Jennifer Gardy

Deputy Director, Surveillance, Data, & Epidemiology





Tornheim JA, Starks AM, Rodwell TC, Gardy JL, Walker TM, Cirillo DM, Jayashankar L, Miotto P, Zignol M, Schito M. (2019). Building the Framework for Standardized Clinical Laboratory Reporting of Next-generation Sequencing Data for Resistance-associated Mutations in Mycobacterium tuberculosis Complex. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 69(9)

Jackson C, Gardy JL, Shadiloo HC, Silva DS. (2019). Trust and the ethical challenges in the use of whole genome sequencing for tuberculosis surveillance: a qualitative study of stakeholder perspectives. BMC medical ethics, 20(1)

Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A. (2019). Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature reviews. Microbiology, 17(9)

Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C. (2019). Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Molecular biology and evolution, 36(3)

Mangan DF, Cloyd ET, Romo JA, Wessner DR, Westenberg DJ, Adukwu E, Menninger H, Gardy J. (2018). Introducing the JMBE themed issue on science communication. Journal of microbiology & biology education, 19(1)

Martin MA, Lee RS, Cowley LA, Gardy JL, Hanage WP. (2018). Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microbial genomics, 4(10)

Hasan NA, Warren RL, Epperson LE, Malecha A, Alexander DC, Turenne CY, MacMillan D, Birol I, Pleasance S, Coope R, Jones SJM, Romney MG, Ng M, Chan T, Rodrigues M, Tang P, Gardy JL, Strong M. (2017). Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease. Genome announcements, 5(37)

Gardy JL. (2017). Mycobacterium chimaera: unraveling a mystery through genomics. The Lancet. Infectious diseases, 17(10)

Gardy JL. (2016). Translating phylogeny into action for HIV surveillance. The lancet. HIV, 3(5)

Hatherell HA, Didelot X, Pollock SL, Tang P, Crisan A, Johnston JC, Colijn C, Gardy JL. (2016). Declaring a tuberculosis outbreak over with genomic epidemiology. Microbial genomics, 2(5)

Gardy J, Loman NJ, Rambaut A. (2015). Real-time digital pathogen surveillance - the time is now. Genome biology, 16(1)

Miller RR, Reid WD, Mattman A, Yamabayashi C, Steiner T, Parker S, Gardy J, Tang P, Patrick DM. (2015). Submaximal exercise testing with near-infrared spectroscopy in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome patients compared to healthy controls: a case-control study. Journal of translational medicine, (13)

Gardy JL, Naus M, Amlani A, Chung W, Kim H, Tan M, Severini A, Krajden M, Puddicombe D, Sahni V, Hayden AS, Gustafson R, Henry B, Tang P. (2015). Whole-Genome Sequencing of Measles Virus Genotypes H1 and D8 During Outbreaks of Infection Following the 2010 Olympic Winter Games Reveals Viral Transmission Routes. The Journal of infectious diseases, 212(10)

Buxton JA, Omura J, Kuo M, Ross C, Tzemis D, Purssell R, Gardy J, Carleton B. (2015). Genetic determinants of cocaine-associated agranulocytosis. BMC research notes, (8)

Gardy JL. (2015). Towards genomic prediction of drug resistance in tuberculosis. The Lancet. Infectious diseases, 15(10)

Crisan A, Wong HY, Johnston JC, Tang P, Colijn C, Otterstatter M, Hiscoe L, Parker R, Pollock SL, Gardy JL. (2015). Spatio-temporal analysis of tuberculous infection risk among clients of a homeless shelter during an outbreak. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease, 19(9)

Patrick DM, Miller RR, Gardy JL, Parker SM, Morshed MG, Steiner TS, Singer J, Shojania K, Tang P,. (2015). Lyme Disease Diagnosed by Alternative Methods: A Phenotype Similar to That of Chronic Fatigue Syndrome. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 61(7)

Guthrie JL, Gardy JL. (2015). Accelerating tuberculosis elimination in low-incidence settings: the role of genomics. The European respiratory journal, 46(6)

Wlodarska M, Johnston JC, Gardy JL, Tang P. (2015). A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics. Clinical microbiology reviews, 28(2)

Cheng JM, Hiscoe L, Pollock SL, Hasselback P, Gardy JL, Parker R. (2015). A clonal outbreak of tuberculosis in a homeless population in the interior of British Columbia, Canada, 2008-2015. Epidemiology and infection, 143(15)

Tang P, Gardy JL. (2014). Stopping outbreaks with real-time genomic epidemiology. Genome medicine, 6(11)

Colijn C, Gardy J. (2014). Phylogenetic tree shapes resolve disease transmission patterns. Evolution, medicine, and public health, 2014(1)

Didelot X, Gardy J, Colijn C. (2014). Bayesian inference of infectious disease transmission from whole-genome sequence data. Molecular biology and evolution, 31(7)

Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P. (2013). Metagenomics for pathogen detection in public health. Genome medicine, 5(9)

Chaban B, Albert A, Links MG, Gardy J, Tang P, Hill JE. (2013). Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza. PloS one, 8(7)

Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, Johnston JC, Gardy J, Lipsitch M, Fortune SM. (2013). Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nature genetics, 45(7)

Gardy JL. (2013). Investigation of disease outbreaks with genome sequencing. The Lancet. Infectious diseases, 13(2)

Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M. (2013). Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nature genetics, 45(10)

Miller RR, Gardy JL, Tang P, Patrick DM. (2013). A metagenomic approach to investigate the microbial causes of myalgic encephalomyelitis/chronic fatigue syndrome: moving beyond XMRV. Fatigue : biomedicine, health & behavior, 1(4)

Skowronski DM, De Serres G, Janjua NZ, Gardy JL, Gilca V, Dionne M, Hamelin ME, Rhéaume C, Boivin G. (2012). Cross-reactive antibody to swine influenza A(H3N2) subtype virus in children and adults before and after immunisation with 2010/11 trivalent inactivated influenza vaccine in Canada, August to November 2010. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 17(4)

Cook VJ, Shah L, Gardy J. (2012). Modern contact investigation methods for enhancing tuberculosis control in aboriginal communities. International journal of circumpolar health, (71)

Skowronski DM, Hamelin ME, Janjua NZ, De Serres G, Gardy JL, Rhéaume C, Bouhy X, Boivin G. (2012). Cross-lineage influenza B and heterologous influenza A antibody responses in vaccinated mice: immunologic interactions and B/Yamagata dominance. PloS one, 7(6)

Janjua NZ, Skowronski DM, De Serres G, Dickinson J, Crowcroft NS, Taylor M, Winter AL, Hottes TS, Fonseca K, Charest H, Drews SJ, Sabaiduc S, Bastien N, Li Y, Gardy JL, Petric M. (2012). Estimates of influenza vaccine effectiveness for 2007-2008 from Canada's sentinel surveillance system: cross-protection against major and minor variants. The Journal of infectious diseases, 205(12)

Skowronski DM, Janjua NZ, De Serres G, Purych D, Gilca V, Scheifele DW, Dionne M, Sabaiduc S, Gardy JL, Li G, Bastien N, Petric M, Boivin G, Li Y. (2012). Cross-reactive and vaccine-induced antibody to an emerging swine-origin variant of influenza A virus subtype H3N2 (H3N2v). The Journal of infectious diseases, 206(12)

Skowronski DM, Janjua NZ, De Serres G, Winter AL, Dickinson JA, Gardy JL, Gubbay J, Fonseca K, Charest H, Crowcroft NS, Fradet MD, Bastien N, Li Y, Krajden M, Sabaiduc S, Petric M. (2012). A sentinel platform to evaluate influenza vaccine effectiveness and new variant circulation, Canada 2010-2011 season. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 55(3)

Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, Tang P. (2011). Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. The New England journal of medicine, 364(8)

Skowronski DM, Hottes TS, McElhaney JE, Janjua NZ, Sabaiduc S, Chan T, Gentleman B, Purych D, Gardy J, Patrick DM, Brunham RC, De Serres G, Petric M. (2011). Immuno-epidemiologic correlates of pandemic H1N1 surveillance observations: higher antibody and lower cell-mediated immune responses with advanced age. The Journal of infectious diseases, 203(2)

Cook VJ, Shah L, Gardy J, Bourgeois AC. (2011). Recommendations on modern contact investigation methods for enhancing tuberculosis control. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease, 16(3)

Joly Y, Koutrikas G, Ramos-Paque E, Zawati M, Gardy J, Hayden MR, Carleton BC. (2011). Diagnostic testing for vaccinomics: is the regulatory approval framework adequate? A comparison of Canada, the United States, and Europe. Omics : a journal of integrative biology, 15(9)

Lee SM, Chan RW, Gardy JL, Lo CK, Sihoe AD, Kang SS, Cheung TK, Guan YI, Chan MC, Hancock RE, Peiris MJ. (2010). Systems-level comparison of host responses induced by pandemic and seasonal influenza A H1N1 viruses in primary human type I-like alveolar epithelial cells in vitro. Respiratory research, (11)

Brown KL, Falsafi R, Kum W, Hamill P, Gardy JL, Davidson DJ, Turvey S, Finlay BB, Speert DP, Hancock RE. (2010). Robust TLR4-induced gene expression patterns are not an accurate indicator of human immunity. Journal of translational medicine, (8)

Skowronski DM, Hottes TS, Janjua NZ, Purych D, Sabaiduc S, Chan T, De Serres G, Gardy J, McElhaney JE, Patrick DM, Petric M. (2010). Prevalence of seroprotection against the pandemic (H1N1) virus after the 2009 pandemic. CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne, 182(17)

Skowronski DM, De Serres G, Crowcroft NS, Janjua NZ, Boulianne N, Hottes TS, Rosella LC, Dickinson JA, Gilca R, Sethi P, Ouhoummane N, Willison DJ, Rouleau I, Petric M, Fonseca K, Drews SJ, Rebbapragada A, Charest H, Hamelin ME, Boivin G, Gardy JL, Li Y, Kwindt TL, Patrick DM, Brunham RC,. (2010). Association between the 2008-09 seasonal influenza vaccine and pandemic H1N1 illness during Spring-Summer 2009: four observational studies from Canada. PLoS medicine, 7(4)

Mookherjee N, Lippert DN, Hamill P, Falsafi R, Nijnik A, Kindrachuk J, Pistolic J, Gardy J, Miri P, Naseer M, Foster LJ, Hancock RE. (2009). Intracellular receptor for human host defense peptide LL-37 in monocytes. Journal of immunology (Baltimore, Md. : 1950), 183(4)

Lee SM, Gardy JL, Cheung CY, Cheung TK, Hui KP, Ip NY, Guan Y, Hancock RE, Peiris JS. (2009). Systems-level comparison of host-responses elicited by avian H5N1 and seasonal H1N1 influenza viruses in primary human macrophages. PloS one, 4(12)

Mookherjee N, Hamill P, Gardy J, Blimkie D, Falsafi R, Chikatamarla A, Arenillas DJ, Doria S, Kollmann TR, Hancock RE. (2009). Systems biology evaluation of immune responses induced by human host defence peptide LL-37 in mononuclear cells. Molecular bioSystems, 5(5)

Gardy JL, Lynn DJ, Brinkman FS, Hancock RE. (2009). Enabling a systems biology approach to immunology: focus on innate immunity. Trends in immunology, 30(6)

Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan TH, Shah N, Lo R, Naseer M, Que J, Yau M, Acab M, Tulpan D, Whiteside MD, Chikatamarla A, Mah B, Munzner T, Hokamp K, Hancock RE, Brinkman FS. (2008). InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular systems biology, (4)

Cosseau C, Devine DA, Dullaghan E, Gardy JL, Chikatamarla A, Gellatly S, Yu LL, Pistolic J, Falsafi R, Tagg J, Hancock RE. (2008). The commensal Streptococcus salivarius K12 downregulates the innate immune responses of human epithelial cells and promotes host-microbe homeostasis. Infection and immunity, 76(9)

Vivona S, Gardy JL, Ramachandran S, Brinkman FS, Raghava GP, Flower DR, Filippini F. (2008). Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends in biotechnology, 26(4)

Barsky A, Gardy JL, Hancock RE, Munzner T. (2007). Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics (Oxford, England), 23(8)

Brown KL, Cosseau C, Gardy JL, Hancock RE. (2007). Complexities of targeting innate immunity to treat infection. Trends in immunology, 28(6)

Gardy JL, Brinkman FS. (2006). Methods for predicting bacterial protein subcellular localization. Nature reviews. Microbiology, 4(10)

Rey S, Gardy JL, Brinkman FS. (2005). Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria. BMC genomics, (6)

Rey S, Acab M, Gardy JL, Laird MR, deFays K, Lambert C, Brinkman FS. (2005). PSORTdb: a protein subcellular localization database for bacteria. Nucleic acids research, 33(Database issue)

Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS. (2005). PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics (Oxford, England), 21(5)

Lewenza S, Gardy JL, Brinkman FS, Hancock RE. (2005). Genome-wide identification of Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. Genome research, 15(2)

Gardy JL, Spencer C, Wang K, Ester M, Tusnády GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS. (2003). PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic acids research, 31(13)