b013e3182572581.

Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, et al. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3065-70. doi: 10.1073/pnas.1121491109. Epub 2012 Feb 6.

Grad YH, Lipsitch M, Aiello AE. Secular trends in Helicobacter pylori seroprevalence in adults in the United States: evidence for sustained race/ethnic disparities. Am J Epidemiol. 2012 Jan 1;175(1):54-9. doi: 10.1093/aje/kwr288. Epub 2011 Nov 15.

Grad YH, Seifter JL, Levy BD, Loscalzo J. Clinical problem-solving. Bitter pills. N Engl J Med. 2010 Nov 4