Identification of
            <i>Mycobacterium</i>
            spp. by Using a Commercial 16S Ribosomal DNA Sequencing Kit and Additional Sequencing Libraries

Cloud, Joann L.; Neal, Haleina; Rosenberry, R.; Turenne, Christine Y.; Jama, Mohamed; Hillyard, David R.; Carroll, Karen C.

doi:10.1128/jcm.40.2.400-406.2002

Cited by 140 publications

(116 citation statements)

References 29 publications

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“…The DNA sequencing indicated strain 9-003 was close matched with Rhodococcus globerulus, the percent difference between strain 9-003 and Rhodococcus globerulus was 0.20%. The phylogenetic relationships were analyzed by the neighbor-joining method, and the results also supported that strain 9-003 was near-perfect match of the Rhodococcus genus and globerulus species [18][19][20]. Analysis of gene sequence and phylogenetic relationships suggested strain 9-003 is a member of Rhodococcus sp.…”

Section: Identification and Characterization Of Strain 9-003mentioning

confidence: 92%

Microbial degradation of disodium terephthalate by Rhodococcus sp. 9-003

Yamashita

et al. 2012

Sen-i Gakkaishi

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Strain 9-003 was isolated from soil in the textile dying factory for its ability to assimilate disodium terephthalate (DT) as a carbon and energy source. Analysis of the base sequence of 16S ribosomal DNA allowed us to assign the bacterium to Rhodococcus sp., the strain reduced a total concentration of DT from 95.2 to 40.8 mM for 7 d, and showed highest degradation rate (1.0 mM/h) in pH 7.0 culture broth at 25ºC, 180 rpm. Oxygen uptake experiments with the resting cells showed the biodegradation process was aerobic. HPLC analysis of the culture broth revealed there was at least one intermediate-protocatechuic acid (PC) involved the microbial degradation process. Substrate spectrum indicated strain 9-003 assimilated DT, PC and p-hydroxybenzoic acid efficiently. The degradation path way of DT was discussed and we propose that DT was metabolized aerobically by Rhodococcus sp. 9-003 via PC.

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Section: Identification and Characterization Of Strain 9-003mentioning

confidence: 92%

Microbial degradation of disodium terephthalate by Rhodococcus sp. 9-003

Yamashita

et al. 2012

Sen-i Gakkaishi

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“…Until now, there has been no standard cutoff value for the species delineation within mycobacteria (3,21). We chose the 1% criterion (99% similarity) used in the study of Hall et al (6).…”

Section: Discussionmentioning

confidence: 99%

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

Lee

Cho

et al. 2004

Microbiology and Immunology

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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.

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“…Studies evaluating the performance of the MicroSeq systems for identification of mycobacteria have repeatedly shown the advantages of using this technique over traditional biochemical tests and with the increase in available and correct sequences in various database, the sensitivity of the assay continues to increase (Patel et al, 2000;Cloud et al, 2002;Hall et al, 2003;Woo et al, 2011). The main limitation of sequencing for identification of mycobacteria as discussed above remains the inability to distinguish several species of mycobacteria based solely on the 16S rRNA including M. chelonae, M. abscessus, and M. immunogenum and the various members of the Mtb complex (Hall et al, 2003;Woo et al, 2011).…”

Section: Dna Sequencingmentioning

confidence: 99%