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(12) United States Patent (10) Patent No.: US 6,617,156 B1 Doucette-Stamm Et Al

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(12) United States Patent (10) Patent No.: US 6,617,156 B1 Doucette-Stamm Et Al USOO6617156B1 (12) United States Patent (10) Patent No.: US 6,617,156 B1 Doucette-Stamm et al. (45) Date of Patent: Sep. 9, 2003 (54) NUCLEIC ACID AND AMINO ACID 5,624,816 A * 4/1997 Carraway et al. .......... 435/69.1 SEQUENCES RELATING TO ENTEROCOCCUS EAECALIS FOR FOREIGN PATENT DOCUMENTS DLAGNOSTICS AND THERAPEUTICS WO 9850555 11/1998 WO 98/80554 11/1998 ........... C12N/15/31 (76) Inventors: Lynn A. Doucette-Stamm, 14 Flanagan OTHER PUBLICATIONS Dr., Framingham, MA (US) 01701; David Bush, 205 Holland St., Frere et al. J. Basic Microbiol. 36(5):305-310, 1996.* Somerville, MA (US) 02144 Tanaka et al. Molecular and Cellular Biology 9(2):757-768, - 1989.* (*) Notice: Subject to any disclaimer, the term of this Bugert et al. Molecular Microbiology 15(5):917–933, patent is extended or adjusted under 35 1995.* U.S.C. 154(b) by 0 days. Mason et al. Journal of Bacteriology 175(9):2632-2639, 1993.* (21) Appl. No.: 09/134,000 Wagner et al. Journal of Bacteriology 177(21):6144-6152, 1-1. 1995.* (22) Filed: Aug. 13, 1998 Chen et al. Yeast 7:287–299, 1991.* Related U.S. Application Data * cited by examiner (60) Provisional application No. 60/055,778, filed on Aug. 15, 1997. Primary Examiner Mary E. Mosher (51) Int. CI.7 C12N 15/31; C12N 15/63; (74) Attorney, Agent, or Firm-Genome Therapeutics CN is. Cio 1's Corporation (52) U.S. Cl. ................ 435/320.1; 536/23.7:536/24.32; (57) ABSTRACT 435/252.3; 435/69.1; 435/6 - (58) Field of Search 536/23.7, 24.32: The invention provides isolated polypeptide and nucleic acid 435/320.1, 252.3, 6, 69.1, 69.3 Sequences derived from EnterOCOccuS faecalis that are use • us a- a-- a- (-1s ws w - - -us s/ 1 - ful in diagnosis and therapy of pathological conditions, (56) References Cited antibodies against the polypeptides, and methods for the production of the polypeptides. The invention also provides U.S. PATENT DOCUMENTS methods for the detection, prevention and treatment of 4,835,256 A * 5/1989 Taniguchi et al 530/351 pathological conditions resulting from bacterial infection. 5,417,971. A * 5/1995 Potter et al. ............. 424/256.1 5,459,034 A * 10/1995 Tabaqchali et al. ............ 435/6 19 Claims, No Drawings US 6,617,156 B1 1 2 NUCLEIC ACID AND AMINO ACID tion (1993) MMWR 42:597-599). These numbers may not SEQUENCES RELATING TO be an accurate reflection of the actual total, as clinical ENTEROCOCCUS EAECALIS FOR identification of Vancomycin resistance is not consistently DLAGNOSTICS AND THERAPEUTICS detected, especially in the VanB phenotype which confers moderate resistance (Tenover, F C (1993) J Clin Microbiol This application claims priority of U.S. Provisional 31: 1695–1699; and Sahm, D F (1990) Antimicrob Agents application No. 60/055,778, filed Aug. 15, 1997, all of which Chemother 34: 1846–1848; and Zabransky, R J (1994) is hereby incorporated herein by reference in its entirety. Microbiol Infect Dis 20:113-116). Patients can be colonized and carry VRE without symptoms, with chief areas of FIELD OF THE INVENTION colonization being anus, axilla, Stool, perineal, umbilicus, The invention relates to isolated nucleic acids and wounds, foley catheters, and colostomy Sites. polypeptides derived from EnterOCOccuS faecalis that are Epidemiology of E. faecalis is not completely understood, useful as molecular targets for diagnosis, prophylaxis and but it is thought that most infections and colonizations are a treatment of pathological conditions, as well as materials result of the patient's endogenous flora (Murray, BE (1990) and methods for the diagnosis, prevention, and amelioration 15 Clin Microbiol Rev 3:46-65). Recent evidence suggests that of pathological conditions resulting from bacterial infection. E. faecalis can be spread by direct contact with other infected patients, indirect transmission from hospital per BRIEF DESCRIPTION OF THE SEQUENCE sonnel (Boyce, J M et al (1994) J Clin Microbiol LISTING 32:1148–53; and Rhineheart, E et al (1990) N Engl J Med Incorporated herein by reference in its entirety is a 323:1814-1818), or from contaminated hospital surfaces Sequence Listing, comprising SEQ ID NO: 1 to SEQ ID and equipment (Karanfil, L V et al (1992) Infect Control NO: 6812. The Sequence Listing is contained on a Hosp Epidemiol 13:195-200; and Boyce, J Metal (1994) J CD-ROM, three copies of which are filed, the Sequence Clin Microbiol 32:1148–53; and Livornese, LL Jr. (1992) Listing being in a computer-readable ASCII file named Ann Intern Med 117:112-116). Increased risk for the criti 25 cally ill, those with underlying disease of immunosuppres “GTC005.pto', created on Sep. 6, 2001 and of 10.3 mega Sion (i.e. ICU, oncology, and transplant patients), cardio bytes in size, in Windows NT 4.0, ASCII text format. thoracic/intraabdominal Surgical patients and those with BACKGROUND OF THE INVENTION urinary or central venous catheters has been demonstrated. In addition, risk for E. faecalis infection increases for Enterococcus faecalis (E. faecalis) is a gram-positive, patients with long hospital stays or previous multiantimi facultative, anaerobic cocci, that is widely distributed in crobial or vancomycin treatments (Boyce, J M et al (1994) nature, animals, and humans. Enterococci are part of the J Clin Microbiol 32:1148–1153; Boyle, JF et al (1993) J normal gastrointestinal and genital tract flora, and among the Clin Microbiol 31:1280–1285; Karanfil, L V et al (1992) 17 known species, E. faecalis is dominant in humans, Infect Control Hosp Epidemiol 13:195-200; Handwerger, S accounting for 80-90% of clinically isolated specimens, and 35 et al (1993) Clin Infect Dis 16:750–755; Montecalvo, MA it exhibits increasing levels of multidrug resistance et al (1994) Antimicrob Agents Chemother 38:1363–1367). (Kaufhold, A and Klein, R (1995) Zentralblatt fuer Bakite Additional concern stems from the ability of the E. riologie 282 (4): 507–518; and Svec, P, Sedlacek, I, and faecalis plasmid borne VanA gene, which conferS high level Pakrova, E (1996) Epidemiologie Mikrobiologie Imunologie Vancomycin resistance, to transfer in vitro to Several gram 45: 153–157). E. faecalis infections include urinary tract 40 positive microorganisms. Such as StaphylococcuS aureuS infections (UTI), bacteremia, endocarditis, and wound and (Leclercq, R et al (1989) Antimicrob Agents Chemother abdominal-pelvic infections, accounting for 16% of all 33:10-15; and Noble, WC, et al (1992) FEMS Microbiology UTIs, and 8% of all becteremias (Ardino, RC, and Murray, Letters 72:195-198). To date, no clinical isolates of S. B E (1990) Principles and Practice of Infectious Diseases, aureuS or S. epidermidis have shown Vancomycin resistance 3rd ed., Mandell et al, eds., Update Vol. 2, No. 4). 45 Vancomycin resistant enterococci (VRE) have emerged in conferred by plasmid transfer, but clinically isolated Strains the midst of high level resistance to penicillin and aminogly of S. haemolyticus have (Degner, J E, et al (1994) J Clin cosides (Centers for Disease Control and Prevention (1993) Microbiol32:2260–2265; and Veach, LA, et al (1990).J Clin MMWR 42:597-599; and Handwerger, S, et al (1993) Clin Microbiol 28:2064–2068). Infect Dis 16:750-755). Resistance can be intrinsic 50 These concerns point to the need for diagnostic tools and (chromosomally mediated), or acquired (plasmid or trans therapeutics aimed at proper identification of Strain and poson mediated), with higher levels of resistance in eradication of virulence. The design of vaccines that will acquired. VRE are characterized by resistance to virtually all limit the Spread of infection and halt transfer of resistance available antibiotics, including Vancomycin, considered the factorS is very desirable. “last resort' antibiotic effective against gram-positive bac 55 SUMMARY OF THE INVENTION teria. Treatment options for physicians are limited, with the latest Strategy being combinations of antimicrobials or the The present invention fulfills the need for diagnostic tools use of new unproven compounds (Moellering, RCJr. (1991) and therapeutics by providing bacterial-specific composi J Antimicrob Chemother 28: 1-12; and Hayden, M Ketal tions and methods for detecting, treating, and preventing (1994) Antimicrob Agents Chemother 38 1225–1229; and 60 bacterial infection, in particular E. faecalis infection. Mobarakai, N et al (1994) J Antimicrob Chemother 33: The present invention encompasses isolated nucleic acids 319-321). From 1989 through 1993, the percentage of and polypeptides derived from E. faecalis that are useful as nosocomial (hospital incurred) infections by VRE increased reagents for diagnosis of bacterial disease, components of from 0.3% to 7.9% (Centers for Disease Control and Pre effective antibacterial vaccines, and/or as targets for anti vention (1993) MMWR 42:597-599). There was a 34-fold 65 bacterial drugs, including anti-E. faecalis drugs. They can increase in ICU patients, and a increasing trend among also be used to detect the presence of E. faecalis and other non-ICU patients (Centers for Disease Control and Preven EnterococcuS Species in a Sample, and in Screening com US 6,617,156 B1 3 4 pounds for the ability to interfere with the E. faecalis life media having recorded thereon a nucleotide Sequence of the cycle or to inhibit E. faecalis infection. They also has use as present invention. The choice of the data Storage Structure biocontrol agents for plants. will generally be based on the means chosen to access the The present invention also provides a genome-wide com Stored information. In addition, a variety of data processor 5 programs and formats can be used to Store the nucleotide parison by FASTA of the predicted amino acid Sequences of Sequence information of the present invention on computer several E.
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