CA2263992C - Sequential hybridization of fungal cell dna and method for the detection of fungal cells in clinical material - Google Patents

Abstract

In order to detect fungal cells in clinical material, fungal DNA is extracted from whole blood, after which the extracted fungal DNA
is analysed. On the basis of this analyse a fungal infection can be indicated.
For further diagnosis the fungal species is subsequently determined from the extracted fungal DNA. The process for the extraction of fungal DNA from whole blood encompasses the isolation of predominantly intact fungal cells from whole blood and the extraction of DNA
from the isolated fungal cells. In order to analyse the fungal DNA at least one segment of said fungal DNA is amplified, whereupon the amplification products are, if required, analysed. 1n order to provide further identification of the fungal species nucleotide sequence segments characteristic of the species of fungus are determined.

Description

?CA 02263992 l999-02- l9SEQUENTIAL HYBRIDIZATION OF FUNGAL CELL DNA AND METHOD FOR THEDETECTION OF FUNGAL CELLS IN CLINICAL MATERIALThe present invention relates to a method for detectingfungal cells in clinical material.Methods for detecting fungal cells in clinical materialare of great interest because, especially in recent years, fun-gal species have acquired considerable importance as signifi-cant nosocomial pathogens, in particular for immunosuppressedpatients. If fungal infections are not recognized in time insuch patients, they propagate in the patient's body and resultin a high mortality rate. Treatment success can be improvedonly by timely diagnosis.?CA 02263992 l999-02- 19The standard methods known for the detection of fungal in-fections, which are based on the culturing of isolated fungi,are complex and time-consuming. On the other hand, fungal in-fections can be detected sensitively and promptly using newtechniques based on nmlecular biology methods. These methodsrequire, however, the ability to efficiently extract fungus-specific nucleic acids from clinical material. In order toidentify, from these extracted nucleic acids, the fungal spe-cies responsible for the infection, specific sequences of dif-ferent pathogenic fungal species must be known. This requiresdifferentiating among the various fungal species, since theparticular therapy depends on the individual fungal infection.Against this background, a method has been developed withwhich fungal DNA can be extracted from patient material, thefungal DNA can be analyzed, and various fungal species can beidentified on the basis of the extracted DNA. This method isdescribed in DE Patent Application 195 30 336.9 as follows:First the fungal DNA is extracted from the patient's wholeblood. This is done by first isolating fungal cells from bloodcells. Then the fungal cells are lysed and their DNA is puri-fied from the lysate. Fungus-specific DNA segments from thefungal cell DNA thus obtained is amplified in a polymerasechain reaction (PCR). This polymerase chain reaction is per-formed with two primers which amplify a region, comprising ap-proximately 500 nucleotides, from the gene for l8ssu rRNA. Theprimers are selected so as to amplify only the correspondinggene region from fungi, but not gene regions from other organ-isms, for example the patient's own body cells. The sequences?CA 02263992 l999-02- 19of these primers are listed in the attached Sequence Listing asSEQ ID No. 1 and 2.A DNA fragment is thus amplified in the polymerase chainreaction only if a fungal infection is present. Considered inand of itself, the PCR thus serves to detect the existence ofan infection with pathogenic fungi.In order then to differentiate among different fungal spe-cies, the amplified 500-base—pair fragment is hybridized withone or more of a total of six probes. Each probe is specificfor one fungal species. According to DE Patent Application 19530 336.9, specific probes are indicated for a total of fiveCandida species and the genus Aspergillus. The probes are alsolisted in the Sequence Listing attached hereto, as SEQ ID No. 3through 8.The fungal genera Candida and Aspergillus are those by farmost often involved in nosocomial infections. Less—common fun-gal species, for which so far no detection methods are avail-able, are nevertheless also gaining in clinical significance.Against this background, the present application makesavailable species-specific probes for the hitherto unknown rRNAgene region of uncommon fungal species. These probes have al-ready been successfully used experimentally for the detectionof the uncommon fungal species.The sequences of these probes are listed in the attachedSequence Listing as SEQ ID No. 9, 10, 11, and 12.?CA 02263992 l999-02- 19The probe with the nucleotide sequence SEQ ID No. 9 isused to detect the fungal species Pneumocystis carinii. Theprobe with the nucleotide sequence SEQ ID No. 10 is used to de-tect the species Malassezia furfur. The letter K at position 21stands for "G or T"; i.e. there are strains which require the Gbase here, and strains which require the T base here. The probewith the nucleotide sequence SEQ ID No. 11 is used to detectthe species Trichosporon cutaneum and Trichosporon capitatum.Lastly, the probe with the sequence SEQ ID No. 12 is used todetect the fungal species Fusariunl solani and Fusariun1 oxy-sporum.Using these specific probes, it is possible for the firsttime to make even the uncommon pathogenic fungal species Pneu-mocystis, Malassezia, Trichosporon, and Fusarium accessible.to.a prompt, sensitive, and easily performed molecular biology de-tection method.It is preferred in this context if these probes are util-ized in a method of the kind described in DE Patent Application195 30 336.9 described above. After extraction of the fungalDNA from clinical material and detection of the extracted fun-gal DNA via a polymerase chain reaction with primers SEQ ID No.1 and 2, the probes presented here (SEQ ID No. 9 through 12)can be used as hybridization probes directly on the DNA frag-ment amplified in the PCR. It is possible in this context touse them individually, or in a sequential hybridization methodtogether with the probes described in DE Patent Application 19530 336.9.?CA 02263992 l999-02- 19It is understood, however, that the probes described herecan also be used in other analysis methods, for example in adirect hybridization of total fungal DNA or fungal RNA, or as aprimer for polymerase chain reactions.Provision is also made for integrating the specific probespresented here into a kit with which fungal species can beidentified. The kit can contain either only the DNA probes oralso additional necessary solutions, thus considerably simpli-fying the everyday laboratory work of identifying the particu-lar fungal species.It is also possible, in this context, to include in a kitall the essential solutions for performing a method of the kindcited above. It can contain not only the probes specific forthe uncommon fungal species, but also the probes described inDE Patent Application 195 30 336.9 for identifying Candida andAspergillus species.The Examples below illustrate the entire method for ex-tracting fungal DNA from clinical material, detecting the ex-tracted fungal DNA by polymerase chain reaction, and determin-ing the fungal species from the extracted DNA.Examples 1 and 2 illustrate how fungal cells can be ob-tained from blood cells contained in whole blood. Example 3 ex-plains how predominantly intact fungal cells can be separatedfrom cellular human DNA; Example 4 shows how fungal cells aredisintegrated, and Example 5 shows how the fungal DNA is thenisolated. Example 6 describes how the aforesaid fungus—specific500-base-pair fragment from the gene region for l8ssu rRNA is?CA 02263992 l999-02- l9amplified by polymerase chain reaction. Examples 7 and 8 demon-strate how the fungus—specific probes can be used to identifyindividual fungal species.Example 1: Lysis of red blood cells by osmotic hemo-lysisRed blood cells are lysed with a hypotonic solution, usingthe following buffer with the following final concentrations:Tris pH 7.6 10 mMMgCl2 5 mMNaCl 10 mMThe solution is incubated at room temperature for 10 min?utes, and then centrifuged.A volume of 3 ml of whole blood is sufficient for thisfirst step.Example 2: Enzymatic disintegration of white bloodcellsThe white blood cells, which may contain fungal cells, arecarefully broken up by enzymatically treating the cells withProteinase K (200 pg/ml) of the Boehringer Mannheim company, inthe following buffer with the indicated final concentrations,in which the pellet from Example 1 is placed:?CA 02263992 l999-02- l97Tris pH 7.6 10 mMEDTA pH 3.0 10 mMNaCl 50 mMSDS 0.2%Proteinase K 200 pg/mlThis buffer is incubated for two hours at 65° C.Example 3: Separation of predominantly intact fungalcells, principally from cellular DNAOnce the blood cells have been disintegrated as describedin Examples 1 and 2 to release the cellular DNA, a centrifuga-tion step at 5000 rpm is performed; this results in a consider-able loss of cellular DNA, which does not sediment at this cen—‘trifuge speed.The sediment now contains exclusively the free or releasedfungal cells, to which NaOH is added for further processing.Example 4: Disintegration of fungal cellsNext the fungal cells are lysed in alkaline solution andenzymatically treated to release the fungal DNA.This involves first an alkaline lysing step with 200 pl 50mM NaOH for 10 minutes at 95° C.That is followed by a neutralization step with 1 M Tris-HCl (pH 7.0) and centrifuging at 5000 rpm for 10 minutes.?CA 02263992 l999-02- 19500 pl Zymolyase of JCN (300 pg/ml) is then added, and thesolution is incubated at 37° C for 60 minutes in order to enzy-matically disintegrate the fungal cells.500 pl Tris/EDTA and 50 pl 10% SDS are then added, and thesolution is incubated at 65° C for 20 minutes to denature theprotein.Example 5: Isolation of fungal DNAThe solution thus obtained contains fungal cell debris aswell as free fungal DNA, which must now be isolated.This is done by first precipitating the protein with 5 Mpotassium acetate, after which the supernatant is removed, and‘the DNA is precipitated by adding ice-cold isopropanol. Thisprecipitation product is then used for the remaining processsteps.The process steps described in Examples 1 through 5 thusmake it possible to extract from whole blood, in highly selec-tive fashion, fungal DNA which is then present as a precipitatewith very little cellular DNA contamination, so that the detec-tion process which now takes place can be performed in verysensitive and highly specific fashion.Example 6: Amplification of a fungus—specific DNAsegmentThe purpose of this process step is first to determinewhether any fungal DNA at all is present in the precipitate?CA 02263992 l999-02- 19from the process step in Example 5. The fact that the DNA se-quences cited in the Sequence Listing as SEQ ID No. 1 and 2specifically bind to binding regions on the fungal gene for 18ssu rRNA of many fungal strains and species is exploited here.The inventors of the present application have recognizednot only that this fungal gene has, in the various fungalstrains and species, a sequence segment of this kind which isflanked by two binding regions for primers that are identicalfor all fungal strains and species; but also that the sequenceof this segment for the various fungal strains and species isso different that it can be used to identify the individualfungal strains and species.In this context, DNA sequence SEQ ID No. 1 binds to thesense strand, while DNA sequence SEQ ID No. 2 binds to theanti-sense strand, the spacing between the two binding regionsbeing approximately 500 base pairs. These two DNA sequences SEQID No. 1 and SEQ ID No. 2 are thus suitable as primers for apolymerase chain reaction (PCR) which consequently generates asufficient quantity of amplification products (amplicon) with alength of approximately 500 base pairs.The PCR conditions are as follows:Buffer (50 pl):10 mM Tris (pH 9.6)50 mM NaC110 mM MgCl20.2 mg/ml BSA?CA 02263992 l999-02- 1910Polymerase0.5 mM of each nucleotide100 pM of each primerInitial denaturing: 3 min at 94° CCycle denaturing: 0.5 min at 94° CAnnealing: 1 min at 62° CExtension: 2 min at 72°CTerminal extension: 5 min at 72°CNo. of cycles: 34The high concentration of magnesium in the buffer ensureshigh specificity for the polymerase, which can operate in theextension step at its optimum temperature (72°C).Example 7: Detection of the amplification productsfrom Example 6The next step is intended to determine whether the po-lymerase chain reaction in Example 6 has actually resulted inthe amplification of DNA segments with a length of approxi-mately 500 base pairs. This detection of fungus—specific DNAsegments is performed by ethidium bromide staining of the spe-cific band in a 2% agarose gel.If the specific band is found there, it can be assumedthat a fungal infection is present, since primers SEQ ID No. 1and 2 bind to all the aforementioned fungal species. In otherwords, if the process steps in Examples 1 through 5 resulted inthe extraction of fungal DNA, it is so far amplified by the PCRstep of Example 6 that it can be detected here by ethidium bro-mide staining.?CA 02263992 l999-02- 1911Example 8: Assignment of the amplification productsfrom Example 6 to individual fungalspeciesFor specific therapy, it is now also necessary to specifymore accurately the fungal infection already detected in step7. This now reveals a further advantage of the PCR step of Ex-ample 6, namely that it generates so much fungus-specific DNAsegment that further detection methods are possible so as todetermine the fungal species.This is done by utilizing the nucleotide sequences SEQ IDNo. 3 through 12 listed in the Sequence Listing, which serve asspecies—specific probes that specifically hybridize with a se-quence portion of the DNA segment generated in Example 6.It has been found that probe SEQ ID No. 3 hybridizes withCandida albicans, SEQ ID No. 4 with Candida glabrata, SEQ IDNo. 5 with Candida krusei, SEQ ID No. 6 with Candida tropi-calis, SEQ ID No. 7 with Candida parapsilosis, and SEQ ID No; 8with Aspergillus fumigatus, A. flavus, A. versiculor, A. niger,A. nidulans, and A. terreus. Nucleotide sequence SEQ ID No. 8is thus a general Aspergillus probe, while nucleotide sequencesSEQ ID No. 3 through 5 can distinguish among fungal species ofthe Candida genus.Probe SEQ ID No. 9 hybridizes with Pneumocystis carinii,probe SEQ ID No. 10 with Malassezia furfur, probe SEQ ID No. 11with Trichosporon cutaneum and Trichosporon capitatum, andprobe SEQ ID No; 12 with Fusarium solani and Fusarium?CA 02263992 l999-02- 1912oxysporum. It should also be noted that in SEQ ID No. 10, Kstands for "G or T".In order to detect hybridization once it has occurred, theprobes are marked with digoxigenin using the transferase kit ofthe Boehringer Mannheim company, detection being accomplishedusing the Southern Blot method with the usual color reaction.It is thus possible in ‘this fashion, by sequential hy-bridization based on the amplification products generated inthe step of Example 6, to identify the fungal species and thento initiate specific therapy.? iv, 5-..;4i:, _—.,—,- ;CA 02263992 2003-04-17v--—- —--y v.......-.—._1SEQUENCE LISTING(1) GENERAL INFORMATION:(i) APPLICANT:(A) NAME: Eberhard-Karls—Universitaet Tuebingen(B) STREET: Geissweg 3(C) CITY: T?bingen(E) COUNTRY: Germany(F) POSTAL CODE (ZIP): 72076‘(G) TELEPHONE: (7071) 29-1(H) TELEFAX: (7071) 29-3966(ii) TITLE-OF INVENTION: SEQUENTIAL HYBRIDIZATION OF FUNGAL CELLDNA AND MTHODS FOR THE DETECTION OFFUNGAL CELLS IN CLINICAL MATERIAL(iii) NUMBER OF SEQUENCES: 12(iv) CORRESPONDENCE ADDRESS:(A) ADDRESSEE: Robic(B) STREET: 55 $t—Jacques(C) CITY: Montréal(D) STATE: QC(E) COUNTRY: CA(F) ZIP: H2Y 3x2(G) TELEPHONE: 514—9e7—6242(H) TELEFAX: 514-345-7374(v) COMPUTER READABLE FORM: _(A) MEDIUM TYPE: Disk 3.5" / 1.44 MB(B) COMPUTER: IBM*Pc compatible(C) OPERATING SYSTEM: PC~DOS/MS~DOS(D) SOFTWARE: TXT ASCII(vi) CURRENT APPLICATION DATA:(A) APPLICATION NUMBER:(B) FILING DATE:(vii) PRIOR'APPLICATION DATA:(A) APPLICATION NUMBER: PCT/EP97/03687(3) FILING DATE: July 11, 1997(2) INFORMATION FOR SEQ ID NO: 1:(1) SEQUENCE CHARACTERISTICS:(A) LENGTH: 20 base pairs(B) TYPE: Nucleic acidI‘ 1: rademarkPage 1.......‘»~»»mu.M~o«-:4-«m..w.......... , . . .w).‘.s.~.I.........µâ€”v~.._u....~...-)---~~- ?PCT-EP97—03687.seq(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO. 1:ATTGGAGGGC AAGTCTGGTG 20(2) INFORMATION FOR SEQ ID NO: 2:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 20 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO. 2:CCGATCCCTA GTCGGCATAG 20(2) INFORMATION FOR SEQ ID NO: 3:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(xi) SEQUENCE DESCRIPTION: SEQ ID NO. 3:TCTGGGTAGC CATTTATGGC GAACCAGGAC 30(2) INFORMATION FOR SEQ ID NO: 4:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single Strand(C) TOPOLOGY: LinearCA 02263992 1999-02-19 Page 2?PCT—EP97—03687.seq(iii) HYPOTHETICAL: YES(xi) SEQUENCE DESCRIPTION: SEQ ID NO. 4:TTCTGGCTAA CCCCAAGTCC TTGTGGCTTG 30(2) INFORMATION FOR SEQ ID NO: 5:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO. 5:GTCTTTCCTT CTGGCTAGCC TCGGGCGAAC 30(2) INFORMATION FOR SEQ ID NO: 6:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO. 6:GTTGGCCGGT CCATCTTTCT GATGCGTACT 30(2) INFORMATION FOR SEQ ID NO: 7:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YESCA 02263992 1999-02-19 Page 3?PCT-EP97-O3687.seq(Xi) SEQUENCE DESCRIPTION: SEQ ID NO.TTTCCTTCTG GCTAGCCTTT TTGGCGAACC(2) INFORMATION FOR SEQ ID NO: 8:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO.CATGGCCTTC ACTGGCTGTG GGGGGAACCA(2) INFORMATION FOR SEQ ID NO: 9:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO.ATTACCGGCT GCCCTTCGCT GGGTGTGCCG(2) INFORMATION FOR SEQ ID NO: l0:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 26 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO.AGAGTGTTCA AAGCAGGCTT KACGCCCA 02263992 1999-02-19 Page 410:30303026?PCT-EP97-O3687.seq(2) INFORMATION FOR SEQ ID NO: 11:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 30 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO.AGGCCGTATG CCCTTCATTG GGTGTGCGGT(2) INFORMATION FOR SEQ ID NO: 12:(i) SEQUENCE CHARACTERISTICS:(A) LENGTH: 24 base pairs(B) TYPE: Nucleic acid(C) STRAND FORM: Single strand(C) TOPOLOGY: Linear(iii) HYPOTHETICAL: YES(Xi) SEQUENCE DESCRIPTION: SEQ ID NO.TGCTCCAGGC AGGCCTATGC TCGACA 02263992 1999-02-19 Page 5 ll:12:3O24

Claims (11)

1. Claims:
   
   I. A method for detecting and identifying fungi in clinical material, comprising the steps:
   a) extraction of Fungal DNA from clinical material;
   b) detection of the extracted fungal DNA;
   c) determination of the fungal species by hybridization of the extracted DNA with fungus-specific probes;
   where one or more of the nucleotide sequences SEQ ID No. 9 through 12 are used as DNA probes.
2. 2. The method as in Claim 1, wherein for detection of the extracted fungal DNA, an amplification of a DNA segment is performed by a polymerise chain reaction (PCR) using the prim-ers with the nucleotide sequences SEQ ID No. 1 and 2.
3. 3. The nucleotide sequence SEQ ID No. 9 from the at-tached Sequence Listing.
4. 4. The nucleotide sequence SEQ ID No. 10 from the at-tached Sequence Listing.
5. 5, The nucleotide sequence SEQ ID No. 11 from the at-tached Sequence Listing.
6. 6. The nucleotide seguence SEQ ID No. 12 from the at-tached Sequence Listing.
7. 7. Usa of the nucleotide sequence of Claim 3 for detec-tion of the fungal species Pneumocystis carinii.
8. 8. Use of the nucleotide sequence of Claim 4 for detec-tion of the fungal species Malassezia furfur.
9. 9. Use of the nucleotide sequence of Claim 5 for detec-tion of the fungal species Trichosporon cutaneum and Trichospo-ron capitatum.
10. 10. Use of the nucleotide sequence of Claim 6 for detec-tion of the fungal species Fusarium solani and Fusarium oxyspo-ron.
11. 11. A kit for identifying fungal species, which comprises nucleutide sequence SEQ ID N o 1 and 2 as PCR- primers and one or more of the nucleotide sequence of any one of claims 3 to 6, as probes.