Genomic Analysis of Mycobacterium massiliense Strain M115, an Isolate from Human Sputum

Abstract

We report the draft genome sequence of a clinical isolate, strain M115, identified as Mycobacterium massiliense, a member of the newly created taxon of Mycobacterium abscessus subspecies bolletii comb. nov.

GENOME ANNOUNCEMENT

The genus Mycobacterium consists of more than 100 species of acid-fast bacteria exhibiting diverse genotypic and phenotypic characteristics. Among the rapidly growing nontuberculous species, M. abscessus is the one most frequently associated with human infections (2, 3). This species has recently been divided into two subspecies: M. abscessus subspecies bolletii, comprising the former taxa of M. bolletii and M. massiliense; and M. abscessus subspecies abscessus (4). The classification of these bacteria has been based on the polymorphism in various target genes (5), but following the introduction of whole-genome sequencing, much more genetic information has been made available for the better identification of organisms. In our ongoing research to characterize members of the M. abscessus subspecies, we sequenced a series of genomes to identify sequence polymorphisms for comparative genome analysis. Here we present the whole-genome sequence of M. massiliense M115, an isolate from sputum from a Malaysian patient presenting with persistent cough and loss of body weight suggestive of pulmonary tuberculosis. The identification of this strain as M. massiliense was based on its clustering with the reference M. massiliense type strain CIP108297 in a dendrogram drawn up with multilocus sequence data from 7 housekeeping genes, constructed using the unweighted-pair group method using average linkages (UPGMA) algorithm (6).

The M115 genome was shotgun sequenced using the high-throughput Illumina genome analyzer IIX technology, generating 9,283,398 reads with an average read length of 61.6 bp. The de novo assembly of these sequencing reads was performed using a commercial CLCBio Genomics Workbench 4.9. This resulted in 50 contigs with an N₂₅ contig size of 683,939 bp, N₅₀ contig size of 307,155 bp, and N₇₅ contig size of 188,276 bp. The resulting contigs were annotated using the Rapid Annotation using Subsystem Technology (RAST) pipeline (1).

The draft genome sequence showed a genome size of 4,977,264 bp and 4,997 putative open reading frames (ORFs) with a mean genomic length of 892 bp (range, 71 to 22,620 bp). There were 50 RNAs (47 tRNAs and 3 rRNAs) and 4,947 coding sequences (CDSs), of which, 1,533 (31%) were involved in 382 subsystems; the remaining 3,413 (69%) CDSs were not categorized in any subsystem. The RAST annotation predicted 433 genes for amino acids and derivatives and 36 putative genes for virulence, intracellular existence, disease, and defense, the majority of which were related to resistance to antibiotics and toxic compounds.

Nucleotide sequence accession numbers.

The M. massiliense strain M115 genome sequence and annotation data have been deposited in NCBI GenBank under accession no. AJLZ00000000. The version described in this paper is the first version, AJLZ01000000.