Genome analysis reveals three genomospecies in Mycobacterium abscessus

BMC Genomics

Michel Drancourt¹  Mohamed Sassi² 

[1] Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine, 27, Boulevard Jean Moulin, Marseille cedex 5, France;Aix Marseille Université, URMITE, UMR63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France

关键词: Prophage;    Mycobacteriophage;    Araucaria;    Mycobacterium massiliense;    Mycobacterium bolletii;    Mycobacterium abscessus;   

Others  :  1217240
DOI  :  10.1186/1471-2164-15-359

 received in 2013-09-05, accepted in 2014-04-30,  发布年份 2014

【 摘 要 】

Background

Mycobacterium abscessus complex, the third most frequent mycobacterial complex responsible for community- and health care-associated infections in developed countries, comprises of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii reviously referred as Mycobacterium bolletii and Mycobacterium massiliense. The diversity of this group of opportunistic pathogens is poorly described.

Results

In-depth analysis of 14 published M. abscessus complex genomes found a pan-genome of 6,153 proteins and core-genome of 3,947 (64.1%) proteins, indicating a non-conservative genome. Analysing the average percentage of amino-acid sequence identity (from 94.19% to 98.58%) discriminates three main clusters C1, C2 and C3: C1 comprises strains belonging to M. abscessus, C2 comprises strains belonging to M. massiliense and C3 comprises strains belonging to M. bolletii; and two sub-clusters in clusters C2 and C3. The phylogenomic network confirms these three clusters. The genome length (from 4.8 to 5.51-Mb) varies from 5.07-Mb in C1, 4.89-Mb in C2A, 5.01-Mb in C2B and 5.28-Mb in C3. The mean number of prophage regions (from 0 to 7) is 2 in C1; 1.33 in C2A; 3.5 in C2B and five in C3. A total of 36 genes are uniquely present in C1, 15 in C2 and 15 in C3. These genes could be used for the detection and identification of organisms in each cluster. Further, the mean number of host-interaction factors (including PE, PPE, LpqH, MCE, Yrbe and type VII secretion system ESX3 and ESX4) varies from 70 in cluster C1, 80 in cluster C2A, 74 in cluster C2B and 93 in clusters C3A and C3B. No significant differences in antibiotic resistance genes were observed between clusters, in contrast to previously reported in-vitro patterns of drug resistance. They encode both penicillin-binding proteins targeted by β-lactam antibiotics and an Ambler class A β-lactamase for which inhibitors exist.

Conclusions

Our comparative analysis indicates that M. abscessus complex comprises three genomospecies, corresponding to M. abscessus, M. bolletii, and M. massiliense. The genomics data here reported indicate differences in virulence of medical interest; and suggest targets for the refined detection and identification of M. abscessus.

【 授权许可】

   
2014 Sassi and Drancourt; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Kubica GP, Baess I, Gordon RE, Jenkins PA, Kwapinski JB, McDurmont C, Pattyn SR, Saito H, Silcox V, Stanford JL, Takeya K, Tsukamura M: A co-operative numerical analysis of rapidly growing mycobacteria. J Gen Microbiol 1972, 73:55-70.
• [2]Ross AJ: Mycobacterium salmoniphilum sp. nov. from salmonid fishes. Am Rev Respir Dis 1960, 81:241-250.
• [3]Wilson RW, Steingrube VA, Böttger EC, Springer B, Brown-Elliott BA, Vincent V, Jost KC Jr, Zhang Y, Garcia MJ, Chiu SH, Onyi GO, Rossmoore H, Nash DR, Wallace RJ Jr: Mycobacterium immunogenum sp. nov., a novel species related to Mycobacterium abscessus and associated with clinical disease, pseudo-outbreaks, and contaminated metalworking fluids: an international cooperative study on mycobacterial taxonomy. Int J Syst Evol Microbiol 2001, 51:1751-1764.
• [4]Adékambi T, Reynaud-Gaubert M, Greub G, Gevaudan MJ, La Scola B, Raoult D, Drancourt M: Amoebal coculture of “Mycobacterium massiliense” sp. nov. from the sputum of a patient with hemoptoic pneumonia. J Clin Microbiol 2004, 42:5493-5501.
• [5]Adékambi T, Berger P, Raoult D, Drancourt M: 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 2006, 56:133-143.
• [6]Simmon KE, Brown-Elliott BA, Ridge PG, Durtschi JD, Mann LB, Slechta ES, Steigerwalt AG, Moser BD, Whitney AM, Brown JM, Voelkerding KV, McGowan KL, Reilly AF, Kirn TJ, Butler WR, Edelstein PH, Wallace RJ Jr, Petti CA: Mycobacterium chelonae-abscessus complex associated with sinopulmonary disease, Northeastern USA. Emerg Infect Dis 2011, 9:1692-1700.
• [7]Petrini B: Mycobacterium abscessus: an emerging rapid-growing potential pathogen. APMIS 2006, 5:319-328.
• [8]Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, Reacher M, Aworth CSH, Curran MD, Harris SR, Peacock SJ, Parkhill J, Floto RA: Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. The Lancet 2013, 381:1551-1560.
• [9]Medjahed H, Gaillard JL, Reyrat JM: Mycobacterium abscessus: a new player in the mycobacterial field. Trends Microbiol 2010, 3:117-123.
• [10]Jassies-van der Lee A, Houwers DJ, Meertens N, van der Zanden AG, Willemse T: Localised pyogranulomatous dermatitis due to Mycobacterium abscessus in a cat: a case report. Vet J 2009, 2:304-306.
• [11]Albini S, Mueller S, Bornand V, Gutzwiller ME, Burnand C, Hüssy D, Abril C, Reitt K, Korczak BM, Miserez R: Cutaneous atypical mycobacteriosis due to Mycobacterium massiliense in a cat. (Article in German). Schweiz Arch Tierheilkd 2007, 12:553-558.
• [12]Whitaker BR, Hadfield CA, Clayton LA, Neiffer D, Stamper MA: Mycobacterium abscessus infection in an Atlantic bottlenose dolphin (Tursiops truncatus). Proceedings of the 36th Annual Conference of the International Association of Aquatic Animal Medicine 2012, 49-51.
• [13]Wiinschmann A, Armien A, Harris NB, Brown-Elliott BA, Wallace RJ Jr, Rasmussen J, Willette M, Wolf T: Disseminated panniculitis in a bottlenose dolphin (Tursiops truncatus) due to Mycobacterium chelonae infection. J Zoo Wildl Med 2008, 39:412-440.
• [14]Clayton LA, Stamper MA, Whitaker BR, Hadfield CA, Simons B, Mankowski JL: Mycobacterium abscessus pneumonia in an Atlantic bottlenose dolphin (Tursiops truncatus). J Zoo Wildl Med 2012, 43:961-965.
• [15]Zerihun MA, Nilsen H, Hodneland S, Colquhoun DJ: Mycobacterium salmoniphilum infection in farmed Atlantic salmon, Salmo salar L. J Fish Dis 2011, 34:769-781.
• [16]Leao SC, Tortoli E, Euzéby JP, Garcia MJ: Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus. Int J Syst Evol Microbiol 2011, 61:2311-2313.
• [17]Adékambi T, Colson P, Drancourt M: rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol 2003, 41:5699-5708.
• [18]Viana-Niero C, Lima KV, Lopes ML, Rabello MC, Marsola LR, Brilhante VC, Durham AM, Leao SC: Molecular characterization of Mycobacterium massiliense and Mycobacterium bolletii in isolates collected from outbreaks of infections after laparoscopic surgeries and cosmetic procedures. J Clin Microbiol 2008, 46:850-855.
• [19]Arnold C, Barrett A, Cross L, Magee JG: The use of rpoB sequence analysis in the differentiation of Mycobacterium abscessus and Mycobacterium chelonae: a critical judgement in cystic fibrosis? Clin Microbiol Infect 2012, 18:E131-133.
• [20]Leao SC, Tortoli E, Viana-Niero C, Ueki SY, Lima KV, Lopes ML, Yubero J, Menendez MC, Garcia MJ: Characterization of mycobacteria from a major Brazilian outbreak suggests that revision of the taxonomic status of members of the Mycobacterium chelonae - M. abscessus group is needed. J Clin Microbiol 2009, 47:2691-2698.
• [21]Macheras E, Roux AL, Ripoll F, Sivadon-Tardy V, Gutierrez C, Gaillard JL, Heym B: Inaccuracy of single-target sequencing for discriminating species of the Mycobacterium abscessus group. J Clin Microbiol 2009, 47:2596-2600.
• [22]Macheras E, Roux AL, Bastian S, Leão SC, Palaci M, Sivadon-Tardy V, Gutierrez C, Richter E, Rusch-Gerdes S, Pfyffer G, Bodmer T, Cambau E, Gaillard JL, Heym B: Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains. J Clin Microbiol 2011, 49:491-499.
• [23]Zelazny AM, Root JM, Shea YR, Colombo RE, Shamputa IC, Stock F, Conlan S, McNulty S, Brown-Elliott BA, Wallace RJ Jr, Olivier KN, Holland SM, Sampaio EP: Cohort study of molecular identification and typing of Mycobacterium abscessus, Mycobacterium massiliense, and Mycobacterium bolletii. J Clin Microbiol 2009, 47:1985-1995.
• [24]Sassi M, Ben Kahla I, Drancourt M: Mycobacterium abscessus multispacer sequence typing. BMC Microbiol 2013, 13:1-3. BioMed Central Full Text
• [25]Ripoll F, Pasek S, Schenowitz C, Dossat C, Barbe V, Rottman M, Macheras E, Heym B, Herrmann JL, Daffé M, Brosch R, Risler JL, Gaillard JL: Non-mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus. PLoS One 2009, 4:e5660.
• [26]Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ: Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11:119. BioMed Central Full Text
• [27]Wozniak M, Wong L, Tiuryn J: CAMBer: an approach to support comparative analysis of multiple bacterial strains. BMC Genomics 2011, 12(2):S6.
• [28]Li L, Stoeckert CJ Jr, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13:2178-2189.
• [29]Sentausa E, Fournier PE: Advantages and limitations of genomics in prokaryotic taxonomy. Clin Microbiol Infect 2013, 19:790-795.
• [30]Darling AE, Mau B, Perna NT: progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5:e11147.
• [31]Bryant D, Moulton V: Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 2004, 21:255-265.
• [32]Raiol T, Ribeiro GM, Maranhão AQ, Bocca AL, Silva-Pereira I, Junqueira-Kipnis AP, Brigido Mde M, Kipnis A: Complete genome sequence of Mycobacterium massiliense. J Bacteriol 2012, 194:5455.
• [33]Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41. BioMed Central Full Text
• [34]Konstantinidis KT, Ramette A, Tiedje JM: The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 2006, 361:1929-1940.
• [35]Konstantinidis KT, Tiedje JM: Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007, 10:504-509.
• [36]Canchaya C, Proux C, Fournous G, Bruttin A, Brüssow H: Prophage genomics. Microbiol Mol Biol Rev 2003, 67:238-276.
• [37]Choi GE, Cho YJ, Koh WJ, Chun J, Cho SN, Shin SJ: Draft genome sequence of Mycobacterium abscessus subsp. bolletii BD (T). J Bacteriol 2012, 194:2756-2757.
• [38]Wong YL, Choo SW, Tan JL, Ong CS, Ng KP, Ngeow YF: Draft genome sequence of Mycobacterium bolletii strain M24, a rapidly growing mycobacterium of contentious taxonomic status. J Bacteriol 2012, 194:4475.
• [39]Sassi M, Bebeacua C, Drancourt M, Cambillau C: The first structure of a mycobacteriophage, Araucaria. J Virol 2013. Epub ahead of print
• [40]Choo SW, Wong YL, Leong ML, Heydari H, Ong CS, Ng KP, Ngeow YF: Analysis of the genome of Mycobacterium abscessus strain M94 reveals an uncommon cluster of tRNAs. J Bacteriol 2012, 194:5724.
• [41]Adékambi T, Drancourt M: Mycobacterium bolletii respiratory infections. Emerg Infect Dis 2009, 15:302-305.
• [42]Iyer A, Barbour E, Azhar E, Qadri I, Chaudhary A, Abuzenadah A, Kumosani T, Damanhouri G, Bahijri S, Al-Hejin A, Abdel Nour AM, Harakeh S: Bacteriophages in Escherichia coli antimicrobial resistance. Adv Bioscience Biotechnol 2013, 4:469-476.
• [43]Kim HY, Kim BJ, Kook Y, Yun YJ, Shin JH, Kim BJ, Kook YH: Mycobacterium massiliense is differentiated from Mycobacterium abscessus and Mycobacterium bolletii by erythromycin ribosome methyltransferase gene (erm) and clarithromycin susceptibility patterns. Microbiol Immunol 2010, 54:347-353.
• [44]Koh WJ, Jeon K, Lee NY, Kim BJ, Kook YH, Lee SH, Park YK, Kim CK, Shin SJ, Huitt GA, Daley CL, Kwon OJ: Clinical significance of differentiation of Mycobacterium massiliense from Mycobacterium abscessus. Am J Respir Crit Care Med 2011, 183:405-410.
• [45]Paulsen IT, Skurray RA, Tam R, Saier MH Jr, Turner RJ, Weiner JH, Goldberg EB, Grinius LL: The SMR family: a novel family of multidrug efflux proteins involved with the efflux of lipophilic drugs. Mol Microbiol 1996, 19:1167-1175.
• [46]Ramón-García S, Martín C, De Rossi E, Aínsa JA: Contribution of the Rv2333c efflux pump (the Stp protein) from Mycobacterium tuberculosis to intrinsic antibiotic resistance in Mycobacterium bovis BCG. J Antimicrob Chemother 2007, 59:544-547.
• [47]Nessar R, Cambau E, Reyrat JM, Murray A, Gicquel B: Mycobacterium abscessus: a new antibiotic nightmare. J Antimicrob Chemother 2012, 67:810-818.
• [48]Hu GZ, Pan YS, Wu H, Hu H, Xu R, Yuan L, Liu JH, Feng JK: Prevalence of tetracycline resistance genes and identification of tet(M) in clinical isolates of E. coli from sick ducks in China. J Med Microbiol 2013, 62:851-858.
• [49]Duarte RS, Lourenço MC, Fonseca Lde S, Leão SC, Amorim Ede L, Rocha IL, Coelho FS, Viana-Niero C, Gomes KM, da Silva MG, Lorena NS, Pitombo MB, Ferreira RM, Garcia MH, de Oliveira GP, Lupi O, Vilaça BR, Serradas LR, Chebabo A, Marques EA, Teixeira LM, Dalcolmo M, Senna SG, Sampaio JL: Epidemic of postsurgical infections caused by Mycobacterium massiliense. J Clin Microbiol 2009, 47:2149-2155.
• [50]Maurer FP, Rüegger V, Ritter C, Bloemberg GV, Böttger EC: Acquisition of clarithromycin resistance mutations in the 23S rRNA gene of Mycobacterium abscessus in the presence of inducible erm(41). J Antimicrob Chemother 2012, 67:2606-2611.
• [51]Monego F, Duarte RS, Nakatani SM, Araújo WN, Riediger IN, Brockelt S, Souza V, Cataldo JI, Dias RC, Biondo AW: Molecular identification and typing of Mycobacterium massiliense isolated from postsurgical infections in Brazil. Braz J Infect Dis 2011, 15:436-441.
• [52]de Moura VC, da Silva MG, Gomes KM, Coelho FS, Sampaio JL, Mello FC, Lourenço MC, Amorim Ede L, Duarte RS: Phenotypic and molecular characterization of quinolone resistance in Mycobacterium abscessus subsp. bolletii recovered from postsurgical infections. J Med Microbiol 2012, 61:115-125.
• [53]Cattoir V, Poirel L, Nordmann P: Plasmid-mediated quinolone resistance pump QepA2 in an Escherichia coli isolate from France. Antimicrob Agents Chemother 2008, 52:3801-3804.
• [54]Basu J, Chattopadhyay R, Kundu M, Chakrabarti P: Purification and partial characterization of a penicillin-binding protein from Mycobacterium smegmatis. J Bacteriol 1992, 174:4829-4832.
• [55]Cayrou C, Henrissat B, Gouret P, Pontarotti P, Drancourt M: Peptidoglycan: a post-genomic analysis. BMC Microbiol 2012, 18:294.
• [56]Catherinot E, Clarissou J, Etienne G, Ripoll F, Emile JF, Daffé M, Perronne C, Soudais C, Gaillard JL, Rottman M: Hypervirulence of a rough variant of the Mycobacterium abscessus type strain. Infect Immun 2007, 75:1055-1058.
• [57]Nessar R, Reyrat JM, Davidson LB, Byrd TF: Deletion of the mmpL4b gene in the Mycobacterium abscessus glycopeptidolipid biosynthetic pathway results in loss of surface colonization capability, but enhanced ability to replicate in human macrophages and stimulate their innate immune response. Microbiology 2011, 157:1187-1195.
• [58]Davidson LB, Nessar R, Kempaiah P, Perkins DJ, Byrd TF: Mycobacterium abscessus glycopeptidolipid prevents respiratory epithelial TLR2 signaling as measured by HβD2 gene expression and IL-8 release. PLoS One 2011, 6:e29148.
• [59]Recht J, Martínez A, Torello S, Kolter R: Genetic analysis of sliding motility in Mycobacterium smegmatis. J Bacteriol 2000, 182:4348-4351.
• [60]Recht J, Kolter R: Glycopeptidolipid acetylation affects sliding motility and biofilm formation in Mycobacterium smegmatis. J Bacteriol 2001, 183:5718-5724.
• [61]Villeneuve C, Etienne G, Abadie V, Montrozier H, Bordier C, Laval F, Daffe M, Maridonneau-Parini I, Astarie-Dequeker C: Surface-exposed glycopeptidolipids of Mycobacterium smegmatis specifically inhibit the phagocytosis of mycobacteria by human macrophages. Identification of a novel family of glycopeptidolipids. J Biol Chem 2003, 278:5129-5130.
• [62]El-Shazly S, Ahmad S, Mustafa AS, Al-Attiyah R, Krajci D: Internalization by HeLa cells of latex beads coated with mammalian cell entry (Mce) proteins encoded by the mce3 operon of Mycobacterium tuberculosis. J Med Microbiol 2007, 56:1145-1151.
• [63]Stavrum R, Valvatne H, Stavrum AK, Riley LW, Ulvestad E, Jonassen I, Doherty TM, Grewal HM: Mycobacterium tuberculosis Mce1 protein complex initiates rapid induction of transcription of genes involved in substrate trafficking. Genes Immun 2012, 13:496-502.
• [64]Ishikawa J, Yamashita A, Mikami Y, Hoshino Y, Kurita H, Hotta K, Shiba T, Hattori M: The complete genomic sequence of Nocardia farcinica IFM 10152. Proc Natl Acad Sci U S A 2004, 101:14925-14930.
• [65]Abdallah AM, van Pittius Gey NC, Champion PA, Cox J, Luirink J, Vandenbroucke-Grauls CM, Appelmelk BJ, Bitter W: Type VII secretion-mycobacteria show the way. Nat Rev Microbiol 2007, 5:88-91.
• [66]Simeone R, Bottai D, Brosch R: ESX/type VII secretion systems and their role in host-pathogen interaction. Curr Opin Microbiol 2009, 12:4-10.
• [67]Mukhopadhyay S, Balaji KN: The PE and PPE proteins of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2011, 91:441-447.
• [68]Snel B, Bork P, Huynen MA: Genome phylogeny based on gene content. Nat Genet 1999, 21:108-110.