Description and complete genome sequence of Mycobacterium venezuelense sp. nov., a rapidly growing species recovered from a soft tissue infection

Abstract

We describe a rapidly growing mycobacterial (RGM) species closely related to <i>Mycobacterium wolinskyi</i>. The bacterium was isolated from three biopsies obtained from a 78-year-old Venezuelan woman who presented with a chronic superficial erythematous plaque in the right nasal cavity. The three isolates, LTG2003(1-3), exhibited identical phenotypic, biochemical, and molecular characteristics and showed susceptibility to amikacin and linezolid, intermediate susceptibility to cefoxitin and imipenem, and resistance to ciprofloxacin, clarithromycin, sulfamethoxazole-trimethoprim, and tobramycin. Conventional diagnostic methods, including biochemical assays, <i>hsp65</i> PCR restriction enzyme analysis (PRA-<i>hsp65</i>), the Genotype Mycobacterium CM v2.0 linear probe assay, and Sanger sequencing of the <i>16S rRNA</i>, <i>hsp65</i>, and <i>rpoB</i> genes, failed to identify the microorganism to the species level. MALDI-TOF mass spectrometry yielded genus-level scores suggestive of <i>M. wolinskyi</i>. Whole-genome sequencing confirmed that the isolates represent a new species. The type strain, designated LTG 2003-1 (WFCC 1312 = P7483 = CDBB-500-3), has been deposited in two internationally recognized microbial culture collections in Mexico and Brazil. The genome of this organism has also been deposited in GenBank as <i>Mycobacterium</i> sp. LTG2003 with accession number JBONDW000000000. Based on our findings, we propose that the LTG2003(1-3) isolates represent a new species, for which we propose the name <i>Mycobacterium venezuelense</i> sp. <i>nov</i>.