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PLOS ONE  2013 

MabsBase: A Mycobacterium abscessus Genome and Annotation Database

DOI: 10.1371/journal.pone.0062443

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Summary Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterial species that has been associated with a wide spectrum of human infections. As the classification and biology of this organism is still not well understood, comparative genomic analysis on members of this species may provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections. The MabsBase described in this paper is a user-friendly database providing access to whole-genome sequences of newly discovered M. abscessus strains as well as resources for whole-genome annotations and computational predictions, to support the expanding scientific community interested in M. abscessus research. The MabsBase is freely available at


[1]  Moore M, Frerichs JB (1953) An unusual acid-fast infection of the knee with subcutaneous, abscess-like lesions of the gluteal region; report of a case with a study of the organism, Mycobacterium abscessus, n. sp. J Invest Dermatol 20: 133–169.
[2]  Kusunoki S, Ezaki T (1992) Proposal of Mycobacterium peregrinum sp. nov., nom. rev., and Elevation of Mycobacterium chelonae subsp. abscessus (Kubica et al.) to Species Status: Mycobacterium abscessus comb. nov. International Journal of Systematic Bacteriology 42: 240–245.
[3]  Yakrus MA, Hernandez SM, Floyd MM, Sikes D, Butler WR, et al. (2001) Comparison of methods for Identification of Mycobacterium abscessus and M. chelonae isolates. J Clin Microbiol 39: 4103–4110.
[4]  Esther CR Jr, Esserman DA, Gilligan P, Kerr A, Noone PG (2010) Chronic Mycobacterium abscessus infection and lung function decline in cystic fibrosis. J Cyst Fibros 9: 117–123.
[5]  Griffith DE, Girard WM, Wallace RJ Jr (1993) Clinical features of pulmonary disease caused by rapidly growing mycobacteria. An analysis of 154 patients. Am Rev Respir Dis 147: 1271–1278.
[6]  Sanguinetti M, Ardito F, Fiscarelli E, La Sorda M, D'Argenio P, et al. (2001) Fatal pulmonary infection due to multidrug-resistant Mycobacterium abscessus in a patient with cystic fibrosis. J Clin Microbiol 39: 816–819.
[7]  Macheras E, Roux AL, Bastian S, Leao SC, Palaci M, et al. (2011) Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains. J Clin Microbiol 49: 491–499.
[8]  Kim HY, Kim BJ, Kook Y, Yun YJ, Shin JH, et al. (2010) Mycobacterium massiliense is differentiated from Mycobacterium abscessus and Mycobacterium bolletii by erythromycin ribosome methyltransferase gene (erm) and clarithromycin susceptibility patterns. Microbiol Immunol 54: 347–353.
[9]  Ripoll F, Pasek S, Schenowitz C, Dossat C, Barbe V, et al. (2009) Non Mycobacterial Virulence Genes in the Genome of the Emerging Pathogen Mycobacterium abscessus. PLoS ONE 4: e5660.
[10]  Choo SW, Wong YL, Yusoff AM, Leong ML, Wong GJ, et al. (2012) Genome Sequence of the Mycobacterium abscessus Strain M93. Journal of Bacteriology 194: 3278.
[11]  Ngeow YF, Wong YL, Tan JL, Arumugam R, Wong GJ, et al. (2012) Genome Sequence of Mycobacterium massiliense M18, Isolated from a Lymph Node Biopsy Specimen. Journal of Bacteriology 194: 4125.
[12]  Wong YL, Choo SW, Tan JL, Ong CS, Ng KP, et al. (2012) Draft Genome Sequence of Mycobacterium bolletii Strain M24, a Rapidly Growing Mycobacterium of Contentious Taxonomic Status. Journal of Bacteriology 194: 4475.
[13]  Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, et al. (2010) Draft genome sequence of the oilseed species Ricinus communis. Nat Biotech 28: 951–956.
[14]  Varshney RK, Paulo MJ, Grando S, van Eeuwijk FA, Keizer LCP, et al. (2012) Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.). Field Crops Research 126: 171–180.
[15]  Aziz R, Bartels D, Best A, DeJongh M, Disz T, et al. (2008) The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75.
[16]  Meyer F, Overbeek R, Rodriguez A (2009) FIGfams: yet another set of protein families. Nucleic Acids Research 37: 6643–6654.
[17]  Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH (2009) JBrowse: A next-generation genome browser. Genome Research 19: 1630–1638.
[18]  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.
[19]  Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
[20]  Yu NY, Wagner JR, Laird MR, Melli G, Rey S, et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26: 1608–1615.
[21]  Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, et al. (2010) Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformtics. 11: 461.
[22]  Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 28(10): 2731–2739.
[23]  Choo SW, Wong YL, Tan JL, Ong CS, Wong GJ, et al. (2012) Annotated genome sequence of Mycobacterium massiliense strain M154, belonging to the recently created taxon,Mycobacterium abscessus subspecies bolletii comb. nov. Journal of Bacteriology 194 (17): 4778.
[24]  Choo SW, Mohamed Yusoff A, Wong YL, Wee WY, Ong CS, et al. (2012) Genome Analysis of Mycobacterium massiliense strain M172 with a putative mycobacteriophage. Journal of Bacteriology 194(18): 5128.
[25]  Ngeow YF, Wong YL, Lokanathan N, Wong GJ, Ong CS, et al. (2012) Genomic analysis of Mycobacterium massiliense strain M115, an isolate from human sputum. Journal of Bacteriology 194(17): 4786.
[26]  Choo SW, Wong YL, Leong ML, Heydari H, Ong CS, et al. (2012) Analysis of the genome of Mycobacterium abscessus strain M94 reveals an uncommon cluster of tRNAs. Journal of Bacteriology 194(20): 5724.
[27]  Ngeow YF, Wee WY, Wong YL, Tan JL, Ong CS, et al. (2012) Genomic analysis of Mycobacterium abscessus strain M139 with an ambiguous subspecies taxonomic position. Journal of Bacteriology 194(21): 6002–3.
[28]  Ngeow YF, Wong YL, Tan JL, Ong CS, Ng KP, et al. (2012) Genome Sequence of the Mycobacterium abscessus strain M152. Journal of Bacteriology 194 (23): 6662.


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