Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Recombinant dna technique included in method of making a...
Reexamination Certificate
1999-02-18
2003-04-22
Allen, Marianne P. (Department: 1631)
Chemistry: molecular biology and microbiology
Micro-organism, tissue cell culture or enzyme using process...
Recombinant dna technique included in method of making a...
C536S023100, C536S023700, C435S006120, C435S320100, C435S253300, C435S325000
Reexamination Certificate
active
06551795
ABSTRACT:
FIELD OF THE INVENTION
The invention relates to isolated nucleic acids and polypeptides derived from
Pseudomonas aeruginosa
that are useful as molecular targets for diagnostics, prophylaxis and treatment of pathological conditions, as well as materials and methods for the diagnosis, prevention, and amelioration of pathological conditions resulting from bacterial infection.
BRIEF DESCRIPTION OF THE SEQUENCE LISTING
Incorporated herein by reference in its entirety is a Sequence Listing, comprising SEQ ID NO: 1 to SEQ ID NO: 33,142. The Sequence Listing is contained on a CD-ROM, three copies of which are filed, the Sequence Listing being in a computer-readable ASCII file named “Path9904.pto”, created on Oct. 20, 2000 and of 68,982,000 bytes in size, in IBM-PC Windows®NT v4.0 format.
BACKGROUND OF THE INVENTION
Pseudomonas aeruginosa
(
P. aeruginosa
) is an aerobic, motile, gram-negative, rod.
P. aeruginosa
normally inhabits soil, water, and vegetation. Although it seldom causes disease in healthy people,
P. aeruginosa
is an opportunistic pathogen which accounts for ~10% of all nosocomial infections (National Nosocomial Infection Survey report-Data Summary from October 1986-April 1996).
P. aeruginosa
is the most common pathogen affecting Cystic Fibrosis patients with 61% of the specimens culturing positive (Govan, J. R. W. and V. Deretic, 1996, Microbiol. Reviews, 60(3):530-574) as well as one of the two most common pathogens observed in intensive care units (Jarvis, W. R. et al., 1992, J. Antimicrob. Chemother., 29(a supp.):19-24). Mortality from some
P. aeruginosa
infections can be as high as 50%. Presently,
P. aeruginosa
infection can still be effectively controlled by antibiotics particularly using a combination of drugs. However, resistance to several of the common antibiotics has been shown and is particularly problematic in ICUs (Archibald, L. et al., 1997, Clin. Infectious Dis., 24(2):211-215; Fish, D. N., et al., 1995, Pharmacotherapy, 15(3):279-291). In addition,
P. aeruginosa
has already demonstrated mechanisms for acquiring plasmids containing antibiotic resistance genes (Jakoby, G. A. (1986), The bacteria, Vol. X, The biology of Pseudomonas, pp. 265-294, J. R. Sokach (ed.) Academic Press, London) and at present thare are no approved vaccines for Pseudomonas infection.
Like many other bacterial species, strain variability in
P. aeruginosa
is quite significant. Variability has been shown to occur by a number of different mechanisms, these include but are not limited to the integration into the genome of prophages (Zierdt, C. H. and P. J. Schmidt, 1964, J. Bacteriol. 87:1003-1010), the addition of the cytotoxin gene and pyocins from bacteriophages (Hayashi, T., et al., 1994, FEMS Microbiol. Lett. 122:239-244) and via transposons (Sinclair, M. I. and B. W. Holloway, 1982, J. Bacteriol. 151:569-579). Through this type of diversity, new pathogenic mechanisms have been incorporated into
P. aeruginosa.
These and other transitions such as the conversion to the mucoidy phenotype commonly seen in CF clearly illustrate the need for continued vigilance.
These concerns point to the need for diagnostic tools and therapeutics aimed at proper identification of strain and eradication of virulence. The design of vaccines that will limit the spread of infection and halt transfer of resistance factors is very desirable.
SUMMARY OF THE INVENTION
The present invention fulfills the need for diagnostic tools and therapeutics by providing bacterial-specific compositions and methods for detecting Pseudomonas species including
P. aeruginosa,
as well as compositions and methods useful for treating and preventing Pseudomonas infection, in particular,
P. aeruginosa
infection, in vertebrates including mammals.
The present invention encompasses isolated nucleic acids and polypeptides derived from
P. aeruginosa
that are useful as reagents for diagnosis of bacterial disease, components of effective antibacterial vaccines, and/or as targets for antibacterial drugs including anti-
P. aeruginosa
drugs. They can also be used to detect the presence of
P. aeruginosa
and other Pseudomonas species in a sample; and in screening compounds for the ability to interfere with the
P. aeruginosa
life cycle or to inhibit
P. aeruginosa
infection. They also has use as biocontrol agents for plants.
In one aspect, the invention features compositions of nucleic acids corresponding to entire coding sequences of
P. aeruginosa
proteins, including surface or secreted proteins or parts thereof, nucleic acids capable of binding mRNA from
P. aeruginosa
proteins to block protein translation, and methods for producing
P. aeruginosa
proteins or parts thereof using peptide synthesis and recombinant DNA techniques. This invention also features antibodies and nucleic acids useful as probes to detect
P. aeruginosa
infection. In addition, vaccine compositions and methods for protection against or treatment of infection by
P. aeruginosa
are within the scope of this invention.
The nucleotide sequences provided in SEQ ID NO: 1-SEQ ID NO: 16571, a fragment thereof, or a nucleotide sequence at least about 99.5% identical to a sequence contained within SEQ ID NO: 1-SEQ ID NO: 16571 may be “provided” in a variety of medias to facilitate use thereof. As used herein, “provided” refers to a manufacture, other than an isolated nucleic acid molecule, which contains a nucleotide sequence of the present invention, i.e., the nucleotide sequence provided in SEQ ID NO: 1-SEQ ID NO: 16571, a fragment thereof, or a nucleotide sequence at least about 99.5% identical to a sequence contained within SEQ ID NO: 1-SEQ ID NO: 16571. Uses for and methods for providing nucleotide sequences in a variety of media are well known in the art (see e.g., EPO Publication No. EP 0 756 006).
In one application of this embodiment, a nucleotide sequence of the present invention can be recorded on computer readable media. As used herein, “computer readable media” refers to any media which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage media, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media. A person skilled in the art can readily appreciate how any of the presently known computer readable media can be used to create a manufacture comprising computer readable media having recorded thereon a nucleotide sequence of the present invention.
As used herein, “recorded” refers to a process for storing information on computer readable media. A person skilled in the art can readily adopt any of the presently known methods for recording information on computer readable media to generate manufactures comprising the nucleotide sequence information of the present invention.
A variety of data storage structures are available to a person skilled in the art for creating a computer readable media having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable media. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and Microsoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A person skilled in the art can readily adapt any number of data processor structuring formats (e.g. text file or database) in order to obtain computer readable media having recorded thereon the nucleotide sequence information of the present invention.
By providing the nucleotide sequence of SEQ ID NO: 1-SEQ ID NO: 16571, a fragment thereof, or a nucleotide sequence at least about 99.5% identical to
Bush David
Deloughery Craig
Nolling Jork
Rubenfield Marc J.
Allen Marianne P.
Genome Therapeutics Corporation
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