title: Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State.
abstract: Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterizeMycobacterium tuberculosisand otherM. tuberculosiscomplex (MTBC) strains, composed of a novel DNA extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics pipeline. This new assay was assessed using 608 MTBC isolates, with 146 isolates during the validation portion of this study and 462 samples received prospectively. In February 2016, this assay was implemented to test all clinical cases of MTBC in New York State, including isolates and early positive Bactec mycobacterial growth indicator tube (MGIT) 960 cultures from primary specimens. Since the inception of the assay, we have assessed the accuracy of identification of MTBC strains to the species level, concordance with culture-based drug susceptibility testing (DST), and turnaround time. Species identification by WGS was determined to be 99% accurate. Concordance between drug resistance profiles generated by WGS and culture-based DST methods was 96% for eight drugs, with an average resistance-predictive value of 93% and susceptible-predictive value of 96%. This single comprehensive WGS assay has replaced seven molecular assays and has resulted in resistance profiles being reported to physicians an average of 9 days sooner than with culture-based DST for first-line drugs and 32 days sooner for second-line drugs.
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Shea
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Tanya A
authors.initials: TA
authors.lastname: Halse
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Pascal
authors.initials: P
authors.lastname: Lapierre
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Shudt
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Donna
authors.initials: D
authors.lastname: Kohlerschmidt
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Van Roey
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Ronald
authors.initials: R
authors.lastname: Limberger
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Jill
authors.initials: J
authors.lastname: Taylor
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Vincent
authors.initials: V
authors.lastname: Escuyer
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA kimberlee.musser@health.ny.gov.
authors.forename: Kimberlee A
authors.initials: KA
authors.lastname: Musser
mesh_terms: D019295:Computational Biology / Q000379:methods; D024881:Drug Resistance, Bacterial; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D009518:New York; D011446:Prospective Studies; D012189:Retrospective Studies; D014376:Tuberculosis / Q000175:diagnosis* / Q000382:microbiology; D000073336:Whole Genome Sequencing / Q000379:methods*
keywords: MGIT; Mycobacterium tuberculosis; WGS; drug resistance prediction; reporting