title: Genome sequence comparisons of serial multi-drug-resistantMycobacterium tuberculosisisolates over 21 years of infection in a single patient.
abstract: We report a case of chronic pulmonary multi-drug-resistant tuberculosis. Despite 14 years of treatment,Mycobacterium tuberculosiswas persistently isolated from sputum. Following treatment cessation the patient remained well, althoughM. tuberculosiswas isolated from sputum for a further 8 years. Genome sequencing of eight serialM. tuberculosisisolates cultured between 1991 and 2011 revealed 17 mutations (0.8 mutations per genome year- 1). Eight of these were persisting mutations and only two mutations were detected in the 7 years following cessation of treatment in 2004. In four isolates there were mixed alleles, suggesting the likely presence of bacterial subpopulations. The initial 1991 isolate demonstrated genotypic resistance to isoniazid (katGW91R), rifampicin (rpoBS531L), ethambutol (embBM306V), streptomycin (gidBL16R), quinolones (gyrAS95T) and P-aminosalicylic acid (thyAT202A). Subsequent resistance mutations developed for pyrazinamide (pncAI31F) and ethionamide (ethAframeshift). Such information might have been instructive when developing a treatment regimen. In retrospect and with the benefit of high-resolution genomic hindsight we were able to determine that the patient received only one or two active anti-tuberculous agents for most of their treatment. Additionally, mutations inbacAand Rv2326c were detected, which may have contributed to the persistent but mild disease course. BacA is likely to be associated with maintenance of chronic infection and Rv2326c with a decreased bacterial metabolic state. These results expand our understanding ofM. tuberculosisevolution during human infection and underline the link between antibiotic resistance and clinical persistence.
authors.affiliation: Victorian Infectious Disease Service, Melbourne Health, Melbourne, Victoria 3000, Australia.|Doherty Institute for Infection and Immunity, Victoria 3000, Australia.
authors.forename: Ella M
authors.initials: EM
authors.lastname: Meumann
authors.affiliation: Doherty Institute for Infection and Immunity, Victoria 3000, Australia.|Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Melbourne Health, Melbourne, Victoria 3000, Australia.
authors.forename: Maria
authors.initials: M
authors.lastname: Globan
authors.affiliation: Doherty Institute for Infection and Immunity, Victoria 3000, Australia.|Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Melbourne Health, Melbourne, Victoria 3000, Australia.
authors.forename: Janet A M
authors.initials: JAM
authors.lastname: Fyfe
authors.affiliation: Doherty Institute for Infection and Immunity, Victoria 3000, Australia.|Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Melbourne Health, Melbourne, Victoria 3000, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Leslie
authors.affiliation: Doherty Institute for Infection and Immunity, Victoria 3000, Australia.|Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Porter
authors.affiliation: Victorian Life Sciences Computation Initiative, University of Melbourne, Parkville, Victoria 3010, Australia.|Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.
authors.forename: Torsten
authors.initials: T
authors.lastname: Seemann
authors.affiliation: Victorian Tuberculosis Program, Melbourne, Victoria 3000, Australia.|Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.|Doherty Institute for Infection and Immunity, Victoria 3000, Australia.|Victorian Infectious Disease Service, Melbourne Health, Melbourne, Victoria 3000, Australia.
authors.forename: Justin
authors.initials: J
authors.lastname: Denholm
authors.affiliation: Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria 3000, Australia.|Doherty Applied Microbial Genomics, Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.|Doherty Institute for Infection and Immunity, Victoria 3000, Australia.
authors.forename: Timothy P
authors.initials: TP
authors.lastname: Stinear
keywords: Mycobacterium tuberculosis; antibiotic resistance; clinical persistence; evolution