Pre-prints and publications

Mortimer TD, Grad YH (2023) A Genomic Perspective on the Near-term Impact of Doxycycline Post-exposure Prophylaxis on Neisseria gonorrhoeae Antimicrobial Resistance. Clinical Infectious Diseases 77:788–791.
Rubin DHF, Mortimer TD, Grad YH (2023) Neisseria gonorrhoeae ciprofloxacin susceptibility testing and gyrA targets – Authors’ reply. The Lancet Microbe 4:e575.
Rubin DH, Mortimer TD, Grad YH (2023) 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. The Lancet Microbe 4:e247–e254.
Bristow CC, Mortimer TD, Morris S, Grad YH, Soge OO, Wakatake E, Pascual R, Murphy SM, Fryling KE, Adamson PC, Dillon J-A, Parmar NR, Le HHL, Van Le H, Ovalles Ureña RM, Mitchev N, Mlisana K, Wi T, Dickson SP, Klausner JD (2023) Whole-Genome Sequencing to Predict Antimicrobial Susceptibility Profiles in Neisseria gonorrhoeae. The Journal of Infectious Diseases 227:917–925.
Martin SL, Mortimer TD, Grad YH (2023) Machine learning models for Neisseria gonorrhoeae antimicrobial susceptibility tests. Annals of the New York Academy of Sciences 1520:74–88.
Smith TM, Youngblom MA, Kernien JF, Mohamed MA, Fry SS, Bohr LL, Mortimer TD, O’Neill MB, Pepperell CS (2022) Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis. eLife 11:e78454.
Mortimer TD, Zhang JJ, Ma KC, Grad YH (2022) Loci for prediction of penicillin and tetracycline susceptibility in Neisseria gonorrhoeae: a genome-wide association study. The Lancet Microbe 3:e376–e381.
Hadjineophytou C, Anonsen JH, Svingerud T, Mortimer TD, Grad YH, Scott NE, Koomey M (2022) Sculpting the Bacterial O-Glycoproteome: Functional Analyses of Orthologous Oligosaccharyltransferases with Diverse Targeting Specificities. mBio 13:e03797-21.
Mortimer TD (2022) Interactions between Loci Contributing to Antimicrobial Resistance and Virulence in Neisseria gonorrhoeae. mBio 13:e00412-22.
Mortimer TD, Pathela P, Crawley A, Rakeman JL, Lin Y, Harris SR, Blank S, Schillinger JA, Grad YH (2021) The Distribution and Spread of Susceptible and Resistant Neisseria gonorrhoeae Across Demographic Groups in a Major Metropolitan Center. Clinical Infectious Diseases 73:e3146–e3155.
Pečerska J, Kühnert D, Meehan CJ, Coscollá M, de Jong BC, Gagneux S, Stadler T (2021) Quantifying transmission fitness costs of multi-drug resistant tuberculosis. Epidemics 36:100471.
Sánchez-Busó L, Yeats CA, Taylor B, Goater RJ, Underwood A, Abudahab K, Argimón S, Ma KC, Mortimer TD, Golparian D, Cole MJ, Grad YH, Martin I, Raphael BH, Shafer WM, Town K, Wi T, Harris SR, Unemo M, Aanensen DM (2021) A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch. Genome Medicine 13:61.
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 (2021) Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae. Genome Medicine 13:51.
Murphy TC, Mortimer TD, Nicholas RA, Wadsworth CB (2021) Draft Genome Sequences of Three Penicillin-Resistant Neisseria gonorrhoeae Strains Isolated in Cincinnati, Ohio, in 1994. Microbiol Resour Announc 10:.
Ogbebor O, Mortimer TD, Fryling K, Zhang JJ, Bhanot N, Grad YH (2021) Disseminated Gonococcal Infection Complicated by Prosthetic Joint Infection: Case Report and Genomic and Phylogenetic Analysis. Open Forum Infectious Diseases 8:.
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 (2020) Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea. Eurosurveillance 25:1900210.
Ma KC, Mortimer TD, Duckett MA, Hicks AL, Wheeler NE, Sánchez-Busó L, Grad YH (2020) Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae. Nature Communications 11:5374.
Ma KC, Mortimer TD, Grad YH (2020) Efflux Pump Antibiotic Binding Site Mutations Are Associated with Azithromycin Nonsusceptibility in Clinical Neisseria gonorrhoeae Isolates. mBio 11:e01509-20.
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 (2020) Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae. Nature Communications 11:4126.
Hicks AL, Kissler SM, Mortimer TD, Ma KC, Taiaroa G, Ashcroft M, Williamson DA, Lipsitch M, Grad YH (2020) Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants. eLife 9:e56367.
Palace SG, Wang Y, Rubin DH, Welsh MA, Mortimer TD, Cole K, Eyre DW, Walker S, Grad YH (2020) RNA polymerase mutations cause cephalosporin resistance in clinical Neisseria gonorrhoeae isolates. eLife 9:e51407.
Bohr LL, Mortimer TD, Pepperell CS (2020) Lateral Gene Transfer Shapes Diversity of Gardnerella spp. Front Cell Infect Microbiol 10:293.
Mortimer TD, Grad YH (2019) Applications of genomics to slow the spread of multidrug-resistant Neisseria gonorrhoeae. Annals of the New York Academy of Sciences 1435:93–109.
Doroshenko A, Pepperell CS, Heffernan C, Egedahl ML, Mortimer TD, Smith TM, Bussan HE, Tyrrell GJ, Long R (2018) Epidemiological and genomic determinants of tuberculosis outbreaks in First Nations communities in Canada. BMC Medicine 16:128.
Mortimer TD, Weber AM, Pepperell CS (2018) Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis. mSystems 3:e00108-17.
Mortimer TD, Annis DS, O’Neill MB, Bohr LL, Smith TM, Poinar HN, Mosher DF, Pepperell CS (2017) Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus. mSphere 2:e00511-17.
Mortimer TD, Weber AM, Pepperell CS (2017) Evolutionary Thrift: Mycobacteria Repurpose Plasmid Diversity during Adaptation of Type VII Secretion Systems. Genome Biol Evol 9:398–413.
Devault AM, Mortimer TD, Kitchen A, Kiesewetter H, Enk JM, Golding GB, Southon J, Kuch M, Duggan AT, Aylward W, Gardner SN, Allen JE, King AM, Wright G, Kuroda M, Kato K, Briggs DE, Fornaciari G, Holmes EC, Poinar HN, Pepperell CS (2017) A molecular portrait of maternal sepsis from Byzantine Troy. eLife 6:e20983.
Dang UJ, Devault AM, Mortimer TD, Pepperell CS, Poinar HN, Golding GB (2016) Estimation of Gene Insertion/Deletion Rates with Missing Data. Genetics 204:513–529.
O’Neill MB, Mortimer TD, Pepperell CS (2015) Diversity of Mycobacterium tuberculosis across Evolutionary Scales. PLoS Pathog 11:e1005257.
Mortimer TD, Pepperell CS (2014) Genomic Signatures of Distributive Conjugal Transfer among Mycobacteria. Genome Biol Evol 6:2489–2500.
Moncla LH, Ross TM, Dinis JM, Weinfurter JT, Mortimer TD, Schultz-Darken N, Brunner K, Iii SVC, Boettcher C, Post J, Johnson M, Bloom CE, Weiler AM, Friedrich TC (2013) A Novel Nonhuman Primate Model for Influenza Transmission. PLOS ONE 8:e78750.