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Items: 1 to 50 of 90

1.

Detection of Antimicrobial Resistance Using Proteomics and the Comprehensive Antibiotic Resistance Database: a Case Study.

Chen CY, Clark CG, Langner S, Boyd DA, Bharat A, McCorrister SJ, McArthur AG, Graham MR, Westmacott GR, Van Domselaar G.

Proteomics Clin Appl. 2019 Dec 24:e1800182. doi: 10.1002/prca.201800182. [Epub ahead of print]

PMID:
31872964
2.

Whole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada.

Tsang RSW, Shuel M, Ahmad T, Hayden K, Knox N, Van Domselaar G, Hoang L, Tyrrell GJ, Minion J, Van Caeseele P, Kus JV, Ulanova M, Lefebvre B, Haldane D, Garceau R, German G, Zahariadis G, Hanley B, Kandola K, Patterson M.

Can J Microbiol. 2019 Oct 29:1-12. doi: 10.1139/cjm-2019-0406. [Epub ahead of print]

PMID:
31661630
3.

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.

Tyson S, Peterson CL, Olson A, Tyler S, Knox N, Griffiths E, Dooley D, Hsiao W, Cabral J, Johnson RP, Laing C, Gannon V, Lynch T, Van Domselaar G, Brinkman F, Graham M.

Microbiol Resour Announc. 2019 Oct 10;8(41). pii: e00625-19. doi: 10.1128/MRA.00625-19.

4.

Comparative diversity of microbiomes and Resistomes in beef feedlots, downstream environments and urban sewage influent.

Zaheer R, Lakin SM, Polo RO, Cook SR, Larney FJ, Morley PS, Booker CW, Hannon SJ, Van Domselaar G, Read RR, McAllister TA.

BMC Microbiol. 2019 Aug 27;19(1):197. doi: 10.1186/s12866-019-1548-x.

5.

PD-1 of Sigmodon hispidus: Gene identification, characterization and preliminary evaluation of expression in inactivated RSV vaccine-induced enhanced respiratory disease.

Muralidharan A, Larocque L, Russell M, Creskey M, Li C, Chen W, Van Domselaar G, Cao J, Cyr T, Rosu-Myles M, Wang L, Li X.

Sci Rep. 2019 Aug 12;9(1):11638. doi: 10.1038/s41598-019-48225-x.

6.

The evolving nature of Bordetella pertussis in Ontario, Canada, 2009-2017: strains with shifting genotypes and pertactin deficiency.

Tsang RSW, Shuel M, Cronin K, Deng S, Whyte K, Marchand-Austin A, Ma J, Bolotin S, Crowcroft N, Schwartz K, Van Domselaar G, Graham M, Jamieson FB.

Can J Microbiol. 2019 Nov;65(11):823-830. doi: 10.1139/cjm-2019-0128. Epub 2019 Jul 11.

PMID:
31295416
7.

The Gut Microbiome in Inflammatory Bowel Disease: Lessons Learned From Other Immune-Mediated Inflammatory Diseases.

Knox NC, Forbes JD, Peterson CL, Van Domselaar G, Bernstein CN.

Am J Gastroenterol. 2019 Jul;114(7):1051-1070. doi: 10.14309/ajg.0000000000000305.

PMID:
31232832
8.

Unveiling Integrated Functional Pathways Leading to Enhanced Respiratory Disease Associated With Inactivated Respiratory Syncytial Viral Vaccine.

Russell MS, Creskey M, Muralidharan A, Li C, Gao J, Chen W, Larocque L, Lavoie JR, Farnsworth A, Rosu-Myles M, Hashem AM, Yauk CL, Cao J, Van Domselaar G, Cyr T, Li X.

Front Immunol. 2019 Mar 29;10:597. doi: 10.3389/fimmu.2019.00597. eCollection 2019.

9.

A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease?

Forbes JD, Bernstein CN, Tremlett H, Van Domselaar G, Knox NC.

Front Microbiol. 2019 Jan 9;9:3249. doi: 10.3389/fmicb.2018.03249. eCollection 2018. Review.

10.

The Gut Microbiome as a Target for IBD Treatment: Are We There Yet?

Knox NC, Forbes JD, Van Domselaar G, Bernstein CN.

Curr Treat Options Gastroenterol. 2019 Mar;17(1):115-126. doi: 10.1007/s11938-019-00221-w. Review.

PMID:
30661163
11.

Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria.

Reimer A, Weedmark K, Petkau A, Peterson CL, Walker M, Knox N, Kent H, Mabon P, Berry C, Tyler S, Tschetter L, Jerome M, Allen V, Hoang L, Bekal S, Clark C, Nadon C, Van Domselaar G, Pagotto F, Graham M, Farber J, Gilmour M.

Microb Genom. 2019 Jan;5(1). doi: 10.1099/mgen.0.000237. Epub 2019 Jan 16.

12.

A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?

Forbes JD, Chen CY, Knox NC, Marrie RA, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN, Van Domselaar G.

Microbiome. 2018 Dec 13;6(1):221. doi: 10.1186/s40168-018-0603-4.

13.

Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus.

Ji H, Enns E, Brumme CJ, Parkin N, Howison M, Lee ER, Capina R, Marinier E, Avila-Rios S, Sandstrom P, Van Domselaar G, Harrigan R, Paredes R, Kantor R, Noguera-Julian M.

J Int AIDS Soc. 2018 Oct;21(10):e25193. doi: 10.1002/jia2.25193.

14.

Whole genome sequencing and phylogenetic analysis of strains of the agent of Lyme disease Borrelia burgdorferi from Canadian emergence zones.

Tyler S, Tyson S, Dibernardo A, Drebot M, Feil EJ, Graham M, Knox NC, Lindsay LR, Margos G, Mechai S, Van Domselaar G, Thorpe HA, Ogden NH.

Sci Rep. 2018 Jul 12;8(1):10552. doi: 10.1038/s41598-018-28908-7.

15.

Identification of immunodominant CD8 epitope in the stalk domain of influenza B viral hemagglutinin.

Muralidharan A, Gravel C, Duran A, Larocque L, Li C, Zetner A, Van Domselaar G, Wang L, Li X.

Biochem Biophys Res Commun. 2018 Jul 12;502(2):226-231. doi: 10.1016/j.bbrc.2018.05.148. Epub 2018 May 24.

PMID:
29792863
16.

Impact of sequencing depth on the characterization of the microbiome and resistome.

Zaheer R, Noyes N, Ortega Polo R, Cook SR, Marinier E, Van Domselaar G, Belk KE, Morley PS, McAllister TA.

Sci Rep. 2018 Apr 12;8(1):5890. doi: 10.1038/s41598-018-24280-8.

17.

Whole genome typing of the recently emerged Canadian serogroup W Neisseria meningitidis sequence type 11 clonal complex isolates associated with invasive meningococcal disease.

Tsang RSW, Ahmad T, Tyler S, Lefebvre B, Deeks SL, Gilca R, Hoang L, Tyrrell G, Van Caeseele P, Van Domselaar G, Jamieson FB.

Int J Infect Dis. 2018 Apr;69:55-62. doi: 10.1016/j.ijid.2018.01.019. Epub 2018 Feb 4.

18.

Universal type/subtype-specific antibodies for quantitative analyses of neuraminidase in trivalent influenza vaccines.

Xu K, Li C, Gravel C, Jiang Z, Jaentschke B, Van Domselaar G, Li X, Wang J.

Sci Rep. 2018 Jan 18;8(1):1067. doi: 10.1038/s41598-017-18663-6.

19.

A primer on microbial bioinformatics for nonbioinformaticians.

Carriço JA, Rossi M, Moran-Gilad J, Van Domselaar G, Ramirez M.

Clin Microbiol Infect. 2018 Apr;24(4):342-349. doi: 10.1016/j.cmi.2017.12.015. Epub 2018 Jan 5. Review.

20.

Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.

Marinier E, Zaheer R, Berry C, Weedmark KA, Domaratzki M, Mabon P, Knox NC, Reimer AR, Graham MR, Chui L, Patterson-Fortin L, Zhang J, Pagotto F, Farber J, Mahony J, Seyer K, Bekal S, Tremblay C, Isaac-Renton J, Prystajecky N, Chen J, Slade P, Van Domselaar G.

Nucleic Acids Res. 2017 Oct 13;45(18):e159. doi: 10.1093/nar/gkx702.

21.

First description of rpsJ and mepA mutations associated with tigecycline resistance in Staphylococcus aureus isolated from a cystic fibrosis patient during antibiotic therapy.

Haim MS, Di Gregorio S, Galanternik L, Lubovich S, Vázquez M, Bharat A, Zaheer R, Golding GR, Graham M, Van Domselaar G, Cardona ST, Mollerach M.

Int J Antimicrob Agents. 2017 Dec;50(6):739-741. doi: 10.1016/j.ijantimicag.2017.10.003. Epub 2017 Oct 13. No abstract available.

PMID:
29038088
22.

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.

Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, Nadon C, Reimer A, Taboada E, Beiko RG, Hsiao W, Brinkman F, Graham M, Van Domselaar G.

Microb Genom. 2017 Jun 8;3(6):e000116. doi: 10.1099/mgen.0.000116. eCollection 2017 Jun 30.

23.

Application of whole genome sequence analysis to the study of Mycobacterium tuberculosis in Nunavut, Canada.

Tyler AD, Randell E, Baikie M, Antonation K, Janella D, Christianson S, Tyrrell GJ, Graham M, Van Domselaar G, Sharma MK.

PLoS One. 2017 Oct 5;12(10):e0185656. doi: 10.1371/journal.pone.0185656. eCollection 2017.

24.

Visualizing and comparing circular genomes using the CGView family of tools.

Stothard P, Grant JR, Van Domselaar G.

Brief Bioinform. 2019 Jul 19;20(4):1576-1582. doi: 10.1093/bib/bbx081.

25.

Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.

Griffiths E, Dooley D, Graham M, Van Domselaar G, Brinkman FSL, Hsiao WWL.

Front Microbiol. 2017 Jun 26;8:1068. doi: 10.3389/fmicb.2017.01068. eCollection 2017.

26.

A Primer on Infectious Disease Bacterial Genomics.

Lynch T, Petkau A, Knox N, Graham M, Van Domselaar G.

Clin Microbiol Rev. 2016 Oct;29(4):881-913. doi: 10.1128/CMR.00001-16. Epub 2016 Sep 7. Review.

27.

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.

Taboada EN, Graham MR, Carriço JA, Van Domselaar G.

Front Microbiol. 2017 May 23;8:909. doi: 10.3389/fmicb.2017.00909. eCollection 2017. Review.

28.

Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing.

Demczuk WHB, Martin I, Hoang L, Van Caeseele P, Lefebvre B, Horsman G, Haldane D, Gubbay J, Ratnam S, German G, Daley Bernier J, Strudwick L, McGeer A, Zhanel GG, Van Domselaar G, Graham M, Mulvey MR.

PLoS One. 2017 May 22;12(5):e0178040. doi: 10.1371/journal.pone.0178040. eCollection 2017.

29.

A Robust PCR Protocol for HIV Drug Resistance Testing on Low-Level Viremia Samples.

Gupta S, Taylor T, Patterson A, Liang B, Bullard J, Sandstrom P, Van Domselaar G, Ji H.

Biomed Res Int. 2017;2017:4979252. doi: 10.1155/2017/4979252. Epub 2017 Apr 3.

30.

A randomized trial to determine the impact of a digestion resistant starch composition on the gut microbiome in older and mid-age adults.

Alfa MJ, Strang D, Tappia PS, Graham M, Van Domselaar G, Forbes JD, Laminman V, Olson N, DeGagne P, Bray D, Murray BL, Dufault B, Lix LM.

Clin Nutr. 2018 Jun;37(3):797-807. doi: 10.1016/j.clnu.2017.03.025. Epub 2017 Mar 31.

31.

A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens.

Katz LS, Griswold T, Williams-Newkirk AJ, Wagner D, Petkau A, Sieffert C, Van Domselaar G, Deng X, Carleton HA.

Front Microbiol. 2017 Mar 13;8:375. doi: 10.3389/fmicb.2017.00375. eCollection 2017.

32.

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains.

Demczuk W, Sidhu S, Unemo M, Whiley DM, Allen VG, Dillon JR, Cole M, Seah C, Trembizki E, Trees DL, Kersh EN, Abrams AJ, de Vries HJC, van Dam AP, Medina I, Bharat A, Mulvey MR, Van Domselaar G, Martin I.

J Clin Microbiol. 2017 May;55(5):1454-1468. doi: 10.1128/JCM.00100-17. Epub 2017 Feb 22.

33.

Baseline Practices for the Application of Genomic Data Supporting Regulatory Food Safety.

Lambert D, Pightling A, Griffiths E, Van Domselaar G, Evans P, Berthelet S, Craig D, Chandry PS, Stones R, Brinkman F, Angers-Loustau A, Kreysa J, Tong W, Blais B.

J AOAC Int. 2017 May 1;100(3):721-731. doi: 10.5740/jaoacint.16-0269. Epub 2017 Jan 19.

PMID:
28105974
34.

First Complete Genome Sequence of Haemophilus influenzae Serotype a.

Iskander M, Hayden K, Van Domselaar G, Tsang R.

Genome Announc. 2017 Jan 19;5(3). pii: e01506-16. doi: 10.1128/genomeA.01506-16.

35.

Draft Genome Sequences of Burkholderia contaminans FFI-28, a Strain Isolated from a Contaminated Pharmaceutical Solution.

Haim MS, Mollerach M, Van Domselaar G, Teves SA, Degrossi J, Cardona ST.

Genome Announc. 2016 Oct 27;4(5). pii: e01177-16. doi: 10.1128/genomeA.01177-16.

36.

The Gut Microbiota in Immune-Mediated Inflammatory Diseases.

Forbes JD, Van Domselaar G, Bernstein CN.

Front Microbiol. 2016 Jul 11;7:1081. doi: 10.3389/fmicb.2016.01081. eCollection 2016. Review.

37.

Microbiome profiling of drinking water in relation to incidence of inflammatory bowel disease.

Forbes JD, Van Domselaar G, Sargent M, Green C, Springthorpe S, Krause DO, Bernstein CN.

Can J Microbiol. 2016 Sep;62(9):781-93. doi: 10.1139/cjm-2016-0219. Epub 2016 May 18.

PMID:
27420183
38.

A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker.

Peterson SW, Knox NC, Golding GR, Tyler SD, Tyler AD, Mabon P, Embree JE, Fleming F, Fanella S, Van Domselaar G, Mulvey MR, Graham MR.

PLoS One. 2016 Mar 28;11(3):e0152493. doi: 10.1371/journal.pone.0152493. eCollection 2016.

39.

Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients.

Forbes JD, Van Domselaar G, Bernstein CN.

Inflamm Bowel Dis. 2016 Apr;22(4):817-25. doi: 10.1097/MIB.0000000000000684.

PMID:
26937623
40.

Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014.

Demczuk W, Martin I, Peterson S, Bharat A, Van Domselaar G, Graham M, Lefebvre B, Allen V, Hoang L, Tyrrell G, Horsman G, Wylie J, Haldane D, Archibald C, Wong T, Unemo M, Mulvey MR.

J Clin Microbiol. 2016 May;54(5):1304-13. doi: 10.1128/JCM.03195-15. Epub 2016 Mar 2.

41.

Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis.

Tyler AD, Christianson S, Knox NC, Mabon P, Wolfe J, Van Domselaar G, Graham MR, Sharma MK.

PLoS One. 2016 Feb 5;11(2):e0148676. doi: 10.1371/journal.pone.0148676. eCollection 2016.

42.

Sequence database versioning for command line and Galaxy bioinformatics servers.

Dooley DM, Petkau AJ, Van Domselaar G, Hsiao WW.

Bioinformatics. 2016 Apr 15;32(8):1275-7. doi: 10.1093/bioinformatics/btv724. Epub 2015 Dec 12.

43.

Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations.

Bekal S, Berry C, Reimer AR, Van Domselaar G, Beaudry G, Fournier E, Doualla-Bell F, Levac E, Gaulin C, Ramsay D, Huot C, Walker M, Sieffert C, Tremblay C.

J Clin Microbiol. 2016 Feb;54(2):289-95. doi: 10.1128/JCM.02200-15. Epub 2015 Nov 18.

44.

Clostridium botulinum Group II Isolate Phylogenomic Profiling Using Whole-Genome Sequence Data.

Weedmark KA, Mabon P, Hayden KL, Lambert D, Van Domselaar G, Austin JW, Corbett CR.

Appl Environ Microbiol. 2015 Sep 1;81(17):5938-48. doi: 10.1128/AEM.01155-15. Epub 2015 Jun 26.

45.

Tatumella saanichensis sp. nov., isolated from a cystic fibrosis patient.

Tracz DM, Gilmour MW, Mabon P, Beniac DR, Hoang L, Kibsey P, Van Domselaar G, Tabor H, Westmacott GR, Corbett CR, Bernard KA.

Int J Syst Evol Microbiol. 2015 Jun;65(Pt 6):1959-66. doi: 10.1099/ijs.0.000207. Epub 2015 Mar 25.

PMID:
25807976
46.

Development and applications of universal H7 subtype-specific antibodies for the analysis of influenza H7N9 vaccines.

Gravel C, Elmgren C, Muralidharan A, Hashem AM, Jaentschke B, Xu K, Widdison J, Arnold K, Farnsworth A, Rinfret A, Van Domselaar G, Wang J, Li C, Li X.

Vaccine. 2015 Feb 25;33(9):1129-34. doi: 10.1016/j.vaccine.2015.01.034. Epub 2015 Jan 22.

PMID:
25620245
47.

Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations.

Ji H, Kozak RA, Biondi MJ, Pilon R, Vallee D, Liang BB, La D, Kim J, Van Domselaar G, Leonard L, Sandstrom P, Brooks J.

Virology. 2015 Mar;477:1-9. doi: 10.1016/j.virol.2014.12.037. Epub 2015 Jan 17.

48.

Whole-genome phylogenomic heterogeneity of Neisseria gonorrhoeae isolates with decreased cephalosporin susceptibility collected in Canada between 1989 and 2013.

Demczuk W, Lynch T, Martin I, Van Domselaar G, Graham M, Bharat A, Allen V, Hoang L, Lefebvre B, Tyrrell G, Horsman G, Haldane D, Garceau R, Wylie J, Wong T, Mulvey MR.

J Clin Microbiol. 2015 Jan;53(1):191-200. doi: 10.1128/JCM.02589-14. Epub 2014 Nov 5.

49.

Two novel toxin variants revealed by whole-genome sequencing of 175 Clostridium botulinum type E strains.

Weedmark KA, Lambert DL, Mabon P, Hayden KL, Urfano CJ, Leclair D, Van Domselaar G, Austin JW, Corbett CR.

Appl Environ Microbiol. 2014 Oct;80(20):6334-45. doi: 10.1128/AEM.01573-14. Epub 2014 Aug 8.

50.

Sylvatic plague in a Canadian black-tailed prairie dog (Cynomys ludovicianus).

Antonation KS, Shury TK, Bollinger TK, Olson A, Mabon P, Van Domselaar G, Corbett CR.

J Wildl Dis. 2014 Jul;50(3):699-702. doi: 10.7589/2013-08-215. Epub 2014 May 7.

PMID:
24807359

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