The Genomic Heterogeneity among Mycobacterium terrae Complex Displayed by Sequencing of 16S rRNA and hsp65 Genes

Abstract

Nontuberculous mycobacteria are opportunistic pathogens and can pose a serious threat to infected individuals (24). Mycobacterium terrae complex is composed of M. nonchromogenicum, M. terrae, and M. triviale. They are uncommon colonizers of human epithelia and generally regarded as nonpathogenic. However, M. nonchromogenicum may occasionally cause human disease such as pulmonary infection and tenosynovitis (10). M. terrae can cause debilitating diseases that are relatively resistant to antibiotic therapy. Disseminated M. terrae infection in a patient with advanced human immunodeficiency virus disease was recently reported (2).The identification of pathogenic versus nonpathogenic species is important for patient management, since treatment regimens for infection caused by one Mycobacterium species are often not effective against another.Conventional methods for species identification of mycobacteria mainly depend on morphological, cultural, and biochemical tests. These methods require diverse techniques and complex procedures that take a long time and yet the efficiency of identification is still limited (11,15). Other methods such as thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) are more powerful, but are cumbersome, expensive and limited by the need for standardized growth conditions. Currently, these methods are used in very few clinical laboratories (1,5,8).In addition to these phenotypic methods, genotypic and phylogenetic methods were introduced for polyphasic taxonomy and complete identification of microor- Abstract: The species identification within Mycobacterium terrae complex has been known to be very difficult. In this study, the genomic diversity of M. terrae complex with eighteen clinical isolates, which were initially identified as M. terrae complex by phenotypic method, was investigated, including that of three type strains (M. terrae, M. nonchromogenicum, and M. triviale). 16S rRNA and 65-kDa heat shock protein (hsp65) gene sequences of mycobacteria were determined and aligned with eleven other references for the comparison using similarity search against the GenBank and Ribosomal Database Project II (RDP) databases. 16S rRNA and hsp65 genes of M. terrae complex showed genomic heterogeneity. Amongst the eighteen clinical isolates, nine were identified as M. nonchromogenicum, eight as M. terrae, one as M. mucogenicum with the molecular characteristic of rapid growth. M. nonchromogenicum could be subdivided into three subgroups, while M. terrae could be subdivided into two subgroups using a 5 bp criterion (>1% difference). Seven isolates in two subgroups of M. nonchromogenicum were Mycobacterium sp. strain MCRO 6, which was closely related to M. nonchromogenicum. The hsp65 gene could not differentiate one M. nonchromogenicum from M. avium or one M. terrae from M. intracellulare. The nucleotide sequence analysis of 16S rRNA and hsp65 genes was shown to be useful in identifying the M. terrae complex, but hsp65 was less discriminating than 16S rRNA.

Mycobacterium algericum sp. nov., a novel rapidly growing species related to the Mycobacterium terrae complex and associated with goat lung lesions

“…nov. (type strain, TBE 500028/10 T ). Previous publications have shown that phenotypic and biochemical analyses often do not provide an accurate identification of Mycobacterium species (Cloud et al, 2006;Lee et al, 2004;Mun et al, 2008;Springer et al, 1996). Therefore, using a combination of both biochemical and molecular techniques, we showed that isolate TBE 500028/10 T , collected from a pulmonary lesion on a goat in Algeria, was representative of a novel Mycobacterium species related to the M. terrae complex, in particular M. terrae sensu stricto and M. senuense.…”

Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens

“…X93032). MCRO 6 is genotypically related to the Mycobacterium terrae complex, which includes M. terrae, Mycobacterium nonchromogenicum and Mycobacterium triviale (Lee et al, 2004). Over a 5-year period, our laboratory has isolated and identified via partial 16S rRNA gene sequencing (positions 7-530 of the Escherichia coli sequence) a genotypic match to Mycobacterium sp.…”

“…MCRO 6 from 65 human clinical samples. Several investigators have reported 'MCRO 6' being isolated from human specimens, suggesting that the organism is clinically relevant (Torkko et al, 1998;Pauls et al, 2003;Lee et al, 2004).…”

Nontuberculous Mycobacterial Lung Disease Caused byMycobacterium terraein a Patient with Bronchiectasis

“…Furthermore, previous studies have had difficulty identifying the exact species of clinical isolates, as commercial DNA probes and high performance liquid chromatography (HPLC) are not suitable methods to distinguish between different member species of the M. terrae complex. A recent study analyzing 16S rRNA and hsp65 genes demonstrated genomic heterogeneity among M. terrae complex members 13 . Therefore, we were able to confirm that our patient had M. terrae infection using modern molecular techniques that enabled sequencing of the rpoB and hsp65 genes.…”