Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
  • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
  • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

Definitions

• molecular diagnostic methods have been developed based on the detection of the nucleic acids of the pathogenic agent in the blood or plasma samples, or in the cell cultures, taken from the patient. These assays are generally much more sensitive than the immunological assays. However, they may require the presence of special equipment and qualified personnel. Furthermore, the biological samples — in the case of plasma, blood, or cell cultures — are difficult to store unaltered, except under controlled temperature conditions, and are considered to be biohazardous to personnel who handle them.
• Tr-DNA transrenal DNA
• U.S. Patent No. 6,251,638 describes an analytical method for detecting male fetal DNA in the urine of pregnant women.
• U.S. Patent No. 6,287,820 describes a system aimed at the diagnosis of tumors, particularly of adenocarcinomas of the colon and pancreas.
• Tr-DNA nucleic-acid analysis method may be used to monitor the progress of allogeneic transplants.
• the presence of transrenal DNA in urine, in the form of nucleic-acid fragments of fewer than 1000 base pairs was also described in Al- Yatama et al. (2001), Prenat Diagn, 21 :399-402; and Utting, M., et al. (2002), Clin Cancer Res, 8:35-40.
• transrenal DNA has been explained through the apoptosis phenomenon. During cell death most of the nuclear DNA is converted into nucleosomes and oligomers (Umansky, S.R., et al. 1982, Biochim. Biophys. Acta 655:9-17), which are finally digested by macrophages or neighboring cells. However, a portion of this degraded DNA escapes phagocytic metabolism, and can be found in the bloodstream (Lichtenstein, A. V., et al. 2001, Ann NY Acad Sd, 945:239-249), and, as confirmed in the above-indicated patents, also in urine.
• prokaryotic DNA could be isolated from urine sediment that contained bacteria (Frasier, et al. 1992, Acta Virol, 36:83-89).
• prokaryotes and parasites are generally ingested by the cells of the immune system, such as macrophages and dendritic cells.
• the prokaryotes are then dissolved by the phagolysosome vesicles.
• the prokaryotic DNA is then released by the cell and a portion of this DNA enters the bloodstream in either of two ways. Either the ingesting cell becomes apoptotic and breaks apart (Navarre, W.V.
• the instant invention describes a method of detecting the presence of non- viral pathogens in a subject through the detection of DNA sequences from those pathogens in the urine of the subject.
• the invention provides compositions and methods for the diagnosis of an infection of a subject through the detection of the presence of pathogens by the presence of pathogen nucleic acids in a urine sample of the subject.
• the methods of the invention are also used to validate the diagnosis of an infection of a subject through the detection of the presence of pathogen nucleic acids in a urine sample of the subject, wherein a previous diagnosis has already been performed by a method of this invention or another diagnosis method.
• the compositions and methods of the invention are also used to determine the efficacy of a treatment of non- viral pathogen infection in a subject by detecting the presence or absence of a nucleic acid of the non- viral pathogen in the urine of the subject.
• compositions and methods of the invention are used to identify a drug resistant non- viral pathogenic infection in a subject by detecting the presence or absence of a nucleic acid of the non- viral pathogen in the urine of the subject after the subject has been treated for the infection with a drug.
• the compositions and methods of the invention are also used to determine the likelihood of pathology from the infection of the subject by a non- viral pathogen in a subject at risk therefrom. More specifically, the compositions and methods of the invention may be used to genotype a non- viral pathogen which has infected a subject by detecting and genotyping nucleic acids from the pathogen in the urine of the subject.
• the invention provides a method of isolating a nucleic acid from urine, the method comprising providing urine from a subject; separating cells and cell debris from the urine by filtration or centrifugation; adding EDTA and Tris-HCl to the urine; adding a chaotropic salt to the urine; adding a resin, wherein the resin binds the nucleic acid in the presence of the chaotropic salt; removing the resin from the urine; and eluting the nucleic acid from the resin; thereby isolating the nucleic acid from urine.
• the concentration of EDTA and Tris-HCl after it is added to the urine is about 10 mM, and pH between about 8.0 and about 8.5.
• the filtration is performed with a filter with a pore size between about 0.1 ⁇ m and about 5.0 ⁇ m.
• the chaotropic salt is guanidine isothiocyanate.
• the guanidine isothiocyanate has a concentration after being added to the urine of at least about 3 M, and at most about 6 M.
• the resin is constructed of silica.
• the subject is a mammal. In one aspect of this embodiment, the mammal is a human.
• the invention also provides a method of detecting a non- viral pathogen in a subject comprising detecting the presence of a nucleic acid from the non- viral pathogen in urine of the subject, wherein the non-viral pathogen is selected from Helicobacter pylori,
• the method further comprises the step of quantitating the nucleic acid.
• the detecting is performed by a method selected from polymerase chain reaction (PCR), nested PCR, semi-nested PCR, hybridization, Single-Strand Conformation Polymorphism analysis (SSCP), ligase chain reaction (LCR), strand displacement amplification (SDA), and pairing with molecular probes that are specific for the non- viral pathogen.
• PCR polymerase chain reaction
• SSCP Single-Strand Conformation Polymorphism analysis
• LCR ligase chain reaction
• SDA strand displacement amplification
• the subject is a mammal.
• the mammal is a human.
• the invention also provides a method for diagnosing a Helicobacter pylori infection in a subject, comprising detecting the presence of a Helicobacter pylori nucleic acid in a urine sample from the subject, thereby diagnosing the Helicobacter pylori infection.
• the method further comprises the step of quantitating the nucleic acid.
• the detecting is performed by a method selected from PCR, nested PCR, semi- nested PCR, hybridization, SSCP, LCR, SDA, and pairing with molecular probes that are specific for the non- viral pathogen.
• a primer set is used in the method, and the primer set comprises a forward primer and a reverse primer.
• the forward primer is selected from SEQ ID NOs: 5, 8, 10, 11, 12 and 15 and the reverse primer is selected from SEQ ID NOs: 6, 7, 9, 13, 14, 16 and 17.
• the Helicobacter pylori nucleic acid comprises transrenal DNA.
• the subject is a mammal. In one aspect of this embodiment, the mammal is a human.
• the method further comprises the step of genotyping the Helicobacter pylori which infected the subject.
• the Helicobacter pylori is genotyped for the presence of a cag pathogenicity island.
• the Helicobacter pylori is genotyped for the presence of a vacA genotype selected from sl/ml, slm2, s2ml and s2m2.
• the invention also provides a method for diagnosing a Mycobacterium tuberculosis infection in a subject, comprising detecting the presence of a Mycobacterium tuberculosis nucleic acid in a urine sample from the subject, wherein the Mycobacterium tuberculosis nucleic acid has crossed the kidney barrier and is from cells outside a urinary tract of the subject, thereby diagnosing the Mycobacterium tuberculosis infection.
• the method further comprises the step of quantitating the nucleic acid.
• the detecting is performed by a method selected from PCR, nested PCR, semi-nested PCR, hybridization, SSCP, LCR, SDA, and pairing with molecular probes that are specific for the non- viral pathogen.
• a primer set is used for the method, wherein the primer set comprises a forward primer and a reverse primer.
• the forward primer is selected from SEQ ID NOs: 34, 37 and 39 and the reverse primer is selected from SEQ ID NOs: 35, 36, 38 and 40.
• the Mycobacterium tuberculosis nucleic acid comprises transrenal DNA.
• the subject is a mammal.
• the mammal is a human.
• the invention also provides a method for diagnosing a Bacillus anthracis infection in a subject, comprising detecting the presence of & Bacillus anthracis nucleic acid in a urine sample from the subject, thereby diagnosing the Bacillus anthracis infection.
• the method further comprises the step of quantitating the nucleic acid.
• the detecting is performed by a method selected from PCR, nested PCR, semi- nested PCR, hybridization, SSCP, LCR, SDA, and pairing with molecular probes that are specific for the non- viral pathogen.
• a primer set is used for the method, wherein the primer set comprises a forward primer and a reverse primer.
• the forward primer is selected from SEQ ID NOs: 41, 43, 45, 47, 48 and 50 and the reverse primer is selected from SEQ ID NOs: 42, 44, 46 and 49.
• the Bacillus anthracis nucleic acid comprises transrenal DNA.
• the subject is a mammal. In one aspect of this embodiment, the mammal is a human.
• the invention also provides a method for diagnosing a Plasmodium species infection in a subject, comprising detecting the presence of a Plasmodium species nucleic acid in a urine sample from the subject, thereby diagnosing the Plasmodium species infection.
• the method further comprises the step of quantitating the nucleic acid.
• the detecting is performed by a method selected from PCR, nested PCR, semi- nested PCR, hybridization, SSCP, LCR, SDA, and pairing with molecular probes that are specific for the non- viral pathogen.
• a primer set is used for the method, wherein the primer set comprises a forward primer and a reverse primer.
• the forward primer is selected from SEQ ID NOs: 18, 21 and 23 and the reverse primer is selected from SEQ ID NOs: 19, 20 and 22.
• the Plasmodium species nucleic acid comprises transrenal DNA.
• the subject is a mammal.
• the mammal is a human.
• the invention also includes a method for diagnosing a Leishmania species infection in a subject, comprising detecting the presence of a. Leishmania species nucleic acid in a urine sample from the subject, thereby diagnosing the Leishmania species infection.
• the method further comprises the step of quantitating the nucleic acid.
• the detecting is performed by a method selected from PCR, nested PCR, semi- nested PCR, hybridization, SSCP, LCR, SDA, and pairing with molecular probes that are specific for the non- viral pathogen.
• a primer set is used for the method, wherein the primer set comprises a forward primer and a reverse primer.
• the forward primer is selected from SEQ ID NOs: 26, 28, 30, 32 and 51 and the reverse primer is selected from SEQ ID NOs: 24, 25, 27, 29, 31 and 33.
• the Leishmania species nucleic acid comprises transrenal DNA.
• the subject is a mammal. In one aspect of this embodiment, the mammal is a human.
• the invention also provides a composition for use in the detection of Helicobacter pylori, wherein the composition comprises a nucleic acid sequence selected from SEQ ID NOs: 5-17.
• the composition for use in the detection of Helicobacter pylori, the composition consists of a nucleic acid sequence selected from SEQ ID NOs: 5-17.
• the invention also provides a composition for use in the detection of Plasmodium species, wherein the composition comprises a nucleic acid sequence selected from SEQ ID NOs: 18-23.
• the composition for use in the detection of Plasmodium species, consists of a nucleic acid selected from SEQ ID NOs: 18-23.
• the invention also provides a composition for use in the detection of Leishmania species, wherein the composition comprises a nucleic acid sequence selected from SEQ ID NOs: 24-33 and 51.
• the composition consists of a nucleic acid selected from SEQ ID NOs: 24-33 and 51.
• the invention also provides a composition for use in the detection of Mycobacterium tuberculosis, wherein the composition comprises a nucleic acid sequence selected from SEQ ID NOs: 34-40.
• the composition for use in the detection of Mycobacterium tuberculosis, consists of a nucleic acid selected from SEQ ID NOs: 34-40.
• the invention also provides a composition for use in the detection of Bacillus anthracis, wherein the composition comprises a nucleic acid sequence selected from SEQ ID NOs: 41-50.
• the composition comprises a nucleic acid sequence selected from SEQ ID NOs: 41-50.
• the composition consists of a nucleic acid selected from SEQ ID NOs: 41-50.
• the invention also provides a kit for detecting Helicobacter pylori in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 5, 8, 10, 11, 12 and 15 and at least one reverse primer selected from SEQ ID NOs: 6, 7, 9, 13, 14, 16 and 17, either in the same or separate packaging, and instructions for its use.
• the invention also provides a kit for detecting Mycobacterium tuberculosis in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 34, 37 and 39 and at least one reverse primer selected from SEQ ID NOs: 35, 36, 38 and 40, either in the same or separate packaging, and instructions for its use.
• the invention also provides a kit for detecting Bacillus anthracis in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 41, 43, 45, 47, 48 and 50 and at least one reverse primer selected from SEQ ID NOs: 42, 44, 46 and 49, either in the same or separate packaging, and instructions for its use.
• the invention also provides a kit for detecting Plasmodium species in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 18, 21 and 23 and at least one reverse primer selected from SEQ ID NOs: 19, 20 and 22, either in the same or separate packaging, and instructions for its use.
• the invention also provides a kit for detecting Leishmania species in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 26, 28, 30, 32 and 51 and at least one reverse primer selected from SEQ ID NOs: 24, 25, 27, 29, 31 and 33, either in the same or separate packaging, and instructions for its use.
• Figure 1 is a photograph of PCR reactions performed on human urine with primers specifc for human b-actin resolved by electrophoresis.
• Figure 2 is a photograph of PCR reactions performed on rabbit urine with primers specifc for rabbit b-globin resolved by electrophoresis.
• Figure 3 A is a photograph of semi-nested PCR reactions performed on human urine with primers specifc for H. pylori ureA sequences resolved by electrophoresis.
• Figure 3B is a photograph of semi-nested PCR reactions performed on human urine with primers specifc for H. pylori cagA sequences resolved by electrophoresis.
• Figure 4 is a photograph of semi-nested PCR reactions performed on human urine with primers specifc for Plasmodium falciparum sequences resolved by electrophoresis.
• Figure 5 is a photograph of semi-nested PCR reactions performed on human urine with primers specifc for Leishmania infantum sequences resolved by electrophoresis.
• Figure 6 is a photograph of semi-nested PCR reactions performed on human urine from TB infected and healthy patients with primers specifc for Mycobacterium tuberculosis sequences resolved by electrophoresis.
• Figure 7 is a photograph of semi-nested PCR reactions performed on the supernatants and pellets of centrifuged human urine from TB infected and healthy patients before and after treatment with primers specifc for Mycobacterium tuberculosis sequences resolved by electrophoresis.
• Figure 8 shows photographs of semi-nested PCR reactions performed on human urine from TB infected patients with primers specific for Mycobacterium tuberculosis sequences of 129/67 bp (left panel) and 330/69 bp (right panel) resolved by electrophoresis.
• Figure 9 is a photograph of semi-nested PCR reactions performed on human urine from TB actively infected patients and patients two months after treatment for TB with primers specifc for Mycobacterium tuberculosis sequences resolved by electrophoresis.
• Figure 10 is a photograph of semi-nested PCR reactions performed on rabbit urine from B. anthracis infected and uninfected subjects with primers specifc for Bacillus anthracis sequences resolved by electrophoresis.
• the invention is based, in part, upon the discovery described herein that pathogenic nucleic acids are detectable in the urine of a subject infected with the pathogen.
• nucleic acids from pathogenic organisms cross the kidney barrier and pass into the urine of mammals.
• the nucleic acids which cross the renal barrier termed herein as transrenal nucleic acids, and more specifically transrenal DNA tend to be shorter than 1,000 bp in length, but are preferably less than 500 bp in length, and more preferably shorter than 250-300 bp in length or shorter than 250 bp in length.
• the invention provides compositions and methods for the detection of non- viral pathogens in the urine of a subject.
• compositions and methods of the invention are used to detect transrenal-nucleic acids derived from pathogenic microorganisms which traverse the renal barrier and are present in the urine of a subject.
• the invention includes methods for the isolation, amplification and detection of these transrenal nucleic acids.
• the invention also includes compositions which may be used to isolate, amplify these transrenal nucleic acids.
• One method of the invention for the isolation of urinary DNA from a subject includes the following steps. Urine is first centrifuged or filtered to separate cells and cell debris from the urine. EDTA/Tris HCl is then added to the urine to bind bivalent ions and to adjust pH to approximately pH 8.
• a chaotropic salt for example guanidine isothiocyanate to a final concentration of at least 3 M.
• a silica resin is added to the urine to which DNA binds. This resin is then washed, and the DNA eluted from it, thereby isolating the transrenal DNA.
• DNA isolated from the urine of a subject may then be amplified in order to be detected.
• Amplification methods include polymerase chain reaction (PCR), nested PCR, semi-nested PCR, Single-Strand Conformation Polymorphism analysis (SSCP), ligase chain reaction (LCR) and strand displacement amplification (SDA). Detection of transrenal DNAs is also performed through hybridization of at least one labeled probe.
• the amplification and detection of urinary nucleic acids from non- viral pathogens may be used to detect the presence of these pathogens, and thus diagnose the infection of a subject with these pathogens and to diagnose pathologies associated with the infection of a subject by these pathogens. Further, the detection of these pathogens may be used to monitor treatment of the infections and pathologies associated with these pathogens. Also, detection of these pathogens may be used to suggest treatments for a subject in which the pathogens are detected. These treatments may be used to relieve symptoms which are associated with the detection of pathogens or diagnosis with infection of the pathogens.
• Non- viral pathogens which are able to be detected by the presence of their nucleic acids in mammalian urine include bacteria and parasites.
• Bacterial species which are detectable using the compositions and methods of the invention include Helicobacter pylori (H pylori), Mycobacterium tuberculosis (M. tuberculosis, MTB or TB), and Bacillus anthracis (B. anthracis).
• Parasite species which are detectable using the compositions and methods of the invention include Plasmodium species including Plasmodium falciparum and Leishmania species.
• H. pylori infection Most cases of peptic ulcer disease, gastric mucosa associated lymphoid tissue (MALT) lymphoma and cancer of the distal stomach are complications of Helicobacter pylori infection. (Axon AT. Gut. 1999 JuI; 45 Suppl 1 :Il-4). However, most H pylori- positive individuals remain symptom free throughout their life. Symptoms associated with H. pylori infection include abdominal discomfort, weight loss, poor appetite, bloating, burping, nausea and vomiting. A widely accepted explanation of this phenomenon is that the outcome of H. pylori colonization is determined by combination of several factors including the genotypes of the bacteria and the host and the environmental cofactors such as diet and smoking.
• the test should give information about the genotype of the bacteria in the carrier. Colonizing human stomach H. pylori strains are genetically very diverse. Observed diversity is attributed to both horizontal transfer of genetic material between coexisting strains as well as to the instability of the bacterial genome. Polymorphism occurs due to point mutations, substitutions, insertions, deletions that may involve one or more genes (Akopyanz, N.S., et al. 1992. Nucleic Acids Res. 20:5137-5142; Achtman, M., et al. 1999. MoI. Microbiol.
• H. pylori virulence A major genetic determinant of H. pylori virulence is the cag pathogenicity island ⁇ cag PAI) (Blaser, M. J., et al. 1995. Cancer Res. 55:2111-2115; Cover, T. h.,et al. 2001. Helicobacter pylori pathogenesis. Academic Press, San Diego, Calif; Mobley, ⁇ . L. 1996. Am. J. Med. 100:2S-l IS.), a 40-kb region of chromosomal DNA that is present in some H. pylori strains but absent from others.
• the cag PAI encodes a type IV secretion system and an immunodominant antigen, CagA, which is translocated into gastric epithelial cells.
• CagA an immunodominant antigen
• infection with cag PAI-positive strains is associated with an increased severity of gastric mucosal inflammation, an increased risk for development of peptic ulceration, and an increased risk of gastric cancer (Ho, S. A., et al 1991. J. Clin. Microbiol. 29:2543-2549).
• cagA is present in only 60-70% of H pylori isolates in Western countries. Over 80% of patients with ulcers harbor cagA positive strains (Atherton JC. Gut. 1997 Jun;40(6):701-3; Tummuru MKR, et al. Infect Immun 1993 ;61: 1799-809; Atherton JC, etal. Curr Microbiol. 1999 Oct;39(4):211-8.).
• the gene encoding the vacuolating cytotoxin is present in all H. pylori strains analyzed so far. But only 50% of them produce an active vacuolating cytotoxin. Production and cytotoxicity of the vacA protein is determined by its structure. There are two polymorphic regions in the vacA gene: the region encoding the signal sequence with two distinct types of si and s2, and midregion marked as ml and m2. Existence of combination of all s and m types was registered except s2/ml . Most active genotype of vac A gene is shown to be si /ml followed by sl/m2. Very little activity or no activity was seen for the type s2/m2.
• H. pylori genetic markers studied such as: 16S rRNA gene, the random chromosome sequence, the 26-kDa species-specific antigen (SSA) gene, the urease A (ureA) gene, and the urease C (ureQ gene (Valentine, J. L., et al. 1991. J. Clin. Microbiol. 29:689-695; Hammer, M., T. et al. 1992. J. Clin. Microbiol. 30:54-58; Clayton, C. L., et al. 1992. J. Clin. Microbiol. 30:192-200; Bickley, J., et al. 1993. J. Med. Microbiol. 39:338- 344; Lu JJ, et al. J Clin Microbiol. 1999 Mar;37(3):772-4.).
• H. pylori presence and virulence can be detected through the isolation and detection of H. pylori transrenal-DNA. Methods of detecting the presence and genotype of H. pylori in urine have not been shown before.
• Tuberculosis remains the second most common cause of death from an infectious disease in the world in spite of advances in the implementation of control strategies during the last decade (Elzinga G, et al. Lancet 2004;363:814-9). Symptoms of tuberculosis include cough that is worse in the morning (sometimes with hemoptysis, blood in the sputum), chest pain, breathlessness, night sweats, and signs of pneumonia. In advanced disease, there may be extreme weight loss. However, no highly sensitive molecular-based test for the detection of M. tuberculosis has yet been discovered.
• tuberculosis in the sputum using PCR generally exceeds 98% and sensitivity is also high in patients whose sputum smear is positive for acid-fast bacilli on microscopic examination.
• the sensitivity of such tests may be less than 50% for patients with negative sputum smear.
• the present invention allows for the detection of M. tuberculosis through identifying its transrenal DNA in the urine of patients with pulmonary tuberculosis. This approach is more attractive than tests using sputum samples because urine specimens are easier and safer to collect than sputum which can generate infectious aerosols and prove to be difficult to obtain, especially in children.
• M. tuberculosis DNA fragments originating from sites of infection outside the urogenital tract are present in the urine in this previously unrecognized range of molecular sizes of less than approximately 200 bp.
• M. tuberculosis specific DNA sequences can be easily detected as short fragments of less than 200 bp in the soluble fraction of urine specimens from patients with pulmonary tuberculosis. These specific DNA fragments disappear following successful tuberculosis treatment. This is demonstrated in more detail in the Examples below.
• the data on M. tuberculosis Tr-DNA disappearance during the course of treatment supports the potential utility of this test in monitoring the clinical course of the disease.
• Tr-DNA testing for diagnosis of tuberculosis would have particular value for clinics located in regions having limited resources.
• PCR is currently the preferred method for detecting specific nucleic acid sequences
• new emerging technologies can be expected to eventually provide the tools to perform the relatively simple Tr-DNA test in the field (Storhoff J.J., et al. (2004) Biosensors & Bioelectronics 19:875-883; Nam J.M., et al. (2002) J. Am. Chem. Soc 124:3820-3821; Ho HA, et al. (2005) J Am Chem Soc.
• Bacillus anthracis Bacillus anthracis is a spore-forming gram-positive bacterium well known for its recent use as a bioterrorist agent. Bacillus anthracis is a large, Gram-positive, spore forming rod shaped bacterium, 1 - 1.2 ⁇ m in width x 3 - 5 ⁇ m in length. The bacterium grows in most media under aerobic or anaerobic conditions.
• Bacillus anthracis infection can cause anthrax.
• anthrax was primarily associated with contact with domestic animals.
• Bacillus anthracis has been associated with weaponized forms used in terrorism.
• the incidence of naturally-acquired anthrax is extremely rare (1-2 cases of cutaneous disease per year).
• 22 cases of anthrax 11 inhalation cases, 11 cutaneous cases were identified in the United States following intentional contamination of the mail.
• cutaneous anthrax which is usually acquired via injured skin or mucous membranes. A minor scratch or abrasion of the skin is contacted by Bacillus anthracis spores. The spores germinate, vegetative cells replicate, and an edema develops at the site. This develops into papule within 12-36 hours which changes rapidly to a vesicle, then a pustule (malignant pustule), and finally into a necrotic ulcer from which infection may disseminate, giving rise to septicemia. Lymphatic swelling also occurs and in severe cases, where the blood stream is eventually invaded, the disease is frequently fatal.
• inhalation anthrax results from the inhalation of spore-containing dust.
• the disease begins with a high fever and chest pain and progresses to a systemic hemorrhagic pathology. It is often fatal if treatment cannot stop the invasive aspect of the infection.
• the plasmid pXOl (110-MDa) carries three anthrax toxin proteins coding genes, edema factor (cya), lethal factor (lef), and protective antigen (pag) (Uchida, L, K. et a 1986. J. Gen. Microbiol. 132(Pt. 2):557-559.). Products of these genes act in paired combinations to produce the two anthrax toxins: edema toxin (pag and cya) and lethal toxin (pag and lef) (Leppla, S. H. 1995. Bacterial toxins and virulence factors in disease, p.543-572. Marcel Dekker, New York, N. Y.).
• toxicity loci on pXOl are commonly used as specific genetic markers for PCR detection of B. anthracis.
• Chromosomal genetic markers such as rpoB, gyrA, rRNA were also successfully utilized for the same purposes.
• B. anthracis can be done clinically by Gram stain, colony morphology, and various biochemical tests (Logan, N. A., and P. C. B. Turnbull. 2004. Bacillus and other aerobic endospore-forming bacteria, p. 445-460. In P. R. Murray, et al. (ed.), Manual of clinical microbiology, 8th ed. American Society for Microbiology, Washington, D.C.). However, these methods are time-consuming, therefore more rapid tests, such as PCR, have been developed to detect B. anthracis in clinical samples (Oggioni, M. R., et al . 2002. J. Clin. Microbiol. 40:3956-3963.). PCR assays have been widely used to identify B. anthracis on the basis of genes associated with pXOl and pXO2 plasmids.
• Plasmodium falciparum can infect humans under natural conditions: Plasmodium falciparum, P. vivax, P. ovale and P. malariae. The first two species cause the most infections worldwide. Plasmodium falciparum is the agent of severe, potentially fatal malaria, causing an estimated 700,000 - 2.7 million deaths annually, most of them in young children in Africa. Plasmodium vivax and P. ovale have dormant liver stage parasites
• Plasmodium malariae produces long-lasting infections and if left untreated can persist asymptomatically in the human host for years, even a lifetime.
• Molecular diagnostic methods have been developed based on the detection of the nucleic acids of the pathogenic agent in the blood or plasma samples, or in the cell cultures, taken from the patient. These assays are generally much more sensitive than the immunological assays. However, they may require the presence of special equipment and qualified personnel.
• the biological samples in the case of plasma, blood, or cell cultures — are difficult to store unaltered, except under controlled temperature conditions. For example, methods for the detection of Plasmodium in blood have been reported by Gal S., et al. (2001), Ann N Y Acad ScI 945: 234-238.
• the present invention provides compositions and methods for the detection of Plasmodium species, potentially very soon after infection, by isolating and detecting Plasmodium species transrenal DNA in subjects. A more detailed description of these compositions and methods are found below in the Examples. Leishmania species
• the biological samples in the case of plasma, blood, or cell cultures — are difficult to store unaltered, except under controlled temperature conditions.
• methods for the detection of Leishmania in blood have been reported by Disch J, et al. Acta Trop. 2004 Nov-Dec;92(3):279-83; Disch J, et al., Trans R Soc Trop Med Hyg. 2003 Jul-Aug;97(4):391-5; and Lee N, et al, Cell Death Differ. 2002 Jan;9(l):53-64.
• leishmaniasis The symptoms of leishmaniasis include fever, fatigue, weakness, appetite loss, weight loss, abdominal discomfort, vomiting, diarrhea, cough, scaly skin, thinning hair, macule or papule forming on the skin, skin ulcer, nasal stuffiness, nosebleed, difficulty swallowing and difficulty breathing.
• the present invention provides compositions and methods for the detection of Leishmania species, potentially very soon after infection, by isolating and detecting Leishmania species transrenal DNA in subjects. A more detailed description of these compositions and methods are found below in the Examples.
• Urinary nucleic acids in non-viral pathogen infections are found below in the Examples.
• the present invention describes a method for diagnosing and/or monitoring of a non- viral pathogen infection by detecting and quantification of the nucleic acids of pathogenic agents in urine. It has been discovered that the nucleic acids of these pathogenic agents are detectable in urine. Many of these pathogen specific nucleic acids cross the transrenal barrier (Tr-NA) and can be detected in urine as low-molecular- weight fragments (which tend to be shorter than 1,000 bp in length, but are preferably less than 500 bp in length, and more preferably shorter than 250-300 bp in length or shorter than 250 bp in length) through molecular methods known in the art.
• Tr-NA transrenal barrier
• pathogen specific nucleic acids may be shed by cells that are within the kidney, and thus do not have to cross the transrenal barrier in order to be detected in the urine. Further, some pathogen specific nucleic acids may be found in the urine through other mechanisms besides crossing the transrenal barrier or being generated by cells in the kidney.
• transrenal nucleic acids are nucleic acids that have crossed the kidney barrier.
• the transrenal nucleic acids (Tr-NA) according to the invention are not associated with, and are not derived from, the DNA of cells that are lost or released in the urinary tract. Instead, the transrenal nucleic acids that are detected in the present invention generally have crossed the kidney barrier as a cell- free material.
• Tr-NAs are DNA fragments.
• the discovery confirms the presence of urinary nucleic acids or transrenal nucleic acids derived from pathogenic bacteria and parasites in urine, and therefore is applicable to the diagnosis of all infectious diseases caused by non- viral pathogens.
• the invention relates to a method for the diagnosis a non-viral pathogenic infection in a subject by detection of pathogen-related transrenal nucleic acids in a urine sample from the subject.
• the invention further includes the step of quantifying the pathogen-related transrenal nucleic acids.
• the invention provides for methods of monitoring a parasite infection by repeated detection of pathogen-related transrenal nucleic acids in a subject over a period of time.
• the invention relates to a method for diagnosis of an infection in a subject, including the step of detection of the presence pathogen-related transrenal nucleic- acid sequences in a urine sample of the subject.
• the invention relates to the above method in which the transrenal nucleic acids are isolated from the urine sample prior to detecting the nucleic acids.
• the method according to the invention may include an initial treatment of the urine sample prior to detection.
• the invention includes the pretreatment of the urine sample with agents that inhibit the degradation of the nucleic acids. Included are the enzymatic inhibitors, such as chelating agents, detergents, or denaturing agents, and preferably DNase or RNase inhibitors, which include EDTA, guanidine HCl, guanidine isothiocyanate, N-lauryl sarcosine, and sodium dodecyl sulfate.
• the enzymatic inhibitors such as chelating agents, detergents, or denaturing agents, and preferably DNase or RNase inhibitors, which include EDTA, guanidine HCl, guanidine isothiocyanate, N-lauryl sarcosine, and sodium dodecyl sulfate.
• the urine sample may be centrifuged (at a speed between 300Og and 5000g, such as between 3500g and 450Og) or filtered in order to separate the fraction consisting of cells and their fragments from the supernatant containing the soluble DNA or RNA and their proteinous complexes.
• the urine sample may also be subjected to nucleic acid detection procedures without this fractionation.
• the optional isolation or purification and quantification of the transrenal nucleic acids are achieved through the use of chemical or physical methods that are already known in the art. It includes at least one purification step, using methods selected from among extraction with organic solvents, filtration, precipitation, absorption on solid matrices (e.g., via ion exchange), affinity chromatography or else molecular exclusion chromatography or combinations of these methods.
• the purification method must be appropriate for the isolation of DNA (single- or double-helix) that are less than 1000 nucleotides in length, with a corresponding molecular weight, assuming, as the average molecular weight, that of a nucleotide having a value of 330 Daltons.
• the purification is specific for fragments that are smaller than 500 nucleotides (nt) in length, with a corresponding molecular weight, such as fragments whose lengths are less than 300 nt, fragments less than 250 nt in length, or fragments whose lengths are between 100 and 200 base pairs of nucleic acids (nt).
• the DNA isolation method is implemented by pretreating the urine sample with a denaturing agent, such as urea, guanidine HCl, or guanidine isothiocyanate.
• a denaturing agent such as urea, guanidine HCl, or guanidine isothiocyanate.
• the sample is then caused to pass through a solid phase, such as a matrix consisting of a silica-based resin which, in the presence of chaotropic salts, such as guanidine isothiocyanate, binds the nucleic acids.
• a resin such as Wizard Purification Resin ® (Promega ® ) is utilized.
• the sample is then collected by elution in a buffer, such as Tris- EDTA (Tris 1-10 mM, EDTA 1-10 mM), or in water.
• the characterization and the determination of the presence of DNA of the pathogenic agent is performed through a technique selected from the group consisting of: hybridization of the nucleic acids, a cycling probe reaction (F. Bekkaoui et al. , in BioTechniques 20:240-248 [1996]), a polymerase chain reaction (PCi? Protocols: A Guide to Methods and Applications, by M. Innis et al; Elsevier Publications, 1990), a nested polymerase chain reaction, single-strand conformation polymorphism, or ligase chain reaction (LCR) (F. Barany, inPNAS USA, 88:189-93 [1991]), strand displacement amplification (SDA) (G.K.
• PCR Polymerase chain reaction
• nucleic acid refers to an oligonucleotide, nucleotide, polynucleotide, or fragments/parts thereof and to DNA or RNA of natural (e.g., genomic) or synthetic origin. It may have a double or single helix, and may also represent the sense or antisense direction of a sequence. Parallel helix (5'— »3'); antiparallel helix (3'->5').
• oligonucleotide, polynucleotide and nucleic-acid polymer are equivalent, and are understood as referring to a molecule consisting of more than two deoxyribonucleic or ribonucleic acid bases.
• nucleotides bases
• length of the oligonucleotide fragment may vary. They may be synthesized in different ways. The sequences are traditionally defined as starting with 5' and ending with a 3'. These numbers indicate the direction of the sequence.
• DNA isolated from the urine of a subject may then be amplified in order to be detected.
• Amplification methods include polymerase chain reaction (PCR), nested PCR, semi-nested PCR, Single-Strand Conformation Polymorphism analysis (SSCP), ligase chain reaction (LCR) and strand displacement amplification (SDA). Detection of transrenal DNAs is also performed through hybridization of at least one labeled primer.
• Hybridization is a method that allows two nucleic-acid sequences to recognize each other as complementary and to join together (annealing).
• Complementarity / Complementary sequences are sequences of polynucleotides that interact with each other, depending on the interaction between the bases.
• the AGTC sequence is complementary to TCAG according to standard Watson Crick base pairing.
• Hoogstein base pairing are well known to those having ordinary skill in the art. It is possible to have a folly or partially complementary sequence, and this is what determines the efficiency or attractive force between the two sequences. Average complementarity would prevent a strong complementarity from hybridizing, under conditions that would allow it to remain attached.
• hybridization includes, among others, slot/dot and blot hybridization.
• the conditions that allow nucleotide sequences to recognize each other can be modified in such a way as to produce complete hybridization (complementarity with high specificity) or partial hybridization (complementarity with average specificity).
• hybridization the conditions should be understood as referring to those that allow average or high complementarity.
• the technician in the field can calculate how many artificial sequences are needed to encourage hybridization between two complementary sequences in the opposite direction, known as antiparallel association.
• a probe is an oligonucleotide that can be produced artificially or naturally, and that forms a combination with another nucleic-acid sequence.
• the probes are useful in discovering specific sequences in a sample containing unknown DNA.
• all of the probes can be bound to a signaling molecule (or reporter).
• the reporter molecule makes it possible to detect the probe (for example, through enzymatic reactions (e.g., ELISA (Enzyme-Linked Immunosorbent Assay)), radioactivity, fluorescence, or other systems).
• PCR Polymerase chain reaction
• a primer is oligonucleotides from which, under proper conditions, the synthesis of a polynucleotide sequence can be initiated.
• a primer may exist naturally (for example, in an enzymatic digestion of a polynucleotide), or may be obtained through chemical synthesis.
• the product amplified in PCR is often referred to as an amplicon.
• Nested PCR is a second PCR which is performed on the product of an earlier PCR using a second set of primers which are internal to the first set of primers, referred to as nested primers. This significantly improves the sensitivity and specificity of the PCR.
• Nested primers are primers internal to an amplicon obtained with a first PCR cycle. The amplification process that uses at least one nested primer improves specificity, because the non-specific products of the first cycle are not amplified in the second cycle, because they lack the sequence that corresponds to the nested primer.
• Semi-nested PCR is a second PCR which uses one new primer and one of the original primers. This process also improves specificity.
• LCR Ligase Chain Reaction
• SSCP Single-Strand Conformation Polymorphism
• Strand displacement amplification is an isothermal nucleic acid amplification method based on the primer-directed nicking activity of a restriction enzyme and the strand displacement activity of an exonuclease-deficient polymerase.
• purification or isolation refers to a process for removing contaminants from a sample, where the result is a sample containing 50%, 60%, 75%, 90% or over 90% of the material toward which the purification procedure is directed.
• Tm a maximum temperature between a maximum, for a nucleic acid, represented by Tm less 5 °C, and a minimum represented by Tm less 25 0 C.
• the technique used in the field utilizes stringent temperature conditions, in combination with other parameters (e.g., saline concentration), to distinguish sequences with a quasi-exact homology.
• Stringent conditions are known to those skilled in the art and can be found in Ausubel, et ah, (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, N. Y. (1989), 6.3.1-6.3.6.
• the conditions are such that sequences at least about 65%, 70%, 75%, 85%, 90%, 95%, 98%, or 99% homologous to each other typically remain hybridized to each other.
• a non-limiting example of stringent hybridization conditions are hybridization in a high salt buffer comprising 6X SSC, 50 niM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 mg/ml denatured salmon sperm DNA at 65°C, followed by one or more washes in 0.2X SSC, 0.01% BSA at 50°C.
• a nucleic acid sequence that is hybridizable to the nucleic acid molecule comprising the nucleotide sequence, or fragments, analogs or derivatives thereof, under conditions of moderate stringency is provided.
• moderate stringency hybridization conditions are hybridization in 6X SSC, 5X Reinhardt's solution, 0.5% SDS and 100 mg/ml denatured salmon sperm DNA at 55 °C, followed by one or more washes in IX SSC 5 0.1% SDS at 37 °C.
• Other conditions of moderate stringency that may be used are well-known within the art. See, e.g., Ausubel, et al.
• nucleic acid that is hybridizable to the nucleic acid molecule, or fragments, analogs or derivatives thereof, under conditions of low stringency, is provided.
• low stringency hybridization conditions are hybridization in 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 mg/ml denatured salmon sperm DNA, 10% (wt/vol) dextran sulfate at 40°C, followed by one or more washes in 2X SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1% SDS at 50°C.
• Other conditions of low stringency that may be used are well known in the art ⁇ e.g., as employed for cross-species hybridizations).
• the invention also provides a kit for detecting and/or genotyping Helicobacter pylori in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 5, 8, 10, 11, 12 and 15 and at least one reverse primer selected from SEQ ID NOs: 6, 7, 9, 13, 14, 16 and 17, either in the same or separate packaging, and instructions for its use.
• the invention also provides a kit for detecting and/or genotyping Mycobacterium tuberculosis in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 34, 37 and 39 and at least one reverse primer selected from SEQ ID NOs: 35, 36, 38 and 40, either in the same or separate packaging, and instructions for its use.
• the invention also provides a kit for detecting and/or genotyping Bacillus anthracis in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 41, 43, 45, 47, 48 and 50 and at least one reverse primer selected from SEQ ID NOs: 42, 44, 46 and 49, either in the same or separate packaging, and instructions for its use.
• the invention also provides a kit for detecting and/or genotyping Plasmodium species in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 18, 21 and 23 and at least one reverse primer selected from SEQ ID NOs: 19, 20 and 22, either in the same or separate packaging, and instructions for its use.
• the invention also provides a kit for detecting and/or genotyping Leishmania species in a urine sample from a subject in need thereof, comprising at least one forward primer selected from SEQ ID NOs: 26, 28, 30, 32 and 51 and at least one reverse primer selected from SEQ ID NOs: 24, 25, 27, 29, 31 and 33, either in the same or separate packaging, and instructions for its use.
• Example 1 Stabilization and preparation of the samples.
• EDTA inhibits the activity of DNase I and phosphodiesterase by chelating divalent metals such as Mg 2+ , Ca 2+ and/or others that are required for their activity.
• DNase II is maximally active in acidic environment. Supplementing the urine with Tris-HCl pH 8.0 buffer increases the pH of urine thereby inhibiting the activity of DNase II.
• the stabilized urine samples can be stored, in aliquots of 5 ml, at -80°C. Optionally, 25 mL of saline solution is frozen to act as a control.
• Tr-DNA based applications that involve quantitative Tr-DNA analysis
• urine fractionation is often required. It reduces the impact of nucleoproteins from cells present in urine on accurate quantitation of Tr-DNA/protein complex, total Tr-DNA, or specific genetic markers.
• centrifugation and filtration Both were carried out immediately after urine collection and, before supplementing the specimen with EDTA-Tris stabilizing mixture.
• Urine may be kept in this condition as long as urine cells are intact and their constituents do not leak into urine and contaminate Tr-DNA by cellular DNA.
• filters For filtration one can use filters with pore size ranging from 0.1 to 5 ⁇ m with reduced nucleic acid and protein binding capacity. The choice of the filter depends on target under analysis.
• Urine cellular fraction can be harvested by extracting it from the filter by applying a solution (high concentrations of salts or chaotropic agents) that is known to dissolve cells.
• Urine fractionation by centrifugation in our experiments was carried immediately after sample collection, before addition of preservation mixture. Centrifugation was performed at room temperature at RCF ranging between 3500 and 4000xg for approximately 15 min. Supernatant was carefully collected and manipulated per the procedure described above for urine filtration. The pellet consisting mainly of cells and cellular debris was resuspended in physiological solution and stored at -80 °C.
• Example 3 Extraction and purification of the nucleic acids from urine.
• Resin was collected by applying vacuum, washed twice with 5 ml of 3M GITC solution. The resin was further washed twice by a solution consisting of 80% ethanol and 50 mM NaCl. Then the minicolumn was detached and the resin was additionally washed twice with 96% ethanol by centrifugation on a benchtop microcentrifuge in 1.5 ml tubes. DNA was eluted by brief centrifugation with hot water in a volume of not more than 1/20 of urine initial volume. Centrifugation Based Procedure
• Example 4 Monitoring of the integrity of DNA extraction procedure.
• the DNA extraction procedure was routinely monitored by testing the purified DNA for the presence of selected control DNA sequences.
• For the purposes of detection of Tr- DNA of infectious agents the integrity of DNA purification procedure was monitored using beta-actin and beta-globin as markers for human and rabbit urine, respectively.
• PCR amplification of above targets is a surrogate for the estimation of DNA yield and quality. Primer pairs used in these studies are presented in Table 1. Table 1.
• PCR conditions for both targets were identical. Amplification of isolated DNA equivalent to 300 ⁇ l of urine was carried out in 25 ⁇ l mixture containing 0.2 ⁇ mol/liter of primers ES0007 and ES0008 or LEBGJF and LEBGJR. for human b-actin or rabbit b-globin, respectively, 200 ⁇ mol/liter dNTP each, and 1 U GoTaq Polymerase (Promega). Thermal profile for both types of reactions was: 94 0 C for 5 minutes followed by 35 cycles of 94 °C for 30 seconds, 60 °C for 30 seconds, 72 °C for 1 minute, and 1 cycle of 72 °C for 5 minutes. Ten ⁇ l the products were resolved by electrophoresis in 7% polyacrylamide gel, and visualized by ethidium bromide staining.
• Figure 1 and Figure 2 depict the results of PCR of DNA purified from human urine and rabbit urine, respectively.
• Figure 1 shows the results of PCR performed to control the integrity of DNA extraction from human urine.
• Urine samples are from patients attending doctor's office for endogastroscopy for a test for Helicobacter pylori.
• M DNA molecular weight standards, 50 bp ladder; NTC - no template control; 1 - 13 urine from patients.
• Figure 2. shows the results of PCR performed to control the integrity of DNA extraction from rabbit urine. Urine samples were harvested from rabbits infected with Bacillus anthracis spores.
• M DNA molecular weight standards, 50 bp ladder; NTC - no template control; 1 - DNA from urine of uninfected rabbit; 2 and 3 - urine of infected rabbit collected 6 an 14 hours after infection, respectively; +c - rabbit genomics DNA
• primers for the PCR based analysis of Tr-DNA were designed for target amplicons not more than 200 bp in length.
• PCR primers were designed based on consensus DNA sequences created by alignment of corresponding genetic markers nucleotide sequences. DNA sequences of target genes were extracted from GeneBank at NCBI and aligned using BioEdit package (IBIS Therapeutics, Carlsbad, CA). Primers are listed in Table 2. For the purposes of present invention two sets of genetic markers were selected: ureA as specie specific marker and cagA as a marker of virulence.
• cagA Gene primers for semi-nested-PCR External primers cagA-f (SEQ ID NO:5): TCRGAAATTTGGGRMTCAGCGTTAC cagA-r (SEQ ID NO:6): TCCATAAAATTTYGGATBBDTYGGGTGTTG Product: 102 bp.
• cagA-f SEQ ID NO:5: TCRGAAATTTGGGRMTCAGCGTTAC
• cagA-rn SEQ ID NO:7: ACGGATCDTTTTGAWGGGACAC Product: 65 bp.
• HG16s-f (SEQ ID NO:15) CACTGGGCGTAAAGAGYGCGTAG HG16s-r (SEQ ID NO:16) CCACCTRCCTCTCCCAYACTC Product 113 bp
• HG16s-f (SEQ ID NO:15) CACTGGGCGTAAAGAGYGCGTAG HG16s-nr (SEQ ID NO:17) GGTTAAGCCATAGGATTTCACAYCTGAC Product 63 bp
• Example 7 Detection of H. pylori in urine of patients.
• Urine specimens were obtained before the endoscopy, and the DNA from whole urine was purified following the protocol described in Examples 1, 2 and 3.
• Detection of we A and cagA specific sequences in urine was carried out by semi- nested PCR. Initial twenty cycles of PCR amplification were performed as following: isolated DNA equivalent to that contained in 5 ml of urine was added to a 25 ⁇ l mixture containing 0.2 ⁇ mol/liter of outer primers specific for ureA or cagA (SEQ ID NO 12 and 13, or SEQ ID NO 5 and 6, respectively), 5 ⁇ l 5X PCR buffer (Promega), 200 ⁇ mol/liter dNTP each, and 1 U GoTaq Polymerase (Promega), denatured at 94 °C for 5 minutes followed by 20 cycles of 94 °C for 30 seconds, 62 °C for 30 seconds, 72 °C for 1 minute, and 1 cycle of 72 °C for 5 minutes.
• One ⁇ l of the product from this amplification was diluted 1:10 and 1 ⁇ l of the dilution was re-amplified 35 cycles using internal ureA and cagA primers (SEQ ID NO 12 and 13, or SEQ ID NO 5 and 6, respectively), under the same conditions as in the first reaction.
• the products from the second amplification were resolved by electrophoresis in 7% polyacrylamide gel, and visualized by ethidium bromide staining.
• Figure 3 shows semi-nested PCR detection of ureA (A) and cagA (B) genes specific DNA sequences in urine of patients (lanes 1-13). NTC - no template control; -c - DNA from the urine of a healthy volunteer; +c — positive control.
• Primers were designed to detect 18S rRNA genes of all four human pathogenic subtypes Plasmodium sp: P. falciparum; P. vivax; P. malariae, and P. ovale (accession numbers: M19172; X13926; M54897 and L48987, respectively).
• PCR primers were designed based on consensus DNA sequences created by alignment of corresponding genes' nucleotide sequences. Nucleotide sequences were aligned using BioEdit package (IBIS Therapeutics, Carlsbad, CA). Primers are presented in the Table 3.
• Urine sample was taken from a malaria patient infected with Plasmodium falciparum. DNA isolated from the whole urine of non-infected patients or from blood of malaria patients was used as negative and positive controls, respectively.
• semi-nested PCR was performed using two sets of primers targeting two conserved regions of Sl 8 ribosomal RNA gene.
• Figure 4 illustrates the electrophoresis of the DNA fragments that were amplified via two amplification cycles (semi-nested PCR). Two sets of reactions were carried out:
• Primer pairs F-358/R-456 for the first PCR and F-358/R-405 for subsequent semi- nested reaction lanes 1; 2 and 3 are negative control; Tr-DNA from infected patient and DNA extracted from the whole blood of an infected patient, respectively.
• Example 11 Detection of Leishmaniasis species.
• Urine sample was taken from a leishmaniasis patient infected with Leishmania infantum. DNA isolated from the whole urine of non-infected patients or from blood of leishmaniasis patients was used as negative and positive controls, respectively.
• PCR amplification reaction was carried out using a set of primers specific for kinetoplast minicircle DNA conserved domain (primers 13 A/13B).
• Figure 5 illustrates the electrophoresis of the DNA fragments that were amplified using primers specific for pathogenic Leishmania sp Lane M-DNA molecular weight standards; Lane 2- Tr-DNA from non-infected subject; Lane 3- Tr-DNA from an infected patient Lanes 4 and 5 - DNA extracted from blood of infected patients was used as a positive control.
• the size of the PCR product is 120 bp (see Table 4).
• Example 12 Selection of PCR Primer Sets for the Detection of Mycobacterium tuberculosis.
• tuberculosis DNA 8 of the patients with pulmonary tuberculosis were asked to return to donate urine specimens two months after initiating anti-tuberculosis therapy. In addition, ten healthy individuals were included as controls in the study.
• Urine specimens were processed as described in Examples 1-3 above. Twenty cycles of PCR amplification were performed as following: isolated DNA equivalent to that contained in 300 ⁇ l of urine was added to a 25 ⁇ l mixture containing 0.2 ⁇ mol/liter of outer primers F-785 and R-913, 5 ⁇ l 5X PCR buffer (Promega), 200 ⁇ mol/liter dNTP each, and 1 U GoTaq Polymerase (Promega), denatured at 94 °C for 5 minutes followed by 20 cycles of 94 °C for 30 seconds, 62 °C for 30 seconds, 72 °C for 1 minute, and 1 cycle of 72 °C for 5 minutes.
• M. tuberculosis-specific product of 67 bp was found in urine specimens from all 20 patients analyzed. Eight healthy individuals used as controls were all found to be negative for the presence of M. tuberculosis-specific sequences. The last lane in the gels is the genomic DNA of Mycobacterium tuberculosis strain H37RV, as a positive control.
• Example 14 Demonstration that TB specific DNA sequences found in urine are cell free.
• Primer pairs F-785/R-913 and semi-nested primers F-785/Rn-851 specific for short amplicon were used (see Table 5). As shown in Figure 7, 6 of 8 of the supernatant samples display the presence of M. tuberculosis DNA, whereas only 2 of 8 of the pellet samples were positive.
• Lanes 3-9 represent products of PCR amplification of DNA purified from patients urine. Lanes 1 in both gels show the DNA standards, Lanes 2 in both gels are negative controls, and Lanes 10 in both gels are positive genomic DNA controls. These data confirmed that bacterial DNA fragments extracted from urine are relatively short fragment. Furthermore, these results strongly suggest that it is unlikely that MTB DNA can be reproducibly detected in urine specimens of pulmonary TB patients when using urine sediment PCR analysis combined with large amplicon sizes.
• Example 15 Analysis of TB Patients Before and After Treatment.
• One of the critical problems faced in the management and eradication of pulmonary tuberculosis worldwide is the accurate and early detection of the efficacy of therapeutic treatment of patients.
• Currently general practice of monitoring of the success of a treatment is based on clinical symptoms, which are relatively late indicators and therefore do not provide information for a "real time" adjustment of the regiment of therapy.
• Tr-DNA platform technology is twofold. First, it gives a safe, easy and inexpensive means for detection of mutations known to be associated with increased drug resistance, and second, it ideally fits to the early monitoring tasks owing to its inherent capabilities of detection and quantification of non-host origin genetic markers in urine.
• Example 16 Selection of PCR Primer Sets for the Detection of Bacillus anthracis and Diagnosis of Anthrax.
• a virulent strain of B. anthracis, A0843 was used for spore production. This strain, isolated from an outbreak of anthrax, which occurred in Italy, was microbiologically characterized by Turnbull et al. (Bacillus, p. 187-210. In M. T. Parker and L. H. Collier (ed.), Topley and Wilson's principles of bacteriology, virology and immunity, VII ed.
• Rabbits were randomly clustered in several groups of 4 animals. Each rabbit was infected by subcutaneous injection of 100,000 spores of the pathogen strain A0843. Animals from each group were sacrificed post-infection at time intervals 6 and 14 hr. After euthanasia urine was harvested from the bladder by syringe aspiration. The volume of collected urine specimens varied from 2 to 10 ml. Four uninfected rabbits were used as controls.
• Tr-DNA isolated from the urine of 4 non-infected rabbits were used as negative controls.
• PCR primers were designed using Beacon Designer software (Premier Biosoft, Palo Alto, CA).
• Detection of pag specific sequences in urine was carried out by semi-nested PCR using the primer set specific for the pag loci (see Table 6). PCR amplification and electrophoresis analysis was performed per the protocol used in previous Examples. Briefly, twenty cycles of PCR amplification were performed in a 25 ⁇ l mixture with primers PAG_F and PAGJR.. One ⁇ l of the product from this amplification was diluted 1:10 and 1 ⁇ l of the dilution was re-amplified 35 cycles using primers PAG_R and PAG_FSN under the same conditions as in the first reaction.
• Figure 10 shows the detection of B. anthracis A0843 specific DNA sequences in the urine of experimentally infected rabbits. Lanes: M - 50 bp ladder DNA molecular weight markers; 1 - no template control; 2 - urine from uninfected rabbit; 3 and 4 - urine collected from infected rabbits 6 and 14 hr post-infection, respectively ; 5 -B. anthracis A0843 genomic DNA, positive control.

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