{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T12:45:23Z","timestamp":1792673123725,"version":"4.5.0"},"reference-count":34,"publisher":"MyJove Corporation","issue":"130","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoVE"],"DOI":"10.3791\/56714","type":"journal-article","created":{"date-parts":[[2017,12,28]],"date-time":"2017-12-28T19:00:08Z","timestamp":1514487608000},"source":"Crossref","is-referenced-by-count":10,"title":["Whole Genome Sequencing of &lt;em&gt;Candida glabrata&lt;\/em&gt; for Detection of Markers of Antifungal Drug Resistance"],"prefix":"10.3791","author":[{"given":"Chayanika","family":"Biswas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon C-A.","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catriona","family":"Halliday","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Martinez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca J.","family":"Rockett","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinning","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verlaine J.","family":"Timms","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rajat","family":"Dhakal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosemarie","family":"Sadsad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karina J.","family":"Kennedy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geoffrey","family":"Playford","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah J.","family":"Marriott","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Monica A.","family":"Slavin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tania C.","family":"Sorrell","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vitali","family":"Sintchenko","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2098","published-online":{"date-parts":[[2017,12,28]]},"reference":[{"issue":"6","key":"ref1","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1093\/cid\/ciu407","type":"journal-article","article-title":"FKS mutant Candida glabrata: risk factors and outcomes in patients with candidemia","volume":"59","author":"Beyda","year":"2014","unstructured":"Beyda, N. D. et al.FKS. mutant Candida glabrata.: risk factors and outcomes in patients with candidemia. Clin Infect Dis. 59 (6), 819-25 (2014).","journal-title":"Clin Infect Dis"},{"issue":"3","key":"ref2","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1128\/AAC.01138-09","type":"journal-article","article-title":"Acquisition of flucytosine, azole, and caspofungin resistance in Candida glabrata. bloodstream isolates serially obtained from a hematopoietic stem cell transplant recipient","volume":"54","author":"Chapeland-Leclerc","year":"2010","unstructured":"Chapeland-Leclerc, F. et al. Acquisition of flucytosine, azole, and caspofungin resistance in Candida glabrata. bloodstream isolates serially obtained from a hematopoietic stem cell transplant recipient. Antimicrob Agents Chemother. 54 (3), 1360-2 (2010).","journal-title":"Antimicrob Agents Chemother"},{"issue":"8","key":"ref3","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1111\/myc.12348","type":"journal-article","article-title":"Candida glabrata-unique features and challenges in the clinical management of invasive infections","volume":"58","author":"Glockner","year":"2015","unstructured":"Glockner, A., Cornely, O. A. Candida glabrata.-unique features and challenges in the clinical management of invasive infections. Mycoses. 58 (8), 445-50 (2015).","journal-title":"Mycoses"},{"issue":"4","key":"ref4","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1128\/JCM.06112-11","type":"journal-article","article-title":"Frequency of decreased susceptibility and resistance to echinocandins among fluconazole-resistant bloodstream isolates of Candida glabrata","volume":"50","author":"Pfaller","year":"2012","unstructured":"Pfaller, M. A. et al. Frequency of decreased susceptibility and resistance to echinocandins among fluconazole-resistant bloodstream isolates of Candida glabrata. J Clin Microbiol. 50 (4), 1199-203 (2012).","journal-title":"J Clin Microbiol"},{"issue":"9","key":"ref5","doi-asserted-by":"crossref","first-page":"4559","DOI":"10.1128\/AAC.01144-13","type":"journal-article","article-title":"Rapid emergence of echinocandin resistance in Candida glabrata resulting in clinical and microbiologic failure","volume":"57","author":"Lewis","year":"2013","unstructured":"Lewis, J. S., 2nd, Wiederhold, N. P., Wickes, B. L., Patterson, T. F., Jorgensen, J. H. Rapid emergence of echinocandin resistance in Candida glabrata. resulting in clinical and microbiologic failure. Antimicrob Agents Chemother. 57 (9), 4559-61 (2013).","journal-title":"Antimicrob Agents Chemother"},{"issue":"3","key":"ref6","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.diagmicrobio.2007.10.001","type":"journal-article","article-title":"Therapy and outcome of Candida glabrata versus Candida albicans bloodstream infection","volume":"60","author":"Klevay","year":"2008","unstructured":"Klevay, M. J. et al. Therapy and outcome of Candida glabrata. versus Candida albicans. bloodstream infection. Diagn Microbiol Infect Dis. 60 (3), 273-7 (2008).","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"7","key":"ref7","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1111\/j.1469-0691.2012.03880.x","type":"journal-article","article-title":"EUCAST technical note on the EUCAST definitive document EDef 7.2: method for the determination of broth dilution minimum inhibitory concentrations of antifungal agents for yeasts EDef 7.2 (EUCAST-AFST)","volume":"18","author":"Arendrup","year":"2012","unstructured":"Arendrup, M. C., Cuenca-Estrella, M., Lass-Florl, C., Hope, W., Eucast, A. EUCAST technical note on the EUCAST definitive document EDef 7.2: method for the determination of broth dilution minimum inhibitory concentrations of antifungal agents for yeasts EDef 7.2 (EUCAST-AFST). Clin Microbiol Infect. 18 (7), E246-7 (2012).","journal-title":"Clin Microbiol Infect"},{"key":"ref8","type":"journal-article","article-title":"Reference Method for Broth Dilution Antifungal Susceptibility Testing of Yeasts","year":"2012","unstructured":"Clinical and Laboratory Standards Institute. Reference Method for Broth Dilution Antifungal Susceptibility Testing of Yeasts; Fourth Informational Supplement. (M27-S4), USA (2012).","journal-title":"Clinical and Laboratory Standards Institute"},{"issue":"7","key":"ref9","doi-asserted-by":"crossref","first-page":"3965","DOI":"10.1128\/AAC.00355-12","type":"journal-article","article-title":"Danish Fungaemia Study, G. Caspofungin Etest susceptibility testing of Candida species: risk of misclassification of susceptible isolates of C. glabrata and C. krusei when adopting the revised CLSI caspofungin breakpoints","volume":"56","author":"Arendrup","year":"2012","unstructured":"Arendrup, M. C., Pfaller, M. A., Danish Fungaemia Study, G. Caspofungin Etest susceptibility testing of Candida. species: risk of misclassification of susceptible isolates of C. glabrata.and C. krusei.when adopting the revised CLSI caspofungin breakpoints. Antimicrob Agents Chemother. 56 (7), 3965-8 (2012).","journal-title":"Antimicrob Agents Chemother"},{"issue":"5","key":"ref10","doi-asserted-by":"crossref","first-page":"1002718","DOI":"10.1371\/journal.ppat.1002718","type":"journal-article","article-title":"Global analysis of the evolution and mechanism of echinocandin resistance in Candida glabrata","volume":"8","author":"Singh-Babak","year":"2012","unstructured":"Singh-Babak, S. D. et al. Global analysis of the evolution and mechanism of echinocandin resistance in Candida glabrata. PLoS Pathog. 8 (5), e1002718 (2012).","journal-title":"PLoS Pathog"},{"issue":"6","key":"ref11","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1097\/QCO.0000000000000215","type":"journal-article","article-title":"Clinical perspectives on echinocandin resistance among Candida species","volume":"28","author":"Shields","year":"2015","unstructured":"Shields, R. K., Nguyen, M. H., Clancy, C. J. Clinical perspectives on echinocandin resistance among Candida. species. Curr Opin Infect Dis. 28 (6), 514-22 (2015).","journal-title":"Curr Opin Infect Dis"},{"issue":"7","key":"ref12","doi-asserted-by":"crossref","first-page":"2609","DOI":"10.1128\/JCM.01038-14","type":"journal-article","article-title":"Set of classical PCRs for detection of mutations in Candida glabrata FKS. genes linked with echinocandin resistance","volume":"52","author":"Dudiuk","year":"2014","unstructured":"Dudiuk, C. et al. Set of classical PCRs for detection of mutations in Candida glabrata FKS. genes linked with echinocandin resistance. J Clin Microbiol. 52 (7), 2609-14 (2014).","journal-title":"J Clin Microbiol"},{"issue":"1","key":"ref13","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.cell.2013.09.006","type":"journal-article","article-title":"The next-generation sequencing revolution and its impact on genomics","volume":"155","author":"Koboldt","year":"2013","unstructured":"Koboldt, D. C., Steinberg, K. M., Larson, D. E., Wilson, R. K., Mardis, E. R. The next-generation sequencing revolution and its impact on genomics. Cell. 155 (1), 27-38 (2013).","journal-title":"Cell"},{"issue":"2","key":"ref14","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.jcv.2013.03.003","type":"journal-article","article-title":"Next-generation sequencing technologies in diagnostic virology","volume":"58","author":"Barzon","year":"2013","unstructured":"Barzon, L. et al. Next-generation sequencing technologies in diagnostic virology. J Clin Virol. 58 (2), 346-50 (2013).","journal-title":"J Clin Virol"},{"issue":"9","key":"ref15","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/nrg3226","type":"journal-article","article-title":"Transforming clinical microbiology with bacterial genome sequencing","volume":"13","author":"Didelot","year":"2012","unstructured":"Didelot, X., Bowden, R., Wilson, D. J., Peto, T. E. A., Crook, D. W. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Gen. 13 (9), 601-12 (2012).","journal-title":"Nat Rev Gen"},{"issue":"8","key":"ref16","doi-asserted-by":"crossref","first-page":"1002824","DOI":"10.1371\/journal.ppat.1002824","type":"journal-article","article-title":"Routine use of microbial whole genome sequencing in diagnostic and public health microbiology","volume":"8","author":"Koser","year":"2012","unstructured":"Koser, C. U. et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog. 8 (8), e1002824 (2012).","journal-title":"PLoS Pathog"},{"issue":"2","key":"ref17","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/nrmicro2949","type":"journal-article","article-title":"The changing face of pathogen discovery and surveillance","volume":"11","author":"Lipkin","year":"2013","unstructured":"Lipkin, W. I. The changing face of pathogen discovery and surveillance. Nat Rev Microbiol. 11 (2), 133-41 (2013).","journal-title":"Nat Rev Microbiol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1136\/bmj.h1314","type":"journal-article","article-title":"The role of pathogen genomics in assessing disease transmission","volume":"350","author":"Sintchenko","year":"2015","unstructured":"Sintchenko, V., Holmes, E. C. The role of pathogen genomics in assessing disease transmission. BMJ. 350 h1314 (2015).","journal-title":"BMJ"},{"issue":"9","key":"ref19","doi-asserted-by":"crossref","first-page":"2556","DOI":"10.1093\/jac\/dkv139","type":"journal-article","article-title":"Next-generation sequencing offers new insights into the resistance of Candida spp. to echinocandins and azoles","volume":"70","author":"Garnaud","year":"2015","unstructured":"Garnaud, C. et al. Next-generation sequencing offers new insights into the resistance of Candida.spp. to echinocandins and azoles. J Antimicrob Chemother. 70 (9), 2556-65 (2015).","journal-title":"J Antimicrob Chemother"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1007\/978-1-61779-040-9_4","type":"journal-article","article-title":"Next-generation sequencing and potential applications in fungal genomics","volume":"722","author":"Sanmiguel","year":"2011","unstructured":"Sanmiguel, P. Next-generation sequencing and potential applications in fungal genomics. Methods Mol Biol. 722 51-60 (2011).","journal-title":"Methods Mol Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1146\/annurev-anchem-062012-092628","type":"journal-article","article-title":"Next-generation sequencing platforms","volume":"6","author":"Mardis","year":"2013","unstructured":"Mardis, E. R. Next-generation sequencing platforms. Annu Rev Anal Chem. 6 287-303 (2013).","journal-title":"Annu Rev Anal Chem"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/s12281-016-0253-6","type":"journal-article","article-title":"Next-Generation Sequencing in the mycology lab","volume":"10","author":"Zoll","year":"2016","unstructured":"Zoll, J., Snelders, E., Verweij, P. E., Melchers, W. J. Next-Generation Sequencing in the mycology lab. Curr Fungal Infect Rep. 10 37-42 (2016).","journal-title":"Curr Fungal Infect Rep"},{"issue":"5","key":"ref23","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1373\/clinchem.2013.209213","type":"journal-article","article-title":"Whole genome sequencing as a diagnostic test: challenges and opportunities","volume":"60","author":"Chrystoja","year":"2014","unstructured":"Chrystoja, C. C., Diamandis, E. P. Whole genome sequencing as a diagnostic test: challenges and opportunities. Clin Chem. 60 (5), 724-33 (2014).","journal-title":"Clin Chem"},{"key":"ref24","doi-asserted-by":"crossref","DOI":"10.1016\/j.cmi.2017.03.014","type":"journal-article","article-title":"Identification of genetic markers of resistance to echinocandins, azoles and 5-fluorocytosine in Candida glabrata by next-generation sequencing: a feasibility study","author":"Biswas","year":"2017","unstructured":"Biswas, C. et al. Identification of genetic markers of resistance to echinocandins, azoles and 5-fluorocytosine in Candida glabrata. by next-generation sequencing: a feasibility study. Clin Microbiol Infect. (2017).","journal-title":"Clin Microbiol Infect"},{"issue":"1","key":"ref25","first-page":"62","type":"journal-article","article-title":"Validity of nucleic acid purities monitored by 260nm\/280nm absorbance ratios","volume":"18","author":"Glasel","year":"1995","unstructured":"Glasel, J. A. Validity of nucleic acid purities monitored by 260nm\/280nm absorbance ratios. BioTechniques. 18 (1), 62-3 (1995).","journal-title":"BioTechniques"},{"issue":"2","key":"ref26","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1128\/CMR.00051-08","type":"journal-article","article-title":"Efflux-mediated antifungal drug resistance","volume":"22","author":"Cannon","year":"2009","unstructured":"Cannon, R. D. et al. Efflux-mediated antifungal drug resistance. Clin Microbiol Rev. 22 (2), 291-321 (2009).","journal-title":"Clin Microbiol Rev"},{"issue":"1","key":"ref27","doi-asserted-by":"crossref","first-page":"1000268","DOI":"10.1371\/journal.ppat.1000268","type":"journal-article","article-title":"Gain of function mutations in CgPDR1. of Candida glabrata not only mediate antifungal resistance but also enhance virulence","volume":"5","author":"Ferrari","year":"2009","unstructured":"Ferrari, S. et al. Gain of function mutations in CgPDR1. of Candida glabrata.not only mediate antifungal resistance but also enhance virulence. PLoS Pathog. 5 (1), e1000268 (2009).","journal-title":"PLoS Pathog"},{"issue":"5","key":"ref28","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1007\/s10096-013-2009-3","type":"journal-article","article-title":"Candida glabrata: a review of its features and resistance","volume":"33","author":"Rodrigues","year":"2014","unstructured":"Rodrigues, C. F., Silva, S., Henriques, M. Candida glabrata.: a review of its features and resistance. Eur J Clin Microbiol Infect Dis. 33 (5), 673-88 (2014).","journal-title":"Eur J Clin Microbiol Infect Dis"},{"issue":"9","key":"ref29","doi-asserted-by":"crossref","first-page":"3690","DOI":"10.1128\/AAC.00443-09","type":"journal-article","article-title":"Effect of Candida glabrata FKS1 and FKS2 mutations on echinocandin sensitivity and kinetics of 1,3-beta-D-glucan synthase: implication for the existing susceptibility breakpoint","volume":"53","author":"Garcia-Effron","year":"2009","unstructured":"Garcia-Effron, G., Lee, S., Park, S., Cleary, J. D., Perlin, D. S. Effect of Candida glabrataFKS1. and FKS2. mutations on echinocandin sensitivity and kinetics of 1,3-beta-D-glucan synthase: implication for the existing susceptibility breakpoint. Antimicrob Agents Chemother. 53 (9), 3690-9 (2009).","journal-title":"Antimicrob Agents Chemother"},{"issue":"6","key":"ref30","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1097\/QCO.0000000000000111","type":"journal-article","article-title":"Echinocandin resistance: an emerging clinical problem","volume":"27","author":"Arendrup","year":"2014","unstructured":"Arendrup, M. C., Perlin, D. S. Echinocandin resistance: an emerging clinical problem? Curr Opin Infect Dis. 27 (6), 484-92 (2014).","journal-title":"Curr Opin Infect Dis"},{"issue":"8","key":"ref31","doi-asserted-by":"crossref","first-page":"0135110","DOI":"10.1371\/journal.pone.0135110","type":"journal-article","article-title":"New Mechanisms of Flucytosine Resistance in C. glabrata Unveiled by a Chemogenomics Analysis in S. cerevisiae","volume":"10","author":"Costa","year":"2015","unstructured":"Costa, C. et al. New Mechanisms of Flucytosine Resistance in C. glabrata.Unveiled by a Chemogenomics Analysis in S. cerevisiae. PLoS One. 10 (8), e0135110 (2015).","journal-title":"PLoS One"},{"issue":"4","key":"ref32","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1128\/EC.00364-12","type":"journal-article","article-title":"Adhesins in human fungal pathogens: glue with plenty of stick","volume":"12","author":"de Groot","year":"2013","unstructured":"Groot, P. W., Bader, O., de Boer, A. D., Weig, M., Chauhan, N. Adhesins in human fungal pathogens: glue with plenty of stick. Eukaryot Cell. 12 (4), 470-81 (2013).","journal-title":"Eukaryot Cell"},{"issue":"11","key":"ref33","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1128\/EC.00284-08","type":"journal-article","article-title":"The cell wall of the human pathogen Candida glabrata: differential incorporation of novel adhesin-like wall proteins","volume":"7","author":"de Groot","year":"2008","unstructured":"Groot, P. W. et al. The cell wall of the human pathogen Candida glabrata.: differential incorporation of novel adhesin-like wall proteins. Eukaryot Cell. 7 (11), 1951-64 (2008).","journal-title":"Eukaryot Cell"},{"issue":"2","key":"ref34","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00065-15","type":"journal-article","article-title":"Upregulation of the adhesin gene EPA1 mediated by PDR1 in Candida glabrata leads to enhanced host colonization","volume":"1","author":"Vale-Silva","year":"2016","unstructured":"Vale-Silva, L. A. et al. Upregulation of the adhesin gene EPA1. mediated by PDR1. in Candida glabrata. leads to enhanced host colonization. mSphere. 1 (2), (2016).","journal-title":"mSphere"}],"container-title":["Journal of Visualized Experiments"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.jove.com\/video\/56714\/whole-genome-sequencing-candida-glabrata-for-detection-markers","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T12:00:44Z","timestamp":1792670444000},"score":1,"resource":{"primary":{"URL":"https:\/\/app.jove.com\/t\/56714"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12,28]]},"references-count":34,"journal-issue":{"issue":"130","published-online":{"date-parts":[[2017]]}},"URL":"https:\/\/doi.org\/10.3791\/56714","relation":{},"ISSN":["1940-087X"],"issn-type":[{"value":"1940-087X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,12,28]]}}}