Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

Roth, Andreas; Fischer, Marga; Hamid, Mohamed E.; Michalke, Sabine; Ludwig, Wolfgang; Mauch, H.

doi:10.1128/jcm.36.1.139-147.1998

Cited by 317 publications

(157 citation statements)

References 41 publications

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“…The relationships between ITS sequences from slow-growing Mycobacterium spp. showed only partial agreement with those based on SSU rDNA sequences (Roth et al, 1998), whereas a similar analysis for the genus Bifidobacterium showed much better agreement (Leblond-Bourget et al, 1996).…”

Section: Discussionmentioning

confidence: 71%

Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton

Suzuki

Béjà

Taylor

et al. 2001

Environmental Microbiology

160

140

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Analyses of small subunit ribosomal RNA genes (SSU rDNAs) have significantly influenced our understanding of the composition of aquatic microbial assemblages. Unfortunately, SSU rDNA sequences often do not have sufficient resolving power to differentiate closely related species. To address this general problem for uncultivated bacterioplankton taxa, we analysed and compared sequences of polymerase chain reaction (PCR)-generated and bacterial artificial chromosome (BAC)-derived clones that contained most of the SSU rDNAs, the internal transcribed spacer (ITS) and the large subunit ribosomal RNA gene (LSU rDNA). The phylogenetic representation in the rRNA operon PCR library was similar to that reported previously in coastal bacterioplankton SSU rDNA libraries. We observed good concordance between the phylogenetic relationships among coastal bacterioplankton inferred from SSU or LSU rDNA sequences. ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses. We also found strong support for homologous recombination between the ITS regions of operons from the SAR11 clade.

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Section: Discussionmentioning

confidence: 71%

Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton

Suzuki

Béjà

Taylor

et al. 2001

Environmental Microbiology

160

140

View full text Add to dashboard Cite

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“…Several methods based on molecular biological techniques have been reported. The sequences that have been reported include hsp65, 16S rRNA gene, and ITS (Plikaytis et al, 1992;De Smet et al, 1995;Springer et al, 1996;Messer & Weigel, 1997;Roth et al, 1998;Brunello et al, 2001). Each gene has several advantages and disadvantages.…”

Section: Discussionmentioning

confidence: 99%

Identification ofMycobacteriumspecies by comparative analysis of thednaAgene

Mukai

Miyamoto

Yamazaki

et al. 2006

FEMS Microbiology Letters

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For the establishment of a diagnostic tool for mycobacterial species, a part of the dnaA gene was amplified and sequenced from clinically relevant 27 mycobacterial species as well as 49 clinical isolates. Sequence variability in the amplified segment of the dnaA gene allowed the differentiation of all species except for Mycobacterium tuberculosis, Mycobacterium africanum and Mycobacterium microti, which had identical sequences. Partial sequences of dnaA from clinical isolates belonging to three frequently isolated species revealed a very high intraspecies similarity, with a range of 96.0-100%. Based on the dnaA sequences, a species-specific primer set for Mycobacterium kansasii and Mycobacterium gastri was successfully designed for a simple loop-mediated isothermal amplification method. These results demonstrate that the variable sequences in the dnaA gene were species specific and were sufficient for the development of an accurate and rapid diagnosis of Mycobacterium species.

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“…However, as certain groups of bacteria are known to present difficulties in identification by 16S rDNA sequencing, these bacteria should be excluded, and other housekeeping gene targets, e.g. rpoB, if available, are required [39][40][41][42]47,[50][51][52][53][54]153]. Regarding the interpretation of sequence data, this involves requirements concerning the length and quality of sequences, the choice of appropriate programs for analysis, and the final species assignment based on similarity search results.…”

Section: U S E F U L N E S S a N D L I M I T A T I O N S O F U S I N mentioning

confidence: 99%

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

Woo

Lau

Teng

et al. 2008

Clinical Microbiology and Infection

694

424

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In the last decade, as a result of the widespread use of PCR and DNA sequencing, 16S rDNA sequencing has played a pivotal role in the accurate identification of bacterial isolates and the discovery of novel bacteria in clinical microbiology laboratories. For bacterial identification, 16S rDNA sequencing is particularly important in the case of bacteria with unusual phenotypic profiles, rare bacteria, slow-growing bacteria, uncultivable bacteria and culture-negative infections. Not only has it provided insights into aetiologies of infectious disease, but it also helps clinicians in choosing antibiotics and in determining the duration of treatment and infection control procedures. With the use of 16S rDNA sequencing, 215 novel bacterial species, 29 of which belong to novel genera, have been discovered from human specimens in the past 7 years of the 21st century (2001-2007). One hundred of the 215 novel species, 15 belonging to novel genera, have been found in four or more subjects. The largest number of novel species discovered were of the genera Mycobacterium (n = 12) and Nocardia (n = 6). The oral cavity/dental-related specimens (n = 19) and the gastrointestinal tract (n = 26) were the most important sites for discovery and/or reservoirs of novel species. Among the 100 novel species, Streptococcus sinensis, Laribacter hongkongensis, Clostridium hathewayi and Borrelia spielmanii have been most thoroughly characterized, with the reservoirs and routes of transmission documented, and S. sinensis, L. hongkongensis and C. hathewayi have been found globally. One of the greatest hurdles in putting 16S rDNA sequencing into routine use in clinical microbiology laboratories is automation of the technology. The only step that can be automated at the moment is input of the 16S rDNA sequence of the bacterial isolate for identification into one of the software packages that will generate the result of the identity of the isolate on the basis of its sequence database. However, studies on the accuracy of the software packages have given highly varied results, and interpretation of results remains difficult for most technicians, and even for clinical microbiologists. To fully utilize 16S rDNA sequencing in clinical microbiology, better guidelines are needed for interpretation of the identification results, and additional/supplementary methods are necessary for bacterial species that cannot be identified confidently by 16S rDNA sequencing alone.

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Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

Cited by 317 publications

References 41 publications

Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton

Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton

Identification ofMycobacteriumspecies by comparative analysis of thednaAgene

Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories

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