Nucleotide fragment of the 23S ribosomal RNA of mycobacteria, de

Details Nucleotide fragment of the 23S ribosomal RNA of mycobacteria, de Nucleotide fragment of the 23S ribosomal RNA of mycobacteria, de

1995-03-23

1997-12-30

Jones, W. Gary

Organic compounds -- part of the class 532-570 series

Organic compounds

Carbohydrates or derivatives

435 6, 435 912, 536 2432, C07H 2102, C07H 2104, C12Q 168, C12P 1934

Patent

active

057032173

DESCRIPTION:

BRIEF SUMMARY
BACKGROUND

The present invention belongs to the field of techniques of detection and/or identification of bacteria of the genus Mycobacterium, and more especially of those which use a genetic marker.
The importance of a reliable and sufficiently rapid bacterial diagnosis has been highlighted again with the current epidemic of acquired immunodeficiency syndrome (AIDS), which is giving rise, on the one hand to a resurgence of cases of tuberculosis due to Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum and Mycobacterium microti, species taxonomically very closely related and grouped together under the name "M. tuberculosis complex", and on the other hand to the appearance of atypical mycobacterial infections caused, more especially, by Mycobacterium intracellulare, Mycobacterium avium and Mycobacterium paratuberculosis, gathered under the name "avian complex".
Thus, the technique using a genetic marker in a method of detection by hybridization of nucleic acids, combining specificity, sensitivity and speed, has already formed the subject of several specific applications to the diagnosis of mycobacteria.
More especially, the ribosomal RNA of the bacteria is used as target since, in the first place, it is to be found in substantial amounts in all cells of all living organisms, and secondly it possesses a particular nucleotide sequence made up of a succession of regions characterized by a variable rate of evolution.
The taxonomic value of the 16S and 23S ribosomal subunits of various bacterial species has been demonstrated in hybridization processes for quantifying levels of homologies between these species. Thus, Woese et al., Microbiological Reviews 47:621-669 (1983), and Grayet et al., Nucleic Acids Research 12:5837-5852 (1984) show, by comparisons of 16S RNA sequences, that highly conserved regions are interspersed with regions of moderate and low homologies, even in the case of closely related species.
Patent Application WO-88/03957describes detection probes specific for mycobacteria, the nucleotide sequences of which are capable of hybridizing with the 16S and 23S subunits of the ribosomal RNAs of said bacteria.
The probes described are 7 species probes, or probes for groups of species, and 4 genus probes, and are gathered in Table 1 below in which are listed, respectively, the target ribosomal RNA subunit, the target nucleotide sequence, taking as reference the nucleotide sequence of E. coli ribosomal RNA, and the specificity of the probes with respect to the species, the group of species or the genus Mycobacterium.


TABLE 1 ______________________________________ PROBE Ribosomal Position in No. RNA subunit the sequence Species ______________________________________ 1 16S 185-225 M. avium 2 16S 185-225 M. intracellulare 3 16S 185-225 M. tuberculosis complex 4 23S 1155-1190 M. tuberculosis complex 5 23S 540-575 M. tuberculosis complex 6 23S 2195-2235 M. tuberculosis complex 7 23S 2195-2235 M. tuberculosis complex 8 16S 1025-1060 genus Mycobacterium 9 23S 1440-1475 genue Mycobacterium 10 23S 1515-1555 genus Mycobacterium 11 23S 1570-1610 genus Mycobacterium ______________________________________
It is apparent from this table that, at the species level, only two probes have been developed, one specific for the species M. avium, the other specific for the species M. intracellulare, and they have been developed on the basis of the sequencing of the 16S ribosomal subunits.
While two species of the "avian complex" which are very closely related from the taxonomic standpoint can be independently identified by these methods, the same does not yet apply to the different species of the "tuberculosis complex".
It emerges, in addition, from this prior art that, on the one hand the regions which are variable from one species to another or from one species to a group of species and which have been adopted for producing probes are located on the 16S subunit of the ribosomal RNA, and that on the other hand the 23S subunit comprises regions which are homologous

REFERENCES:
patent: 5521300 (1996-05-01), Shah et al.
Keller and Manak, In DNA Probes and Applications, Stockton Press, 1994, pp. 565-583. (vol. not applicable).
Erlich et al. In PCR Technology, Freeman and Company, pp. 235-244, 1992. (vol. not applicable).
Gura, Science 270: 575-577, 1995.
Gutierrez et al., The Lancet, 339: 715-721, 1992.
Liesack Febs 281: 114,1991.
Fleurbaaij et al. Genbank Sequence Listing, 1992.
U. Sjobring et al., "Polymerase Chain Reaction for Detection of Mycobacterium tuberculosis," J. of Clinical Microbiology, vol. 28, No. 10, pp. 2200-2204, Oct. 1990.
A.R. Dunn et al., "A Novel Method to Map Transcripts: Evidence for Homology between an Adenovirus mRNA and Discrete Multiple Regions of the Viral Genome," Cell, vol. 12, pp. 23-36, Sep. 1977.
M.W. Gray et al., "On the Evolutionary Descent of Organisms and Organelles: A Global Phylogeny Based on a Highly Conserved Structural Core in small Subunit Ribosomal RNA," Nucleic Acids Research, vol. 12, No. 14, 1984.
C.R. Woese et al., "Detailed Analysis of the Higher-Order Structure of 16S-Like Ribosomal Ribonucleic Acids," Microbiology Reviews, vol. 47, No. 4, pp. 621-669, Dec. 1983.
P.E. Nielsen et al., "Sequence-Selective Recognition of DNA by Strand Displacement with a Thymine-Substituted Polyamide," Science, vol. 254, pp. 1497-1500, Dec. 1991.

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