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Jennifer Gardy

Deputy Director, Surveillance, Data, & Epidemiology

Education

Affiliations

Projects

Papers

Guthrie JL, Ronald LA, Cook VJ, Johnston J, Gardy JL. (2019). The problem with defining foreign birth as a risk factor in tuberculosis epidemiology studies. PloS one, 14(4)

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)

Bouquet J, Li T, Gardy JL, Kang X, Stevens S, Stevens J, VanNess M, Snell C, Potts J, Miller RR, Morshed M, McCabe M, Parker S, Uyaguari M, Tang P, Steiner T, Chan WS, De Souza AM, Mattman A, Patrick DM, Chiu CY. (2019). Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing. PloS one, 14(3)

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)

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)

Crisan A, Munzner T, Gardy JL. (2019). Adjutant: an R-based tool to support topic discovery for systematic and literature reviews. Bioinformatics (Oxford, England), 35(6)

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)

Guthrie JL, Marchand-Austin A, Cronin K, Lam K, Pyskir D, Kong C, Jorgensen D, Rodrigues M, Roth D, Tang P, Cook VJ, Johnston J, Jamieson FB, Gardy JL. (2019). Universal genotyping reveals province-level differences in the molecular epidemiology of tuberculosis. PloS one, 14(4)

Guthrie JL, Strudwick L, Roberts B, Allen M, McFadzen J, Roth D, Jorgensen D, Rodrigues M, Tang P, Hanley B, Johnston J, Cook VJ, Gardy JL. (2019). Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region. Epidemiology and infection, (147)

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)

Crisan A, Gardy JL, Munzner T. (2019). A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT. Bioinformatics (Oxford, England), 35(10)

Guthrie JL, Kong C, Roth D, Jorgensen D, Rodrigues M, Tang P, Thejoe M, Elwood K, Cook VJ, Johnston J, Gardy JL. (2018). Universal Genotyping for Tuberculosis Prevention Programs: a 5-Year Comparison with On-Request Genotyping. Journal of clinical microbiology, 56(5)

Guthrie JL, Delli Pizzi A, Roth D, Kong C, Jorgensen D, Rodrigues M, Tang P, Cook VJ, Johnston J, Gardy JL. (2018). Genotyping and Whole-Genome Sequencing to Identify Tuberculosis Transmission to Pediatric Patients in British Columbia, Canada, 2005-2014. The Journal of infectious diseases, 218(7)

Feijao P, Yao HT, Fornika D, Gardy J, Hsiao W, Chauve C, Chindelevitch L. (2018). MentaLiST - A fast MLST caller for large MLST schemes. Microbial genomics, 4(2)

Günther OP, Gardy JL, Stafford P, Fluge Ø, Mella O, Tang P, Miller RR, Parker SM, Johnston SA, Patrick DM. (2019). Immunosignature Analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Molecular neurobiology, 56(6)

Crisan A, McKee G, Munzner T, Gardy JL. (2018). Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory. PeerJ, (6)

Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. (2018). Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. The New England journal of medicine, 379(15)

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)

Comas I, Gardy JL. (2018). TB Transmission: Closing the Gaps. EBioMedicine, (34)

Guthrie JL, Kong C, Roth D, Jorgensen D, Rodrigues M, Hoang L, Tang P, Cook V, Johnston J, Gardy JL. (2018). Molecular Epidemiology of Tuberculosis in British Columbia, Canada: A 10-Year Retrospective Study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 66(6)

Didelot X, Fraser C, Gardy J, Colijn C. (2017). Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks. Molecular biology and evolution, 34(4)

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

Guthrie JL, Fisman D, Gardy JL. (2017). Self-rated health and reasons for non-vaccination against seasonal influenza in Canadian adults with asthma. PloS one, 12(2)

Gardy JL, Loman NJ. (2018). Towards a genomics-informed, real-time, global pathogen surveillance system. Nature reviews. Genetics, 19(1)

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)

Bouquet J, Gardy JL, Brown S, Pfeil J, Miller RR, Morshed M, Avina-Zubieta A, Shojania K, McCabe M, Parker S, Uyaguari M, Federman S, Tang P, Steiner T, Otterstater M, Holt R, Moore R, Chiu CY, Patrick DM,. (2017). RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 64(4)

Tsui CKM, Wong D, Narula G, Gardy JL, Hsiao WWH, Av-Gay Y. (2017). Genome Sequences of the Mycobacterium tuberculosis H37Rv-ptkA Deletion Mutant and Its Parental Strain. Genome announcements, 5(44)

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

Ip CL, Pybus OG, Gardy JL. (2016). Virus genomics and evolution: the transformative effect of new technologies and multidisciplinary collaboration on virus research and outbreak management. Genome biology, 17(1)

Guthrie JL, Gardy JL. (2017). A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Annals of the New York Academy of Sciences, 1388(1)

Miller RR, Uyaguari-Diaz M, McCabe MN, Montoya V, Gardy JL, Parker S, Steiner T, Hsiao W, Nesbitt MJ, Tang P, Patrick DM,. (2016). Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects. PloS one, 11(11)

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)

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)

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

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)

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)

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)

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)

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)

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

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

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

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

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

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

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)

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)

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)

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, 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)

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)

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

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)

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)

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)

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)

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, 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)

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)

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)

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)

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)

Barsky A, Munzner T, Gardy J, Kincaid R. Cerebral: visualizing multiple experimental conditions on a graph with biological context. IEEE transactions on visualization and computer graphics, 14(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)

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)

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, 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)

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, 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)

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