WO1999037804A2 - EF-Tu mRNA AS A MARKER FOR VIABILITY OF BACTERIA - Google Patents

EF-Tu mRNA AS A MARKER FOR VIABILITY OF BACTERIA Download PDF

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WO1999037804A2
WO1999037804A2 PCT/EP1999/000323 EP9900323W WO9937804A2 WO 1999037804 A2 WO1999037804 A2 WO 1999037804A2 EP 9900323 W EP9900323 W EP 9900323W WO 9937804 A2 WO9937804 A2 WO 9937804A2
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sequence
amplification
seq
mrna
depicted
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PCT/EP1999/000323
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French (fr)
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WO1999037804A3 (en
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Pieter Oudshoorn
Paul Klatser
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Akzo Nobel N.V.
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Priority to CA002318726A priority Critical patent/CA2318726C/en
Priority to DE69933755T priority patent/DE69933755T2/en
Priority to JP2000528711A priority patent/JP4634604B2/en
Priority to AU27176/99A priority patent/AU2717699A/en
Priority to EP99907386A priority patent/EP1049809B1/en
Priority to US09/600,770 priority patent/US6489110B1/en
Publication of WO1999037804A2 publication Critical patent/WO1999037804A2/en
Publication of WO1999037804A3 publication Critical patent/WO1999037804A3/en

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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
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria

Definitions

  • the present invention is related to the detection of bacteria, such as Mycobacteria, in human or animal body fluids such as blood, sputum and urine
  • the present invention provides a method for assessing the viability of bacteria such as Mycobacte ⁇ um tuberculosis without the need for propagation of the bacteria
  • tuberculosis caused by Mycobactenum tuberculosis is a major public health problem in many countries world-wide with particular significance in developing countries
  • Tuberculosis control programmes are faced with an increased burden of cases, a shift towards diagnostically more difficult categories of patients such as extrapulmonary and smear-negative cases, and the emergence of multidrug-resistant strains of M tuberculosis Improved diagnosis would be a valuable contribution in the struggle to solve this global public health emergency
  • the method of the present invention is concerned with the amplification of specific nucleic acid sequences
  • Nucleic acid amplification reactions promise to reduce the time for diagnosis from weeks to hours, while surpassing the sensitivity and specificity of the classical methods Besides their potential value in diagnosis, amplification reactions offer the possibility of a rapid identification and drug-susceptibility determination
  • Amplification of DNA target molecules to a detectable level by the polymerase chain reaction (PCR) is the best analyzed system for detecting Mycobacteria
  • PCR Polymerase Chain Reaction
  • PCR is a cyclic process which has double stranded DNA as target
  • Each cycle in the PCR process starts with the separation of a double stranded DNA target in its two complementary strands
  • a primer will anneal and DNA polymerases present will extend the primers along the DNA strand to which it annealed thus forming two new DNA duplexes
  • the reaction mixture is heated the strands of the DNA duplexes will be separated again and a new PCR cycle can start
  • the PCR process produces multiple DNA copies of a DNA target Amplification using PCR, can also be based on an RNA template
  • the actual PCR needs to be preceded by a reverse transcription step to copy the RNA into DNA (RT-PCR)
  • RT-PCR reverse transcription step to copy the RNA into DNA
  • RNA polymerase a different class of nucleic acid amplification methods namely the "transcription based amplification techniques" was developed.
  • the techniques involve the transcription of multiple RNA copies from a template comprising a promoter recognized by an RNA polymerase. Said copies are used as input for further amplification.
  • Such methods have been described by Gingeras et al. in WO88/10315 and Burg et al. in WO89/1050.
  • Isothermal transcription based amplification techniques have been described by Davey et al. in EP 323822 (relating to the NASBA method), by Gingeras et al. in EP 373960 and by Kacian et al. in EP 408295 (the TMA method).
  • Transcription based amplification reactions may also be performed with thermostable enzymes. Such a thermostable method is described in EP 682121 filed in the name of Toyo Boseki KK.
  • the isothermal transcription based nucleic acid amplification techniques have been utilized to detect mycobacteria, such as the NASBA method [Vliet, G.M.E. van der, Schukkink, R.A.F., Gemen, B. van, Schepers, P. and Klatser, P.R. (1993) Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria. J. Gen. Microbiol. 139, 2423- 2429.] and another transcription-mediated RNA amplification test (TMA)[Jonas, V., Alden, M.J., Curry, J.I., Kamisango, K., Knott, C.A., Lankford, R., Wolfe, J.
  • TMA transcription-mediated RNA amplification test
  • Amplification reactions targeted at the 16S rRNA or the gene encoding it are usually directed to a conserved region which comprises species-specific variable sequences [Vliet, G.M.E. van der, Schukkink, R.A.F., Gemen, B. van, Schepers, P. and Klatser, P.R. (1993) Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria. J. Gen. Microbiol. 139, 2423-2429., Jonas, V., Alden, M.J., Curry, J.I., Kamisango, K., Knott, C.A., Lankford, R., Wolfe, J. and Moore, D.F.
  • species-specific variable sequences [Vliet, G.M.E. van der, Schukkink, R.A.F., Gemen, B. van, Schepers, P. and Klatser, P.R. (1993) Nucleic acid sequence-based amplification (NASBA
  • the present invention is based on the detection of mRNA encoding the elongation factor EF-Tu.
  • the elongation factor EF-Tu is essential in (myco)bactehal translation. Elongation factors play an ancillary role in the elongation step of translation and are thus an indicator of the cell's metabolic activity. For every translation EF-Tu is required. The amount of EF-Tu protein can be as high as 50% of their total protein content in active proliferating cells. EF-Tu encoding gene sequences (DNA) have been used as a marker to detect the presence of bacterial cells.
  • EP133288 a method is disclosed for the detection of bacterial DNA with a probe comprising a base sequence of at least a portion of one of the strands of a tuf or fus gene.
  • the present invention is concerned with the detection of EF-Tu mRNA as a marker for bacterial viability.
  • the present invention thus provides a method for the assessment of bacterial viability whereby mRNA coding for the elongation factor EF-Tu is used as a target in a nucleic acid amplification reaction and the presence and/or amount of said mRNA is determined.
  • the presumably short-lived mRNA coding for the EF-Tu is most likely highly abundant in the (myco)bacterial cell and a decrease therein will indicate a decline in metabolic activity.
  • a transcription based amplification technique such as a NASBA
  • NASBA which is based on RNA transcription by T7 RNA polymerase (Kievits et al., 1991 ; Compton, 1991 )
  • T7 RNA polymerase RNA polymerase
  • RNA- and DNA- derived amplification products since it uses RNA as its principal target.
  • the amplified products may be detected using a complementary labeled probe.
  • Numerous protocols have been described for the detection of amplified products [Klatser, PR. (1995) Amplification reactions in mycobacteriology. J. Microbiol. Meth. 23, 75-87.].
  • Preferably homogeneous assays are used, because they would allow amplification reaction mixtures to be sealed before amplification is initiated.
  • ECL electro- chemiluminescence
  • Mycobacteria species such as are M. tuberculosis or M.leprae.
  • oligonucleotides are also provided that can be used as primers and probes for the amplification of bacterial EF-Tu mRNA.
  • the use of the oligonucleotides according to the invention is not limited to any particular amplification technique or any particular modification thereof. It is evident that the oligonucleotides according to the invention find their use in many different nucleic acid amplification techniques and various methods for detecting the presence of (amplified) bacterial EF-Tu mRNA.
  • the oligonucleotides of the present invention can likewise be used in quantitative amplification methods. An example of such quantitative method is described in EP 525882.
  • oligonucleotide refers to a molecule comprised of two or more deoxyribonucleotides or ribonucleotides. Such oligonucleotides may be used as primers and probes.
  • analogues of oligonucleotides can also be prepared.
  • Such analogues may constitute alternative structures such as "PNA” (molecules with a peptide-like backbone instead of the phosphate sugar backbone of normal nucleic acid) or the like. It is evident that these alternative structures, representing the sequences of the present invention are likewise part of the present invention.
  • the term "primer” as used herein refers to an oligonucleotide either naturally occurring
  • a primer must be sufficiently long to prime the synthesis of extension products in the presence of an agent for polymerization.
  • a typical primer contains at least about 10 nucleotides in length of a sequence substantially complementary or homologous to the target sequence, but somewhat longer primers are preferred.
  • primers contain about 15-26 nucleotides but longer primers may also be employed, especially when the primers contain additional sequences such as a promoter sequence for a particular polymerase.
  • a set of primers will consist of at least two primers, one 'upstream' and one 'downstream' primer which together define the amplificate (the sequence that will be amplified using said primers).
  • the oligonucleotides according to the invention may also be linked to a promoter sequence.
  • promoter sequence defines a region of a nucleic acid sequence that is specifically recognized by an RNA polymerase that binds to a recognized sequence and initiates the process of transcription by which an RNA transcript is produced. In principle any promoter sequence may be employed for which there is a known and available polymerase that is capable of recognizing the initiation sequence.
  • promoters are those that are recognized by certain bacteriophage RNA polymerases such as bacteriophage T3, T7 or SP6. Oligonucleotides linked to a promoter sequence are commonly referred to as "promoter primers”. Oligonucleotides according to the invention are substantially complementary to a sequence of a bacterial EF-Tu mRNA sequence, said oligonucleotide being 10-50 nucleotides in length and comprising at least 10 consecutive nucleotides of one of the sequences depicted in SEQ ID 1-8 or the complementary sequence thereof.
  • Oligonucleotides comprising (a part of) SEQ ID's 1 and 2 have proven to be suitable for the amplification of Ef-Tu mRNA sequences of M.tuberculosis.
  • one of said oligonucleotides may also comprise a promoter sequence.
  • promoter-oligonucleotides are likewise art of the invention.
  • T7 promoter has been linked to the sequence as depicted in SEQ ID 1.
  • these sequences are indicated as TUF15 (SEQ ID 9) and TUF 18 (SEQ ID 2).
  • the present invention also provides a pair of oligonucleotides for the amplification of
  • M.leprae derived EF-Tu sequences This pair consists of an oligonucleotide comprising at least
  • one of the oligonucleotides may be linked to a promoter sequence, and an oligonucleotide provided with the T7 promoter sequence is depicted in SEQ ID 10.
  • TUF 20 SEQ ID 10
  • TUF 22 SEQ ID 4
  • the present invention further provides a pair of oligonucleotides that are suitable for the amplification of E.coli derived EF-Tu sequences.
  • This pair consists of an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 5 and an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 6 respectively.
  • one of the oligonucleotides may be linked to a promoter sequence, and an oligonucleotide provided with the T7 promoter sequence is depicted in SEQ ID 1 1.
  • TUF 27 SEQ ID 11
  • TUF 22 SEQ ID 6
  • oligonucleotides consisting of the sequences of the present invention may contain minor deletions, additions and/or substitutions of nucleic acid bases, to the extent that such alterations do not negatively affect the yield or product obtained to a significant degree. Where oligonucleotides according to the present invention are used as probes, the alterations should not result in lowering the hybridization efficiency of the probe.
  • the sequences of the present invention are reflected as DNA sequences. The RNA equivalents of these sequences are likewise part of the present invention.
  • oligonucleotides according to the invention are particularly suitable for use as a probe in the detection of nucleic acid amplified with a pair of oligonucleotides according to the invention.
  • said oligonucleotides may be provided with a detectable label.
  • Various labeling moieties are known in the art. Said moiety may, for example, either be a radioactive compound, a detectable enzyme (e.g. horse radish peroxidase (HRP)), a hapten like biotin, or any other moiety capable of generating a detectable signal such as a colorimetric, fluorescent, chemiluminescent or electrochemiluminescent signal.
  • HRP horse radish peroxidase
  • Hybrids between oligonucleotides according to the invention and (amplified) target nucleic acid may also be detected by other methods known to those skilled in the art.
  • Oligonucleotides according to the invention that are especially suitable as a probe for the detection of Mycobacterial Ef-Tu sequences consist essentially of the sequences as depicted in SEQ ID 7 and 8 (In the experimental part said sequences are depicted as TUF 25 and TUF 26 respectively.). Together these probes can be used in a sandwich hybridization assay, whereby one can be used as capture probe and the other can be labeled with a detectable label.
  • a test kit for the detection of Mycobacterial EF-Tu mRNA in a sample is likewise part of the present invention.
  • a kit may comprise a pair of oligonucleotides according to the invention and at least one oligonucleotide comprising a nucleic acid sequence substantially complementary to at least part of the amplified nucleic acid sequence , provided with a detectable label, as well as suitable amplification reagents. These reagents are for example the suitable enzymes for carrying out the amplification reaction.
  • a kit, adapted for use with NASBA for example, may contain suitable amounts of reverse transcriptase, RNase H and T7 RNA polymerase.
  • Said enzymes may be present in the kit in a buffered solution but can likewise be provided as a lyophilized composition, for example, a lyophilized spherical particle. Such lyophilized particles have been disclosed in PCT appl. no. EP95/01268.
  • the kit may further be furnished with buffer compositions, suitable for carrying out an amplification reaction.
  • Said buffers may be optimized for the particular amplification technique for which the kit is intended as well as for use with the particular oligonucleotides that are provided with the kit. In transcription based amplification techniques, such as NASBA, said buffers may contain, for example, DMSO, which enhances the amplification reaction (as is disclosed in PCT appl. no. US90/04733).
  • kit may be provided with an internal control as a check on the amplification procedure and to prevent the occurrence of false negative test results due to failures in the amplification procedure.
  • internal controls in transcription based amplification techniques is described in PCT appl. no. EP 93/02248.
  • An optimal control sequence is selected in such a way that it will not compete with the target nucleic acid in the amplification reaction.
  • Kits may also contain reagents for the isolation of nucleic acid from biological specimen prior to amplification. A suitable method for the isolation of nucleic acid is disclosed in EP389063.
  • Figure 1a The analytical sensitivity of NASBA using in vitro produced mycobacterial EF-Tu RNA.
  • Figure 1 b The analytical sensitivity of NASBA using in vitro produced mycobacterial EF-Tu RNA.
  • RNA Sources of RNA. Table 1 shows the sources of RNAs that were used in the experiments described in this and the following examples.
  • the cultivable mycobacteria were grown on Lowenstein-Jensen slants for 2-3 weeks. M.leprae was isolated from spleen tissue of an experimentally infected armadillo (Dasypus novemcinctus Linn.), as recommended by the World Health Organization [WHO Expert Committee on Leprosy. (1988) Sixth Report Tech. Rep. Ser. 8. 768. World Health Organization, Geneva.].
  • Other bacteria which might be found in human and/or animal samples or which are closely related to mycobacteria (see Table 1 ), were used for controls. For Actinomyces israelii lyophilized bacteria were used. The strains used for the production of in vitro RNA are described below.
  • RIVM National Institute of Public Health and Environment, Bilthoven, The Netherlands
  • SSI Statens Serum Institute, Copenhagen, Denmark
  • ATCC American Type Culture Collection, Rockvilie, USA.
  • nucleic acid isolation To perform the experiments described in all examples nucleic acids were isolated as we described previously [Vliet, G.M.E. van der, Schepers, P.,
  • the NA were eluted from the silica with 50 ⁇ l or 100 ⁇ l RNAse-free H 2 0 and stored at -20°C.
  • ECTUF E. coli EF-Tu gene sequence (GenBank accession number J01717)
  • MTTUF M.tuberculosis EF-Tu gene sequence (GenBank accession number X63539)
  • MLTUF M.leprae EF-Tu gene sequence (GenBank accession number D13869)
  • TUF 15, 20 and 27 include the T7 promoter sequence which is shown in lower case.
  • the promoter sequence is followed by a purine rich region (AGAG) which is shown in italics.
  • AGAG purine rich region
  • the purified fragments were sequenced directly using primers TUF 3F, 4F and 8F by applying the Autocycle Sequencing Kit (Pharmacia) and the A.L.F. automatic DNA sequencer (Pharmacia). Sequences were edited by using the DNASIS software programme (Pharmacia) and clustal alignments were then made using the PCGene software programme.
  • Table 3 shows the seven variable regions of the EF- Tu sequences which were defined based on the clustal alignments. From these variable regions it is possible to select primers and probes enabling species-specific detection of EF-Tu mRNA of different organisms (Table 4).
  • Table 5 shows the clustal alignments of two (region IV and VI) of the seven variable regions of the EF-Tu sequence on the basis of which the primers and probes were selected for specific amplification of M.tuberculosis, M.leprae and E.coli EF-Tu mRNA through NASBA. The criteria to select these two areas were: the availability of species-specific primers, a genus-specific probe and a length of ⁇ 200 nucleotides of the fragment to be amplified. Table 3. Seven variable regions on the EF-Tu sequences
  • Parts of the EF-Tu mRNA variable sequences which can be used for the selection of primers and/or probes enabling species-specific detection of EF-Tu mRNA from different organisms.
  • Probe TUF 25 is homologous to the EF-Tu sequence of M.leprae and not to that of M.tuberculosis; the difference is one nucleotide (G ⁇ A; see Table 2). However, this difference did not affect the detection of amplicons generated from RNA originating from M.tuberculosis.
  • E.coli RNA amplicons we used the specific capture and detection probes TUF 29 and TUF 30, respectively. In region IV one nucleotide difference was found with the published sequence of EF-
  • a 764 bp fragment of the EF-Tu gene of M.tuberculosis H37Rv, M.leprae and E.coli (Table 1 ) was amplified via PCR using the primer set TUF 4 and TUF 7 (Table 2), as described above.
  • the amplified product was cloned into the pCR II vector using the TA- cloning kit (Invitrogen) following the manufacture's instructions. Selection of the appropriate clone with the insert in the correct orientation, size and specificity was determined by restriction enzyme analysis and PCR.
  • the cloned insert within the polylinker region was transcribed from the T7 promoter site using the SP6/T7 transcription kit (Boehringer, Mannheim).
  • the DNA template was removed by digestion with RQI DNAse (Promega) and the RNA was purified by the RNeasy kit from Qiagen according the manufacturer's protocol. Purity was checked by agarose gel electrophoresis and Northern blotting with digoxigenine-labelled probe TUF 24 according to standard procedures. The in vitro RNA was quantified by measuring the extinction at 260 nm. RNA Amplification.
  • M.leprae and E.coli were amplified by the NASBA technique essentially as described before [Vliet, G.M.E. van der, Schepers, P., Schukkink, R.A.F., Gemen, B. van and Klatser, P.R. (1994) Assessment of mycobacterial viability by RNA amplification. Antimicrob. Agents Chemother. 38, 1959-1965.].
  • the 20 ⁇ l reaction mix was composed of 40 mM Tris-HCI, pH 8.5, 12 mM MgCI 2 , 70 mM KCI, 5 mM DTT, 1.5 M sorbitol, 2.1 mg BSA, 1 mM of each dNTP, 2 mM of ATP, CTP, UTP, 1.5 mM of GTP and 0.5 mM ITP, 15% -. (v/v) DMSO, 0.2 mM Primer 1 and Primer 2, 0.08 U RNase H, 32 U T7 RNA polymerase, 6.4 U AMV-RT polymerase and the RNA target. Isothermal amplification of the RNA target was performed by incubation of these samples at 41 °C for 2.0 h.
  • RNA NASBA nucleic acid amplification assay using electrochemiluminescent (ECL) labelled probes. J. Virol. Methods, 49, 1] with minor modifications: 5 ⁇ l of NASBA amplified RNA was either diluted 20-fold in RNase-free water or used undiluted. A 5'-biotinylated probe was used to capture the NASBA product.
  • the detection probe used was tris [2,2-bipyridine] ruthenium [II] complex labelled. This label emits light as a result of chemical reactions taking place at the surface of an electrode.
  • the cutoff value was set at 3000.
  • the ECL detection assay was measured on a scale of 0 to 10 8 .
  • Negative controls water only were included in each experiment in order to check for carry-over contamination during NA-extraction and amplification. These control samples were extracted and amplified by NASBA in the same manner as described above.
  • M.tuberculosis ATCC 35801 was grown in liquid Tween/Albumin medium at 37 °C. The concentration at the start of the culture was 8.10 6 bacteria/ml. Growth of the bacteria was monitored by measuring the extinction at 420 nm. After 13 days of culture a sample was taken and diluted in lysis buffer [Boom, R., C.J.A. Sol, M.M.M. Salimans, C.L. Jansen, P.M.E. Wertheim-Van Dillen and J. Van der Noordaa (1990). Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495-503.].
  • E.coli was grown in Luria Broth (LB) liquid medium at 37 °C for 18 h.
  • a serial dilution was made and mRNA was purified as described above.
  • the same dilutions were plated onto LB agar plates which were incubated at 37 °C for 18 h after which colonies were counted.
  • the analytical sensitivity of NASBA was determined using serial dilutions of in vitro
  • M.leprae NASBA had a detection of 50 molecules of RNA (Fig 1a).
  • the detection limit of the M.tuberculosis NASBA when using bacteria as starting material for detection was
  • the analytical sensitivity of the E.coli NASBA was shown to be 100 molecules (Fig. 1b).
  • the detection limit of the E.coli NASBA when using bacteria as starting material for detection was 0.4 (result not shown).
  • NASBA specificity of the M.tuberculosis NASBA and the M.leprae NASBA is illustrated in Figures 2 and 3, respectively.
  • the M.tuberculosis NASBA showed specificity for the RNA purified from bacteria belonging to the M.tuberculosis complex only.
  • the M.tuberculosis NASBA showed a positive reaction when homologous in vitro produced EF- Tu RNA was used as target.
  • the M.leprae NASBA showed specificity for M.leprae RNA only and its homologous in vitro produced RNA.
  • Example 4 The M.leprae NASBA showed specificity for M.leprae RNA only and its homologous in vitro produced RNA.
  • E.coli was grown in LB liquid medium at 37 °C for 18 h.
  • the suspension was then divided in two equal parts.
  • a cocktail of antibiotics was added to kill the bacteria: ampicillin, rifampicin and kanamycin (each 50 ⁇ g/ml); the other part was left untouched. Both were incubated at 37 °C for another 3 h and 30 min. Every 30 min the OD at 600 nm was monitored and a 100 sample from each culture was taken and added to 900 lysis buffer; mRNA was purified as described above (9).
  • viability of the E.coli bacteria was monitored by overlaying a sample (100 ) onto LB agar plates. Colonies were counted after 18 h incubation at 37 °C.
  • the NASBA signals increased and reached its maximum level when E.coli was left to grow untouched ( Figure 4). However, when antibiotics were added to the exponentially growing E.coli culture, the NASBA signal decreased 1 h after the addition of the antibiotics.

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Abstract

The present invention is related to the detection of bacteria, such as Mycobacteria, in human or animal body fluids such as blood, sputum and urine. The present invention provides a method for assessing the viability of bacteria such as Mycobacterium tuberculosis without the need for propagation of the bacteria. The method of the present invention is in particular useful for assessing the viability of Mycobacteria species such as are M. tuberculosis or M. leprae. With the present invention oligonucleotides are provided that can be used as primers and probes for the amplification of bacterial EF-Tu mRNA. The use of the oligonucleotides according to the invention is not limited to any particular amplification technique or any particular modification thereof. It is evident that the oligonucleotides according to the invention find their use in many different nucleic aid amplification techniques and various methods for detecting the presence of (amplified) bacterial EF-Tu mRNA.

Description

EF-Tu mRNA as a marker for viability of bacteria
The present invention is related to the detection of bacteria, such as Mycobacteria, in human or animal body fluids such as blood, sputum and urine The present invention provides a method for assessing the viability of bacteria such as Mycobacteπum tuberculosis without the need for propagation of the bacteria
For example, tuberculosis (TB) caused by Mycobactenum tuberculosis is a major public health problem in many countries world-wide with particular significance in developing countries Tuberculosis control programmes are faced with an increased burden of cases, a shift towards diagnostically more difficult categories of patients such as extrapulmonary and smear-negative cases, and the emergence of multidrug-resistant strains of M tuberculosis Improved diagnosis would be a valuable contribution in the struggle to solve this global public health emergency
The method of the present invention is concerned with the amplification of specific nucleic acid sequences
Nucleic acid amplification reactions promise to reduce the time for diagnosis from weeks to hours, while surpassing the sensitivity and specificity of the classical methods Besides their potential value in diagnosis, amplification reactions offer the possibility of a rapid identification and drug-susceptibility determination Amplification of DNA target molecules to a detectable level by the polymerase chain reaction (PCR) is the best analyzed system for detecting Mycobacteria
The "Polymerase Chain Reaction" (PCR) is described in European patent applications EP 200362 and EP 201 148 PCR is a cyclic process which has double stranded DNA as target Each cycle in the PCR process starts with the separation of a double stranded DNA target in its two complementary strands To each strand a primer will anneal and DNA polymerases present will extend the primers along the DNA strand to which it annealed thus forming two new DNA duplexes When the reaction mixture is heated the strands of the DNA duplexes will be separated again and a new PCR cycle can start Thus, the PCR process produces multiple DNA copies of a DNA target Amplification using PCR, can also be based on an RNA template The actual PCR needs to be preceded by a reverse transcription step to copy the RNA into DNA (RT-PCR) However, if RT-PCR is used for the detection of transcripts differentiation of mRNA- and DNA-denved PCR products is necessary DNAse treatment prior to RT-PCR can be employed (Bitsch, A et al , J Infect Dis 167, 740-743 , 1993, Meyer, T et al., Mol. Cell Probes. 8, 261-271., 1994), but sometimes fails to remove contaminating DNA sufficiently [Bitsch, A. et al.,1993].
More recently a different class of nucleic acid amplification methods namely the "transcription based amplification techniques" was developed. The techniques involve the transcription of multiple RNA copies from a template comprising a promoter recognized by an RNA polymerase. Said copies are used as input for further amplification. Such methods have been described by Gingeras et al. in WO88/10315 and Burg et al. in WO89/1050. Isothermal transcription based amplification techniques have been described by Davey et al. in EP 323822 (relating to the NASBA method), by Gingeras et al. in EP 373960 and by Kacian et al. in EP 408295 (the TMA method). Transcription based amplification reactions may also be performed with thermostable enzymes. Such a thermostable method is described in EP 682121 filed in the name of Toyo Boseki KK.
The isothermal transcription based nucleic acid amplification techniques have been utilized to detect mycobacteria, such as the NASBA method [Vliet, G.M.E. van der, Schukkink, R.A.F., Gemen, B. van, Schepers, P. and Klatser, P.R. (1993) Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria. J. Gen. Microbiol. 139, 2423- 2429.] and another transcription-mediated RNA amplification test (TMA)[Jonas, V., Alden, M.J., Curry, J.I., Kamisango, K., Knott, C.A., Lankford, R., Wolfe, J. and Moore, D.F. (1993) Detection and identification of Mycobactehum tuberculosis directly from sputum sediments by amplification of rRNA. J. Clin. Microbiol. 31 , 241] both targeted at 16S hbosomal RNA.
Amplification reactions targeted at the 16S rRNA or the gene encoding it are usually directed to a conserved region which comprises species-specific variable sequences [Vliet, G.M.E. van der, Schukkink, R.A.F., Gemen, B. van, Schepers, P. and Klatser, P.R. (1993) Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria. J. Gen. Microbiol. 139, 2423-2429., Jonas, V., Alden, M.J., Curry, J.I., Kamisango, K., Knott, C.A., Lankford, R., Wolfe, J. and Moore, D.F. (1993) Detection and identification of Mycobactehum tuberculosis directly from sputum sediments by amplification of rRNA. J. Clin. Microbiol. 31 , 241]. They have the advantage that a single amplification reaction can identify the mycobacterial species. An additional advantage of the transcription-mediated RNA amplification assays targeted at 16S rRNA, is the high number of target molecules per cell - ± 2000; sensitivity is thereby favoured. Since RNA, especially mRNA, has a generally much shorter half-life time than DNA, its detection may be useful for the assessment of the viability of mycobacteria [Moore, D.F.,
Curry, J.I., Knott, C.A. and Jonas, V. (1996) Amplification of rRNA for assessment of treatment response of pulmonary tuberculosis patients during antimicrobial therapy. J. Clin. Microbiol. 34, 1745-1749., Vliet, G.M.E. van der, Schepers, P., Schukkink, R.A.F., Gemen, B. van and
Klatser, P.R. (1994) Assessment of mycobacterial viability by RNA amplification. Antimicrob.
Agents Chemother. 38, 1959-1965.], which is relevant to the problems of resistance against drugs and contagiousness of the patient.
The present invention is based on the detection of mRNA encoding the elongation factor EF-Tu.
The elongation factor EF-Tu is essential in (myco)bactehal translation. Elongation factors play an ancillary role in the elongation step of translation and are thus an indicator of the cell's metabolic activity. For every translation EF-Tu is required. The amount of EF-Tu protein can be as high as 50% of their total protein content in active proliferating cells. EF-Tu encoding gene sequences (DNA) have been used as a marker to detect the presence of bacterial cells.
In EP133288 a method is disclosed for the detection of bacterial DNA with a probe comprising a base sequence of at least a portion of one of the strands of a tuf or fus gene.
Southern blot hybridization of the digested mycopiasmal DNAs with the elongation factor (EF- Tu) gene tuf of E.coli was used as a basis to detect polymorphism in mycoplasma strains.fYogev et al. FEMS Microbiol. Lett., 50(2-3), 145-9, 1988].
A PCR based assays for the detection of Mycoplasma tuberculosis, and Mycoplasma fermentans using the gene encoding elongation factor Tu (tuf) as the target sequence had also been described [Berg et al.,Mol. Cell. Probes, 10(1), 7-14,1996 and Luneberg et al., J.CIin.Microbiol., 31 (5), 1088-94, 1993].
The present invention, however, is concerned with the detection of EF-Tu mRNA as a marker for bacterial viability.
The present invention thus provides a method for the assessment of bacterial viability whereby mRNA coding for the elongation factor EF-Tu is used as a target in a nucleic acid amplification reaction and the presence and/or amount of said mRNA is determined.
The presumably short-lived mRNA coding for the EF-Tu is most likely highly abundant in the (myco)bacterial cell and a decrease therein will indicate a decline in metabolic activity.
Furthermore, because of the EF-Tu's essential role, it is plausible to assume that it is present in all mycobacterial species, allowing the development of a general amplification system with species-specific primers and/or probes, analogous to the 16S rRNA NASBA design [Vliet, G.M.E. van der, Schukkink, R.A.F., Gemen, B. van, Schepers, P. and Klatser, P.R. (1993) Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria. J. Gen. Microbiol. 139, 2423-2429.].
With the method of the present invention, preferably a transcription based amplification technique, such a NASBA, is used for the amplification of the bacterial EF-Tu mRNA. In contrast to RT-PCR, NASBA, which is based on RNA transcription by T7 RNA polymerase (Kievits et al., 1991 ; Compton, 1991 ), does not need differentiation between RNA- and DNA- derived amplification products since it uses RNA as its principal target.
The amplified products may be detected using a complementary labeled probe. Numerous protocols have been described for the detection of amplified products [Klatser, PR. (1995) Amplification reactions in mycobacteriology. J. Microbiol. Meth. 23, 75-87.]. Preferably homogeneous assays are used, because they would allow amplification reaction mixtures to be sealed before amplification is initiated. One such system, electro- chemiluminescence (ECL), has already been succesfully applied to detect amplified products in NASBA [Gemen, B. van, Beuningen, R. van, Nabbe, A., Strijp, D. van, Jurriaans, S., Lens, P., Kievits, T. (1994) A one-tube quantitative HIV-I RNA NASBA nucleic acid amplification assay using electrochemiluminescent (ECL) labelled probes. J. Virol. Methods, 49, 157-167.]. The method of the present invention is in particular useful for assessing the viability of
Mycobacteria species such as are M. tuberculosis or M.leprae.
With the present invention oligonucleotides are also provided that can be used as primers and probes for the amplification of bacterial EF-Tu mRNA. The use of the oligonucleotides according to the invention is not limited to any particular amplification technique or any particular modification thereof. It is evident that the oligonucleotides according to the invention find their use in many different nucleic acid amplification techniques and various methods for detecting the presence of (amplified) bacterial EF-Tu mRNA. The oligonucleotides of the present invention can likewise be used in quantitative amplification methods. An example of such quantitative method is described in EP 525882. The term "oligonucleotide" as used herein refers to a molecule comprised of two or more deoxyribonucleotides or ribonucleotides. Such oligonucleotides may be used as primers and probes.
Of course, based on the sequences of the oligonucleotides of the present invention, analogues of oligonucleotides can also be prepared. Such analogues may constitute alternative structures such as "PNA" (molecules with a peptide-like backbone instead of the phosphate sugar backbone of normal nucleic acid) or the like. It is evident that these alternative structures, representing the sequences of the present invention are likewise part of the present invention. The term "primer" as used herein refers to an oligonucleotide either naturally occurring
(e.g. as a restriction fragment) or produced synthetically, which is capable of acting as a point of initiation of synthesis of a primer extension product which is complementary to a nucleic acid strand (template or target sequence) when placed under suitable conditions (e.g. buffer, salt, temperature and pH) in the presence of nucleotides and an agent for nucleic acid polymerization, such as DNA dependent or RNA dependent polymerase. A primer must be sufficiently long to prime the synthesis of extension products in the presence of an agent for polymerization. A typical primer contains at least about 10 nucleotides in length of a sequence substantially complementary or homologous to the target sequence, but somewhat longer primers are preferred. Usually primers contain about 15-26 nucleotides but longer primers may also be employed, especially when the primers contain additional sequences such as a promoter sequence for a particular polymerase.
Normally a set of primers will consist of at least two primers, one 'upstream' and one 'downstream' primer which together define the amplificate (the sequence that will be amplified using said primers). Primarily for the use in transcription based amplification techniques, the oligonucleotides according to the invention may also be linked to a promoter sequence. The term "promoter sequence" defines a region of a nucleic acid sequence that is specifically recognized by an RNA polymerase that binds to a recognized sequence and initiates the process of transcription by which an RNA transcript is produced. In principle any promoter sequence may be employed for which there is a known and available polymerase that is capable of recognizing the initiation sequence. Known and useful promoters are those that are recognized by certain bacteriophage RNA polymerases such as bacteriophage T3, T7 or SP6. Oligonucleotides linked to a promoter sequence are commonly referred to as "promoter primers". Oligonucleotides according to the invention are substantially complementary to a sequence of a bacterial EF-Tu mRNA sequence, said oligonucleotide being 10-50 nucleotides in length and comprising at least 10 consecutive nucleotides of one of the sequences depicted in SEQ ID 1-8 or the complementary sequence thereof. Oligonucleotides comprising (a part of) SEQ ID's 1 and 2 have proven to be suitable for the amplification of Ef-Tu mRNA sequences of M.tuberculosis. In the event amplification is carried out with a transcription based amplification technique one of said oligonucleotides may also comprise a promoter sequence. Of course, such "promoter-oligonucleotides" are likewise art of the invention. In the sequence as depicted in SEQ ID 9 the T7 promoter has been linked to the sequence as depicted in SEQ ID 1. In the experimental part of this application these sequences are indicated as TUF15 (SEQ ID 9) and TUF 18 (SEQ ID 2).
The present invention also provides a pair of oligonucleotides for the amplification of
M.leprae derived EF-Tu sequences. This pair consists of an oligonucleotide comprising at least
10 consecutive nucleotides of the sequence as depicted in SEQ ID 3 and an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 4 respectively.
Again, for use in transcription based methods, one of the oligonucleotides may be linked to a promoter sequence, and an oligonucleotide provided with the T7 promoter sequence is depicted in SEQ ID 10. In the experimental part of the application such a pair is referred to as TUF 20 (SEQ ID 10) and TUF 22 (SEQ ID 4).
The present invention further provides a pair of oligonucleotides that are suitable for the amplification of E.coli derived EF-Tu sequences.
This pair consists of an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 5 and an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 6 respectively.
Again, for use in transcription based methods, one of the oligonucleotides may be linked to a promoter sequence, and an oligonucleotide provided with the T7 promoter sequence is depicted in SEQ ID 1 1. In the experimental part of the application such a pair is referred to as TUF 27 (SEQ ID 11 ) and TUF 22 (SEQ ID 6). These oligonucleotides are thus especially useful in the assessment of the viability of
M.tuberculosis, M.leprae or E.coli.
It is understood that oligonucleotides consisting of the sequences of the present invention may contain minor deletions, additions and/or substitutions of nucleic acid bases, to the extent that such alterations do not negatively affect the yield or product obtained to a significant degree. Where oligonucleotides according to the present invention are used as probes, the alterations should not result in lowering the hybridization efficiency of the probe.
For example, in case of transcription based amplification techniques, wherein one or more of the primers may be provided with a promoter sequence, the introduction of a purine- rich (= G or A) hybridizing sequence, just after the promoter sequence may have positive effects on the transcription (when there are C's and T's abortive transcription may occur). If no such sequence is available in the target nucleic acid a purine-rich sequence can be inserted in the oligonucleotide just following the last three G residues of the promoter sequence. The sequences of the present invention are reflected as DNA sequences. The RNA equivalents of these sequences are likewise part of the present invention.
Part of the oligonucleotides according to the invention are particularly suitable for use as a probe in the detection of nucleic acid amplified with a pair of oligonucleotides according to the invention. When used as a probe, said oligonucleotides may be provided with a detectable label. Various labeling moieties are known in the art. Said moiety may, for example, either be a radioactive compound, a detectable enzyme (e.g. horse radish peroxidase (HRP)), a hapten like biotin, or any other moiety capable of generating a detectable signal such as a colorimetric, fluorescent, chemiluminescent or electrochemiluminescent signal.
Hybrids between oligonucleotides according to the invention and (amplified) target nucleic acid may also be detected by other methods known to those skilled in the art. Oligonucleotides according to the invention that are especially suitable as a probe for the detection of Mycobacterial Ef-Tu sequences consist essentially of the sequences as depicted in SEQ ID 7 and 8 (In the experimental part said sequences are depicted as TUF 25 and TUF 26 respectively.). Together these probes can be used in a sandwich hybridization assay, whereby one can be used as capture probe and the other can be labeled with a detectable label.
A test kit for the detection of Mycobacterial EF-Tu mRNA in a sample is likewise part of the present invention. Such a kit may comprise a pair of oligonucleotides according to the invention and at least one oligonucleotide comprising a nucleic acid sequence substantially complementary to at least part of the amplified nucleic acid sequence , provided with a detectable label, as well as suitable amplification reagents. These reagents are for example the suitable enzymes for carrying out the amplification reaction. A kit, adapted for use with NASBA for example, may contain suitable amounts of reverse transcriptase, RNase H and T7 RNA polymerase. Said enzymes may be present in the kit in a buffered solution but can likewise be provided as a lyophilized composition, for example, a lyophilized spherical particle. Such lyophilized particles have been disclosed in PCT appl. no. EP95/01268. The kit may further be furnished with buffer compositions, suitable for carrying out an amplification reaction. Said buffers may be optimized for the particular amplification technique for which the kit is intended as well as for use with the particular oligonucleotides that are provided with the kit. In transcription based amplification techniques, such as NASBA, said buffers may contain, for example, DMSO, which enhances the amplification reaction (as is disclosed in PCT appl. no. US90/04733).
Furthermore the kit may be provided with an internal control as a check on the amplification procedure and to prevent the occurrence of false negative test results due to failures in the amplification procedure. The use of internal controls in transcription based amplification techniques is described in PCT appl. no. EP 93/02248. An optimal control sequence is selected in such a way that it will not compete with the target nucleic acid in the amplification reaction. Kits may also contain reagents for the isolation of nucleic acid from biological specimen prior to amplification. A suitable method for the isolation of nucleic acid is disclosed in EP389063.
BRIEF DESCRIPTION OF THE FIGURES:
Figure 1a: The analytical sensitivity of NASBA using in vitro produced mycobacterial EF-Tu RNA.
Figure 1 b: The analytical sensitivity of NASBA using in vitro produced mycobacterial EF-Tu RNA.
Figure 2 Specificity of the M.tuberculosis NASBA.
Figure 3 Specificity of the M.leprae NASBA. Figure 4 NASBA for viability assessment. EXAMPLES:
Example 1 :
Selection of primers and probes for the amplification of EF-Tu mRNA of M.tuberculosis, M.leprae and E.coli:
Sources of RNA. Table 1 shows the sources of RNAs that were used in the experiments described in this and the following examples. The cultivable mycobacteria were grown on Lowenstein-Jensen slants for 2-3 weeks. M.leprae was isolated from spleen tissue of an experimentally infected armadillo (Dasypus novemcinctus Linn.), as recommended by the World Health Organization [WHO Expert Committee on Leprosy. (1988) Sixth Report Tech. Rep. Ser. 8. 768. World Health Organization, Geneva.]. Other bacteria which might be found in human and/or animal samples or which are closely related to mycobacteria (see Table 1 ), were used for controls. For Actinomyces israelii lyophilized bacteria were used. The strains used for the production of in vitro RNA are described below.
Table 1. Sources of RNA and specificity of NASBA
Figure imgf000012_0001
Figure imgf000013_0001
Figure imgf000014_0001
Figure imgf000015_0001
AMC= Academic Medical Centre, Amsterdam, The Netherlands; CBS= Netherlands Culture Collections of Micro-Organisms, Baarn, The Netherlands; CDI= Central Veterinary Institute, Lelystad, The Netherlands; KIT= Royal Tropical Institute, Amsterdam, The
Netherlands; RIVM= National Institute of Public Health and Environment, Bilthoven, The Netherlands; SSI= Statens Serum Institute, Copenhagen, Denmark; ATCC= American Type Culture Collection, Rockvilie, USA.
Nucleic acid (NA) isolation. To perform the experiments described in all examples nucleic acids were isolated as we described previously [Vliet, G.M.E. van der, Schepers, P.,
Schukkink, R.A.F., Gemen, B. van and Klatser, P.R. (1994) Assessment of mycobacterial viability by RNA amplification. Antimicrob. Agents Chemother. 38, 1959-1965.]. In summary, all bacterial strains were adjusted to the turbidity equivalent of no. 4 McFarland barium sulphate nephelometer standard as described earlier [Verstijnen, C. P. H. J., H. M.
Ly, K. Polman, C. Richter, S. P. Smits, S. Y. Maselle, P. Peerbooms, D. Rienthong, N.
Montreewasuwat, S. Koanjanart, D. D. Trach, S. Kuijper, and A. H. J. Kolk (1991 ) Enzyme- . linked immunosorbent assay using monoclonal antibodies for identification of mycobacteria from early cultures. J. Clin. Microbiol. 29, 1372-1375.]. Fifty μl of the diluted samples contained approximately 105 viable mycobacteria as determined by counting the number of colony-forming units (not done for M.leprae). This volume was used for lysis and NA- isolation according to "protocol Y/SC" described by Boom et al. (1990) [ Boom, R., C.J.A.
Sol, M.M.M. Salimans, C.L. Jansen, P.M.E. Wertheim-Van Dillen and J. Van der Noordaa (1990). Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495-
503.]. The NA were eluted from the silica with 50 μl or 100 μl RNAse-free H20 and stored at -20°C.
Human placental NA were isolated in a similar fashion (kindly provided by Dr. H.
Smits, Department of Virology, Academic Medical Hospital, Amsterdam, The Netherlands). Two μl containing 270 ng NA was tested. This amount corresponds to approximately 4 x
105 diploid human cells. Another batch of human NA was obtained commercially from
Pharmacia (Uppsala, Sweden).
Example 2:
Sensitivity and specificity of NASBA in the amplification of EF-Tu mRNA of M.tuberculosis, M.leprae and E.coli:
Selection of primers and probes. The primers and probes used in this study are listed in Table 2. Table 2. Primers and probes
Figure imgf000018_0001
Figure imgf000019_0001
Abbreviations:
ECTUF = E. coli EF-Tu gene sequence (GenBank accession number J01717)
MTTUF = M.tuberculosis EF-Tu gene sequence (GenBank accession number X63539)
MLTUF = M.leprae EF-Tu gene sequence (GenBank accession number D13869)
I = Inosine, M=[A,C], K = [G,T], R = [A,G]
® The sequence shown is homologous to MLTUF and not to MTTUF (where the underlined G is an A).
TUF 15, 20 and 27 include the T7 promoter sequence which is shown in lower case.
The promoter sequence is followed by a purine rich region (AGAG) which is shown in italics.
The published nucleotide sequences of the EF-Tu genes of M.tuberculosis (GenBank accession number X63539), M.leprae (GenBank accession number D13869), E. coli
(GenBank accession number J01717), Micrococcus luteus (GenBank accession number
M17788) and Streptomyces coelicolor (GenBank accession number X77039) were aligned using the software programme GCG (National Institute of Health, USA)) installed on appropriate hardware. Degenerative primers TUF4 and TUF7 (Table 2) were selected to amplify a 764 bp DNA fragment of the EF-Tu genes by PCR from all organisms listed in
Table 1. PCR was performed using 75 mM Tris-HCI, pH9.0, 20 mM (NH4)2S04, 0.01% (v/v)
Tween 20, 4 mM MgCI2, 0.2 mM of each dNTP, 125 ng of each primer and 1 U/reaction of Goldstar DNA polymerase (Eurogentec, Belgium). PCR was initiated by incubation at 94 °C for 3 min followed by 35 cycles of 1.15 min at 94 °C, 1 min at 55 °C and 2 min at 72 °C. The generated PCR fragments of the DNA of the organisms listed in Table 1 , except C.belfanti, H. influenza, S.aureus, S. pneumoniae and H. sapiens were purified using a MicroSpin Sephacryl 300 HR column (Pharmacia) to remove excess of primers. The purified fragments were sequenced directly using primers TUF 3F, 4F and 8F by applying the Autocycle Sequencing Kit (Pharmacia) and the A.L.F. automatic DNA sequencer (Pharmacia). Sequences were edited by using the DNASIS software programme (Pharmacia) and clustal alignments were then made using the PCGene software programme.
Selection of primers and probes. Table 3 shows the seven variable regions of the EF- Tu sequences which were defined based on the clustal alignments. From these variable regions it is possible to select primers and probes enabling species-specific detection of EF-Tu mRNA of different organisms (Table 4). Table 5 shows the clustal alignments of two (region IV and VI) of the seven variable regions of the EF-Tu sequence on the basis of which the primers and probes were selected for specific amplification of M.tuberculosis, M.leprae and E.coli EF-Tu mRNA through NASBA. The criteria to select these two areas were: the availability of species-specific primers, a genus-specific probe and a length of ± 200 nucleotides of the fragment to be amplified. Table 3. Seven variable regions on the EF-Tu sequences
Figure imgf000021_0001
Table 4.
Parts of the EF-Tu mRNA variable sequences which can be used for the selection of primers and/or probes enabling species-specific detection of EF-Tu mRNA from different organisms.
Figure imgf000022_0001
Figure imgf000023_0001
Figure imgf000024_0001
Figure imgf000025_0001
Table 5.
Two clustal alignments (region IV and VI) of the variable regions of the EF-Tu sequence
Figure imgf000026_0001
Figure imgf000027_0002
Figure imgf000027_0001
Based on these alignments species-specific primers for the use in NASBA were selected for M.tuberculosis (TUF 15 and 18), for M.leprae (TUF 20 and 22) and for E.coli (TUF 27 and 28). A generic capture probe TUF 25 and detection probe TUF 26 were chosen for the detection of the mycobacterial RNA amplicons by electrochemiluminescence (ECL). Probe TUF 25 is homologous to the EF-Tu sequence of M.leprae and not to that of M.tuberculosis; the difference is one nucleotide (G→A; see Table 2). However, this difference did not affect the detection of amplicons generated from RNA originating from M.tuberculosis. For the detection of E.coli RNA amplicons we used the specific capture and detection probes TUF 29 and TUF 30, respectively. In region IV one nucleotide difference was found with the published sequence of EF-
Tu of M.tuberculosis [GenBank accession number X63539]: in none of the strains belonging to the M.tuberculosis complex a C at position 855 was found. However, the primer position was chosen in such a way that this discrepancy would not influence the amplification reaction.
Example 3:
Specificity and sensitivity testing of E.coli by amplification of EF-Tu mRNA.
Isolation of in vitro RNA.
A 764 bp fragment of the EF-Tu gene of M.tuberculosis H37Rv, M.leprae and E.coli (Table 1 ) was amplified via PCR using the primer set TUF 4 and TUF 7 (Table 2), as described above. The amplified product was cloned into the pCR II vector using the TA- cloning kit (Invitrogen) following the manufacture's instructions. Selection of the appropriate clone with the insert in the correct orientation, size and specificity was determined by restriction enzyme analysis and PCR.
After linearization of the plasmid with the restriction enzymes Bam HI and Hind 111, the cloned insert within the polylinker region was transcribed from the T7 promoter site using the SP6/T7 transcription kit (Boehringer, Mannheim). The DNA template was removed by digestion with RQI DNAse (Promega) and the RNA was purified by the RNeasy kit from Qiagen according the manufacturer's protocol. Purity was checked by agarose gel electrophoresis and Northern blotting with digoxigenine-labelled probe TUF 24 according to standard procedures. The in vitro RNA was quantified by measuring the extinction at 260 nm. RNA Amplification.
A 203, 197 and 198 nucleotide fragment of the EF-Tu mRNA of M.tuberculosis,
M.leprae and E.coli, respectively, was amplified by the NASBA technique essentially as described before [Vliet, G.M.E. van der, Schepers, P., Schukkink, R.A.F., Gemen, B. van and Klatser, P.R. (1994) Assessment of mycobacterial viability by RNA amplification. Antimicrob. Agents Chemother. 38, 1959-1965.]. The 20 μl reaction mix was composed of 40 mM Tris-HCI, pH 8.5, 12 mM MgCI2, 70 mM KCI, 5 mM DTT, 1.5 M sorbitol, 2.1 mg BSA, 1 mM of each dNTP, 2 mM of ATP, CTP, UTP, 1.5 mM of GTP and 0.5 mM ITP, 15% -. (v/v) DMSO, 0.2 mM Primer 1 and Primer 2, 0.08 U RNase H, 32 U T7 RNA polymerase, 6.4 U AMV-RT polymerase and the RNA target. Isothermal amplification of the RNA target was performed by incubation of these samples at 41 °C for 2.0 h.
Detection of the amplified RNA was done by in-solution hybridization in the ECL detection assay, as described previously [Gemen, B. van, Beuningen, R. van, Nabbe, A., Strijp, D. van, Jurriaans, S., Lens, P., Kievits, T. (1994) A one-tube quantitative HIV-I RNA NASBA nucleic acid amplification assay using electrochemiluminescent (ECL) labelled probes. J. Virol. Methods, 49, 1] with minor modifications: 5 μl of NASBA amplified RNA was either diluted 20-fold in RNase-free water or used undiluted. A 5'-biotinylated probe was used to capture the NASBA product. The detection probe used was tris [2,2-bipyridine] ruthenium [II] complex labelled. This label emits light as a result of chemical reactions taking place at the surface of an electrode. The cutoff value was set at 3000. The ECL detection assay was measured on a scale of 0 to 108.
Controls for amplification.
Negative controls (water only) were included in each experiment in order to check for carry-over contamination during NA-extraction and amplification. These control samples were extracted and amplified by NASBA in the same manner as described above.
Sensitivity and specificity of the mycobacteria NASBA.
For determination of the sensitivity of the NASBA, M.tuberculosis ATCC 35801 was grown in liquid Tween/Albumin medium at 37 °C. The concentration at the start of the culture was 8.106 bacteria/ml. Growth of the bacteria was monitored by measuring the extinction at 420 nm. After 13 days of culture a sample was taken and diluted in lysis buffer [Boom, R., C.J.A. Sol, M.M.M. Salimans, C.L. Jansen, P.M.E. Wertheim-Van Dillen and J. Van der Noordaa (1990). Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495-503.]. Serial dilutions were made in lysis buffer, RNA purified [Boom, R., C.J.A. Sol, M.M.M. Salimans, C.L. Jansen, P.M.E. Wertheim-Van Dillen and J. Van der Noordaa (1990). Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28, 495-503.] and each dilution was tested in NASBA to determine the highest dilution still giving a positive NASBA signal. In addition the analytical sensitivity of NASBA was determined using serial dilutions of in vitro RNA (see above). The specificity of NASBA was determined using the purified RNA from different organisms (Table 1 , see above).
Sensitivity and specificity of the E.coli NASBA.
E.coli was grown in Luria Broth (LB) liquid medium at 37 °C for 18 h. The suspension thus obtained was inoculated in fresh medium (1 :200)(OD 600nm = 0.015) and incubated at 37 °C in a gyratory shaker for 3 h and 15 min (OD 600nm = 0.430). A serial dilution was made and mRNA was purified as described above. In addition, the same dilutions were plated onto LB agar plates which were incubated at 37 °C for 18 h after which colonies were counted. The analytical sensitivity of NASBA was determined using serial dilutions of in vitro
RNA (see above).
Results:
Sensitivity of NASBA. The analytical sensitivity of NASBA using in vitro produced EF- Tu RNA is illustrated in Figure 1a and 1b. Both the M.tuberculosis NASBA and the
M.leprae NASBA had a detection of 50 molecules of RNA (Fig 1a). The detection limit of the M.tuberculosis NASBA when using bacteria as starting material for detection was
12,000 (result not shown).
The analytical sensitivity of the E.coli NASBA was shown to be 100 molecules (Fig. 1b). The detection limit of the E.coli NASBA when using bacteria as starting material for detection was 0.4 (result not shown).
Specificity of NASBA. The specificity of the M.tuberculosis NASBA and the M.leprae NASBA is illustrated in Figures 2 and 3, respectively. The M.tuberculosis NASBA showed specificity for the RNA purified from bacteria belonging to the M.tuberculosis complex only. Furthermore, as illustrated in Figure 2, the M.tuberculosis NASBA showed a positive reaction when homologous in vitro produced EF- Tu RNA was used as target.
The M.leprae NASBA showed specificity for M.leprae RNA only and its homologous in vitro produced RNA. Example 4:
Viability testing of E.coli.
E.coli was grown in LB liquid medium at 37 °C for 18 h. The suspension thus obtained was inoculated in fresh medium (1:1000)(OD 600nm = 0.001) and incubated at 37 °C in a gyratory shaker for 4 h. The suspension was then divided in two equal parts. To one part a cocktail of antibiotics was added to kill the bacteria: ampicillin, rifampicin and kanamycin (each 50 μg/ml); the other part was left untouched. Both were incubated at 37 °C for another 3 h and 30 min. Every 30 min the OD at 600 nm was monitored and a 100 sample from each culture was taken and added to 900 lysis buffer; mRNA was purified as described above (9). In addition, viability of the E.coli bacteria was monitored by overlaying a sample (100 ) onto LB agar plates. Colonies were counted after 18 h incubation at 37 °C.
The NASBA signals increased and reached its maximum level when E.coli was left to grow untouched (Figure 4). However, when antibiotics were added to the exponentially growing E.coli culture, the NASBA signal decreased 1 h after the addition of the antibiotics.
This drop in mRNA concentration as measured by NASBA was coinciding with a decrease in the number of viable counts (Figure 4).

Claims

CLAIMS:
1. Method for the assessment of bacterial viability whereby mRNA coding for the elongation factor EF-Tu is used as a target in a nucleic acid amplification reaction and the presence and/or amount of said mRNA is determined.
2. Method according to claim 1 , wherein said nucleic acid amplification reaction is a transcription based amplification reaction.
3. Method according to claim 2, wherein the transcription based amplification method is NASBA.
4. Method according to any of claims 1-3, wherein the amplified mRNA is detected with a complementary labeled probe.
5. Method according to claim 4, wherein the probe is provided with an electro- chemiluminescent label.
6. Method according any of the preceding claims wherein the bacteria are Mycobacteria.
7. Method according to claim 6, wherein the Mycobacteriae species are M.tuberculosis or M.leprae.
8. Oligonucleotide substantially complementary to a sequence of a bacterial EF-Tu mRNA sequence, said oligonucleotide being 10-50 nucleotides in length and comprising at least 10 consecutive nucleotides of one of the sequences depicted in SEQ ID 1-8 or the complementary sequence thereof.
9. Pair of oligonucleotides for the amplification of a sequence in the EF-Tu gene of M.tuberculosis, said pair consisting of an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 1 and an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 2 respectively.
0. Pair of oligonucleotides for the amplification of a sequence in the EF-Tu gene of M.leprae, said pair consisting of an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 3 and an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 4 respectively.
11. Pair of oligonucleotides for the amplification of a sequence in the EF-Tu gene of E.coli, said pair consisting of an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ ID 5 and an oligonucleotide comprising at least 10 consecutive nucleotides of the sequence as depicted in SEQ
ID 6 respectively.
12. Method for the assessment of the viability of M.tuberculosis, M.leprae or E.coli wherein a pair of oligonucleotides according to claim 9, 10 or 11 is used respectively for amplifying Ef-Tu mRNA and the presence and/or amount of amplified nucleic acid is detected.
13. Method according to claim 12, wherein the viability of M.tuberculosis or M.leprae is assessed and detection of amplified nucleic acid is carried out using a sandwich hybridization assay with a capture probe having at least 10 consecutive nucleotides of a sequence as depicted in SEQ ID 7 and a labeled detection probe having at least 10 consecutive nucleotides of the sequence depicted in SEQ ID 8.
14. Method according to claim 12, wherein the viability of E.coli is assessed and detection of amplified nucleic acid is carried out using a sandwich hybridization assay with a capture probe having at least 10 consecutive nucleotides of a sequence as depicted in SEQ ID 12 and a labeled detection probe having at least 10 consecutive nucleotides of the sequence depicted in SEQ ID 13.
15. Test kit for the detection of Mycobacterial EF-Tu mRNA in a sample comprising:
- a pair of oligonucleotides according to claim 9 or 10 ,
- at least one oligonucleotide comprising a nucleic acid sequence substantially complementary to at least part of the amplified nucleic acid sequence , provided with a detectable label - suitable amplification reagents. Test kit for the detection of E.coli bacterial EF-Tu mRNA in a sample comprising:
- a pair of oligonucleotides according to claim 11 ,
- at least one oligonucleotide comprising a nucleic acid sequence substantially complementary to at least part of the amplified nucleic acid sequence , provided with a detectable label
- suitable amplification reagents.
PCT/EP1999/000323 1998-01-23 1999-01-19 EF-Tu mRNA AS A MARKER FOR VIABILITY OF BACTERIA WO1999037804A2 (en)

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JP2000528711A JP4634604B2 (en) 1998-01-23 1999-01-19 EF-Tu mRNA as a marker for bacterial viability
AU27176/99A AU2717699A (en) 1998-01-23 1999-01-19 Ef-tu mrna as a marker for viability of bacteria
EP99907386A EP1049809B1 (en) 1998-01-23 1999-01-19 EF-Tu mRNA AS A MARKER FOR VIABILITY OF BACTERIA
US09/600,770 US6489110B1 (en) 1998-01-23 1999-01-19 EF-Tu mRNA as a marker for viability of bacteria

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AU2717699A (en) 1999-08-09
US6489110B1 (en) 2002-12-03
EP1049809B1 (en) 2006-10-25
JP2011050387A (en) 2011-03-17
CA2318726A1 (en) 1999-07-29
JP2002500893A (en) 2002-01-15
ATE343642T1 (en) 2006-11-15
DE69933755T2 (en) 2007-09-13
EP1049809A2 (en) 2000-11-08
JP4634604B2 (en) 2011-02-16
ZA99362B (en) 1999-07-19

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