Computational protocol: Draft Genome Sequence of Mycobacterium massiliense Strain M159, Showing Phenotypic Resistance to β-Lactam and Tetracycline Antibiotics

Similar protocols

Protocol publication

[…] The rapidly growing Mycobacterium species M. abscessus is an established human pathogen (). Three subspecies, M. abscessus sensu stricto, M. massiliense, and M. bolletii, have been recognized for many years (, , ), but recently, in 2011, Leao and colleagues () proposed a reclassification into two subspecies, M. abscessus subspecies abscessus and M. abscessus subspecies bollettii, which comprises the former M. bolletii and M. massiliense. There are, however, distinct phenotypic features that distinguish M. bolletii from M. massiliense as well as DNA sequences that differentiate these two former subspecies in phylogenetic studies (, ). Here, we report the draft genome sequence of M159, a strain of M. abscessus subspecies bolletii referred to here as M. massiliense for ease of discussion.Strain M159 was isolated from the bronchial aspirate of a 75-year-old male chronic smoker with prostatic carcinoma. He presented with a cough and chest radiograph signs of lung infection, which improved after a 2-week course of ciprofloxacin. The isolate was identified as Mycobacterium massiliense by its rapid growth (within 5 days in the mycobacterial growth indicator tube [MGIT]960 liquid culture system), acid-fast staining, and clustering with M. massiliense reference strains in rpoB- and hsp65-based phylogenetic analyses. MIC determinations using the Sensititre RGMyco plate (TREK Diagnostic Systems, Cleveland, OH) showed in vitro resistance to doxycycline, minocycline, ceftriaxone, cefepime, and amoxicillin-clavulanic acid and intermediate resistance to cefoxitin and imipenem but susceptibility to ciprofloxacin, clarithromycin, amikacin, and linezolid.The genome sequence of M159 was determined using the Illumina GA IIx platform. The 20,229,857 raw read sequences generated were processed and assembled using Genomics Workbench 4.9. This resulted in 118 contigs with an N50 value of 115,707 bp and a draft genome sequence of 4,935,864 bp with a G+C content of 64%. Functional annotation using the Rapid Annotations using Subsystems Technology (RAST) Server () predicted 4,864 coding sequences (CDS) and 51 RNAs (48 tRNAs and 3 rRNAs). Of the 1,540 (32%) functional genes assigned to functional categories, most are involved in amino acids and derivatives (427 genes), followed by cofactors, vitamins, and prosthetic groups (347 genes), carbohydrates (284 genes), and fatty acids, lipids, and isoprenoids (256 genes). In contrast, there was only 1 putative gene for motility and chemotaxis, and there were 49 genes associated with virulence, disease, and defense. In agreement with its antibiotic susceptibility pattern, M159 showed the typical truncated erm(41) gene associated with susceptibility to macrolides (), bla genes for resistance to cephalosporins and clavulanic acid inhibition, and three genes for tetracycline resistance, namely, the tetA and tetC genes encoding efflux proteins and an intact tetR gene, which is associated with the upregulation of the expression of efflux proteins in the presence of tetracycline (). […]

Pipeline specifications

Software tools geWorkbench, RAST
Application Phylogenetics
Organisms Homo sapiens
Diseases Infection, Lung Diseases, Mycobacterium Infections
Chemicals Tetracycline, Tetracyclines