WO2002040663A1 - Nucleic acids for detecting fungi and method of detecting fungi by using the same - Google Patents
Nucleic acids for detecting fungi and method of detecting fungi by using the same Download PDFInfo
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- WO2002040663A1 WO2002040663A1 PCT/JP2001/009939 JP0109939W WO0240663A1 WO 2002040663 A1 WO2002040663 A1 WO 2002040663A1 JP 0109939 W JP0109939 W JP 0109939W WO 0240663 A1 WO0240663 A1 WO 0240663A1
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- 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
- C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
Definitions
- the present invention relates to a nucleic acid mixture for detecting a fungus and a method for detecting a fungus using the mixture.
- the main pathogens of deep mycosis are Candida (hereinafter abbreviated as G.) genus fungi, Aspergillus (hereinafter abbreviated as A.) genus fungi, and Cryptococcus (abbreviated as Gr. Below). ) Genus fungi are known.
- Major pathogens of the genus Candida include Candida albicans (G. albicans), Candida albicans 'G. glabrata', Candida albicans 'G. tropical is', and Candida albicans (G. parapsi losis) Candida albicans 'G. dubl iniensis and other major pathogens of the genus Cryptococcus include Cryptococcus neoformans (Gr.
- Neoformans The main pathogens of the genus Aspergillus include A. fumigatus, A. flavus, A. niger, and the two gar groups, Aspergillus drans (A. n). idurans) and Aspergillus' terreus (A. terreus), and it is desired to rapidly detect, classify, and identify these strains.
- An object of the present invention is to provide a nucleic acid used for detecting fungi causing deep mycosis, particularly fungi of the genus Candida and Cryptococcus, and to use the nucleic acid in a simple, rapid, specific and specific manner. It is an object of the present invention to provide a highly sensitive method for detecting fungi of deep mycosis, particularly fungi of the genus Candida and cryptococci.
- the present inventors have conducted various studies on the genes of various fungal fungi, especially Candida fungi and Cryptococcus fungi, and as a result, the fungi causing these various fungal diseases have been identified.
- a part of the cytochrome b gene present in mitochondria was amplified and its sequence was successfully decoded.
- the present inventors found specific sequences for each type of Candida fungus, and amplified a part of the cytochrome b gene of each species based on them.
- a universal primer mixture has been designed to be able to do so.
- the present invention relates to the present invention, wherein each of a plurality of base sequences represented by SEQ ID NOS: 1, 2, 3 or 4, each showing a plurality of base sequences (provided that thymine at any position is substituted with peracil. Or at least two or more of its complementary base sequences, each consisting of at least 15 bases continuous from the 3 ′ end, or hybridizing with each base sequence under stringent conditions.
- nucleic acid mixture for detecting a fungus comprising a mixture of at least two or more nucleic acids having a base sequence.
- the present invention relates to at least a plurality of base sequences represented by SEQ ID NOS: 1 and 2 in the sequence listing (though thymine at any position may be substituted with peracyl).
- a base sequence consisting of at least 15 bases continuous from the 3 ′ end or a mixture of the base sequence and a nucleic acid having a base sequence that hybridizes under stringent conditions.
- a primer on one side and has at least two or more of a plurality of base sequences represented by SEQ ID NO: 3 or 4 in the sequence listing (though thymine at any position may be substituted with peracyl).
- SEQ ID NO: 3 or 4 in the sequence listing (though thymine at any position may be substituted with peracyl).
- 'A nucleic acid amplification method using a nucleotide sequence comprising at least 15 nucleotides continuous from the terminal or a mixture of nucleic acids having a nucleotide sequence that hybridizes with the nucleotide sequence under stringent conditions as a reverse primer.
- a method for detecting a fungus comprising amplifying a test nucleic acid and detecting an amplification product.
- the present invention provides a method for identifying a fungus, comprising determining the base sequence of the amplification product.
- the present invention further provides a kit for detecting a fungus containing the nucleic acid of the present invention.
- the present invention provides a fungal detection probe obtained by labeling the nucleic acid mixture of the present invention.
- the present invention provides a capture probe for detecting a fungus, wherein the nucleic acid mixture of the present invention is bound to a carrier.
- the present invention provides the use of the nucleic acid mixture of the present invention for producing a probe or primer for detecting a fungus.
- a fungal nucleic acid for use in detecting various fungi and a method for detecting a fungus using the nucleic acid are provided.
- the nucleic acid mixture of the present invention can be used as a primer for an amplification reaction or as a probe for direct detection.
- the nucleic acid mixture of the present invention as a primer for an amplification reaction, it has become possible to detect a plurality of fungi having different nucleotide sequences by a single amplification reaction.
- the sensitivity and specificity can be further increased by detecting the product amplified by the primer with a probe, and its clinical significance is great.
- the nucleic acid mixture for detecting a fungus of the present invention comprises a plurality of base sequences each represented by SEQ ID NO: 1, 2, 3 or 4 (provided that thymine at any position is substituted with peracil. Or at least two of its complementary base sequences Among them, those having a base sequence consisting of at least 15 bases continuous from at least the 3 'end or a base sequence that hybridizes with the base sequence under stringent conditions.
- the nucleic acids of the present invention may be DNA or RNA.
- nucleic acid mixture of the present invention at least 3 ′ of a plurality of base sequences represented by SEQ ID NOs: 1, 2, 3 or 4 (provided that thymine at any position may be substituted with peracyl)
- a nucleotide sequence consisting of at least 15 bases continuous from the terminal is preferable, and a nucleic acid mixture represented by SEQ ID NO: 1, 2, 3, or 4 and having a plurality of nucleotide sequences is particularly preferable.
- the nucleic acid mixture for detecting a fungus of the present invention comprises a nucleotide sequence represented by SEQ ID NO: 1, 2, 3 or 4 in the sequence listing (however, thymine at any position may be substituted with peracyl) or its complement.
- a basic sequence consisting of at least 15 bases continuous from at least its 3 'end under stringent conditions the base sequence described above may be substituted with at least 3 bases. It may include deletions, insertions or additions.
- “under stringent conditions” means that under the annealing conditions in ordinary PCR as described in the Examples below, the target nucleic acid hybridizes to type II and functions as a primer.
- the buffer commonly used for PCR is PCR buffer (final concentration of 50 mM KG I, 10 mM Tris-HCl (pH 8.4-9. at 25 ° C), 1.5 mM MgG I 2 ) .Kit usually comes with a 10-fold concentration of X10 PGR buffer (or 10X PGR buffer), which is diluted.
- nucleotide sequence represented by SEQ ID NO: 1, 2, 3 or 4 (however, thymine at any position may be substituted with peracyl) or at least the 3 '
- a nucleic acid mixture having a base sequence consisting of at least 15 bases consecutive from the end and a sequence in which only one or two bases are substituted (excluding those in which the 3 'end is substituted) is usually used for the purpose of the present invention. Can be used for
- the nucleic acid of the present invention can be easily produced by chemical synthesis using a commercially available DNA synthesizer or the like.
- SEQ ID NOs: 1 to 4 indicate multiple bases with one letter, such as m, r, and w, respectively. Therefore, one sequence number indicates multiple sequences.
- the nucleic acid of the present invention is a mixture of nucleic acids having at least two or more, and preferably all of these plural nucleotide sequences (including the above-mentioned portions and variants). By using such a mixture, various mutant strains of fungi can be detected.
- the nucleic acid mixture of the present invention may comprise a region within the mitochondrial cytochrome b gene of a fungus, particularly a fungus belonging to the genus Candida, Cryptococcus, Aspergillus or Penicillium, preferably a fungus belonging to the genus Candida or Cryptococcus. It is what hybridizes.
- Preferred fungal species that can be detected using the nucleic acid mixture of the present invention include Candida 'grabrata, Candida parapsilosis, Candida tropicalis, Candida' albicans, Cryptococcus' neoformans and Candida doubryensis But are not limited to these. However, SEQ ID NO: 3 (including the above-mentioned portions and variants) cannot be used for the detection of Candida albicans, Cryptococcus neoformans and Candida doubriniensis.
- the mitochondrial cytochrome b gene is located in mitochondria, is difficult to recombine due to cytoplasmic inheritance, and is thought to undergo base changes in proportion to evolution. Therefore, it is suitable for detecting various fungi.
- the region amplified when the nucleic acid combination of the present invention is used as a primer in a nucleic acid amplification method is a relatively variable portion, and it is easy to distinguish species, It has the advantage that it is easy to distinguish between DNA types within a species. Therefore, the species or strain of fungi can be identified by amplifying the test nucleic acid using the nucleic acid of the present invention as a primer and determining the base sequence of the amplification product.
- the nucleic acid mixture of the present invention hybridizes with a region in the cytochrome b gene of the fungal mitochondria, so that the fungus can be detected by using the nucleic acid mixture of the present invention as a probe or a primer for a nucleic acid amplification method. it can.
- the nucleic acid mixture of the present invention is used as a probe, it is preferable to use a nucleic acid mixture labeled with a labeling agent.
- the labeled nucleic acid mixture of the invention is After the fungal gene in the test sample and the labeled probe are hybridized, the bound product of the fungal gene and the labeled probe or the unbound labeled probe is detected by an appropriate detection method suitable for the labeling agent.
- Labeling agents used for probes are well known in this field, and include fluorescent labels, radioactive labels, enzyme labels, biotin and the like.
- the hybridization of the sample, i.e., the fungal gene in the test sample, to the probe is performed by pretreating and purifying the sample by a usual method to obtain a test sample, and mixing it with a labeled nucleic acid mixture as a probe, and then room temperature. It can be carried out by treating at 10 to 70 ° C for 10 minutes to 48 hours.
- the sample may be subjected to an amplification reaction in advance using the nucleic acid mixture of the present invention as a primer.
- the nucleic acid mixture of the present invention is used as a primer for a nucleic acid amplification method
- the nucleic acid mixture of the present invention is used as a primer to carry out an elongation reaction with a DNA polymerase or the like to amplify the gene, thereby obtaining a cytochrome of a Candida fungus and a Cryptococcus fungus.
- a fungus can be detected by specifically amplifying only the b gene fragment and measuring the amplified product.
- a labeled nucleic acid obtained by labeling the nucleic acid mixture of the present invention with a labeling agent as described above may be used as a primer.
- the gene amplification method used herein include a PCR method, but are not particularly limited to this method. Any method using a short-chain oligonucleic acid as a primer to initiate gene synthesis is used. Can also be used.
- the method for detecting a fungus of the present invention can be performed by detecting an amplification product amplified by the above method, ie, a cytochrome b gene fragment. Alternatively, it can also be carried out by fragmenting the amplified cytochrome b gene fragment with a restriction enzyme and comparing the generated patterns of the fragment.
- the restriction enzymes used here are used alone or in combination.
- Means for detecting a cytochrome b gene fragment amplified with an amplification product or a gene fragment further fragmented with a restriction enzyme is not particularly limited, and a normal gene detection method (for example, an electrophoresis method) can be used.
- the amplification product is fractionated by, for example, electrophoresis and can be easily detected as a specific and sufficiently clear band for detection.
- the primers are also used in the amplification reaction during the amplification reaction. By using a liponucleic acid mixture (ATP, UTP, GTP, CTP) as a raw material for DNA or RNA synthesis, amplification products can be directly detected with high sensitivity.
- the amplified product can be directly detected with high sensitivity.
- the labeling agent used for labeling is preferably a radioactive substance, a fluorescent substance, or the like. It can also be used as a primer for so-called real-time detection PCR, in which case the nucleic acid to be tested can be quantified. Therefore, “detection” as used herein includes quantitative detection.
- a nucleic acid mixture having the nucleotide sequence shown in SEQ ID NO: 1 and SEQ ID NO: 2 (including the above-mentioned part and mutant thereof, the same applies hereinafter) is preferably used as a fore-side primer
- the nucleic acid mixture having the nucleotide sequence shown in SEQ ID NO: 3 or SEQ ID NO: 4 is preferably used as a reverse primer. It is preferable to use a combination of these forward primer and linear primer, whereby a 396 bp region is amplified as specifically described in the Examples below.
- the reagent kit for detecting a fungus of the present invention comprises the nucleic acid mixture of the present invention or a labeled nucleic acid obtained by labeling the nucleic acid mixture with an appropriate labeling agent.
- the reagent kit of the present invention may contain the above-described nucleic acid, and may contain a labeling detection reagent, a buffer, and the like as other components.
- the nucleic acid in the reagent kit of the present invention can be used as a primer or a probe. Whether a nucleic acid is used as a primer or a probe is different in only its means, and is essentially the same for detecting fungi.
- the reagent kit is used as a reagent kit for detecting a fungus by the method using the above-described probe. Can be used as a reagent kit.
- the reagent kit of the present invention when the nucleic acid mixture in the reagent kit is used as a probe May contain, in addition to the nucleic acid mixture for detecting Candida fungi and Cryptococcus fungi or the labeled nucleic acid mixture for detecting Candida fungi and Cryptococcus fungus of the present invention, a labeling detection reagent, a buffer, and the like. Good.
- the reagent kit of the present invention is a nucleic acid mixture for detecting a Candida fungus and a Cryptococcus fungus of the present invention or a labeled Candida fungus and a Cryptococcus fungus detection.
- nucleic acid synthases eg, DNA polymerase, RNA polymerase, reverse transcriptase, etc.
- mixtures of deoxyribonucleotides dATP, dTTP, dGTP, dGTP
- mixtures of ribonucleotides ATP, UTP
- restriction enzymes e.g., restriction enzymes, buffers and the like.
- kits include, for example, those obtained by adding the nucleic acid mixture of the present invention to commercially available PCR kits described in the following Examples.
- the nucleic acid mixture of the present invention can be used as a capture probe by binding to a solid phase carrier.
- the sandwich assay may be performed by combining two of the capture probe and the labeled probe.
- the nucleic acid mixture is labeled with biotin, hybridized, and then captured with an avidin-bound carrier.
- the sandwich assay if the nucleic acid mixture of the present invention is used for either one, specific measurement of the nucleic acid mixture of the present invention becomes possible, and there is no problem even if the specificity of the other nucleic acid mixture is slightly lower. .
- the binding of the nucleic acid to the solid phase carrier can be easily performed by a well-known technique widely used in the field of DNA chips and the like.
- nucleic acid mixtures 1 to 4 in the sequence listing were synthesized by chemical synthesis.
- the various nucleic acid mixtures represented by SEQ ID NOs: 1 to 4 in the sequence listing are referred to as nucleic acid mixtures 1 to 4, respectively.
- Example 2 (Candida albicans cytochrome b gene amplification reaction)
- Candida albicans (Gandida albicans IF 40009) obtained by culturing in a port dextrose liquid medium were treated with 75% ethanol and sterilized.
- the cells were obtained by centrifugation at 1500 g for 10 minutes, and about 40 ml of extraction buffer (0.9 M sorbitol, 10 mM EDTA, 10 mM Tris-HCl buffer, pH 7.1) was added, and the mixture was shaken well. Thereafter, the supernatant was discarded by centrifugation at 1500 g for 10 minutes, 30 ml of the same buffer was added.
- extraction buffer 0.9 M sorbitol, 10 mM EDTA, 10 mM Tris-HCl buffer, pH 7.1
- the supernatant was discarded after centrifugation, and 9 ml of the same buffer was added.
- 1 ml of Zymolyase (Seikagaku Kogyo Co., Ltd. cell wall lysing enzyme, 10 mg / ml) dissolved in the same buffer, and the mixture was incubated at 37 ° C. for 1 hour and then treated with an ultrasonic washer for 1 minute. This was centrifuged at 1500 g for 10 minutes to obtain a supernatant, and further centrifuged at 20000 g for 15 minutes to obtain a precipitate. The precipitate was washed with an extraction buffer and centrifuged again at 20000 g for 15 minutes to obtain a mitochondrial fraction.
- the total volume was made up to 50 I with water.
- the reaction conditions were as follows.
- the amplified DNA was separated and purified by agarose gel electrophoresis, and the nucleotide sequence was analyzed by the following method. Using a DNA sequencer (ABI Prism 377) manufactured by PerkinElmer and analyzed according to the Dye Terminator method according to the operation guide of the company. Nucleic acid mixture 2 was used on the forward side and nucleic acid mixture 4 was used on the reverse side as primers for base sequence analysis. The determined nucleotide sequence is shown in SEQ ID NO: 5 in the sequence listing.
- Example 3 Candida 'glabrata cytochrome b gene amplification reaction
- Example 2 In the same manner as in Example 2, using the nucleic acid mixture 1 and the nucleic acid mixture 3 obtained in Example 1, a part of the cytochrome b gene was amplified from Candida glabrata (Candida glabrata IFM 46843) by a PCR reaction, The nucleotide sequence was determined. Nucleic acid mixture 1 was used on the forward side and nucleic acid mixture 3 was used on the reverse side as primers for nucleotide sequence analysis. The nucleotide sequence is shown in SEQ ID NO: 6 in the sequence listing.
- Example 4 (Amplification reaction of Candida parapsilosis cytochrome b gene) Using the nucleic acid mixture 1 and the nucleic acid mixture 3 obtained in Example 1 in the same manner as in Example 2, Candida parapsilosis was used. losis IFM 46829), a part of the cytochrome b gene was amplified by PCR, and its nucleotide sequence was determined. Nucleic acid mixture 1 was used on the forward side and nucleic acid mixture 3 was used on the reverse side as primers for nucleotide sequence analysis. The nucleotide sequence is shown as SEQ ID NO: 7 in the sequence listing.
- Example 5 (Amplification reaction of Candida tropicalis cytochrome b gene)
- Example 2 In the same manner as in Example 2, using the nucleic acid mixture 1 and the nucleic acid mixture 3 obtained in Example 1, a part of the cytochrome b gene from Candida tropical is (FM 46816) was subjected to a PCR reaction. It was amplified and its nucleotide sequence was determined. Base sequence solution Nucleic acid mixture 1 was used on the forward side and nucleic acid mixture 3 was used on the reverse side as the primer for analysis. The nucleotide sequence is shown in SEQ ID NO: 8 in the sequence listing.
- Example 6 (Amplification reaction of Candida doubriniensis cytochrome b gene) Using the nucleic acid mixture 2 and nucleic acid mixture 4 obtained in Example 1 in the same manner as in Example 2, Candida doubriniensis (Candida doubriniensis) was used. A part of the cytochrome b gene from Candida dubl iniensis IFM 48313) was amplified by PCR, and its nucleotide sequence was determined. The nucleotide sequence analysis primer used was a nucleic acid mixture 2 on the forward side and a nucleic acid mixture 4 on the reverse side. The nucleotide sequence is shown in SEQ ID NO: 9 in the sequence listing.
- Example II (Cryptococcus neoformans cytochrome b gene amplification reaction)
- nucleic acid mixture 2 Using the nucleic acid mixture 2 and the nucleic acid mixture 4 obtained in Example 1 in the same manner as in Example 2, a portion of the cytochrome b gene is amplified from Cryptococcus neoformans (Gryptococcus neoformans IFM 46 138) by PCR. Then, its nucleotide sequence was determined. For the primer for nucleotide sequence analysis, the nucleic acid mixture 2 was used on the forward side, and the nucleic acid mixture 4 was used on the reverse side. The nucleotide sequence is shown as SEQ ID NO: 10 in the sequence listing.
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Abstract
Description
明細書 Specification
真菌検出用核酸及びそれを用いた真菌の検出方法 Nucleic acid for detecting fungi and method for detecting fungi using the same
技術分野 Technical field
本発明は、 真菌検出用核酸混合物及びそれを用いた真菌の検出方法に関する。 The present invention relates to a nucleic acid mixture for detecting a fungus and a method for detecting a fungus using the mixture.
背景技術 Background art
深在性真菌症の主要な病原菌としては、 カンジダ (Candida, 以下 G.と略す。 ) 属真菌、 ァスペルギルス (Aspergillus 以下 A.と略す。 ) 属真菌、 クリブト コッカス (Cryptococcus、 以下 Gr.と略す。 ) 属真菌などが知られている。 カン ジダ属の主要な病原菌としては、 カンジダ -アルビカンス (G. albicans) 、 力 ンジダ 'グラブラータ (G. glabrata) 、 カンジダ ' トロピカリス (G. tropical is) 、 カンジダ'パラプシローシス (G. parapsi losis) カンジダ' ドウブリニ ェンシス (G. dubl iniensis) などが、 クリプトコッカス属の主要な病原菌とし ては、 クリプトコッカス■ネオフオルマンス (Gr. neoformans) が知られている。 ァスペルギルス属の主要な病原菌としては、 ァスペルギルス■フミガタス (A. fumigatus) 、 ァスペルギルス■フラバス (A. f lavus) 、 ァスペルギルス■二 ガー (A. niger) および二ガーグループ、 ァスペルギルス■二ドランス (A. n idurans) 、 ァスペルギルス 'テレウス (A. terreus) などがあり、 これらの菌 種を迅速に検出■分類■同定することが望まれている。 The main pathogens of deep mycosis are Candida (hereinafter abbreviated as G.) genus fungi, Aspergillus (hereinafter abbreviated as A.) genus fungi, and Cryptococcus (abbreviated as Gr. Below). ) Genus fungi are known. Major pathogens of the genus Candida include Candida albicans (G. albicans), Candida albicans 'G. glabrata', Candida albicans 'G. tropical is', and Candida albicans (G. parapsi losis) Candida albicans 'G. dubl iniensis and other major pathogens of the genus Cryptococcus include Cryptococcus neoformans (Gr. Neoformans). The main pathogens of the genus Aspergillus include A. fumigatus, A. flavus, A. niger, and the two gar groups, Aspergillus drans (A. n). idurans) and Aspergillus' terreus (A. terreus), and it is desired to rapidly detect, classify, and identify these strains.
近年、 深在性真菌症は免疫不全患者に日和見感染症として増加しているが、 そ の患者は重篤な基礎疾患を持つことが多く、 早期に起炎菌を明らかにして的確な 治療をすることが必要である。 深在性真菌症の診断は血液培養法が基本であるが 検出感度などに問題がある。 これまでに抗体による診断薬が市販されているが、 抗体による診断は免疫不全状態の患者には役立たない。 このような現状で、 近年、 抗原やその他の菌体成分を直接検出する方法が開発されてきている。 たとえば、 マンナン、 D—ァラビ二トル、 グルカンなどを検出して感染を診断する方法が開 発されている。 一方、 分子生物学の発展につれて、 結核菌やクラミジァなど各種 病原菌の D N Aを抽出し、 いわゆる P C R法などによって核酸を検出することに よって診断する方法が開発されている。 深在性真菌症の分野 もリボゾーム RN Aを検出して診断する方法 (臨床病理、 4 3卷補冊、 1 1 9頁、 1 9 9 5年) な どが提示されている。 本発明者らは、 先にこれら各種真菌症の原因となる真菌の ミ トコンドリアに存在するチ卜クローム bの遺伝子に着目し、 ァスペルギルス属 真菌を検出するために用いられる核酸を提供し、 さらにそれを用いることによる 簡便、 迅速、 特異的かつ高感度な深在性真菌症の原因菌、 さらにはァスペルギル ス属真菌の検出方法を開発した (真菌類の検出用材料及び検出法、 W098/10073) 。 In recent years, deep mycosis has increased as an opportunistic infection in immunodeficient patients, but those patients often have serious underlying illness, and the pathogenic bacteria are identified early and appropriate treatment is performed. It is necessary to. Diagnosis of deep mycosis is based on the blood culture method, but there are problems with detection sensitivity. Antibody-based diagnostics have been marketed so far, but antibody-based diagnosis is not useful for immunodeficient patients. Under these circumstances, in recent years, methods for directly detecting antigens and other bacterial cell components have been developed. For example, methods have been developed to detect mannan, D-arabinitol, glucan, etc. to diagnose infection. On the other hand, with the development of molecular biology, methods of extracting DNA of various pathogens such as Mycobacterium tuberculosis and Chlamydia and diagnosing them by detecting nucleic acids by a so-called PCR method have been developed. Ribosome RN also in the field of deep mycosis Methods for detecting and diagnosing A (Clinical Pathology, Vol. 43, Supplement, pp. 119, 1995) have been proposed. The present inventors have previously focused on the gene of cytochrome b present in the mitochondria of fungi causing these various mycosis, and provided a nucleic acid used for detecting a fungus of the genus Aspergillus. A simple, rapid, specific, and sensitive method for the detection of fungi causing deep mycosis, and a method for the detection of fungi of the genus Aspergillus by using E. coli (Materials and methods for detecting fungi, W098 / 10073) .
発明の開示 Disclosure of the invention
本発明の目的は、 深在性真菌症の原因菌、 特にカンジダ属真菌及びクリプトコ ッカス属真菌を検出するために用いられる核酸を提供し、 さらにそれを用いるこ とによる簡便、 迅速、 特異的かつ高感度な深在性真菌症の原因菌、 特にカンジダ 属真菌及びクリプトコッカス属真菌の検出方法を提供することである。 An object of the present invention is to provide a nucleic acid used for detecting fungi causing deep mycosis, particularly fungi of the genus Candida and Cryptococcus, and to use the nucleic acid in a simple, rapid, specific and specific manner. It is an object of the present invention to provide a highly sensitive method for detecting fungi of deep mycosis, particularly fungi of the genus Candida and cryptococci.
本発明者らは、 各種深在性真菌症の原因菌、 なかでもカンジダ属真菌及びクリ プトコッカス属真菌の遺伝子に関する種々の検討を重ねた結果、 これら各種深在 性真菌症の原因となる真菌のミ トコンドリァに存在するチトクローム bの遺伝子 の一部を増幅し、 その配列を解読することに成功した。 本発明者らは、 その配列 をもとにさらに研究を重ねた結果、 カンジダ属真菌の各種ごとに特異的な配列を 見出し、 それらを基にそれぞれの種のチトクローム bの遺伝子の一部を増幅する ことが可能になる普遍的なプライマー混合物を設計した。 これらプライマー混合 物を用いて核酸増幅反応を行うことにより、 検体中に存在する深在性真菌症の原 因菌の菌種が同定されていなくともプライマー伸長物を得る事が可能となった。 すなわち、 本発明は、 それぞれが複数の塩基配列を示す配列番号 1、 2、 3又 は 4で示される、 それぞれ複数の塩基配列 (ただし、 任意の位置のチミンはゥラ シルと置換されていてもよい) 又はその相補的な塩基配列の少なくとも 2種以上 のそれぞれの、 3'末端から連続する少なくとも 1 5塩基から成る塩基配列又は該 各塩基配列とス卜リンジェントな条件下でハイプリダイズする塩基配列を有する、 少なくとも 2種以上の核酸の混合物から成る真菌検出用核酸混合物を提供する。 また、 本発明は、 配列表の配列番号 1又は 2で示されるそれぞれ複数の塩基配列 (ただし、 任意の位置のチミンはゥラシルと置換されていてもよい) の少なくと も 2種以上のうち、 3'末端から連続する少なくとも 1 5塩基から成る塩基配列又 は該塩基配列とストリンジ: i:ントな条件下でハイプリダイズする塩基配列を有す る核酸の混合物をフォヮ一ド側プライマーとして用い、 配列表の配列番号 3又は 4で示されるそれぞれ複数の塩基配列 (ただし、 任意の位置のチミンはゥラシル と置換されていてもよい) の少なくとも 2種以上のうち、 3'末端から連続する少 なくとも 1 5塩基から成る塩基配列又は該塩基配列とストリンジェントな条件下 でハイブリダィズする塩基配列を有する核酸の混合物をリバース側プライマーと して用いて核酸増幅法によリ被検核酸を増幅し、 増幅産物を検出することを含む 真菌の検出方法を提供する。 さらに、 本発明は、 該増幅産物の塩基配列を決定す ることを含む、 真菌の同定方法を提供する。 さらに本発明は、 上記本発明の核酸 を含む真菌検出用キットを提供する。 さらに、 本発明は、 上記本発明の核酸混合 物を標識して成る真菌検出用プローブを提供する。 さらに、 本発明は、 上記本発 明の核酸混合物を担体に結合して成る真菌検出用捕捉プローブを提供する。 さら に、 本発明は、 上記本発明の核酸混合物の、 真菌検出用プローブ又はプライマー を製造するための使用を提供する。 The present inventors have conducted various studies on the genes of various fungal fungi, especially Candida fungi and Cryptococcus fungi, and as a result, the fungi causing these various fungal diseases have been identified. A part of the cytochrome b gene present in mitochondria was amplified and its sequence was successfully decoded. As a result of further studies based on the sequences, the present inventors found specific sequences for each type of Candida fungus, and amplified a part of the cytochrome b gene of each species based on them. A universal primer mixture has been designed to be able to do so. By performing a nucleic acid amplification reaction using these primer mixtures, a primer extension product can be obtained even if the species of the causative microorganism of deep mycosis present in the sample has not been identified. That is, the present invention relates to the present invention, wherein each of a plurality of base sequences represented by SEQ ID NOS: 1, 2, 3 or 4, each showing a plurality of base sequences (provided that thymine at any position is substituted with peracil. Or at least two or more of its complementary base sequences, each consisting of at least 15 bases continuous from the 3 ′ end, or hybridizing with each base sequence under stringent conditions. Provided is a nucleic acid mixture for detecting a fungus, comprising a mixture of at least two or more nucleic acids having a base sequence. Further, the present invention relates to at least a plurality of base sequences represented by SEQ ID NOS: 1 and 2 in the sequence listing (though thymine at any position may be substituted with peracyl). Out of two or more kinds, a base sequence consisting of at least 15 bases continuous from the 3 ′ end or a mixture of the base sequence and a nucleic acid having a base sequence that hybridizes under stringent conditions. It is used as a primer on one side and has at least two or more of a plurality of base sequences represented by SEQ ID NO: 3 or 4 in the sequence listing (though thymine at any position may be substituted with peracyl). 'A nucleic acid amplification method using a nucleotide sequence comprising at least 15 nucleotides continuous from the terminal or a mixture of nucleic acids having a nucleotide sequence that hybridizes with the nucleotide sequence under stringent conditions as a reverse primer. Provided is a method for detecting a fungus, comprising amplifying a test nucleic acid and detecting an amplification product. Further, the present invention provides a method for identifying a fungus, comprising determining the base sequence of the amplification product. The present invention further provides a kit for detecting a fungus containing the nucleic acid of the present invention. Further, the present invention provides a fungal detection probe obtained by labeling the nucleic acid mixture of the present invention. Further, the present invention provides a capture probe for detecting a fungus, wherein the nucleic acid mixture of the present invention is bound to a carrier. Furthermore, the present invention provides the use of the nucleic acid mixture of the present invention for producing a probe or primer for detecting a fungus.
本発明により、 種々の真菌の検出に用いることができる真菌検出用核酸及びそ れを用いた真菌の検出方法が提供された。 本発明により従来、 分類 <同定に時間 のかかつていたカンジダ属真菌及びクリプトコッカス属真菌を迅速、 簡便に特異 的且つ高感度で検出することが可能となつた。 本発明の核酸混合物は増幅反応の プライマーとしても、 直接検出用のプローブとしても用いることが可能である。 本発明の核酸混合物を増幅反応のプライマーとして用いる事によって、 塩基配列 が異なった複数の種類の真菌を一回の増幅反応によって検出する事が可能になつ た。 また、 プライマ一により増幅した産物をプローブで検出することにより、 感 度、 特異性をさらに高くすることも可能であり、 その臨床的意義は大きい。 According to the present invention, a fungal nucleic acid for use in detecting various fungi and a method for detecting a fungus using the nucleic acid are provided. According to the present invention, it has become possible to detect Candida fungi and Cryptococcus fungi quickly, easily and specifically and with high sensitivity, which have conventionally required classification <time for identification. The nucleic acid mixture of the present invention can be used as a primer for an amplification reaction or as a probe for direct detection. By using the nucleic acid mixture of the present invention as a primer for an amplification reaction, it has become possible to detect a plurality of fungi having different nucleotide sequences by a single amplification reaction. In addition, the sensitivity and specificity can be further increased by detecting the product amplified by the primer with a probe, and its clinical significance is great.
発明を実施するための最良の形態 BEST MODE FOR CARRYING OUT THE INVENTION
上記の通り、 本発明の真菌検出用核酸混合物は、 配列表の配列番号 1、 2、 3 又は 4で示されるそれぞれ複数の塩基配列 (ただし、 任意の位置のチミンはゥラ シルと置換されていてもよい) 若しくはその相補的な塩基配列の少なくとも 2種 以上のうち、 少なくともその 3'末端から連続する少なくとも 1 5塩基から成る塩 基配列又は該塩基配列とス卜リンジェン卜な条件下でハイプリダイズする塩基配 列を有するものである。 チミンはゥラシルと置換されていてもよいことから明ら かなように、 本発明の核酸は D N Aであっても R N Aであってもよい。 本発明の 核酸混合物としては、 配列番号 1、 2、 3又は 4で示されるそれぞれ複数の塩基 配列 (ただし、 任意の位置のチミンはゥラシルと置換されていてもよい) のうち、 少なくともその 3'末端から連続する少なくとも 1 5塩基から成る塩基配列が好ま しく、 とりわけ、 配列番号 1、 2、 3若しくは 4で示される、 それぞれ複数塩基 配列を有する核酸混合物が好ましい。 もっとも、 本発明の真菌検出用核酸混合物 は、 配列表の配列番号 1、 2、 3若しくは 4で示される塩基配列 (ただし、 任意 の位置のチミンはゥラシルと置換されていてもよい) 又はその相補的な塩基配列 のうち、 少なくともその 3'末端から連続する少なくとも 1 5塩基から成る塩基配 列とストリンジェントな条件下でハイブリダイズするものであれば、 上記した塩 基配列に、 塩基の置換、 欠失、 挿入又は付加を含んでいてもよい。 ここで、 Γス トリンジ工ン卜な条件下」 とは、 下記実施例に記載するような通常の P C Rにお けるアニーリング条件下で、 錶型となる標的核酸にハイブリダィズし、 プライマ 一として機能することを意味する (なお、 P C Rにおいて通常用いられている緩 衝液は、 PCR buffer ( P C R反応混合物中の終濃度で 50 mM KG I , 10 mM Tr i s-HC I (pH8. 4-9. 0 at 25°C) , 1 . 5 mM MgG I 2)であり、 通常、 キッ卜にはこの 1 0倍濃 度の X10 PGR buffer (又は 10X PGR buffer)が添付されており、 これを希釈して用 いる) 。 また、 配列番号 1、 2、 3若しくは 4で示される塩基配列 (ただし、 任 意の位置のチミンはゥラシルと置換されていてもよい) 又はその相補的な塩基配 列のうち、 少なくともその 3'末端から連続する少なくとも 1 5塩基から成る塩基 配列と 1塩基又は 2塩基のみが置換した配列 (ただし、 3 ' 末端が置換したもの を除く) を有する核酸混合物は、 通常、 本発明の目的のために使用できる。 As described above, the nucleic acid mixture for detecting a fungus of the present invention comprises a plurality of base sequences each represented by SEQ ID NO: 1, 2, 3 or 4 (provided that thymine at any position is substituted with peracil. Or at least two of its complementary base sequences Among them, those having a base sequence consisting of at least 15 bases continuous from at least the 3 'end or a base sequence that hybridizes with the base sequence under stringent conditions. As is evident from the fact that thymine may be substituted for peracil, the nucleic acids of the present invention may be DNA or RNA. As the nucleic acid mixture of the present invention, at least 3 ′ of a plurality of base sequences represented by SEQ ID NOs: 1, 2, 3 or 4 (provided that thymine at any position may be substituted with peracyl) A nucleotide sequence consisting of at least 15 bases continuous from the terminal is preferable, and a nucleic acid mixture represented by SEQ ID NO: 1, 2, 3, or 4 and having a plurality of nucleotide sequences is particularly preferable. However, the nucleic acid mixture for detecting a fungus of the present invention comprises a nucleotide sequence represented by SEQ ID NO: 1, 2, 3 or 4 in the sequence listing (however, thymine at any position may be substituted with peracyl) or its complement. A basic sequence consisting of at least 15 bases continuous from at least its 3 'end under stringent conditions, the base sequence described above may be substituted with at least 3 bases. It may include deletions, insertions or additions. Here, “under stringent conditions” means that under the annealing conditions in ordinary PCR as described in the Examples below, the target nucleic acid hybridizes to type II and functions as a primer. (Note that the buffer commonly used for PCR is PCR buffer (final concentration of 50 mM KG I, 10 mM Tris-HCl (pH 8.4-9. at 25 ° C), 1.5 mM MgG I 2 ) .Kit usually comes with a 10-fold concentration of X10 PGR buffer (or 10X PGR buffer), which is diluted. Use). In addition, the nucleotide sequence represented by SEQ ID NO: 1, 2, 3 or 4 (however, thymine at any position may be substituted with peracyl) or at least the 3 ' A nucleic acid mixture having a base sequence consisting of at least 15 bases consecutive from the end and a sequence in which only one or two bases are substituted (excluding those in which the 3 'end is substituted) is usually used for the purpose of the present invention. Can be used for
本発明の核酸は、 市販の D N A合成機等を用い、 化学合成により容易に製造す ることができる。 The nucleic acid of the present invention can be easily produced by chemical synthesis using a commercially available DNA synthesizer or the like.
配列番号 1〜 4には、 それぞれ、 m、 r、 wのような、 一文字で複数の塩基を示 す記号が含まれているから 1つの配列番号で複数の配列を示すものである。 本発 明の核酸は、 これらの複数の塩基配列 (上記したその部分及び変異体を包含する ) の少なくとも 2種以上、 好ましくは全種類の塩基配列をそれぞれ有する核酸の 混合物である。 このような混合物を用いることにより、 真菌の種々の変異株をも 検出可能となる。 SEQ ID NOs: 1 to 4 indicate multiple bases with one letter, such as m, r, and w, respectively. Therefore, one sequence number indicates multiple sequences. The nucleic acid of the present invention is a mixture of nucleic acids having at least two or more, and preferably all of these plural nucleotide sequences (including the above-mentioned portions and variants). By using such a mixture, various mutant strains of fungi can be detected.
本発明の核酸混合物は、 真菌、 特にカンジダ属、 クリプトコッカス属、 ァスぺ ルギルス属又はぺニシリウム属に属する真菌、 好ましくは、 カンジダ属又はクリ プトコッカス属に属する真菌のミトコンドリアチトクローム b遺伝子内の領域と ハイブリダィズするものである。 本発明の核酸混合物を用いて検出できる好まし い真菌の種として、 カンジダ 'グラブラ一タ、 カンジダ■パラプシローシス、 力 ンジダ■ トロピカリス、 カンジダ 'アルビカンス、 クリプトコッカス 'ネオフォ ルマンス及び力ンジダ■ ドウブリニェンシスを挙げることができるがこれらに限 定されるものではない。 ただし、 配列番号 3 (上記したその部分及び変異体を包 含する) は、 カンジダ■アルビカンス、 クリプトコッカス■ネオフォルマンス及 びカンジダ ' ドウブリニェンシスの検出に用いることはできない。 The nucleic acid mixture of the present invention may comprise a region within the mitochondrial cytochrome b gene of a fungus, particularly a fungus belonging to the genus Candida, Cryptococcus, Aspergillus or Penicillium, preferably a fungus belonging to the genus Candida or Cryptococcus. It is what hybridizes. Preferred fungal species that can be detected using the nucleic acid mixture of the present invention include Candida 'grabrata, Candida parapsilosis, Candida tropicalis, Candida' albicans, Cryptococcus' neoformans and Candida doubryensis But are not limited to these. However, SEQ ID NO: 3 (including the above-mentioned portions and variants) cannot be used for the detection of Candida albicans, Cryptococcus neoformans and Candida doubriniensis.
ミトコンドリアチトクローム b遺伝子は、 ミ トコンドリアにあり、 細胞質遺伝 のため DNAの組み換えがおこりにくく、 進化に比例して塩基の変化が起こってい ると考えられる。 従って、 種々の真菌を検出するのに適している。 また、 後でよ リ詳しく述べるように、 本発明の核酸の組合せを核酸増幅法のプライマーとして 用いた場合に増幅される領域は、 比較的変化の多い部分で、 種の区別をつけやす く、 種内の DNA type による区別もっけやすいという利点がある。 従って、 本発 明の核酸をプライマーとして用いて被検核酸を増幅し、 増幅産物の塩基配列を決 定することによつて真菌の種又は菌株の同定が可能となる。 The mitochondrial cytochrome b gene is located in mitochondria, is difficult to recombine due to cytoplasmic inheritance, and is thought to undergo base changes in proportion to evolution. Therefore, it is suitable for detecting various fungi. Further, as will be described in more detail later, the region amplified when the nucleic acid combination of the present invention is used as a primer in a nucleic acid amplification method is a relatively variable portion, and it is easy to distinguish species, It has the advantage that it is easy to distinguish between DNA types within a species. Therefore, the species or strain of fungi can be identified by amplifying the test nucleic acid using the nucleic acid of the present invention as a primer and determining the base sequence of the amplification product.
上記の通り、 本発明の核酸混合物は、 真菌のミトコンドリアのチトクローム b 遺伝子内の領域とハイブリダィズするので、 本発明の核酸混合物をプローブ又は 核酸増幅法用プライマーとして用いることにより、 真菌を検出することができる。 本発明の核酸混合物をプローブとして用いる場合、 標識剤で標識した核酸混合 物を用いることが好ましい。 この場合、 標識された本発明の核酸混合物をプロ一 ブとし、 被験試料中の真菌遺伝子と該標識プローブをハイブリダィズさせた後に、 真菌遺伝子と標識プローブとの結合物もしくは非結合の標識プローブを、 標識剤 に適した適当な検出法で検出する。 プローブに用いる標識剤はこの分野において 周知であり、 蛍光標識、 放射標識、 酵素標識、 ビォチン等を挙げることができる。 検体、 すなわち被験試料中の真菌遺伝子とプローブとのハイブリダィゼーシヨン は、 検体を通常の方法で前処理、 精製したものを被験試料とし、 それとプローブ としての標識核酸混合物とを混合し、 室温から 70°Cで 10分から 48時間処理す ることにより実施できる。 また、 検体はあらかじめ本発明の核酸混合物をプライ マーとして増幅反応を行っておいてもよい。 As described above, the nucleic acid mixture of the present invention hybridizes with a region in the cytochrome b gene of the fungal mitochondria, so that the fungus can be detected by using the nucleic acid mixture of the present invention as a probe or a primer for a nucleic acid amplification method. it can. When the nucleic acid mixture of the present invention is used as a probe, it is preferable to use a nucleic acid mixture labeled with a labeling agent. In this case, the labeled nucleic acid mixture of the invention is After the fungal gene in the test sample and the labeled probe are hybridized, the bound product of the fungal gene and the labeled probe or the unbound labeled probe is detected by an appropriate detection method suitable for the labeling agent. Labeling agents used for probes are well known in this field, and include fluorescent labels, radioactive labels, enzyme labels, biotin and the like. The hybridization of the sample, i.e., the fungal gene in the test sample, to the probe is performed by pretreating and purifying the sample by a usual method to obtain a test sample, and mixing it with a labeled nucleic acid mixture as a probe, and then room temperature. It can be carried out by treating at 10 to 70 ° C for 10 minutes to 48 hours. The sample may be subjected to an amplification reaction in advance using the nucleic acid mixture of the present invention as a primer.
本発明の核酸混合物を核酸増幅法用のプライマーとして用いる場合、 本発明の 核酸混合物をプライマーとして、 D N Aポリメラーゼ等による伸長反応を行い遺 伝子増幅することによりカンジダ属真菌及びクリプトコッカス属真菌のチトク口 ーム b遺伝子断片のみを特異的に増幅させ、 この増幅産物を測定することによつ て真菌を検出することができる。 またこの場合、 プライマーとして本発明の核酸 混合物を前述したごとく標識剤で標識化して得られる標識核酸を用いてもよい。 ここで用いられる遺伝子増幅法としては、 具体的には P C R法が例示されるが、 特にこの方法に限定されるものではなく、 短鎖のオリゴ核酸をプライマーとして 遺伝子合成の開始のために用いるいずれの遺伝子増幅法をも用いることができる。 本発明の真菌の検出法は、 上記方法により増幅された増幅産物すなわちチトク口 —厶 b遺伝子断片を検出することにより行うことができる。 あるいは増幅された チトクローム b遺伝子断片を制限酵素によって断片化し、 その断片の生成バタ一 ンを比較することによつても行うことができる。 ここで用いる制限酵素は単独、 あるいは組み合わせて使用される。 増幅産物増幅されたチトクローム b遺伝子断 片、 または制限酵素でさらに断片化された遺伝子断片の検出手段は特に限定され ることはなく、 通常の遺伝子の検出方法 (例えば電気泳動法など) が使用できる。 増幅産物は、 例えば電気泳動により分画され、 特異的かつ検出に十分な程度に鮮 明なバンドとして容易に検出できる。 プライマーがまた増幅反応時に、 適当な標 識剤で標識化されたデォキシリポ核酸混合物 (dATP、 dTTP、 dGTP、 dCTP) もしく はリポ核酸混合物 (ATP、 UTP、 GTP、 CTP) を D N Aもしくは R N A合成の原料と して使用することにより、 増幅産物を高感度に直接検出することが可能である。 もしくは、 プライマーとして本発明の核酸を標識化して得られる標識核酸混合物 を用いることにより、 増幅産物を同様に高感度に直接検出することができる。 か かる場合、 標識化に用いられる標識剤として、 好ましくは放射性物質、 蛍光物質 などである。 また、 いわゆるリアルタイム検出 P C Rのプライマーとしても用い ることができ、 この場合には被検核酸の定量も可能になる。 従って、 本明細書に おける 「検出」 には、 定量的な検出も包含される。 When the nucleic acid mixture of the present invention is used as a primer for a nucleic acid amplification method, the nucleic acid mixture of the present invention is used as a primer to carry out an elongation reaction with a DNA polymerase or the like to amplify the gene, thereby obtaining a cytochrome of a Candida fungus and a Cryptococcus fungus. A fungus can be detected by specifically amplifying only the b gene fragment and measuring the amplified product. In this case, a labeled nucleic acid obtained by labeling the nucleic acid mixture of the present invention with a labeling agent as described above may be used as a primer. Specific examples of the gene amplification method used herein include a PCR method, but are not particularly limited to this method.Any method using a short-chain oligonucleic acid as a primer to initiate gene synthesis is used. Can also be used. The method for detecting a fungus of the present invention can be performed by detecting an amplification product amplified by the above method, ie, a cytochrome b gene fragment. Alternatively, it can also be carried out by fragmenting the amplified cytochrome b gene fragment with a restriction enzyme and comparing the generated patterns of the fragment. The restriction enzymes used here are used alone or in combination. Means for detecting a cytochrome b gene fragment amplified with an amplification product or a gene fragment further fragmented with a restriction enzyme is not particularly limited, and a normal gene detection method (for example, an electrophoresis method) can be used. . The amplification product is fractionated by, for example, electrophoresis and can be easily detected as a specific and sufficiently clear band for detection. The primers are also used in the amplification reaction during the amplification reaction. By using a liponucleic acid mixture (ATP, UTP, GTP, CTP) as a raw material for DNA or RNA synthesis, amplification products can be directly detected with high sensitivity. Alternatively, by using a labeled nucleic acid mixture obtained by labeling the nucleic acid of the present invention as a primer, the amplified product can be directly detected with high sensitivity. In such a case, the labeling agent used for labeling is preferably a radioactive substance, a fluorescent substance, or the like. It can also be used as a primer for so-called real-time detection PCR, in which case the nucleic acid to be tested can be quantified. Therefore, “detection” as used herein includes quantitative detection.
プライマーとして用いる場合、 配列番号 1及び配列番号 2に示される塩基配列 を有する核酸混合物 (上記したその一部分及び変異体を包含する、 以下同様) は、 フォヮ一ド側ブライマ一として用いることが好ましく、 配列番号 3及び配列番号 4に示される塩基配列を有する核酸混合物はリバース側プライマ一として用いる ことが好ましい。 これらのフォワード側プライマーとリノ 一ス側プライマーとを 組み合わせて用いることが好ましく、 それにより、 下記実施例に具体的に記載さ れるように 396 bpの領域が増幅される。 得られた増幅産物を各種電気泳動法など によって分離■検出することによって、 真菌が検体中に存在するかを判定できる。 また、 得られた増幅産物の塩基配列を決定することにより種の同定が可能になる。 本発明の真菌検出用の試薬キットは、 本発明の核酸混合物又はこの核酸混合物 を適当な標識剤で標識した標識核酸を含むことを特徴とするものである。 本発明 の試薬キットは上記核酸を含んでいればよく、 他の成分として標識検出用試薬や 緩衝液などを含んでいてもよい。 本発明の試薬キット中の核酸は、 プライマーと して用いることもできるし、 またプローブとして用いることもできる。 核酸をプ ライマーとして用いるかプローブとして用いるかは、 その手段が異なるのみであ つて、 真菌の検出に関しては本質的には同じである。 当該試薬キットは、 核酸を プローブとして使用する場合は、 上述のプローブを用いた方法による真菌検出の ための試薬キットとして、 またプライマーとして使用する場合は、 上述の核酸増 幅法による真菌検出のための試薬キッ卜として用いることができる。 When used as a primer, a nucleic acid mixture having the nucleotide sequence shown in SEQ ID NO: 1 and SEQ ID NO: 2 (including the above-mentioned part and mutant thereof, the same applies hereinafter) is preferably used as a fore-side primer, The nucleic acid mixture having the nucleotide sequence shown in SEQ ID NO: 3 or SEQ ID NO: 4 is preferably used as a reverse primer. It is preferable to use a combination of these forward primer and linear primer, whereby a 396 bp region is amplified as specifically described in the Examples below. By separating and detecting the obtained amplification product by various electrophoresis methods or the like, it is possible to determine whether a fungus is present in the sample. Also, species can be identified by determining the base sequence of the obtained amplification product. The reagent kit for detecting a fungus of the present invention comprises the nucleic acid mixture of the present invention or a labeled nucleic acid obtained by labeling the nucleic acid mixture with an appropriate labeling agent. The reagent kit of the present invention may contain the above-described nucleic acid, and may contain a labeling detection reagent, a buffer, and the like as other components. The nucleic acid in the reagent kit of the present invention can be used as a primer or a probe. Whether a nucleic acid is used as a primer or a probe is different in only its means, and is essentially the same for detecting fungi. When the nucleic acid is used as a probe, the reagent kit is used as a reagent kit for detecting a fungus by the method using the above-described probe. Can be used as a reagent kit.
試薬キッ卜中の核酸混合物をプローブとして用いる場合の本発明の試薬キッ卜 は、 本発明のカンジダ属真菌及びクリプトコッカス属真菌検出用核酸混合物もし くは標識化されたカンジダ属真菌及びクリプトコッカス属真菌検出用核酸混合物 以外に、 標識検出用試薬、 緩衝液などを含んていてもよい。 試薬キット中の核酸 混合物をプライマーとして用いる場合の本発明の試薬キッ卜は、 本発明のカンジ ダ属真菌及ぴクリプトコッカス属真菌検出用核酸混合物もしくは標識化された力 ンジダ属真菌及びクリプトコッカス属真菌検出用核酸混合物以外に、 核酸合成酵 素 (例えば、 D N Aポリメラ一ゼ, R N Aポリメラーゼ, 逆転写酵素など) 、 デ ォキシリボヌクレオチド混合物 (dATP、 dTTP、 dGTP、 dGTP) 、 リボヌクレオチド 混合物 (ATP、 UTP、 GTP、 CTP) 、 制限酵素、 緩衝液などを含んでいてもよい。 こ れらのキットの具体例としては、 例えば、 下記実施例に記載されている市販の P C R用キッ卜に本発明の核酸混合物を追加したものを挙げることができる。 また、 本発明の核酸混合物は固相担体に結合して、 捕捉プローブとして用いる こともできる。 この場合、 捕捉プローブと標識プローブの 2つを組合せてサンド イッチアツセィを行ってもよい。 また標的核酸を標識して捕捉する方法もある。 さらに核酸混合物をビォチンで標識し、 ハイブリダィゼーシヨン後、 アビジン結 合担体で捕捉する方法もある。 サンドイッチアツセィにおいてはどちらか一方に 本発明の核酸混合物を用いれば、 本発明の核酸混合物にて特異的な測定が可能と なり、 他方の核酸混合物の特異性は若干低くてもなんら問題はない。 なお、 核酸 の固相担体への結合は、 D N Aチップの分野等で広く用いられている周知技術に より容易に行うことができる。 The reagent kit of the present invention when the nucleic acid mixture in the reagent kit is used as a probe May contain, in addition to the nucleic acid mixture for detecting Candida fungi and Cryptococcus fungi or the labeled nucleic acid mixture for detecting Candida fungi and Cryptococcus fungus of the present invention, a labeling detection reagent, a buffer, and the like. Good. When the nucleic acid mixture in the reagent kit is used as a primer, the reagent kit of the present invention is a nucleic acid mixture for detecting a Candida fungus and a Cryptococcus fungus of the present invention or a labeled Candida fungus and a Cryptococcus fungus detection. In addition to nucleic acid mixtures for use, nucleic acid synthases (eg, DNA polymerase, RNA polymerase, reverse transcriptase, etc.), mixtures of deoxyribonucleotides (dATP, dTTP, dGTP, dGTP), and mixtures of ribonucleotides (ATP, UTP) , GTP, CTP), restriction enzymes, buffers and the like. Specific examples of these kits include, for example, those obtained by adding the nucleic acid mixture of the present invention to commercially available PCR kits described in the following Examples. Further, the nucleic acid mixture of the present invention can be used as a capture probe by binding to a solid phase carrier. In this case, the sandwich assay may be performed by combining two of the capture probe and the labeled probe. There is also a method of labeling and capturing a target nucleic acid. Furthermore, there is a method in which the nucleic acid mixture is labeled with biotin, hybridized, and then captured with an avidin-bound carrier. In the sandwich assay, if the nucleic acid mixture of the present invention is used for either one, specific measurement of the nucleic acid mixture of the present invention becomes possible, and there is no problem even if the specificity of the other nucleic acid mixture is slightly lower. . The binding of the nucleic acid to the solid phase carrier can be easily performed by a well-known technique widely used in the field of DNA chips and the like.
実施例 Example
以下、 本発明を実施例に基づきより具体的に説明する。 もっとも、 本発明は下 記実施例に限定されるものではない。 Hereinafter, the present invention will be described more specifically based on examples. However, the present invention is not limited to the following examples.
実施例 1 (各種核酸混合物の合成) Example 1 (Synthesis of various nucleic acid mixtures)
配列表の配列番号 1〜4で表される配列を有する核酸混合物を化学合成によリ 合成した。 以下、 配列表の配列番号 1〜 4に示される各種核酸混合物を、 それぞ れ核酸混合物 1〜 4と呼ぶ。 A nucleic acid mixture having the sequences represented by SEQ ID NOs: 1 to 4 in the sequence listing was synthesized by chemical synthesis. Hereinafter, the various nucleic acid mixtures represented by SEQ ID NOs: 1 to 4 in the sequence listing are referred to as nucleic acid mixtures 1 to 4, respectively.
実施例 2 (カンジダ■アルビカンスのチトクローム b遺伝子増幅反応) ポ亍トデキストロース液体培地で培養して得たカンジダ■アルビカンス (Gand ida albicans IF 40009) の菌体を、 75 %エタノール処理し殺菌した。 1500g、 10分間の遠心分離で菌体を得、 これに約 40mlの抽出用緩衝液 (0.9M ソルビ卜 ール、 10mM EDTA、 10mM トリス塩酸緩衝液 pH7.1 ) を加え、 良く振り混 ぜた後、 1500g、 10分間の遠心分離で上澄みを捨て、 30mlの同緩衝液を加え、 同様に遠心分離後上澄みを捨て、 9mlの同緩衝液を加えた。 これに同緩衝液に溶 解した Zymolyase (生化学工業社製細胞壁溶解酵素、 10mg/ml) を 1ml加え、 37 °Cで 1時間保温した後、 超音波洗浄機にて 1分間処理した。 これを 1500g、 10 分間の遠心分離で上澄みを得、 さらに 20000gで 15分間、 遠心分離して沈殿を 得た。 この沈殿を抽出用緩衝液で洗浄し、 再度 20000 gで 15分間、 遠心分離し てミ トコンドリア画分を得た。 このミトコンドリア画分に 1mg/mlのプロテア一 ゼ K (Protease ) を 0.5tnl加え、 37°Cで 1時間保温した。 これにフエノール、 クロ口ホルム、 イソアミルアルコール混合液 (25:24:1) を 1ml加え、 振り混ぜ た後、 1500g、 10分間の遠心分離で上層を取り、 これに水飽和フヱノールを 1ml 加え、 振り混ぜた後、 1500g、 10分間の遠心分離で上層を取った。 これに 0.1ml の 3M酢酸ナトリウム、 0.1M塩化マグネシウム溶液を加え、 3mlのエタノールを 加えて、 -20°Cにー晚放置した。 これを 1500g、 10分間遠心分離して沈殿を得、 この沈殿を - 20°Cの 75%エタノールで洗浄し、 1500g、 10分間遠心分離後、 上清 を捨て、 核酸を得、 乾燥後、 - 20°Cに保存した。 Example 2 (Candida albicans cytochrome b gene amplification reaction) The cells of Candida albicans (Gandida albicans IF 40009) obtained by culturing in a port dextrose liquid medium were treated with 75% ethanol and sterilized. The cells were obtained by centrifugation at 1500 g for 10 minutes, and about 40 ml of extraction buffer (0.9 M sorbitol, 10 mM EDTA, 10 mM Tris-HCl buffer, pH 7.1) was added, and the mixture was shaken well. Thereafter, the supernatant was discarded by centrifugation at 1500 g for 10 minutes, 30 ml of the same buffer was added. Similarly, the supernatant was discarded after centrifugation, and 9 ml of the same buffer was added. To this was added 1 ml of Zymolyase (Seikagaku Kogyo Co., Ltd. cell wall lysing enzyme, 10 mg / ml) dissolved in the same buffer, and the mixture was incubated at 37 ° C. for 1 hour and then treated with an ultrasonic washer for 1 minute. This was centrifuged at 1500 g for 10 minutes to obtain a supernatant, and further centrifuged at 20000 g for 15 minutes to obtain a precipitate. The precipitate was washed with an extraction buffer and centrifuged again at 20000 g for 15 minutes to obtain a mitochondrial fraction. To this mitochondrial fraction was added 0.5 tnl of 1 mg / ml protease K (Protease), and the mixture was incubated at 37 ° C for 1 hour. Add 1 ml of a mixture of phenol, black form and isoamyl alcohol (25: 24: 1), shake, and remove the upper layer by centrifugation at 1500 g for 10 minutes. Add 1 ml of water-saturated phenol and shake. After mixing, the upper layer was removed by centrifugation at 1500 g for 10 minutes. To this, 0.1 ml of a 3 M sodium acetate and 0.1 M magnesium chloride solution was added, 3 ml of ethanol was added, and the mixture was allowed to stand at -20 ° C. This was centrifuged at 1500 g for 10 minutes to obtain a precipitate.This precipitate was washed with 75% ethanol at -20 ° C. After centrifugation at 1500 g for 10 minutes, the supernatant was discarded, nucleic acid was obtained, and after drying,- Stored at 20 ° C.
この核酸を鏡型にし、 実施例 1で得られた核酸混合物 2と核酸混合物 4をブラ イマ一として、 宝酒造 (株) の TaKaRa PGR Ampl ification Kit (R011)を用い、 サ ンョ一の D N A増幅装置 (M I R-D30)を使用して以下の方法で P C R反応を行い、 チトクローム b遺伝子の一部を増幅した。 反応液の組成は次の通りであった。 x10 PGR緩衝液 (キッ卜の試薬) 5 I Using this nucleic acid as a mirror, using the nucleic acid mixture 2 and the nucleic acid mixture 4 obtained in Example 1 as a primer and using TaKaRa PGR Amplification Kit (R011) of Takara Shuzo Co., Ltd. Using (MIR-D30), PCR was performed by the following method to amplify a part of the cytochrome b gene. The composition of the reaction solution was as follows. x10 PGR buffer (kit reagent) 5 I
PGR dNTP混合液 (キッ卜の試薬) 4 I PGR dNTP mixed solution (kit reagent) 4 I
Taq DNA合成酵素 (キッ卜の試薬) 1 I (2.5U) Taq DNA synthase (kit reagent) 1 I (2.5U)
核酸混合物 2 1 1 Nucleic acid mixture 2 1 1
核酸混合物 4 1 1 ミ トコンドリア DNA 1 1 Nucleic acid mixture 4 1 1 Mitochondrial DNA 1 1
水にて全量を 50 Iにした。 The total volume was made up to 50 I with water.
反応条件は次の通リであつた。 The reaction conditions were as follows.
熱変性: 94°C、 I分 Thermal denaturation: 94 ° C, I min
ァニーリング: 50°C、 1分 Annealing: 50 ° C, 1 minute
伸長反応: 72°C、 2分 Extension reaction: 72 ° C, 2 minutes
サイクル数: 30回 Number of cycles: 30
増幅された D N Aをァガロースゲル電気泳動法で分離精製し、 以下の方法で塩 基配列を解析した。 パーキンエルマ一社製 DN Aシーケンサー (ABI Prism 377 ) を用い、 同社の操作ガイドに従い、 ダイターミネータ一法により解析した。 塩 基配列解析用プライマーにはフォヮ一ド側に核酸混合物 2を、 リバース側に核酸 混合物 4を用いた。 決定された塩基配列を、 配列表の配列番号 5に示した。 実施例 3 (カンジダ 'グラブラータのチ卜クローム b遺伝子増幅反応) The amplified DNA was separated and purified by agarose gel electrophoresis, and the nucleotide sequence was analyzed by the following method. Using a DNA sequencer (ABI Prism 377) manufactured by PerkinElmer and analyzed according to the Dye Terminator method according to the operation guide of the company. Nucleic acid mixture 2 was used on the forward side and nucleic acid mixture 4 was used on the reverse side as primers for base sequence analysis. The determined nucleotide sequence is shown in SEQ ID NO: 5 in the sequence listing. Example 3 (Candida 'glabrata cytochrome b gene amplification reaction)
実施例 2と同様な方法で、 実施例 1で得られた核酸混合物 1 と核酸混合物 3を 用い、 カンジダ 'グラブラータ(Candida glabrata IFM 46843)からチトクローム b遺伝子の一部を PC R反応で増幅し、 その塩基配列を決定した。 塩基配列解析 用プライマーにはフォワード側に核酸混合物 1を、 リバース側に核酸混合物 3を 用いた。 その塩基配列を、 配列表の配列番号 6に示した。 In the same manner as in Example 2, using the nucleic acid mixture 1 and the nucleic acid mixture 3 obtained in Example 1, a part of the cytochrome b gene was amplified from Candida glabrata (Candida glabrata IFM 46843) by a PCR reaction, The nucleotide sequence was determined. Nucleic acid mixture 1 was used on the forward side and nucleic acid mixture 3 was used on the reverse side as primers for nucleotide sequence analysis. The nucleotide sequence is shown in SEQ ID NO: 6 in the sequence listing.
実施例 4 (カンジダ■パラプシローシスのチ卜クロ一厶 b遺伝子増幅反応) 実施例 2と同様な方法で、 実施例 1で得られた核酸混合物 1 と核酸混合物 3を 用い、 カンジダ'パラプシローシス(Candida parapsi losis IFM 46829)からチト クローム b遺伝子の一部を PCR反応で増幅し、 その塩基配列を決定した。 塩基 配列解析用プライマーにはフォワード側に核酸混合物 1を、 リバース側に核酸混 合物 3を用いた。 その塩基配列を、 配列表の配列番号 7に示した。 Example 4 (Amplification reaction of Candida parapsilosis cytochrome b gene) Using the nucleic acid mixture 1 and the nucleic acid mixture 3 obtained in Example 1 in the same manner as in Example 2, Candida parapsilosis was used. losis IFM 46829), a part of the cytochrome b gene was amplified by PCR, and its nucleotide sequence was determined. Nucleic acid mixture 1 was used on the forward side and nucleic acid mixture 3 was used on the reverse side as primers for nucleotide sequence analysis. The nucleotide sequence is shown as SEQ ID NO: 7 in the sequence listing.
実施例 5 (カンジダ ' トロピカリスのチトクローム b遺伝子増幅反応) Example 5 (Amplification reaction of Candida tropicalis cytochrome b gene)
実施例 2と同様な方法で、 実施例 1で得られた核酸混合物 1 と核酸混合物 3を 用い、 カンジダ ' トロピカリス(Candida tropical is IFM 46816)からチトクロ一 ム b遺伝子の一部を PCR反応で増幅し、 その塩基配列を決定した。 塩基配列解 析用プライマーにはフォワード側に核酸混合物 1を、 リバース側に核酸混合物 3 を用いた。 その塩基配列を、 配列表の配列番号 8に示した。 In the same manner as in Example 2, using the nucleic acid mixture 1 and the nucleic acid mixture 3 obtained in Example 1, a part of the cytochrome b gene from Candida tropical is (FM 46816) was subjected to a PCR reaction. It was amplified and its nucleotide sequence was determined. Base sequence solution Nucleic acid mixture 1 was used on the forward side and nucleic acid mixture 3 was used on the reverse side as the primer for analysis. The nucleotide sequence is shown in SEQ ID NO: 8 in the sequence listing.
実施例 6 (カンジダ ' ドウブリニェンシスのチトクローム b遺伝子増幅反応) 実施例 2と同様な方法で、 実施例 1で得られた核酸混合物 2と核酸混合物 4を 用い、 カンジダ ' ドウブリニェンシス (Candida dubl iniensis IFM 48313) から チトクローム b遺伝子の一部を P C R反応で増幅し、 その塩基配列を決定した。 塩基配列解析用プライマーにはフォヮ一ド側に核酸混合物 2を、 リバース側に核 酸混合物 4を用いた。 その塩基配列を、 配列表の配列番号 9に示した。 Example 6 (Amplification reaction of Candida doubriniensis cytochrome b gene) Using the nucleic acid mixture 2 and nucleic acid mixture 4 obtained in Example 1 in the same manner as in Example 2, Candida doubriniensis (Candida doubriniensis) was used. A part of the cytochrome b gene from Candida dubl iniensis IFM 48313) was amplified by PCR, and its nucleotide sequence was determined. The nucleotide sequence analysis primer used was a nucleic acid mixture 2 on the forward side and a nucleic acid mixture 4 on the reverse side. The nucleotide sequence is shown in SEQ ID NO: 9 in the sequence listing.
実施例 Ί (クリプトコッカス 'ネオフォルマンスのチトクローム b遺伝子増幅反 応) Example II (Cryptococcus neoformans cytochrome b gene amplification reaction)
実施例 2と同様な方法で、 実施例 1で得られた核酸混合物 2と核酸混合物 4を 用い、 クリプトコッカス 'ネオフォルマンス (Gryptococcus neoformans IFM 46 138) からチトクローム b遺伝子の一部を PCR反応で増幅し、 その塩基配列を 決定した。 塩基配列解析用プライマ一にはフォワード側に核酸混合物 2を、 リバ ース側に核酸混合物 4を用いた。 その塩基配列を、 配列表の配列番号 1 0に示し た。 Using the nucleic acid mixture 2 and the nucleic acid mixture 4 obtained in Example 1 in the same manner as in Example 2, a portion of the cytochrome b gene is amplified from Cryptococcus neoformans (Gryptococcus neoformans IFM 46 138) by PCR. Then, its nucleotide sequence was determined. For the primer for nucleotide sequence analysis, the nucleic acid mixture 2 was used on the forward side, and the nucleic acid mixture 4 was used on the reverse side. The nucleotide sequence is shown as SEQ ID NO: 10 in the sequence listing.
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| EP0860503A1 (en) * | 1996-09-09 | 1998-08-26 | SS Pharmaceutical Co., Ltd. | Material and method for detecting fungi |
| WO2000066773A2 (en) * | 1999-04-30 | 2000-11-09 | Syngenta Limited | Method of detection of cytochrome b mutations in funghi leading to resistance against anti-fungal agents |
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| EP0860503A1 (en) * | 1996-09-09 | 1998-08-26 | SS Pharmaceutical Co., Ltd. | Material and method for detecting fungi |
| WO2000066773A2 (en) * | 1999-04-30 | 2000-11-09 | Syngenta Limited | Method of detection of cytochrome b mutations in funghi leading to resistance against anti-fungal agents |
Non-Patent Citations (3)
| Title |
|---|
| WANG L. ET AL.: "Mitochondrial cytochrome beta gene analysis of aspergillus fumigatus and related species", J. CLIN. MICROBIOL., vol. 38, no. 4, April 2000 (2000-04-01), pages 1352 - 1358, XP002908819 * |
| WANG L. ET AL.: "The identification and phylogenetic relationship of pathogenic species of aspergillus based on the mitochondrial cytochrome beta gene", MED. MYCOL., vol. 36, no. 3, 1998, pages 153 - 164, XP002908820 * |
| YOKOYAMA K. ET AL.: "Identification and phylogenetic relationship of the most common pathogenic candida species inferred from mitochondrial cytochrome beta gene sequences", J. CLIN. MICROBIOL., vol. 38, no. 12, December 2000 (2000-12-01), pages 4503 - 4510, XP002908818 * |
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| CN116875721A (en) * | 2022-12-21 | 2023-10-13 | 广州医科大学附属第一医院 | Application of cfDNA of cryptococcus in diagnosis of cryptococcus infection |
| CN116875721B (en) * | 2022-12-21 | 2024-03-19 | 广州医科大学附属第一医院 | Application of cfDNA of cryptococcus in diagnosis of cryptococcus infection |
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