References
- Falkinham JO. Environmental sources of nontuberculous mycobacteria. Clin Chest Med. 2015;36:35–41. doi: 10.1016/j.ccm.2014.10.003
- Halstrom S, Price P, Thomson R. Review: environmental mycobacteria as a cause of human infection. Int J Mycobacteriology. 2015;4:81–91. doi: 10.1016/j.ijmyco.2015.03.002
- Namkoong H, Kurashima A, Morimoto K, et al. Epidemiology of pulmonary nontuberculous Mycobacterial disease, Japan1. Emerg Infect Dis. 2016;22:1116–1117. doi: 10.3201/eid2206.151086
- Smith GS, Ghio AJ, Stout JE, et al. Epidemiology of nontuberculous mycobacteria isolations among central North Carolina residents, 2006–2010. J Infect. 2016;72:678–686. doi: 10.1016/j.jinf.2016.03.008
- Agizew T, Basotli J, Alexander H, et al. Higher-than-expected prevalence of non-tuberculous mycobacteria in HIV setting in Botswana: Implications for diagnostic algorithms using Xpert MTB/RIF assay. PLoS One. 2017;12:e0189981. doi: 10.1371/journal.pone.0189981
- Hoza AS, Mfinanga SGM, Rodloff AC, et al. Increased isolation of nontuberculous mycobacteria among TB suspects in Northeastern, Tanzania: public health and diagnostic implications for control programmes. BMC Res Notes. 2016;9:109. doi: 10.1186/s13104-016-1928-3
- Prevots DR, Marras TK. Epidemiology of human pulmonary Infection with nontuberculous mycobacteria: A Review. Clin Chest Med. 2015;36:13–34. doi: 10.1016/j.ccm.2014.10.002
- Hoefsloot W, van Ingen J, Andrejak C, et al. The geographic diversity of nontuberculous mycobacteria isolated from pulmonary samples: an NTM-NET collaborative study. Eur Respir J. 2013;42:1604–1613. doi: 10.1183/09031936.00149212
- Fedrizzi T, Meehan CJ, Grottola A, et al. Genomic characterization of nontuberculous mycobacteria. Sci Rep. 2017;7:45258. doi: 10.1038/srep45258
- Gupta RS, Lo B, Son J. Phylogenomics and comparative genomic studies robustly support division of the genus mycobacterium into an emended genus mycobacterium and four novel Genera. Front Microbiol. 2018;9:67. doi: 10.3389/fmicb.2018.00067
- Philley JV, Griffith DE. Medical Management of pulmonary nontuberculous Mycobacterial disease. Thorac Surg Clin. 2019;29:65–76. doi: 10.1016/j.thorsurg.2018.09.001
- Griffith DE, Aksamit T, Brown-Elliott BA, et al. An Official ATS/IDSA Statement: diagnosis, treatment, and Prevention of nontuberculous Mycobacterial diseases. Am J Respir Crit Care Med. 2007;175:367–416. doi: 10.1164/rccm.200604-571ST
- Nessar R, Cambau E, Reyrat JM, et al. Mycobacterium abscessus: A new antibiotic nightmare. J Antimicrob Chemother. 2012;67:810–818. doi: 10.1093/jac/dkr578
- Uchiya K-I, Asahi S, Futamura K, et al. Antibiotic Susceptibility and Genotyping of Mycobacterium avium strains that Cause pulmonary and Disseminated Infection. Antimicrob Agents Chemother. 2018;62:e02035–17. doi: 10.1128/AAC.02035-17
- Griffith DE, Brown-Elliott BA, Benwill JL, et al. Mycobacterium abscessus . “pleased to Meet You, Hope You Guess My name … ”. Ann Am Thorac Soc. 2015;12:436–439. doi: 10.1513/AnnalsATS.201501-015OI
- Koh W-J, Jeong B-H, Kim S-Y, et al. Mycobacterial characteristics and treatment outcomes in Mycobacterium abscessus Lung disease. Clin Infect Dis. 2017;64:309–316. doi: 10.1093/cid/ciw724
- Claydon MA, Davey SN, Edwards-Jones V, et al. The rapid identification of intact microorganisms using mass spectrometry. Nat Biotechnol. 1996;14:1584–1586. doi: 10.1038/nbt1196-1584
- Jannetto PJ, Fitzgerald RL. Effective Use of Mass spectrometry in the clinical laboratory. Clin Chem. 2016;62:92–98. doi: 10.1373/clinchem.2015.248146
- Stackebrandt E, Goebel BM. Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA sequence analysis in the present species Definition in Bacteriology. Int J Syst Evol Microbiol. 1994;44:846–849. doi: 10.1099/00207713-44-4-846
- Enright MC, Spratt BG. Multilocus sequence typing. Trends Microbiol. 1999;7:482–487. doi: 10.1016/S0966-842X(99)01609-1
- Maiden MCJ, Jansen van Rensburg MJ, Bray JE, et al. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol. 2013;11:728–736. doi: 10.1038/nrmicro3093
- Zolfo M, Tett A, Jousson O, et al. MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. Nucleic Acids Res. 2016;1:1–10.
- Jolley KA, Maiden MC. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11:595. doi: 10.1186/1471-2105-11-595
- Tortoli E, Fedrizzi T, Meehan CJ, et al. The new phylogeny of the genus Mycobacterium : The old and the news. Infect Genet Evol. 2017;56:19–25. doi: 10.1016/j.meegid.2017.10.013
- Miyamoto M, Motooka D, Gotoh K, et al. Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes. BMC Genomics. 2014;15:699. doi: 10.1186/1471-2164-15-699
- Koren S, Walenz BP, Berlin K, et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27:722–736. doi: 10.1101/gr.215087.116
- Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324
- Walker BJ, Abeel T, Shea T, et al. Pilon: An Integrated Tool for comprehensive Microbial Variant detection and genome assembly Improvement. PLoS One. 2014;9:e112963. doi: 10.1371/journal.pone.0112963
- Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid Annotations using Subsystems technology. BMC Genomics. 2008;9:75. doi: 10.1186/1471-2164-9-75
- Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. doi: 10.1016/S0022-2836(05)80360-2
- Katoh K, Misawa K, Kuma K, et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–3066. doi: 10.1093/nar/gkf436
- Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; doi:10.1186/gb-2009-10-3-r25.
- Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; doi:10.1093/bioinformatics/bty191.
- Li H, Handsaker B, Wysoker A, et al. The sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; doi:10.1093/bioinformatics/btp352.
- Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; doi:10.1089/cmb.2012.0021.
- Guerin-Faublee V, Flandrois J-P, Pichat C, et al. Mycobacterium bourgelatii sp. nov., a rapidly growing, non-chromogenic species isolated from the lymph nodes of cattle. Int J Syst Evol Microbiol. 2013;63:4669–4674. doi: 10.1099/ijs.0.051979-0
- Meissner G, Schroder KH, Amadio GE, et al. A Co-operative Numerical analysis of Nonscoto- and Nonphotochromogenic Slowly growing mycobacteria. J Gen Microbiol. 1974;83:207–235. doi: 10.1099/00221287-83-2-207
- Teng S-H, Chen C-M, Lee M-R, et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry can accurately differentiate between Mycobacterium masilliense (M. abscessus subspecies bolletti) and M. abscessus (sensu stricto). J Clin Microbiol. 2013;51:3113–3116. doi: 10.1128/JCM.01239-13
- Sassi M, Drancourt M. Genome analysis reveals three genomospecies in Mycobacterium abscessus. BMC Genomics. 2014;15:359. doi: 10.1186/1471-2164-15-359
- Lee M-R, Sheng W-H, Hung C-C, et al. Mycobacterium abscessus complex infections in humans. Emerg Infect Dis. 2015;21:1638–1646.
- Haworth CS, Banks J, Capstick T, et al. British Thoracic Society guidelines for the management of non-tuberculous mycobacterial pulmonary disease (NTM-PD). Thorax . 2017;72:ii1–ii64. doi: 10.1136/thoraxjnl-2017-210927
- Kodana M, Tarumoto N, Kawamura T, et al. Utility of the MALDI-TOF MS method to identify nontuberculous mycobacteria. J Infect Chemother. 2016;22:32–35. doi: 10.1016/j.jiac.2015.09.006
- Cao Y, Wang L, Ma P, et al. Accuracy of matrix-Assisted Laser Desorption Ionization-time of Flight Mass spectrometry for identification of mycobacteria: a systematic review and meta-analysis. Sci Rep. 2018;8:4131. doi: 10.1038/s41598-018-22642-w
- Pranada AB, Witt E, Bienia M, et al. Accurate differentiation of Mycobacterium chimaera from Mycobacterium intracellulare by MALDI-TOF MS analysis. J Med Microbiol. 2017;66:670–677. doi: 10.1099/jmm.0.000469
- Lecorche E, Haenn S, Mougari F, et al. Comparison of methods available for identification of Mycobacterium chimaera. Clin Microbiol Infect. 2018;24:409–413. doi: 10.1016/j.cmi.2017.07.031
- Votintseva AA, Bradley P, Pankhurst L, et al. Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples. J Clin Microbiol. 2017;55:1285–1298. doi: 10.1128/JCM.02483-16
- Doughty EL, Sergeant MJ, Adetifa I, et al. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ. 2014;2:e585. doi: 10.7717/peerj.585
- Brown AC, Bryant JM, Einer-Jensen K, et al. Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples. J Clin Microbiol. 2015;53:2230–2237. doi: 10.1128/JCM.00486-15