Abstract
Multiple isolates of Mycobacterium abscessus subsp. bolletii, collectively called BRA100, were associated with outbreaks of postsurgical skin infections across various regions of Brazil from 2003 to 2009. We announce the draft genome sequence of a newly sequenced BRA100 strain, M. abscessus subsp. bolletii CRM-0020, isolated from a patient in Rio de Janeiro, Brazil.
GENOME ANNOUNCEMENT
The nontuberculous mycobacterium (NTM) Mycobacterium abscessus is an environmental organism found in soil, water, and other ecological niches, and it acts as an opportunistic pathogen causing diseases ranging from cutaneous to pulmonary infections (1). Bacterial isolates of M. abscessus subsp. bolletii (formerly referred to as M. abscessus subsp. massiliense) (2) were linked to outbreaks of postsurgical skin infections in multiple Brazilian states from 2003 to 2009 (3–5). The epidemic isolates are collectively referred to as BRA100, as they exhibit a unique pulsed-field gel electrophoresis (PFGE) signature and show high levels of resistance to glutaraldehyde, the disinfectant used in most hospital sites that had reported cases (2, 4, 6).
The genome of one BRA100 strain, M. abscessus subsp. bolletii GO-06, from the Brazilian state of Goiás, was previously released (7), but the sequencing of additional outbreak strains is needed for comparative studies of isolates from different geographic regions. Here, we present the draft genome sequence of a BRA100 strain from Rio de Janeiro, Brazil, called M. abscessus subsp. bolletii CRM-0020, which was isolated in 2006 from a soft tissue biopsy specimen (4). The PFGE profile of CRM-0020 showed 13 bands by DraI digestion similar to those of the outbreak strains isolated in the Brazilian states of Goiás and Pará (4).
The genomic sequence data of CRM-0020 were obtained with Illumina MiSeq (150 bp, paired-end) at 130× coverage and with Roche 454 GS-FLX Titanium (average length, 604 bp) at 10× coverage. MiSeq reads were assembled into contigs with the software packages A5 (8) and Velvet (9) that were trimmed into 400-bp pseudo-Sanger reads. A combination of pseudo-Sanger, 454, and MiSeq reads were combined for hybrid assembly using Newbler (Roche). The contigs were ordered by alignment to the M. abscessus subsp. abscessus reference genome ATCC 19977 (10) with Mauve 2.3.1 (11), and genomic features were predicted and annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline.
The draft genome of CRM-0020 consists of 44 contigs with an average contig length of 111,245 bp, a total size of 4,840,000 bp, and a G+C content of 64.3%. A total of 4,750 coding sequences (CDSs) were predicted, including 3,378 CDSs (71.1%) with functional annotations and 1,372 CDSs (28.9%) that were annotated as hypothetical proteins. The genome contains 46 tRNAs and one rRNA cistron. A comparative analysis between CRM-0020 and ATCC 19977 revealed that 4,189 CDSs (88.2%) are shared between the two strains, while 561 (11.8%) CDSs are unique to CRM-0020. A single contig (length, 56,466 bp) aligned with 99% identity to the M. abscessus subsp. bolletii plasmids, pMAB01 (12) and BRA100 (GenBank accession no. CP003505), and includes 63 predicted CDSs.
Whole-genome sequence alignments revealed 6,217 single nucleotide polymorphisms (SNPs) (1.28 SNPs per Kb) between CRM-0020 and GO-06, showing a low level of divergence among the regional outbreak strains from Brazil. In contrast, 49,354 SNPs (10.2 SNPs per Kb) were observed between CRM-0020 and the type strain of M. abscessus subsp. bolletii CCUG 48898 (13), revealing a higher level of divergence between unrelated strains than between outbreak strains.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ATFQ00000000. The version described in this paper is version ATFQ01000000.
ACKNOWLEDGMENTS
R.M.D., P.R.R., and M.S. thank the NTM Center of Excellence at National Jewish Health, funded in part by the Amon G. Carter Foundation. M.S. acknowledges support from the Colorado Bioscience Discovery Evaluation Grant Program, the Eppley Foundation, and the Boettcher Foundation Webb-Waring Biomedical Research Program. E.F.-H. acknowledges support from the Natalie V. Zucker Foundation. This work was supported in part by the National Institutes of Health/National Institute of Allergy and Infectious Diseases grant no. AI089718 (to M.J.).
The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
Footnotes
Citation Davidson RM, Reynolds PR, Farias-Hesson E, Duarte RS, Jackson M, Strong M. 2013. Genome sequence of an epidemic isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil. Genome Announc. 1(4):e00617-13. doi:10.1128/genomeA.00617-13.
REFERENCES
- 1. Primm TP, Lucero CA, Falkinham JO., III 2004. Health impacts of environmental mycobacteria. Clin. Microbiol. Rev. 17:98–106 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Leao SC, Tortoli E, Viana-Niero C, Ueki SY, Lima KV, Lopes ML, Yubero J, Menendez MC, Garcia MJ. 2009. 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. 47:2691–2698 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Cardoso AM, Martins de Sousa E, Viana-Niero C, Bonfim de Bortoli F, Pereira das Neves ZC, Leão SC, Junqueira-Kipnis AP, Kipnis A. 2008. Emergence of nosocomial Mycobacterium massiliense infection in Goiás, Brazil. Microbes Infect. 10:1552–1557 [DOI] [PubMed] [Google Scholar]
- 4. Duarte RS, Lourenço MC, de Souza Fonseca L, Leão SC, de Lourdes T, Amorim E, 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. 2009. Epidemic of postsurgical infections caused by Mycobacterium massiliense. J. Clin. Microbiol. 47:2149–2155 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Viana-Niero C, Lima KV, Lopes ML, Rabello MC, Marsola LR, Brilhante VC, Durham AM, Leão SC. 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 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Shang S, Gibbs S, Henao-Tamayo M, Shanley CA, McDonnell G, Duarte RS, Ordway DJ, Jackson M. 2011. Increased virulence of an epidemic strain of Mycobacterium massiliense in mice. PLoS One 6:e24726. 10.1371/journal.pone.0024726 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Raiol T, Ribeiro GM, Maranhão AQ, Bocca AL, Silva-Pereira I, Junqueira-Kipnis AP, Brigido MDM, Kipnis A. 2012. Complete genome sequence of Mycobacterium massiliense. J. Bacteriol. 194:5455. 10.1128/JB.01219-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Tritt A, Eisen JA, Facciotti MT, Darling AE. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 7:e42304. 10.1371/journal.pone.0042304 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. 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. 2009. Nonmycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus. PLoS One 4:e5660. 10.1371/journal.pone.0005660 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Darling AC, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394–1403 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Leão SC, Matsumoto CK, Carneiro A, Ramos RT, Nogueira CL, Lima JD, Lima KV, Lopes ML, Schneider H, Azevedo VA, da Costa da Silva A. 2013. The detection and sequencing of a broad-host-range conjugative IncP-1β plasmid in an epidemic strain of Mycobacterium abscessus subsp. bolletii. PLoS One 8:e60746. 10.1371/journal.pone.0060746 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Tettelin H, Sampaio EP, Daugherty SC, Hine E, Riley DR, Sadzewicz L, Sengamalay N, Shefchek K, Su Q, Tallon LJ, Conville P, Olivier KN, Holland SM, Fraser CM, Zelazny AM. 2012. Genomic insights into the emerging human pathogen Mycobacterium massiliense. J. Bacteriol. 194:5450. 10.1128/JB.01200-12 [DOI] [PMC free article] [PubMed] [Google Scholar]