Different molecular methods for the identification of rarely isolated non-tuberculous mycobacteria and description of new hsp65 restriction fragment length polymorphism patterns

Häfner, Bernhard; Haag, Heike; Geiss, H. K.; Nolte, Oliver

doi:10.1016/j.mcp.2003.09.003

Cited by 45 publications

(32 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Higher intraspecies variability was observed with M. kansasii and M. gordonae, two species known for their high genetic heterogeneity. At least seven and eight different subtypes have been described for M. kansasii and M gordonae, respectively (12,31,32,35). Nonetheless, all clinical isolates were correctly identified by our method.…”

Section: Discussionmentioning

confidence: 99%

“…The hsp65 genebased PCR restriction pattern analysis (PRA) is also widely used for the identification of Mycobacterium spp. ; however, species with similar patterns, and multiple patterns within a single species, do occur (12,32,34). Recently, McNabb et al assessed the use of partial sequences of the hsp65 gene for routine identification of mycobacteria and reported an overall agreement of 85.2% with other identification methods; discrepancies were most frequently encountered with isolates of M. chelonae, M. fortuitum, M. gordonae, M. scrofulaceum, and M. terrae (18).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Identification of Mycobacterium Species by secA1 Sequences

Zelazny

Calhoun

et al. 2005

J Clin Microbiol

View full text Add to dashboard Cite

We describe a novel molecular method for the differentiation and identification of 29 mycobacterial species. The target is the secA1 gene that codes for the essential protein SecA1, a key component of the major pathway of protein secretion across the cytoplasmic membrane. A 700-bp region of the secA1 gene was amplified and sequenced from 47 American Type Culture Collection strains of 29 Mycobacterium species as well as from 59 clinical isolates. Sequence variability in the amplified segment of the secA1 gene allowed the differentiation of all species except for the members of the Mycobacterium tuberculosis (MTB) complex, which had identical sequences. A range of 83.3 to 100% interspecies similarity was observed. All species could also be differentiated by their amino acid sequences as deduced from the sequenced region of the secA1 gene, with the exception of the MTB complex. Partial sequences of secA1 from clinical isolates belonging to nine frequently isolated species of mycobacteria revealed a very high intraspecies similarity at the DNA level (typically >99%; range, 96.0 to 100%); all clinical isolates were correctly identified. Comparison of the deduced 233-amino-acid sequences among clinical isolates of the same species showed between 99.6 and 100% similarity. To our knowledge, this is the first time a secretion-related gene has been used for the identification of the species within a bacterial genus.The global increase of infections caused by Mycobacterium tuberculosis and nontuberculous mycobacteria (NTM) has received attention worldwide. Traditionally, the definitive diagnosis of mycobacterial infections depends on the isolation and phenotypic identification of the causative agent, a procedure that is time-consuming and labor intensive.The development of DNA probes for identification of mycobacteria greatly improved the identification speed and accuracy in the mycobacteriology laboratory. The Accuprobe system (Gen-Probe, San Diego, Calif.) is a rapid and sensitive method, but it offers only a limited number of species-or complex-specific probes (39). Recently, a new DNA probe kit, INNO-LiPA Mycobacteria (Innogenetics, Ghent, Belgium), targeting the 16S-23S rRNA spacer region, was developed for the identification of Mycobacterium spp. This assay can presently identify 16 mycobacterial species and was reported to be sensitive (100%) and specific (94.4 to 100%) (37). However, its complex procedure makes it difficult to implement in a clinical laboratory, and it is not available in the United States. The transcription-mediated amplification test (Amplified Mycobacterium Tuberculosis Direct [MTD] test) from Gen-Probe is the first approved commercial method for amplification of mycobacterial nucleic acids directly from respiratory specimens. This method is only useful for detecting members of the M. tuberculosis complex. Compared to culture, the sensitivity of the MTD test is variable, ranging from 65 to 97% (29).PCR has been used to analyze various mycobacterial genes for diagnostic purposes, including the 16...

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Identification of Mycobacterium Species by secA1 Sequences

Zelazny

Calhoun

et al. 2005

J Clin Microbiol

View full text Add to dashboard Cite

show abstract

“…paraffinicum' as M. avium, despite a suggestion that 'M. paraffinicum' was 'perhaps synonymous to M. scrofulaceum' (Hafner et al, 2004). Conversely, sequence analysis of this same hsp65 gene region produced a separate branch distribution for 'M.…”

mentioning

confidence: 86%

Revival and emended description of ‘Mycobacterium paraffinicum’ Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev.

Toney

Adékambi

Toney

et al. 2010

International Journal of Systematic and Evolutionary Microbiology

View full text Add to dashboard Cite

The omission of the name 'Mycobacterium paraffinicum' from the Approved Lists of Bacterial Names was due to phenotypic confusion surrounding a close relationship with Mycobacterium scrofulaceum. Correspondingly, 'M. paraffinicum' strains grew slowly in .7 days, stained acidalcohol-fast and produced yellow-pigmented, smooth, waxy colonies in the dark at an optimal temperature of 35 6C. However, 'M. paraffinicum' strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase and lacked growth at 42 6C, unlike M. scrofulaceum. The mycolic acid pattern, as determined by HPLC, clustered 'M. paraffinicum' with M. scrofulaceum, Mycobacterium avium and Mycobacterium parascrofulaceum. Strains were fully susceptible to linezolid, rifabutin, clarithromycin and amikacin. Examination of the historical reference strain of 'M. paraffinicum', ATCC 12670, and five additional isolates using comparative studies with 16S rRNA, hsp65 and rpoB gene and concatenated sequences showed that they formed a tight taxonomic group that was distinct from similar non-tuberculous mycobacteria. Multilocus enzyme electrophoresis (MEE) analysis confirmed a close association of the five additional isolates with the reference strain of 'M. paraffinicum' with a genetic distance of 0.12 and showed that all six strains were distinct from other closely related species. These genetic results provided unambiguous evidence of the uniqueness of this slowly growing, scotochromogenic species and supported the revival of the name as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev. We propose the previously deposited reference strain ATCC 12670 T 5DSM 44181 T 5NCIMB 10420 T , located in collections worldwide, as the type strain.In 1956, multiple strains of a soil bacterium were isolated below the level of grass roots in oily pools. They were characterized as Gram-positive, acid-alcohol-fast, nonmotile, rod-shaped bacilli, with white colonies that became yellow with age and were waxy and wrinkled on selective isolation medium of mineral salts agar in a gaseous atmosphere of 40 % ethane in air. Subsequently, the bacteria were grown on ethanol-and acetate-containing medium and the name 'Mycobacterium paraffinicum' was suggested to represent a paraffinic, gaseous hydrocarbonutilizing, non-tuberculous mycobacterium (NTM). The proposed name was 'meant to connote the general utilization of gaseous and liquid paraffinic hydrocarbons' (Davis et al., 1956). Furthermore, these mycobacteria were abundant in soil samples of petroliferous emanation, principally oilfields, and demonstrated specificity for ethane and higher paraffinic hydrocarbons (Davis et al., 1959). The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, hsp65 and rpoB gene sequences of isolates 90683, 90750, 30760, 70769 and 80776 and 'M. paraffinicum' ATCC 12670 are respectively GQ153265-GQ153270 (16S rRNA gene), GQ153283-GQ153288 (hsp65) and GQ153299-GQ153304 (rpoB).A comparison of mycolic acid patterns, a dendrogram based on ETs and neighbour-joining tree...

show abstract

“…Various molecular based methods for the rapid detection and identification of mycobacterial species have been developed [Hafner et al, 2004;Springer et al, 1996]. Polymerase chain reaction (PCR) has proven to be suitable for the purpose of bacterial typing.…”

Section: Molecular Detection Of Ntmmentioning

confidence: 99%

Molecular Detection of Nontuberculous Mycobacteria: Advantages and Limits of a Broad-Range Sequencing Approach

Slaný

Pavlík²

2012

Microb Physiol

View full text Add to dashboard Cite

The isolation of nontuberculous mycobacteria (NTM) from clinical specimens has become very common in recent years. Such organisms are typically environmental and occasionally pathogenic for humans and animals. Standard diagnosis of mycobacterial infections relies on direct examination and culture. However, molecular tools are now available which allow quicker and more accurate diagnosis. Detection of NTM can be performed directly from clinical samples, although identification is mostly carried out after isolation. Sequencing of genomic targets (such as 16S rRNA, ITS, rpoB or hsp65) allows accurate and rapid identification, but has some technical limitations. A brief summary of the molecular methods available for NTM identification and a discussion of the problems associated with the use of sequencing analysis together with a description of available algorithms for NTM identification are the major objectives of this review.

show abstract

Different molecular methods for the identification of rarely isolated non-tuberculous mycobacteria and description of new hsp65 restriction fragment length polymorphism patterns

Cited by 45 publications

References 19 publications

Identification of Mycobacterium Species by secA1 Sequences

Identification of Mycobacterium Species by secA1 Sequences

Revival and emended description of ‘Mycobacterium paraffinicum’ Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev.

Molecular Detection of Nontuberculous Mycobacteria: Advantages and Limits of a Broad-Range Sequencing Approach

Contact Info

Product

Resources

About