Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1998-03-31
2001-07-17
Jones, W. Gary (Department: 1655)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C536S024320, C536S024330
Reexamination Certificate
active
06261769
ABSTRACT:
BACKGROUND OF THE INVENTION
1. Field of the Invention
This invention relates to a target nucleic acid sequence and to probes and primers that detect that target sequence in laboratory and clinical samples containing Chlamydiaceae.
2. Description of the Prior Art
The order Chlamydiales includes at least four families that are proven or suspected pathogens of humans or other animals: Parachlamydiaceae, Simkaniaceae, Waddliaceae, and Chlamydiaceae [Everett, K. D. E., et al. (1998),
Int J Syst Bacteriol
, Submitted; Rurangirwa, F. R., et al. (1998),
Int J Syst Bacteriol
, Submitted]. These pathogens have been associated with reproductive, respiratory, cardiovascular, gastrointestinal, or systemic disease, and conjunctivitis, arthritis, and encephalitis in the host animal [Everett, K. D. E., et al. (1997),
Int J Syst Bacteriol
47: 461-473; Birtles, R. J., et al. (1997), Lancet 349: 925-926; Kahane, S., et al. (1998a),
J Infect Dis
In press; Kahane, S., et al. (1998b), In Proceedings of the
Third Meeting of the European Society for Chlamydia Research
, p. 18. Edited by A. Stary., Bologna, Italy: Study Group for STD and Dermatological Microbiology of the Austrian Society for Dermatology and Venerology; Lieberman, D., et al. (1997),
Am J Respir Crit Care Med
156: 578-82]. Numerous Chlamydiaceae isolates comprising some 60 strains have been reported since the early 1900's. These belong to two genera and nine species, as determined by genetic and phenotypic criteria, and these species can be identified by DNA sequence analysis (Everett & Andersen, 1998). However, a rapid systematic technique to routinely distinguish all nine Chlamydiaceae species is not available.
Efforts to speciate chlamydial isolates have been ongoing since the early days of chlamydial research. Because chlamydiae only grow inside inclusions in host cells, the only distinguishing criteria that initially could be relied upon were inclusion morphology, sulfadiazine resistance, and the accumulation of glycogen within the cells. Eventually, strains were characterized by PCR-RFLP, type-specific antigens, host associations, and monoclonal antibodies (MAb) [Andersen, A. A. (1991),
J Clin Microbiol
29: 707-711; Moulder, J. W., Hatch, T. P., Kuo, C. -C., Schachter, J. & Storz, J. (1984), Genus Chlamydia. In
Bergey's Manual of Systematic Bacteriology
, vol. 1., pp. 729-739. Edited by N. R. Krieg., Baltimore, Md.: The Williams & Wilkins Co.; Stephens, R. S., et al., (1982),
J Immunol
128: 1083-1089; Wang, S. -P., et al. (1985),
J Infect Dis
152: 791-800]. Today Chlamydiaceae isolates are generally distinguished by a variety of MAb or PCR tests that recognize only one strain or species at a time. These assays were developed using limited numbers of isolates and were not intended for speciating, per se. A number of problems associated with using these tests for speciation has becoming evident. For example, MAbs that recognize a “species-specific”
C. trachomatis
epitope (in variable-segment-IV of the major outer membrane protein) also probably recognize Chlamydia suis, according to DNA sequence analyses [Everett, K. D. E., et al., (1998),
Int J Syst Bacteriol
, Submitted]. Plasmid-based
C. trachomatis
tests originally thought to be species specific, do not detect plasmid-strains [An, Q., et al. (1994),
Mol Cell Probes
8: 429-435; An, Q., et al. (1992),
J Clin Microbiol
30: 2814-2821]. Because all of the species cannot be identified with a single test, they can be mistaken for one another or diagnosis can be missed. With only a limited amount of sequence data in hand, PCR tests have been developed that identify up to four species and two subclades [Holland, S. M., et al., (1990),
J Infect Dis
162: 984-987; Kaltenbock, B., et al., (1997),
J Clin Microbiol
35: 1835-1841; Meijer, A. et al., (1997),
J Clin Microbiol
35: 1179-1183; Messmer, T. O., et al. (1997),
J Clin Microbiol
35; Tong, C. Y., & Sillis, M. (1993), J Clin Pathol 46: 313-317]. For the most part, the primers used in these tests are a reasonable match to most target sequences, but these tests are incapable of distinguishing all nine species. Thus, our ability to examine the epidemiology and pathogenesis of chlamydial species has been critically limited.
PCR-RFLP may be used to identify bacterial species, and requires a target gene that has appropriately conserved and variable segments. The gene that expresses the major outer membrane protein, ompA (omp1), has now been completely sequenced from more than 50 strains and it is evident that excess sequence diversity in this gene limits its usability in PCR-RFLP identification of the nine chlamydial species (Everett et al., 1998, supra). The 7.5 kbp plasmid is also a poor target for systematic PCR-RFLP identification of Chlamydiaceae species because, in many strains, it is either uncharacterized or absent (Everett et al., 1998, supra).
Shah et al. (WO 90/15159) reported a series of oligonucleotide probes, 28-36 nucleotides in length, that were specific for
C. trachomatis
. These probes targeted either the 16S or the 23S rRNA or rDNA.
Longiaru et al. (U.S. Pat. No. 5,232,829) disclose a number of PCR primers and capture probes for amplifying and detecting
C. trachomatis
. These oligonucleotides targeted either the 16S or the 23S rRNA or rDNA.
Yang et al. (U.S. Pat. Nos. 5,512,445 and 5,514,551) show oligonucleotide probes and primers for the amplification and specific detection of
C. trachomatis
. These oligonucleotides are targeted to regions of the 16S and the 23S rRNA/rDNA.
Hogan et al. shows a series of probes and primers specific to rRNA of a number of bacteria. The probes and primer for
C. trachomatis
target variable regions of the 16S and 23S rRNA.
Goessens et al. present a comparison of three commercially available amplification assays for detecting
C. trachomatis
in urine samples. The sensitivity of these assays ranged from 90-96% and the specificities ranged from 98-99%.
SUMMARY OF THE INVENTION
We have now succeeded in identifying the intergenic spacer between the 16S and the 23S genes and a region of the 3′ end of Domain I in the 23S region for 43 strains of Chlamydiaceae and have thereby identified a novel pair of target regions of the genome for assaying and identifying all strains of Chlamydiaceae. The sequence of this target region allows for the construction of suitable probes and primers that can be group-specific for the identification of all species of Chlamydiaceae, or species-specific, or even strain-specific. The appropriate selection of probe or primer set can be used to identify the presence of Chlamydiaceae in a test sample, or to distinguish one strain from another.
In accordance with this discovery, it is an object of the invention to provide a sensitive, specific, and rapid diagnostic tool for positively identifying Chlamydiaceae in a clinical or laboratory sample.
It is also an object of the invention to provide a target region for constructing probes and primer sets tailored to the desired specificity for detecting chlamydial infections.
Another object of the invention is to provide an improved method for diagnosing chlamydial infections in humans and animals.
Yet another object of the invention is to provide a diagnostic test for chlamydial infection that would distinguish the 9 species of Chlamydiaceae.
Other objects and advantages of the invention will become readily apparent from the ensuing description.
REFERENCES:
patent: 5232829 (1993-08-01), Longiaru
patent: 5512445 (1996-04-01), Yang et al.
patent: 5514551 (1996-05-01), Yang et al.
patent: 5693468 (1997-12-01), Hogan et al.
patent: 5756298 (1998-05-01), Burczak et al.
patent: 5814490 (1998-09-01), Spears
patent: WO9015159 (1990-12-01), None
patent: WO9304163 (1993-03-01), None
patent: WO9600298 (1996-01-01), None
patent: WO9612040 (1996-04-01), None
Wilson et al. Journal of Applied Bacteriology 80, 431-438, 1996.*
Amann et al. Applied and Environmental Microbiology, vol. 63(1), 115-121, Jan. 1997.*
Wilson et al. GenBank A
Andersen Arthur A.
Everett Karin D. E.
Einsmann Juliet C.
Fado John D.
Jones W. Gary
Ribando Curtis P.
Silverstein M. Howard
LandOfFree
Intergenic spacer target sequence for detecting and... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Intergenic spacer target sequence for detecting and..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Intergenic spacer target sequence for detecting and... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2512367