Mycobacterium abscessus is an emerging rapidly growing mycobacterium (RGM) causing a pseudotuberculous lung disease to which patients with cystic fibrosis (CF) are particularly susceptible. We report here its complete genome sequence. The genome of M. abscessus (CIP 104536T) consists of a 5,067,172-bp circular chromosome including 4920 predicted coding sequences (CDS), an 81-kb full-length prophage and 5 IS elements, and a 23-kb mercury resistance plasmid almost identical to pMM23 from Mycobacterium marinum. The chromosome encodes many virulence proteins and virulence protein families absent or present in only small numbers in the model RGM species Mycobacterium smegmatis. Many of these proteins are encoded by genes belonging to a “mycobacterial” gene pool (e.g. PE and PPE proteins, MCE and YrbE proteins, lipoprotein LpqH precursors). However, many others (e.g. phospholipase C, MgtC, MsrA, ABC Fe(3+) transporter) appear to have been horizontally acquired from distantly related environmental bacteria with a high G+C content, mostly actinobacteria (e.g. Rhodococcus sp., Streptomyces sp.) and pseudomonads. We also identified several metabolic regions acquired from actinobacteria and pseudomonads (relating to phenazine biosynthesis, homogentisate catabolism, phenylacetic acid degradation, DNA degradation) not present in the M. smegmatis genome. Many of the “non mycobacterial” factors detected in M. abscessus are also present in two of the pathogens most frequently isolated from CF patients, Pseudomonas aeruginosa and Burkholderia cepacia. This study elucidates the genetic basis of the unique pathogenicity of M. abscessus among RGM, and raises the question of similar mechanisms of pathogenicity shared by unrelated organisms in CF patients.
References
[1]
Brown-Elliott BA, Wallace RJ Jr (2002) Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria. Clin Microbiol Rev 15: 716–746.
[2]
Griffith DE, Aksamit T, Brown-Elliott BA, Catanzaro A, Daley C, et al. (2007) An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med 175: 367–416.
[3]
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.
[4]
Kubica GP, Baess I, Gordon RE, Jenkins PA, Kwapinski JB, et al. (1972) A co-operative numerical analysis of rapidly growing mycobacteria. J Gen Microbiol 73: 55–70.
[5]
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. Int J Syst Bacteriol 42: 240–245.
[6]
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.
[7]
Adekambi T, Berger P, Raoult D, Drancourt M (2006) rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov. Int J Syst Evol Microbiol 56: 133–143.
[8]
Adekambi T, Reynaud-Gaubert M, Greub G, Gevaudan MJ, La Scola B, et al. (2004) Amoebal coculture of “Mycobacterium massiliense” sp. nov. from the sputum of a patient with hemoptoic pneumonia. J Clin Microbiol 42: 5493–5501.
[9]
Kim HY, Yun YJ, Park CG, Lee DH, Cho YK, et al. (2007) Outbreak of Mycobacterium massiliense infection associated with intramuscular injections. J Clin Microbiol 45: 3127–3130.
[10]
Viana-Niero C, Lima KV, Lopes ML, Rabello MC, Marsola LR, et al. (2008) Molecular characterization of Mycobacterium massiliense and Mycobacterium bolletii in isolates collected from outbreaks of infections after laparoscopic surgeries and cosmetic procedures. J Clin Microbiol 46: 850–855.
[11]
Griffith DE (2003) Emergence of nontuberculous mycobacteria as pathogens in cystic fibrosis. Am J Respir Crit Care Med 167: 810–812.
[12]
Chalermskulrat W, Sood N, Neuringer IP, Hecker TM, Chang L, et al. (2006) Non-tuberculous mycobacteria in end stage cystic fibrosis: implications for lung transplantation. Thorax 61: 507–513.
[13]
J?nsson BE, Gilljam M, Lindblad A, Ridell M, Wold AE, et al. (2007) Molecular epidemiology of Mycobacterium abscessus, with focus on cystic fibrosis. J Clin Microbiol 45: 1497–1504.
[14]
Olivier KN, Weber DJ, Wallace RJ Jr, Faiz AR, Lee JH, et al. (2003) Nontuberculous mycobacteria. I: multicenter prevalence study in cystic fibrosis. Am J Respir Crit Care Med 167: 828–834.
[15]
Pierre-Audigier C, Ferroni A, Sermet-Gaudelus I, Le Bourgeois M, Offredo C, et al. (2005) Age-related prevalence and distribution of nontuberculous mycobacterial species among patients with cystic fibrosis. J Clin Microbiol 43: 3467–3470.
[16]
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.
[17]
Sermet-Gaudelus I, Le Bourgeois M, Pierre-Audigier C, Offredo C, Guillemot D, et al. (2003) Mycobacterium abscessus and children with cystic fibrosis. Emerg Infect Dis 9: 1587–1591.
[18]
Tomashefski JF Jr, Stern RC, Demko CA, Doershuk CF (1996) Nontuberculous mycobacteria in cystic fibrosis. An autopsy study. Am J Respir Crit Care Med 154: 523–528.
[19]
Galil K, Miller LA, Yakrus MA, Wallace RJ Jr, Mosley DG, et al. (1999) Abscesses due to Mycobacterium abscessus linked to injection of unapproved alternative medication. Emerg Infect Dis 5: 681–687.
[20]
Villanueva A, Calderon RV, Vargas BA, Ruiz F, Aguero S, et al. (1997) Report on an outbreak of postinjection abscesses due to Mycobacterium abscessus, including management with surgery and clarithromycin therapy and comparison of strains by random amplified polymorphic DNA polymerase chain reaction. Clin Infect Dis 24: 1147–1153.
[21]
Byrd TF, Lyons CR (1999) Preliminary characterization of a Mycobacterium abscessus mutant in human and murine models of infection. Infect Immun 67: 4700–4707.
[22]
Rottman M, Catherinot E, Hochedez P, Emile JF, Casanova JL, et al. (2007) Importance of T cells, gamma interferon, and tumor necrosis factor in immune control of the rapid grower Mycobacterium abscessus in C57BL/6 mice. Infect Immun 75: 5898–5907.
[23]
Catherinot E, Clarissou J, Etienne G, Ripoll F, Emile JF, et al. (2007) Hypervirulence of a rough variant of the Mycobacterium abscessus type strain. Infect Immun 75: 1055–1058.
[24]
Howard ST, Rhoades E, Recht J, Pang X, Alsup A, et al. (2006) Spontaneous reversion of Mycobacterium abscessus from a smooth to a rough morphotype is associated with reduced expression of glycopeptidolipid and reacquisition of an invasive phenotype. Microbiology 152: 1581–1590.
[25]
Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, et al. (2001) Massive gene decay in the leprosy bacillus. Nature 409: 1007–1011.
[26]
Stinear TP, Mve-Obiang A, Small PL, Frigui W, Pryor MJ, et al. (2004) Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. Proc Natl Acad Sci U S A 101: 1345–1349.
[27]
Behr MA, Wilson MA, Gill WP, Salamon H, Schoolnik GK, et al. (1999) Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284: 1520–1523.
[28]
Gordon SV, Brosch R, Billault A, Garnier T, Eiglmeier K, et al. (1999) Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol Microbiol 32: 643–655.
[29]
Kim SJ, Kweon O, Jones RC, Edmondson RD, Cerniglia CE (2008) Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19: 859–881.
[30]
Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, et al. (2008) Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res 18: 729–741.
[31]
Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537–544.
[32]
Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, et al. (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113: 171–182.
[33]
Howard ST, Byrd TF, Lyons CR (2002) A polymorphic region in Mycobacterium abscessus contains a novel insertion sequence element. Microbiology 148: 2987–2996.
[34]
Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, et al. (2006) Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol Biol 6: 95.
[35]
Sorensen AL, Nagai S, Houen G, Andersen P, Andersen AB (1995) Purification and characterization of a low-molecular-mass T-cell antigen secreted by Mycobacterium tuberculosis. Infect Immun 63: 1710–1717.
[36]
Arruda S, Bomfim G, Knights R, Huima-Byron T, Riley LW (1993) Cloning of an M. tuberculosis DNA fragment associated with entry and survival inside cells. Science 261: 1454–1457.
[37]
Ishikawa J, Yamashita A, Mikami Y, Hoshino Y, Kurita H, et al. (2004) The complete genomic sequence of Nocardia farcinica IFM 10152. Proc Natl Acad Sci U S A 101: 14925–14930.
[38]
Thoma-Uszynski S, Stenger S, Takeuchi O, Ochoa MT, Engele M, et al. (2001) Induction of direct antimicrobial activity through mammalian toll-like receptors. Science 291: 1544–1547.
[39]
Titball RW (1993) Bacterial phospholipases C. Microbiol Rev 57: 347–366.
[40]
Raynaud C, Guilhot C, Rauzier J, Bordat Y, Pelicic V, et al. (2002) Phospholipases C are involved in the virulence of Mycobacterium tuberculosis. Mol Microbiol 45: 203–217.
[41]
Brodin P, Eiglmeier K, Marmiesse M, Billault A, Garnier T, et al. (2002) Bacterial artificial chromosome-based comparative genomic analysis identifies Mycobacterium microti as a natural ESAT-6 deletion mutant. Infect Immun 70: 5568–5578.
[42]
Moncrief MB, Maguire ME (1998) Magnesium and the role of MgtC in growth of Salmonella typhimurium. Infect Immun 66: 3802–3809.
[43]
Buchmeier N, Blanc-Potard A, Ehrt S, Piddington D, Riley L, et al. (2000) A parallel intraphagosomal survival strategy shared by Mycobacterium tuberculosis and Salmonella enterica. Mol Microbiol 35: 1375–1382.
[44]
Blanc-Potard AB, Lafay B (2003) MgtC as a horizontally-acquired virulence factor of intracellular bacterial pathogens: evidence from molecular phylogeny and comparative genomics. J Mol Evol 57: 479–486.
[45]
St John G, Brot N, Ruan J, Erdjument-Bromage H, Tempst P, et al. (2001) Peptide methionine sulfoxide reductase from Escherichia coli and Mycobacterium tuberculosis protects bacteria against oxidative damage from reactive nitrogen intermediates. Proc Natl Acad Sci U S A 98: 9901–9906.
[46]
Lau GW, Hassett DJ, Ran H, Kong F (2004) The role of pyocyanin in Pseudomonas aeruginosa infection. Trends Mol Med 10: 599–606.
[47]
Arias-Barrau E, Olivera ER, Luengo JM, Fernandez C, Galan B, et al. (2004) The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida. J Bacteriol 186: 5062–5077.
[48]
Ernst RK, D'Argenio DA, Ichikawa JK, Bangera MG, Selgrade S, et al. (2003) Genome mosaicism is conserved but not unique in Pseudomonas aeruginosa isolates from the airways of young children with cystic fibrosis. Environ Microbiol 5: 1341–1349.
[49]
Luengo JM, Garcia JL, Olivera ER (2001) The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications. Mol Microbiol 39: 1434–1442.
[50]
Hunt TA, Kooi C, Sokol PA, Valvano MA (2004) Identification of Burkholderia cenocepacia genes required for bacterial survival in vivo. Infect Immun 72: 4010–4022.
[51]
Zhou X, He X, Liang J, Li A, Xu T, et al. (2005) A novel DNA modification by sulphur. Mol Microbiol 57: 1428–1438.
[52]
Zhang Y, Yakrus MA, Graviss EA, Williams-Bouyer N, Turenne C, et al. (2004) Pulsed-field gel electrophoresis study of Mycobacterium abscessus isolates previously affected by DNA degradation. J Clin Microbiol 42: 5582–5587.
[53]
Nash KA, Brown-Elliott BA, Wallace RJ Jr (2009) A novel gene, erm(41), confers inducible macrolide resistance to clinical isolates of Mycobacterium abscessus but is absent from Mycobacterium chelonae. Antimicrob Agents Chemother 53: 1367–1376.
[54]
Prammananan T, Sander P, Brown BA, Frischkorn K, Onyi GO, et al. (1998) A single 16S ribosomal RNA substitution is responsible for resistance to amikacin and other 2-deoxystreptamine aminoglycosides in Mycobacterium abscessus and Mycobacterium chelonae. J Infect Dis 177: 1573–1581.
[55]
Silver S, Phung LT (1996) Bacterial heavy metal resistance: new surprises. Annu Rev Microbiol 50: 753–789.
[56]
Ordonez E, Letek M, Valbuena N, Gil JA, Mateos LM (2005) Analysis of genes involved in arsenic resistance in Corynebacterium glutamicum ATCC 13032. Appl Environ Microbiol 71: 6206–6215.
[57]
Barkay T, Miller SM, Summers AO (2003) Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol Rev 27: 355–384.
[58]
Wheeler PR, Ratledge C (1994) Tuberculosis: Pathogenesis, Protection and Control. In: Bloom BR, editor. American Society for Microbiology. pp. 353–385.
[59]
Rodriguez-Zaragoza S (1994) Ecology of free-living amoebae. Crit Rev Microbiol 20: 225–241.
[60]
Prithiviraj B, Bais HP, Weir T, Suresh B, Najarro EH, et al. (2005) Down regulation of virulence factors of Pseudomonas aeruginosa by salicylic acid attenuates its virulence on Arabidopsis thaliana and Caenorhabditis elegans. Infect Immun 73: 5319–5328.
[61]
Le Dantec C, Duguet JP, Montiel A, Dumoutier N, Dubrou S, et al. (2002) Occurrence of mycobacteria in water treatment lines and in water distribution systems. Appl Environ Microbiol 68: 5318–5325.
[62]
Danelishvili L, Wu M, Stang B, Harriff M, Cirillo SL, et al. (2007) Identification of Mycobacterium avium pathogenicity island important for macrophage and amoeba infection. Proc Natl Acad Sci U S A 104: 11038–11043.
[63]
Becq J, Gutierrez MC, Rosas-Magallanes V, Rauzier J, Gicquel B, et al. (2007) Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli. Mol Biol Evol 24: 1861–1871.
[64]
Rosas-Magallanes V, Deschavanne P, Quintana-Murci L, Brosch R, Gicquel B, et al. (2006) Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis. Mol Biol Evol 23: 1129–1135.
[65]
Hall-Stoodley L, Lappin-Scott H (1998) Biofilm formation by the rapidly growing mycobacterial species Mycobacterium fortuitum. FEMS Microbiol Lett 168: 77–84.
[66]
Davey ME, O'Toole G A (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev 64: 847–867.
[67]
Jang J, Becq J, Gicquel B, Deschavanne P, et al. (2008) Horizontally acquired genomic islands in the tubercle bacilli. Trends Microbiol 16: 303–308.
[68]
Posfai G, Plunkett G 3rd, Feher T, Frisch D, Keil GM, et al. (2006) Emergent properties of reduced-genome Escherichia coli. Science 312: 1044–1046.
Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406: 959–964.
[71]
Weingart CL, Hooke AM (1999) A nonhemolytic phospholipase C from Burkholderia cepacia. Curr Microbiol 38: 233–238.
[72]
Guina T, Purvine SO, Yi EC, Eng J, Goodlett DR, et al. (2003) Quantitative proteomic analysis indicates increased synthesis of a quinolone by Pseudomonas aeruginosa isolates from cystic fibrosis airways. Proc Natl Acad Sci U S A 100: 2771–2776.
[73]
Maloney KE, Valvano MA (2006) The mgtC gene of Burkholderia cenocepacia is required for growth under magnesium limitation conditions and intracellular survival in macrophages. Infect Immun 74: 5477–5486.
[74]
Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, et al. (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci U S A 105: 3100–3105.
[75]
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, et al. (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100–3108.
[76]
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964.
[77]
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402.
[78]
Glemet E, Codani JJ (1997) LASSAP, a LArge Scale Sequence compArison Package. Comput Appl Biosci 13: 137–143.
Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 16: 560–561.
[81]
Mohseni-Zadeh S, Brezellec P, Risler JL (2004) Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques. Comput Biol Chem 28: 211–218.
[82]
Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22: 2196–2203.
[83]
Luc N, Risler JL, Bergeron A, Raffinot M (2003) Gene teams: a new formalization of gene clusters for comparative genomics. Comput Biol Chem 27: 59–67.
[84]
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797.
[85]
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696–704.
[86]
Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 55: 539–552.
[87]
Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, et al. (2007) Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res 17: 192–200.