Characterization of IS1110-like sequences found in Mycobacterium species other than Mycobacterium avium

Mycolicibacterium cyprinidarum sp. nov., a rapidly growing species isolated from diseased koi carp, Cyprinus carpio

A rapidly growing nontuberculous mycobacterium was isolated from diseased koi carp in Niigata, Japan, which was identified as representing a novel Mycolicibacterium species through whole genome sequence analysis. The bacterial isolates (NGTWS0302, NGTWS1803T and NGTWSNA01) were found to belong to the genus Mycolicibacterium through phylogenetic analysis using whole genome sequences of mycobacteria species. The bacterial colony was smooth, moist and non-chromogenic on 1% Ogawa medium at 30 °C. In biochemical characteristic tests, the bacterial isolates showed positive reactions for catalase activity, Tween 80 hydrolysis and tellurite reduction. The isolates were sensitive to 2-4 µg ml-1 ampicillin, kanamycin and rifampicin. Based on these results, we propose a novel Mycolicibacterium species, Mycolicibacterium cyprinidarum sp. nov. The type strain is NGTWS1803T (=JCM 35117T=ATCC TSD-289T).

Mycobacterium avium in the postgenomic era

The past several years have witnessed an upsurge of genomic data pertaining to the Mycobacterium avium complex (MAC). Despite clear advances, problems with the detection of MAC persist, spanning the tests that can be used, samples required for their validation, and the use of appropriate nomenclature. Additionally, the amount of genomic variability documented to date greatly outstrips the functional understanding of epidemiologically different subsets of the organism. In this review, we discuss how postgenomic insights into the MAC have helped to clarify the relationships between MAC organisms, highlighting the distinction between environmental and pathogenic subsets of M. avium. We discuss the availability of various genetic targets for accurate classification of organisms and how these results provide a framework for future studies of MAC variability. The results of postgenomic M. avium study provide optimism that a functional understanding of these organisms will soon emerge, with genomically defined subsets that are epidemiologically distinct and possess different survival mechanisms for their various niches. Although the status quo has largely been to study different M. avium subsets in isolation, it is expected that attention to the similarities and differences between M. avium organisms will provide greater insight into their fundamental differences, including their propensity to cause disease.

Isolation and characterization of a gene cluster involved in PAH degradation in Mycobacterium sp. strain SNP11: Expression in Mycobacterium smegmatis mc2155

Mycobacterium sp. strain SNP11 is able to grow with pyrene, fluoranthene, phenanthrene and fluorene the sole carbon and energy sources. A probe based on the previously described gene pdoA2, which encodes the alpha subunit of a PAH ring-hydroxylating dioxygenase in Mycobacterium sp. strain 6PY1 [S. Krivobok et al., Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases, J. Bacteriol. 185(13) (2003) 3828-3841], was used to isolate a 14kb DNA fragment from strain SNP11. Twelve putative open reading frames (ORFs), divided into two groups by a promoter intergenic region, were detected in this DNA sequence. The first gene cluster, located upstream of the promoter region, showed low but significant deduced amino acid sequence homologies with enzymes involved in aromatic degradation. The second gene cluster, under control of the promoter, contained pdoA2 (designated phdA in this study) and several other ORFs with deduced amino acid sequences closely related to enzymes involved in the phenanthrene-degrading pathway of Nocardioides sp. strain KP7. Gene expression analysis in Mycobacterium smegmatis mc(2)155 revealed broad substrate specificity of the ring-hydroxylating dioxygenase, since transformant cells containing phdAB strongly oxidized fluoranthene, phenanthrene, anthracene, fluorine and dibenzofuran. Laser desorption/ionization time-of-flight mass spectrometry (LDI-ToF MS) analyses of culture media after PAH degradation by M. smegmatis transformants also revealed that the second gene cluster, located downstream of the promoter, takes an active share in initial phenanthrene and anthracene degradation by allowing transformation of these two PAHs in aromatic ring-cleaved metabolites.