title: Genomic Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis.
abstract: Fluoroquinolones (FQs) are effective second-line drugs for treating antibiotic-resistant tuberculosis (TB) and are being considered for use as first-line agents. Because FQs are used to treat a range of infections, in a setting of undiagnosed TB, there is potential to select for drug-resistant Mycobacterium tuberculosis mutants during FQ-based treatment of other infections, including pneumonia. Here we present a detailed characterization of ofloxacin-resistant M. tuberculosis samples isolated directly from patients in Taiwan, which demonstrates that selection for FQ resistance can occur within patients who have not received FQs for the treatment of TB. Several of these samples showed no mutations in gyrA or gyrB based on PCR-based molecular assays, but genome-wide next-generation sequencing (NGS) revealed minority populations of gyrA and/or gyrB mutants. In other samples with PCR-detectable gyrA mutations, NGS revealed subpopulations containing alternative resistance-associated genotypes. Isolation of individual clones from these apparently heterogeneous samples confirmed the presence of the minority drug-resistant variants suggested by the NGS data. Further NGS of these purified clones established evolutionary links between FQ-sensitive and -resistant clones derived from the same patient, suggesting de novo emergence of FQ-resistant TB. Importantly, most of these samples were isolated from patients without a history of FQ treatment for TB. Thus, selective pressure applied by FQ monotherapy in the setting of undiagnosed TB infection appears to be able to drive the full or partial emergence of FQ-resistant M. tuberculosis, which has the potential to confound diagnostic tests for antibiotic susceptibility and limit the effectiveness of FQs in TB treatment.
authors: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, China.
authors: Danfeng
authors: D
authors: Zhang
authors: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors: James E
authors: JE
authors: Gomez
authors: Graduate Institute of Clinical Medicine, National Taiwan University Medical College, Taipei, Taiwan.|Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University Medical College, Taipei, Taiwan.
authors: Jung-Yien
authors: JY
authors: Chien
authors: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors: Nathan
authors: N
authors: Haseley
authors: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors: Christopher A
authors: CA
authors: Desjardins
authors: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors: Ashlee M
authors: AM
authors: Earl
authors: Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University Medical College, Taipei, Taiwan.|Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University Medical College, Taipei, Taiwan.
authors: Po-Ren
authors: PR
authors: Hsueh
authors: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA hung@molbio.mgh.harvard.edu.|Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.|Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.|Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA.
authors: Deborah T
authors: DT
authors: Hung
mesh_terms: D000995:Antitubercular Agents / Q000494:pharmacology*; D002999:Clone Cells; D027081:DNA Gyrase / Q000235:genetics*; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D019143:Evolution, Molecular; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008826:Microbial Sensitivity Tests; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D015242:Ofloxacin / Q000494:pharmacology*; D010802:Phylogeny; D018410:Pneumonia, Bacterial / Q000175:diagnosis / Q000382:microbiology; D012641:Selection, Genetic; D018088:Tuberculosis, Multidrug-Resistant / Q000175:diagnosis / Q000382:microbiology
chemical_list: D000995:Antitubercular Agents; D015242:Ofloxacin; D027081:DNA Gyrase