DETECTION OF GIARDIA

Abstract: Oligonucleotide molecules for the detection of <i>Giardia lamblia</i> (<i>G. lamblia</i>) which molecules hybridise under medium to high stringency conditions to unique 18S rDNA/rRNA sequences of <i>G. lamblia</i>, and methods for the detection of the presence of viable cells of <i>G. lamblia</i> in samples using the oligonucleotide molecules.

Description: Detection of Giardia Technical Field The present invention is directed to the detection of parasite pathogens, particularly Giardia lamblia. using molecular probes. Backfiround Art Fluorescent in situ hybridisation (FISH) employing nucleic acid probes is one of the most advanced techniques for detection and enumeration of microorganisms. The technique emerged in the early nineties and since then has been improved rapidly and is being used for a wide range of applications which include diagnostics in clinical microbiology and analysis of microbial community structure in environmental and industrial microbiology/biotechnology. Although widely used for bacteria, very few publications describe methods for detection and enumeration of protozoan pathogens. The design of oligonucleotide probes requires skill and experience to determine accessible regions of rRNA in native ribosomes. An additional problem of successful FISH for protozoa is the development of hybridisation protocols that allow oligonucleotide probes to penetrate protozoa cell walls which are fundamentally different to bacterial cell walls. Moreover, the composition of bacterial cell walls has been well documented whereas little knowledge exists about the structure of the cyst walls of protozoa like Cryptosporidium spp. Giardia spp and related organisms. To date, monoclonal antibodies (mabs) are the most important and widely applied tool for detection of Giardia cysts in water samples. The vast majority of commercially available antibodies show a lack of specificity as the antibodies detect all Giardia spp including species that do not infect humans. As a positive antibody reaction does not allow any conclusion regarding the viability (infectivity) of the cysts, viability stains (DAPI, PI) have to be used in conjunction with antibodies. Oligonucleotide probes for FISH have several advantages over mabs in that probes are significantly cheaper to produce and are more stable as probes can be stored for long periods without loosing reactivity or specificity. Furthermore, correctly designed probes should only detect cysts of Giardia lamblia and no other species unable to infect humans. Probes target rRNA and will potentially only detect viable cysts which are able to cause infection. As non-viable (dead) cyst contain no or only small amounts of rRNA, it is envisaged that these cysts will not undergo detection. The present inventors have developed specific oligonucleotides suitable foi detection of potentially viable Giardia spp cysts and hybridisation protocols that allow permeabihzation of the cyst walls and enable oligonucleotide probes to reach their πbosomal nucleic acid targets Disclosure of Invention In a first aspect, the present invention consists in an oligonucleotide molecule foi the detection of Giardia lamblia [G lamblia). the oligonucleotide molecule hvbndises to unique 18S rDNWrRNA sequences of G lamblia Preferablv. the oligonucleotide molecule hybridises specifically to unique 18S rDNA/rRNA sequences of G lamblia under medium to high stringency conditions (Sambrook et al . 1989 Molecular Cloning A Laboratory Manual. Cold Spring Harbour Laboratory Press) In manv cases, however, conditions of high stringency can be used to ensure specific hybridisation to unique G lamblia 18S rDNA/rRNA sequences In a preferred embodiment of the first aspect of the present invention, the oligonucleotide molecule is selected from the group of oligonucleotides having one or more of the following nucleotide sequences Gιar-1 GCG TCC CGG GTG AGC GGG (SEQ ID NO 1) Gιar-2 GCC CGC GGG CGC CCG CCC (SEQ ID NO 2) Gιar-3 TGG GCC CGC CTC GCT CGC (SEQ ID NO 3) Gιar-4 CGG CGG GGG GCC AAC TAC (SEQ ID NO. 4) Gιar-5 GCG GGT CCA ACG GGC CTG (SEQ ID NO 5) Gιar-6 CGG GGC TGC CGC GGC GCG (SEQ ID NO 6) or comprising a part of the sequences, typically at least 10 bases in length. Gιaι-1 to Gιaι-6 above so as to allow specific hybridisation to unique 18S rRNA sequences of G lamblia In a further preferred embodiment, the oligonucleotide molecules are Gιar-4 or Gιar-6 Preferably, the oligonucleotide molecules according to the invention are detectablv labelled so that the oligonucleotides may be utilised as probes in hybridisation assays It will be appreciated, however, that oligonucleotide molecules which are not labelled mav be used, for example, in a polymerase chain reaction (PCR) to amplify a part of the rDNA of G lamblia Stringent conditions are usually defined as those that (1) employ low ionic strength and high temperature for washing, for example. 0 015 M NaCl/0 0015 M sodium cιtrate/0/1% NaDodS0 at 65°C. (2) employ during hybridisation a denaturing agent such as formamide. foi example, up to 50% (vol/vol) formamide with 0 1% bovine serum albumin 0 1% Ficoll. 0 1% polvvinylpyiiohdone. 50 nM sodium phosphate buffei at pH 6 5 with 750 niM NaCl. 75 n M sodium citrate at 42°C or (3) employ up to 50% formamide 5 x SSC (0 75 M NaCl. 0 075 M sodium citrate). 50 rnM sodium phosphate (pH 6 8) 0 1% sodium pviophosphate 5 x Denhardt s solution sonicated salmon sperm DNA (50 g/ml). 0 1% SDS and 10% dextran sulfate at 42°C m 0 2 x SSC and 0 1% SDS Clarification of the term "18S rDNA rRNA" foi Giardia lamblia and Giardia spp is piovided as follows The RNA molecule in question is veπ unusual With approximately 1450 nucleotides. the 18S RNA molecule is significantly shorter than the 18S rRNA of other eukaryotes and in respect of sizes resembles the 16S rRNA of bacteria (Sogin et al 1989 Phylogenetic meaning of the kingdom concept An unusual πbosomal RNA from Giardia lamblia Science 243: 75-77) However, as determined by sequence homology Giardia appears to be an eukaryote representing a phylogenetically 'ancient ' group of species In the following, the term "18S rRNA/DNA will be used for all eukaryotic sequences that were examined for the purpose of designing Giardia lamblia specific probes In a second aspect, the present invention provides a method for the detection of the presence of viable cells of G lamblia in a sample, the method comprising the steps of (a) adding to the sample a probe comprising a detectably labelled oligonucleotide molecule according to the first aspect of the present invention, (b) allowing hybridisation of the probe to the 18S iDNA/rRNA of any G lamblia cells present in the sample, and (c) detecting hybridisation of the probe Detection of any hybridisation of the probe to 18S rDNA/rRNA in the sample is indicative of the presence of viable cells of G lamblia in the sample The sample can be any sample where there is concern that G lamblia may be present Samples include environmental, water sources, waste matenals. medical and body fluids Examination of dunking water samples are paiticularh applicable for the present invention In a preferred embodiment, the method is used in combination with fluorescence m situ hybridisation (FISH) in which the oligonucleotide probe is labelled with a fluorochrome and after hybridisation, the resulting fluorescent cell is detected by epifluorescence microscopy or flow cvtometry Suitable fluorochromes for the probes include but not limited to fluorescein lsothiocvanate (FITC, green), cyanine dyes Cy2. Cy3. Cy3 5. Cy5. Cy5 5 (ranging from green to fai red) oi Texas Red Other labels include radio-isotopes phosphorus 32 P and 33 P and sulfur 3J S Another option is conjugation of piobes to biotin and then add streptavidin-hnked horseradish peroxidase (HRP) to the hybridisation reaction in order to enhance the signal via tvi amide signal amplification (TSA) In oidei to impiove the hybridisation of the probe to the nucleic acid of the cell, the piesent inventors have found that adding formamide (preferably around 20% v/v) to the hybridisation buffer increases the stringency sufficiently to eliminate cross reactions of the probes with Giardia muris) Other agents which act m a similar manner would also be suitable to assist in specific hybridisation In a further preferred embodiment of the second aspect of the present invention several different oligonucleotide probes are used and are distinguished bv the use of different labels on each probe More preferably the oligonucleotide piobes are labelled with different fluorochromes and detected by flow cvtometry While it is preferred that the probes are fluorescently labelled it is to be understood that othei known forms of labelling may be used within the broad scope of the present invention Examples of other forms of labelling are radioactivity and chemiluminescence In a third aspect, the piesent invention provides an oligonucleotide molecule which hybridizes to G lamblia 18S rDNA/rRNA sequences under medium to high stringency conditions wherein the oligonucleotide molecules hybridizes to at least one of target regions of G lamblia rDNA having the following nucleotide sequences CCC GCT CAC CCG GGA CGC (SEQ ID NO 7) GGG CGG GCG CCC GCG GGC (SEQ ID NO 8) GCG AGC GAG GCG GGC CCA (SEQ ID NO 9) GTA GTT GGC CCC CCG CCG (SEQ ID NO 10) CAG GCC CGT TGG ACC CGC (SEQ ID NO 11) CGC GCC GCG GCA GCC CCG (SEQ ID NO 12) The oligonucleotide molecules and methods of the present invention may be used to detect the presence in a sample of any type of viable cell of G lamblia Normally only oocvsts will be found in environmental samples Other cell types trophozoites may. however, be found and detected in clinical samples The oligonucleotide probes according to the present invention have tested successfully in the inventors' laboratories Probes were used on samples that underwent IMS. staining with fluorescently labelled antibodies and sorting of positive particles on a membrane via flow cvtometry FISH was then carried out with these membranes in order to determine species identity and viability of the cysts and the membranes examined by epi- fluorescence microscopy once the hybridisation reaction is completed Further, it has been established that the probes specifically detect cysts of Giardia lamblia Weak cross reactions were observed when the probes were hybridised against cysts of the closely related species Giardia muris Cross reactions were subsequently eliminated by modifying the hybridisation buffer in a manner that increases the stringency of the hybridisation The present inventors demonstrated earlier that an excellent coirelation exists between the FISH signal intensity obtained from Cnφtosporidium parvum oocvsts and viability of the oocysts as measured by excystation (Vesev et al 1995 The use of a πbosomal RNA targeted oligonucleotide probe for fluorescent labelling of viable Cπφtospondium parvum oocysts / Appl Microbiol 85: 429-440) It is likely that Giardia cysts having lost their viability through ageing, which includes degradation of the rRNAs. the target of the oligonucleotide probes, will not show any fluorescent signal Throughout this specification, unless the context requires otherwise, the woid "comprise", or variations such as "comprises" or "comprising", will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps Any description of prior art documents herein is not an admission that the documents foim part of the common general knowledge of the relevant art in Australia In order that the present invention may be more clearly understood, preferred forms will be described with reference to the following examples Modes for Cairymg Out the Invention Design of Oligonucleotide Probes A brief explanation of the svstematics of the genus Giardia is provided as follows Giardia lamblia is the only species of the genus that is known to cause disease in humans Some controversy still surrounds the svstematics of the species which is also referred to as Giardia duodenalis or Giardia intestmalis (Lu et al 1998 Molecular comparison of Giardia lamblia isolates Int J Parasitol 28: 1341-1345) Other representatives of the genus Giardia described to date aie Giardia agihs from amphibians and Giardia muris from rodents, birds and reptiles (Mevei 1994 Giardia as an organism P 3-13 In RCA Thompson. J A Reynoldsen. A J Lymberv (eds ) Giardia From molecules to disease CAB International. Wallingford. Oxon. UK). Giardia ardea from herons (Erlandsen et al 1990 Axenic culture and characterization of Giardia ardea from the great blue heron (Ardea herodias) J Prasitol 76: 717-724) and Giardia microti from muskrats and voles (van Keulen et al 1998 The sequence of Giardia small subunit rRNA shows that voles and muskrats are parasitized by a unique species Giardia microti J Parasitol 84: 294-300) Sequence information of 18S rDNA of Giardia lamblia and phvlogenetically closely related species was obtained from GenBank through ANGIS (Australian National Genonuc Information Service) at Sydney University All relevant sequences of Giardia spp as available in April 2000 were examined Sequences retrieved included Zl7210-Giαrώα ardea M54878-Gιardιa lamblia. U09492-Gιardιa lamblia U09491-Gιardιa lamblia AF00δδ77-Gιardιa microti AF006676-G ardia microti Xd5063-Gιardιa muris U20351-Gιardιa sp L16997 -Cπφtospoπdium parvum. Ll9069-Cnptospoπdιum muris Ll9068-Cnφtospoπdwm bailevi. U40261-Cvclospora sp U40262-fimena mitis. U40264-fi/neπα tenella. UA0263-Eιmena nieschulzi U26532-Nosema fiirnucahs. \J26533-Nosema ceranae. X73894-Nosema apis, and 39110-Ichtvospoπdιum Sequences were aligned using the program ClustalW and screened for diagnostic regions, e g regions that specifically discriminated Giardia lamblia from the other species included in the alignment Six target regions were identified as listed below The positions of the nucleotides given are not based on anv internationally recognised numbering system but refer to the numbering for the Giardia lamblia 18S rRNA (designated 16S rRNA in the reference) given in a secondary structure model published by Sogin et al in 1989 (Phylogenetic meaning of the kingdom concept. An unusual πbosomal RNA from Giardia lamblia Science 243: 75-77) In accord with international agreements, all sequences listed, including oligonucleotide sequences, are shown in 5 ' -3 ' onentation Target Regions Target regions (rDNA) were identified as follows 1 CCC GCT CAC CCG GGA CGC (Position 57-74) (SEQ ID NO. 7) 2 GGG CGG GCG CCC GCG GGC (Position 166-183) (SEQ ID NO. 8) 3 GCG AGC GAG GCG GGC CCA (Position 391-408) (SEQ ID NO: 9) 4 GTA GTT GGC CCC CCG CCG (Position 508-525) (SEQ ID NO 10) 5 CAG GCC CGT TGG ACC CGC (Position 552-569) (SEQ ID NO 11) 6 CGC GCC GCG GCA GCC CCG (Position 596-613) (SEQ ID NO 12) Due to the fact that G lamblia shows a very unusual 18 rRNA regarding sequence and secondary structure, it appeared reasonable to assume that the probes are G lamblia specific and will not show cross reactions with other protozoans under moderately stringent hybridisation conditions Table 1 shows a comparison of the target regions for the two functional FISH probes Giar-4 and Giar-6 from all Giardia spp. 18S rD A/R A target sequences available. A cross reaction observed from probe Giar-4 with G. muris. probably the phvlogenetically closest related species to G. lamblia. occurred under low stringency hybridisation and was eliminated by increased stringency through 20 % formamide in the hybridisation buffer. The alignment of published sequences used to design the probes showed that the corresponding target region of Giar-4 on the G. muris 18S rRNA shows eight mismatches and one deletion compared to the target region on the G. lamblia 18S rRNA. A corresponding target region for Giar-6 does not exist on the G. muris 18S rRNA. It appears that a large part of the rRNA in this region was deleted during the evolution of G. muris. From database searches, it would appear that the Giar-4 and Giar-6 probes might cross react with a species designated G. microti. isolated from muskrats and voles. These sequences show a very high overall sequence homology up to 96.8 % to the G. lamblia sequence. It appears questionable to describe the isolate as a species different to G. lamblia as other Giardia spp. share as little as 72-75 % sequence homology G. lamblia. Given that it has not been demonstrated to date that G. microti does not infect humans, it appears possible that the organism is in fact G. lamblia or a subspecies of G. lamblia which is supported by the high sequence homology of the 18S rRNAs. According to literature available. G. microti is not a generally recognised species and the fact that Giar-4 and Giar-6 will detect the organism is unlikely to contradict the finding that the probes according to the present invention are G. lamblia specific. TABLE 1 Comparison of the target regions of 'Giar-4 ' and 'Giar-6 ' on the 16S rDNA of Giardia spp * Species/ Target 'Giar-4' Target 'Giar-6' Accession G Iambi id GTAG TTGGCCCCCCGCCG CGCGC CGCGGCA GCCCCG M54878 G lamblia GTAG TTGGCCCCCCGCCG CGCGC CGCGGCA GCCCCG U09492 G lamblia GTAG TTGGCCCCCCGCCG CGCGC CGCGGCA GCCCCG U09491 G microti GTAG TTGGCCCCCCGCCG CTCGC CGCGGCA GCCCCG AF006677 G microti GTAG TTGGCCCCCCGCCG CGCGC CGCGGCA GCCCCG AF006676 G ardea GCAGGCGTCGCGCGGCGCTG TGGACCTACCGCCCGGGACGGCG Z17210 G sp GGCGCTGCTG CTGCAGTTA CGC C CGGGAC GCGCG U20351 G mun^ GGAGTCGAGACGTC CAG X65063 Not Applicable * * Nucleotide residues printed in bold indicate mismatch to the G lamblia target sequences of 'Giar-4' and 'Giar-6 ' . blank space represents nucleotide deletions * Analysis include all 16S rDNA sequences of Giardia spp available through GenBank in April 2000 **Comparatιve sequence analysis and secondary structure modeling led to the conclusion that no corresponding target region exists on the 16S rRNA of G muris FISH Probes Fluorescently labelled oligonucleotide probes were produced for the target regions as shown above Naturally, sequences of the oligonucleotides are the reveise complement of the target regions Gιar-1 GCG TCC CGG GTG AGC GGG (SEQ ID NO 1) Gιar-2 GCC CGC GGG CGC CCG CCC (SEQ ID NO 2) Gιaι-3 TGG GCC CGC CTC GCT CGC (SEQ ID NO 3) Gιaι-4 CGG CGG GGG GCC AAC TAC (SEQ ID NO 4) Gιar-5 GCG GGT CCA ACG GGC CTG (SEQ ID NO 5) Giar-6 CGG GGC TGC CGC GGC GCG (SEQ ID NO 6) Preliminary investigations including a universal eukarvotic probe as a positive control showed that only probes Gιaι-4 and Giar-6 were suitable foi ¬ FISH as the other probes yielded no or very weak signals Subsequently, Giar-4 and Giar-6 weie employed for further testing and refinement of hybridisation conditions The other four probes. Gιar-1. Gιar-2. Gιar-3. and Gιar-5. however, can be employed for specific detection of Giardia lamblia rRNA or rDNA in techniques that target free nucleic acids such as Polymerase Chain Reaction (PCR) assays or dot blot hybridisations RESULTS Commercially available viable Giardia lamblia cysts were used Ahquots of cysts were stored at -20°C in 50% ethanol and 50% phosphate buffered saline (PBS), pH 7 2 This method of fixation enables long term storage (> 1 year) prior to hybridisation experiments without diminished FISH signal due to degradation of πbosomal nucleic acids METHOD Protocol for Fluorescent in situ Hybridisation in 1.5 ml Tubes A suspension containing cvsts was centπfuged for 5 mm and the supernatant discarded A centrifugal force greatei than 1200 x g should be avoided as this will cause many cysts to rupture Resuspend cysts in 50% ethanol and 50% PBS. incubate at 80°C for 20 mm Centrifuge cysts, discard supernatant and resuspend in FISH buffer (0 9 M NaCl. 10 mM Tπs/HCl. pH 7 2. 0 1% SDS. 20% formamide) Adding 20% formamide to the hybridisation buffer increased the stringency sufficienth to eliminate the above mentioned cross leactions of the probes with Giardia muris containing 1 picomol per microhter of each fluorescently labelled probe Gιaι-4 and Giar-6 Incubate at 80°C for 2 mm. transfer to 48°C water bath and incubate 60 mm Terminate hybridisation by adding ice cold PBS. spin, discard supernatant and resuspend cysts m ice cold PBS Cvsts are then ready to be examined The hybridisation protocol as detailed above can be applied for cysts concentrated via IMS. stained with FITC-labelled antibodies and sorted on filters bv flow cvtometπ Alternatively. Cnφtospondium oocysts and Giardia lamblia cysts can be detected simultaneously by applying the specific probes described here in conjunction with Cnφtosporidium pari'um specific probes and hybridisation protocols (Deere et al 1998 Rapid method for fluorescent situ πbosomal RNA labelling of Crvptospondium parvum J Appl Microbiol 85: 807-818. Vesey et al 1998 The use of a πbosomal RNA targeted oligonucleotide probe for fluorescent labelling of viable Crvptospondium parvum oocvsts / Appl Microbiol 85: 429-440) Modifications Possible modifications of the invention is the application of methods that allow amplification of the fluorescent FISH signal In brief, molecular beacons are modified, fluorescently labelled oligonucleotides that can only emit a fluorescent signal when attached to their specific nucleic acid target No signal will be obtained from probes that are bound non-specifically to any other matter in a sample In essence, increased signal strength is achieved by eliminating or at least drastically reducing background signals (Schofield et al 1997 Molecular beacons Trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria Appl Envir Microbiol 63: 1143-1147) Tvrannde signal amplification (Schonhuber et al 1997 Improved sensitivity of whole cell hybridization by the combination of hoiseradish peioxidase-labelled oligonucleotides and tyramide signal amplification Appl Envir Microbiol 63: 3268-3273) utilises unlabelled oligonucleotide probes that are conjugated to horseradish peroxidase (HRP) After the hybridisation reaction is completed, the hybridisation buffer is removed and replaced by a buffer solution containing HRP substrate conjugated to a fluorescent dye Subsequently. HRP linked to oligonucleotides converts the substrate into a fluorescent precipitate that accumulates in the taiget cells The present invention is a continuation of the development of specific oligonucleotide probes foi detection and enumeration of protozoan pathogens in watei via fluorescent situ hybridisation (FISH) The investigations led to the first specific FISH probes for detection of viable Cnψtosporidium parvum oocvsts (WO 96/34978 entitled Method for the Detection of Viable Cnψtosporidium pan'um oocvsts) Comparative sequence analysis of the 18S πbosomal DNA (rDNA) from Giardia lamblia and closely related species (in terms of sequence homology) and secondary structure analysis was used to determine the accessibility of the potential target region resulted in the oligonucleotide probes disclosed Based on the above investigations, six potentially specific FISH probe sequences were determined The probes were produced and tested on trophozoites of Giardia lamblia Two of these probes (designated Giar-4 and Giar-6) yielded a strong fluorescent signal and showed the same result when hybridised against potentially viable cvsts The remaining four probes showed either very weak or no fluorescence at all and were subsequently omitted from further FISH experiments However, these four probes can be employed for specific detection of Giardia lamblia rRNA or rDNA in techniques that target free nucleic acids such as Polymerase Cham Reaction (PCR) assays or dot blot hybridisations It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the invention as shown in the specific embodiments without departing from the spirit or scope of the invention as broadly described The present embodiments are, therefore, to be considered in all respects as illustrative and not restrictive

Claims: CLAIMS 1 An oligonucleotide molecule for the detection of Giardia lamblia [G lamblia) the oligonucleotide molecule hybridises undei medium to high stιιngenc\ conditions to unique 18S 1 DNA rRNA sequences of G lamblia 2 The oligonucleotide molecule according to claim 1 which hybridises to unique 18S rDNA/rRNA sequences of G lamblia under conditions of high stringency 3 The oligonucleotide molecule according to claim 1 or 2 selected from the gioup consisting of oligonucleotides having the following nucleotide sequences GCG TCC CGG GTG AGC GGG (SEQ ID NO 1). GCC CGC GGG CGC CCG CCC (SEQ ID NO 2). TGG GCC CGC CTC GCT CGC (SEQ ID NO 3) CGG CGG GGG GCC AAC TAC (SEQ ID NO 4). GCG GGT CCA ACG GGC CTG (SEQ ID NO 5) CGG GGC TGC CGC GGC GCG (SEQ ID NO 6) and oligonucleotides comprising a part of the sequences above having at least ten bases which hvbndise to unique rDNA/rRNA sequences of G lamblia 4 The oligonucleotide molecule according to claim 3 comprising the nucleotide sequence CGG CGG GGG GCC AAC TAC (SEQ ID NO 4) 5 The oligonucleotide molecule accoiding to claim 3 comprising the nucleotide sequence CGG GGC TGC CGC GGC GCG (SEQ ID NO 6) 6 The oligonucleotide molecule according to any one of claims 1 to 5 being detectablv labelled 7 The oligonucleotide molecule according to claim 6 wherein the label is selected fiom the gioup consisting of fluorochrome. ladioisotope. and chemical 8 The oligonucleotide molecule according to claim 7 wherein the label is a fluorochrome 9 The oligonucleotide molecule according to claim 7 wherein the fluorochiome is selected from the group consisting of fluorescem lsothiocyanate (FITC. green) cvanine dyes Cy2. Cy3. Cy3 5. Cy5, Cy5 5 (ranging from green to far red), and Texas Red 10 A method foi the detection of the presence of viable cells of G lamblia in a sample, the method comprising the steps of (a) adding to the sample a probe consisting of a detectablv labelled oligonucleotide molecule which hybridises under medium to high stringency conditions to unique 18S rDNA/rRNA sequences of G lamblia. (b) allowing hybridisation of the probe to the 18S rDNA/rRNA of any G lamblia cells present in the sample, and (c) detecting hybridisation of the probe 11 The method according to claim 10 wherein the probe is selected from the gioup consisting of oligonucleotides having one or more of the following nucleotide sequences GCG TCC CGG GTG AGC GGG (SEQ ID NO 1) GCC CGC GGG CGC CCG CCC (SEQ ID NO 2) TGG GCC CGC CTC GCT CGC (SEQ ID NO 3) CGG CGG GGG GCC AAC TAC (SEQ ID NO 4) GCG GGT CCA ACG GGC CTG (SEQ ID NO 5) CGG GGC TGC CGC GGC GCG (SEQ ID NO 6) and oligonucleotides comprising a part of the sequences above having at least ten bases which hybridise to unique rDNA/rRNA sequences of G lamblia 12 The method according to claim 11 wherein the oligonucleotide molecule comprises the nucleotide sequence CGG CGG GGG GCC AAC TAC (SEQ ID NO 4) 13 The method according to claim 11 wherein the oligonucleotide molecule comprises the nucleotide sequence CGG GGC TGC CGC GGC GCG (SEQ ID NO 6) 14 The method according to any one of claims 10 to 13 is used in combination with fluorescence m situ hybridisation (FISH) in which the oligonucleotide probe is labelled with fluorochrome and after hybridisation, the resulting fluorescent-labelled cell is detected by epifluorescence microscopy or flow cvtometry 15 The method according to any one of claims 10 to 14 wherein several different oligonucleotide probes are used and are distinguished by the use of different labels on each probe 16 The method according to claim 15 wherein the oligonucleotide probes are labelled with different fluorochromes and detected bv flow cvtometry 17. The method according to any one of claims 10 to 16 wherein the sample is an environmental sample. 18. An oligonucleotide molecule which hybridizes to G. lamblia 18S rDNA rRNA sequences under medium to high stringency conditions, wherein the oligonucleotide molecule hybridizes to at least one of target regions of G. lamblia rDNA having the following nucleotide sequences: CCC GCT CAC CCG GGA CGC (SEQ ID NO: 7); GGG CGG GCG CCC GCG GGC (SEQ ID NO: 8): GCG AGC GAG GCG GGC CCA (SEQ ID NO: 9); GTA GTT GGC CCC CCG CCG (SEQ ID NO 10): CAG GCC CGT TGG ACC CGC (SEQ ID NO 11): CGC GCC GCG GCA GCC CCG (SEQ ID NO 12).

Inventors: DORSCH MATTHIAS RUDOLF, VEAL DUNCAN ADAM, DORSCH, MATTHIAS, RUDOLF, VEAL, DUNCAN, ADAM
Applicants: DORSCH MATTHIAS RUDOLF, MACQUARIE RES LTD, VEAL DUNCAN ADAM, DORSCH, MATTHIAS, RUDOLF, MACQUARIE RESEARCH LTD, VEAL, DUNCAN, ADAM
Application year: 2000
Main classification: C07H21
IPC codes: C07H21, C12N15, C12Q1, C12R1