Computational protocol: Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii INCQS 00594

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Protocol publication

[…] Mycobacterium abscessus is a rapidly growing mycobacterium and an emerging human pathogen causing pulmonary infections, especially in patients with cystic fibrosis and other underlying lung disorders (). M. abscessus is also a major cause of sporadic and clustered outbreaks of community-acquired and health care-associated skin and soft tissue infections (). Recently, two subspecies were recognized within M. abscessus: M. abscessus subsp. abscessus and M. abscessus subsp. bolletii (). The latter subspecies includes strains of two previously described taxa, M. massiliense and M. bolletii (–).A prolonged nationwide epidemic of surgical infections related to video surgeries occurred in Brazil between 2004 and 2008 (). The analysis of isolates obtained in different states confirmed that the epidemic was caused by a single strain of M. abscessus subsp. bolletii (–). One isolate, obtained from a patient who underwent laparoscopic surgery in 2004 in Belém, Pará (PA), was deposited as the epidemic prototype strain in the collection of the National Institute for Health Quality Control (INCQS) under the name INCQS 00594 (). This isolate was shown to carry a circular plasmid of the IncP-1β group, named pMAB01, which was the subject of a previous publication by Leão et al. ().The genome of M. abscessus subsp. bolletii INCQS 00594 was sequenced from a fragment library using the 454 GS FLX sequencer (Roche, Nutley, NJ) and the GS FLX Titanium sequencing kit XL+ at the Centre for Advanced Technologies in Genomics (CATG), Chemistry Institute, São Paulo University. A total of 779,074 reads (558,522,880 bp) were extracted from the .sff file with the script “sff_extract_0_2_13” (http://bioinf.comav.upv.es/sff_extract/), which represents a genomic coverage of ~111×. The reads were assembled using the MIRA software (), generating 102 contigs with an N50 of 664 kb. Eighteen contigs matched sequences in the plasmid pMAB01 (GenBank accession no. CP003376), and these were not considered here. The remaining sequences were annotated via RAST (). The draft genome sequence of M. abscessus subsp. bolletii INCQS 00594 has 4,885,146 bp, an overall G+C content of 64.24%, 4,864 open reading frames (ORF), and one rRNA operon. […]

Pipeline specifications

Software tools seq_crumbs, RAST
Application WGS analysis
Organisms Mycobacteroides abscessus, Homo sapiens
Diseases Infection