title: Simultaneous identification of mycobacterial isolates to the species level and determination of tuberculosis drug resistance by PCR followed by electrospray ionization mass spectrometry.
abstract: Mycobacterium tuberculosis that is resistant to both isoniazid (INH) and rifampin (RIF) is spreading. It has become a public health problem in part because the standard culture methods used to determine the appropriate treatment regimen for patients often take months following the presumptive diagnosis of tuberculosis. Furthermore, the misidentification of nontuberculosis mycobacteria (NTM) in patients presumably suffering from tuberculosis results in additional human and health care costs. The mechanisms of resistance for several drugs used to treat Mycobacterium tuberculosis are well understood and therefore should be amenable to determination by rapid molecular methods. We describe here the use of PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) in an assay that simultaneously determines INH and RIF resistance in Mycobacterium tuberculosis and identifies and determines the species of NTMs. The assay panel included 16 primer pairs in eight multiplexed reactions and was validated using a collection of 1,340 DNA samples from cultured specimens collected in the New York City area, the Republic of Georgia, and South Africa. Compared with phenotypic data, the PCR/ESI-MS assay had 89.3% sensitivity and 95.8% specificity in the determination of INH resistance and 96.3% sensitivity and 98.6% specificity in the determination of RIF resistance. Based on a set of 264 previously characterized liquid culture specimens, the PCR/ESI-MS method had 97.0% sensitivity and 99.9% specificity for determination of NTM identity. The assay also provides information on ethambutol, fluoroquinolone, and diarylquinoline resistance and lineage-specific polymorphisms, to yield highly discriminative digital signatures potentially suitable for epidemiology tracking.
authors.affiliation: Ibis Biosciences, Inc., 2251 Faraday Ave., Carlsbad, CA 92008, USA. cmassire@ibisbio.com
authors.forename: Christian
authors.initials: C
authors.lastname: Massire
authors.forename: Cristina Agasino
authors.initials: CA
authors.lastname: Ivy
authors.forename: Robert
authors.initials: R
authors.lastname: Lovari
authors.forename: Natalia
authors.initials: N
authors.lastname: Kurepina
authors.forename: Haijing
authors.initials: H
authors.lastname: Li
authors.forename: Lawrence B
authors.initials: LB
authors.lastname: Blyn
authors.forename: Steven A
authors.initials: SA
authors.lastname: Hofstadler
authors.forename: George
authors.initials: G
authors.lastname: Khechinashvili
authors.forename: Charles W
authors.initials: CW
authors.lastname: Stratton
authors.forename: Rangarajan
authors.initials: R
authors.lastname: Sampath
authors.forename: Yi-Wei
authors.initials: YW
authors.lastname: Tang
authors.forename: David J
authors.initials: DJ
authors.lastname: Ecker
authors.forename: Barry N
authors.initials: BN
authors.lastname: Kreiswirth
mesh_terms: D000995:Antitubercular Agents / Q000494:pharmacology*; D001431:Bacteriological Techniques / Q000379:methods; D017931:DNA Primers / Q000235:genetics; D024881:Drug Resistance, Bacterial; D005846:Georgia (Republic); D006801:Humans; D007538:Isoniazid / Q000494:pharmacology; D009161:Mycobacterium / Q000145:classification* / Q000187:drug effects* / Q000302:isolation & purification; D009519:New York City; D016133:Polymerase Chain Reaction / Q000379:methods*; D012293:Rifampin / Q000494:pharmacology; D013019:South Africa; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D018088:Tuberculosis, Multidrug-Resistant / Q000175:diagnosis* / Q000382:microbiology
chemical_list: D000995:Antitubercular Agents; D017931:DNA Primers; D007538:Isoniazid; D012293:Rifampin