Patent Application
20100159448
The present invention is related, in general, to the detection, identification, and quantification of pathogenic bacteria, and particularly to a method for the detection and multiple, simultaneous quantification of any combination of pathogens, such as Listeria sp, Staphylococcus aureusm Campylobacter jejuni and/or Escherichia coli O157:H7, by means of multiplex amplification reaction, using real-time polymerase chain reaction.
At present, the detection of pathogenic bacteria transmissible by food, such as Listeria sp, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157:H7, is a very important task in the field of medicine and public health and is very important in the agro-foodstuffs, both for the producer and the distributor of food products (raw materials and/or processed products), for which several methods have been described for their detection and identification.
One of the current methodologies, considered among the most effective in the detection, identification and quantification of pathogens, is the one that is based on molecular techniques, as the method of polymerase chain reaction, commonly known as PCR. The PCR procedure is generally regarded as the most sensitive and rapid method used to detect nucleic acids of pathogens in a given sample test in particular, and we can find it described within the state of the art by Kary B. Mullis et al. in the family of U.S. Pat. No. 4,683,195, U.S. Pat. No. 4,683,202, U.S. Pat. No. 4,800,159, U.S. Pat. No. 4,889,818, U.S. Pat. No. 4,965,188, U.S. Pat. No. 5,008,182, U.S. Pat. No. 5,038,852, U.S. Pat. No. 5,079,352, U.S. Pat. No. 5,176,995, U.S. Pat. No. 5,310,652, U.S. Pat. No. 5,310,893, U.S. Pat. No. 5,322,770, U.S. Pat. No. 5,333,675, U.S. Pat. No. 5,352,600, U.S. Pat. No. 5,374,553, U.S. Pat. No. 5,386,022, U.S. Pat. No. 5,405,774, U.S. Pat. No. 5,407,800, U.S. Pat. No. 5,418,149, U.S. Pat. No. 5,420,029 among others.
To perform the PCR technique, basically, you need at least one pair of oligonucleotides for each of the pathogens to be identified, so that each pair of primers include a first nucleotide sequence complementary to a sequence that borders on the extreme 5′ of a sequence of a nucleic acid target and a second nucleotide sequence complementary to a sequence that borders the 3′ end of the sequence of nucleic acid target. Nucleotide sequences should have every pair of oligonucleotide primers which are specific to the pathogen to be detected, so that they do not react or are crossed with other pathogens.
As the PCR technique is a sensitive and quick method to detect pathogens on an individual basis, this can also be used to simultaneously detect multiple pathogens present in a sample. However, the PCR methodology used for simultaneous detection of multiple pathogens in a sample is problematic, since its main obstacle lies in the cross reaction that may be present due to the use of multiple nucleotide sequences in order to have the preferential amplification of certain target sequences, present in the sample at the expense of other target sequences, also present.
Examples of multiple and simultaneous detection of pathogens, using the PCR methodology, are described by John W. Czajka in the issuance of international patent application WO-0314704, and by Linxian Wo and others in the family of U.S. Pat. No. 5,612,473, U.S. Pat. No. 5,738,995, U.S. Pat. No. 5,753,444, U.S. Pat. No. 5,756,701, and U.S. Pat. No. 5,846,783.
The publication of international patent application WO-0314704 describes a method to detect specific and simultaneously pathogen species of Campylobacter in a complex test sample. The pathogen species of Campylobacter to be detected may be Campylobacter jejuni or Campylobacter coli. The complex test sample can be a sample of food, water or a rich array of food. The method uses the PCR amplification with or without an internal positive control and appropriate pairs of primers. Multiple species can be detected in said reaction.
In the family of U.S. Pat. No. 5,612,473, U.S. Pat. No. 5,738,995, U.S. Pat. Nos. 5,753,444, 5,756,701, and U.S. Pat. No. 5,846,783 a multiplex PCR method is described to detect infectious agents quickly and simultaneously in one sample. The infectious agents that are detected, are Salmonella spp, Shigella spp, Campylobacter spp, Yersinia spp and Escherichia coli, in particular Escherichia coli O157:H7. The limitation of the method described in these patents is that it allows a minimum cross-reaction between the oligonucleotides and probes, as well as of the first ones with other sequences of nucleic acid during the amplification.
Other molecular methods that are currently used, there are some on the market to detect pathogens in food, some through DNA hybridization (Gene-Trak systems, Unipath), which is very sensitive but requires about 50 hours, and others by means of nucleic acid amplification (BAX, Dupont and FOMS Probelia, Sanofi Diagnostic Pasteur) requiring at least 24 hours. None of these methods provides results on the same day of the production of food, nor makes any quantification of the present pathogenic contamination.
Among the methods described above, in some cases it will be necessary only to increase the sensitivity of the method to detect the presence or absence of pathogens in particular reliably and rapidly, whereas in other cases it may be necessary, moreover, to further quantify pathogens that may present in order to establish the limits of concentration, starting from which the presence of the pathogen may present a problem for the consumer's health.
According to the former, it is of utmost concern to the food and health industry to have a quick method, which employs less than 5 hours, to detect and quantify simultaneously four of the most important infectious agents or pathogens, transmissible by food and/or contaminated environmental surfaces, such as Listeria sp, Staphylococcus aureus, Campylobacter jejuni, and Escherichia coli O157:H. This detection and multiple, simultaneous and quick quantification of pathogens, through reaction of multiplex amplification using polymerase chain reaction in real time, will allow to save costs and time in an industry where the times on the shelf of the products are extremely important.
According to the above and in order to find solutions to the constraints encountered, it is the object of the invention to offer a method for the detection and multiple, simultaneous quantification of any combination of pathogens, selected from a group consisting of Listeria spp, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157:H7, in one or more test samples, by multiplex amplification reaction, using real-time polymerase chain reaction (PCR), the steps of the method are: (a) extracting DNA from the test sample or samples; (b) preparing a reaction mixture specific for the pathogens to be detected and quantified, such that the reaction mixture contains the necessary reagents for enzymatic amplification of the extracted DNA and identification of the pathogens to be detected and quantified; (c) amplifying the reaction mixture by means of multiplex amplification reaction using PCR; and (d) simultaneously determining the presence or absence of and quantification of the pathogens in the test sample or samples; the method is particular in that (i) the reaction mixture for the enzymatic amplification of DNA extracted and identification of any combination of Listeria spp, Staphylococcus aureus, Campylobacter jejuni and/or Escherichia coli O157:H7 to be detected and quantified contains (a) a first pair of oligonucleotide primers identified as SEQ ID NO: 1 and SEQ ID NO: 2 and a probe identified as SEQ ID NO: 3, which react with an initial target nucleic acid sequence of Listeria sp; (b) a second pair of oligonucleotide primers identified as SEQ ID NO: 4 and SEQ ID NO: 5 and a probe identified as SEQ ID NO: 6, which react with a second target nucleic acid sequence of Staphylococcus aureus, (c) a third pair of oligonucleotide primers identified as SEQ ID NO: 7 and SEQ ID NO: 8 and a probe identified as SEQ ID NO: 9, which react with a third target nucleic acid sequence of Campylobacter jejuni, and/or (d) fourth pair of oligonucleotide primers identified as SEQ ID NO: 10 and SEQ ID NO: 11 and a probe identified as SEQ ID NO: 12, which react with a fourth target nucleic acid sequence of Escherichia coli O157:H7, (ii) the presence or absence of and quantification of said pathogens in any combination of Listeria spp, Staphylococcus aureus, Campylobacter jejuni and/or Escherichia coli O157:H7 in the test sample or samples is determined by means of a fluorescent signal or fluorescence emission specific for each pathogen.
Another object of this invention is to provide an oligonucleotide that has a nucleotide sequence selected from a group consisting of sequences identified as SEQ ID NO: 1, SEQ ID NO: 2 and SEQ ID NO: 3.
It is also the object of the invention to provide an oligonucleotide that has a nucleotide sequence selected from a group consisting of sequences identified as SEQ ID NO: 4, SEQ ID NO: 5 and SEQ ID NO: 6.
Another object of the invention is an oligonucleotide that has a nucleotide sequence selected from a group consisting of sequences identified as SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID NO: 9.
It is also the object of the invention to provide an oligonucleotide that has a nucleotide sequence selected from a group consisting of sequences identified as SEQ ID NO: 10, SEQ ID NO: 11 and SEQ ID NO: 12.
In addition to the above, it is also the object of the invention to provide a marked probe which includes an oligonucleotide identified as SEQ ID NO: 3, and at least one marker.
Another object of the invention is to provide a marked probe which includes an oligonucleotide identified as SEQ ID NO: 6, and at least one marker.
It is also the subject of a marked probe the invention which includes an oligonucleotide identified as SEQ ID NO: 9, and at least one marker.
Another object of the invention is to provide a marked probe which includes an oligonucleotide identified as SEQ ID NO: 12; and at least one marker.
Finally, it is the object of the invention to provide a diagnostic kit for the detection and multiple, simultaneous quantification of any combination of pathogens, selected from a group consisting of Listeria spp, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157:H7, in one or more test samples, by multiplex amplification reaction, using real-time polymerase chain reaction (PCR), the diagnostic kit has (a) one or more oligonucleotides as any group of sequences identified as SEQ ID NO: 1, SEQ ID NO: 2 and SEQ ID NO: 3; SEQ ID NO: 4, SEQ ID NO: 5 and SEQ ID NO: 6; SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID NO: 9; and/or SEQ ID NO: 10, SEQ ID NO: 11 and SEQ ID NO: 12; (b) one or more marked probes that contain any of the oligonucleotides with its sequences identified as SEQ ID NO: 3, SEQ ID NO: 6, SEQ ID NO: 9 and SEQ ID NO: 12; and a different marker for each sequence, and (c) other reagents or compositions needed to perform the test.
The characteristic details of the invention are described in the following paragraphs together with the figures that accompany it, which are for the purpose of defining the invention but not limiting its scope.
The term “enzymatic amplification of DNA,” as used in the context of this description, means the use of polymerase chain reaction (PCR) to increase the concentration of a particular DNA sequence within a combination of DNA sequences. The particular sequence of DNA that is amplified is referred to as a “target sequence.”
The term “pair of primers” is employed under the meaning of a pair of oligonucleotide that are complementary to the sequences bordering the target sequence. The pair of primers is an “upstream” primer which has a nucleic acid sequence that is complementary to a sequence “upstream” of the target sequence, and a “downstream” primer which has a nucleic acid sequence that is a sequence complementary to “downstream” of the target sequence.
The term “multiplex amplification reaction” means, in the context of this description, amplified by PCR procedure, multiple target sequences of DNA in a test sample in particular.
In the present invention four bacteria were detected and quantified simultaneously using the technique of real-time PCR, which compared with other techniques, does not require a pre-enrichment, nor preparing a series of tubes with a mixture of a specific reaction for each bacteria to be detected; it is necessary to stress that it is a breakthrough that four bacteria are detected simultaneously the total time of analysis is reduced to 2.5 hrs minimum, representing a competitive advantage in decreasing the cost of analysis, using the same mixture for the detection test. Additionally, better sensitivity was achieved, as the sample preparation (which is already included in the 2.5 hrs time) has given better results because it has been adapted so that there are no factors that could adversely affect the amplification.
The method provided by this invention allows detecting, identifying and quantifying multiple pathogens simultaneously transmissible via food, contaminated surfaces or environments, such as Listeria sp, Staphylococcus aureus, Campylobacter jejuni and/or Escherichia coli O157:H7, in one or more test samples, through multiplex amplification reaction using polymerase chain reaction in real time. The test sample can be any sample that contains DNA and you want to know the possible contamination of by said pathogens. In a particular realization, said test sample is a sample of a food product, for example, meat and milk products, or a sample of contaminated surfaces or environments.
The oligonucleotides of the invention have been designed in order to identify specifically, Listeria sp, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157:H7 that may be present in a sample test without giving false positives because of the presence of other pathogens it may contain.
There is a couple of oligonucleotide primers for each of the pathogens to be identified (Listeria sp, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157:H7), so that each pair of primers comprises a first synthetic nucleotide “upstream” sequence complementary to a nucleotide “upstream” sequence which borders the extreme 5′ of a nucleic acid sequence target, and a second synthetic nucleotide “downstream” sequence, complementary to a “downstream” sequence which borders the extreme 3′ of the nucleic acid sequence target. Nucleotide sequences should have every pair of oligonucleotide primers which are specific to the pathogen to be detected, so that they do not react or are crossed with other pathogens. Also, for each of the pathogens to be identified, a synthetic sequence of a probe test is developed. Oligonucleotides developed are shown in Table 1.
Listeria sp
Listeria sp
Listeria sp
Staphylococcus
aureus
Staphylococcus
aureus
Staphylococcus
aureus
Campylobacter
jejuni
Campylobacter
jejuni
Campylobacter
jejuni
Escherichia coli
Escherichia coli
Escherichia coli
In a preferential embodiment of the invention sequences SEQ ID NO: 3, SEQ ID NO: 6, SEQ ID NO: 9 and SEQ ID NO: 12, used as test probes are marked in their 5′ extreme with a fluorophoro or a dye capable of emitting energy, and at its 3′ end with an extinguisher or a dye capable of capturing the energy emitted by the fluorophoro excitation. The fluorophores and dyes, used as markers to detect and identify Listeria sp, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157:H7 without producing cross-reactions between them and other components are shown in Table 2.
Listeria sp
Staphylococcus
aureus
Campylobacter
jejuni
Escherichia coli
To develop the methodology of the invention the following steps are considered for the preparation of a test sample:
First, there is a stage of washing, where a food sample, environmental or surface area is subject to a saline solution forming a suspension which was subsequently centrifuged to obtain a first sediment obtained by the elimination of water-soluble substances present in the suspension.
Once the sediment of the sample is obtained, it is incubated with lysozyme to break down the cell wall of the bacteria present in the sample, then proceed with an incubation with proteinase K to cause the hydrolysis of proteins and the lysozyme previously added.
The extraction of proteins and other fat-soluble compounds present is performed through the application of phenol-chloroform-alcohol, so that once extracted, through a precipitation with ethanol, a selective precipitation of the DNA present is performed, forming a concentration of DNA that is dried.
Finally, with the concentration of DNA obtained, a suspension is formed that is heated to approximately 65° C., which causes a quick dissolution of the DNA sample.
In each of the elements tested, quantity tests of added reagent were performed, times of centrifuge-incubation, repetition of the washings, until finding the optimal conditions. The sample preparation was done taking into account that all the reagents and samples should be kept at a cooling temperature during its process.
Examples of the preparation process of the sample or test samples for DNA are described below:
Once the sample or test samples of DNA are obtained, a reaction mix is prepared using components described in Table 3.
1.5X
Listeria sp
Staphylococcus
aureus
Campylobacter
jejuni
Escherichia coli
Subsequently, a cocktail of reaction was prepared for 100 reactions by mixing the ingredients described in Table 4.
Listeria sp
Staphylococcus
aureus
Campylobacter
jejuni
Escherichia coli
The cocktail prepared mixes perfectly by inversion and 19.75 μl are dispensed Eppendorf flasks of 0.5 ml to be stored, frozen, and protected from light.
In a preferential embodiment of the invention, the multiplex amplification reaction using PCR in real-time provides many advantages over the conventional PCR method to detect a single target. The multiplex amplification reaction using multiplex PCR requires the development of oligonucleotide primers and probes, specific for the target sequence of the pathogen to be detected, so that said oligonucleotide primers and probes be compatible with one another within the same optimum temperature of 40° C. to 65° C. and submitted to the same conditions of chemical reaction in order to allow the crossing or tying by hybridization of two segments of complementary nucleic acid. In addition to this, the sets of oligonucleotide primers and probes should not react crossedly or be tied during the amplification to other nucleic acid sequences for which they were not designed.
Given the above, the following pairs of oligonucleotide primers are used to amplify each of the target nucleic acid sequences of each pathogen to be detected. A pair of oligonucleotide primers of Listeria sp identified as SEQ ID NO: 1 and SEQ ID NO: 2, which are crossed or tied to a target sequence of the genome of Listeria sp. A pair of oligonucleotide primers of Staphylococcus aureus identified as SEQ ID NO: 4 and SEQ ID NO: 5 that are crossed or tied to a target sequence of the genome of Staphylococcus aureus. A pair of oligonucleotide primers of Campylobacter jejuni identified as SEQ ID NO: 7 and SEQ ID NO: 8 which are crossed or tied to a target sequence of the genome of Campylobacter jejuni. And a pair of oligonucleotide primers of Escherichia coli O157:H7 identified as SEQ ID NO: 10 and SEQ ID NO: 11, which are crossed or tied to a target sequence of the genome of Escherichia coli O157:H7.
Each probe identified as SEQ ID NO: 3, SEQ ID NO: 6, SEQ ID NO: 9 and SEQ ID NO: 12, which is used in the multiplex amplification reaction using PCR in real-time, is a double-marked oligonucleotide sequence that is complementary to each of the intermediate sequences in the amplified products that were obtained. Each of the probes is marked on its 5′ end with a fluorophore or a dye capable of emitting energy, and on its 3′ end with an extinguisher or a dye, capable of capturing the energy emitted by the excitation of said fluorophore, as described by Nazarenko et al. in the U.S. Pat. No. 5,866,336 which mentions fluorophores that transfer energy and how these are applied in the oligonucleotide primers in the methods of nucleic amplification.
In a preferential embodiment of the invention, the fluorophores used are TET, TxR, Cy5, FAM, while the dyes are BHQ-1, BHQ-2 and BHQ-3. So that the oligonucleotide sequences used as probes (SEQ ID NO: 3, SEQ ID NO: 6, SEQ ID NO: 9 and SEQ ID NO: 12) are marked on their 5′ and 3′ ends according to the combination shown in Table 2 above.
In one particular example of embodiment, the DNA sample is prepared for its amplification under the following conditions:
Sample of milk or of environment: A flask was defrosted with 19.75 μl of a cocktail prepared and added 0.25 μl of Taq DNA polymerase, 4 μl of water and 1 μl of the sample of DNA to be analyzed.
Sample of meat or cheese: A flask was defrosted with 19.75 μl of a cocktail prepared and added 0.25 μl of Taq DNA polymerase, 5 μl of the sample of DNA to be analyzed.
The multiplex amplification reaction using PCR is performed on an apparatus for the simultaneous control of multiple nucleic acid amplifications, as the device described by Russell G. Higuchi and Robert M. Watson in the publication of the European Patent EP-640,828, which usually consists of a thermal cycler with a plurality of holes where tubes are introduced containing the reaction mixture for the enzymatic amplification of DNA from pathogens to be detected and identified; a light source coupled to the thermal cycler and adapted to distribute the light on the plurality of holes, and a sensor or fluorescence detector adapted to simultaneously detect the emitted light.
In order to quantify the micro-organism present in the sample, calibration curves are produced, preparing suspensions of each of the pathogens to be detected (Listeria sp, Staphylococcus aureus, Campylobacter jejuni and Escherichia coli O157:H7), adjusting the turbidity in the Mc Farland tube of 0.5 to prepare dilutions to 10−1, 10−2, 10−3, 104, 105, 106, 107 and 108 and then contaminate 25 grams of food with each of these suspensions (one food for each dilution). Then, proceed to the extraction of DNA as if it were a sample and an account is prepared on a plate of each of the dilutions prepared to be submitted to the thermal cycler, assigning the corresponding concentration of pathogens. Finally, the curve of cT against log ug/g is built, thereby obtaining a calibration curve for Listeria sp (see
In one particular embodiment, the apparatus used comprises a fast thermal cycler in real-time coupled to a fluorescence detection system, allowing real-time monitoring of the process of amplification after each cycle. An example of the thermal cycler used in the method of the invention is the cycler SMART CYCLER® II of CEPHEID®.
The presence or absence and quantification of pathogens in any combination of Listeria spp, Staphylococcus aureus, Campylobacter jejuni and/or Escherichia coli O157:H7 in a sample or test samples is determined by a fluorescent signal or emission of specific fluorescence of each product or amplified DNA sample. Therefore, a specific wave length is pointed out for the excitation of each fluorescence and its emission at specific wavelengths is detected.
In an example of embodiment, Table 5 presents the conditions in which the multiplex amplification reaction was carried out, Table 6 presents the detection limits, and Table 7 shows the readings of concentrations that were obtained as a result of detection and quantification of the four pathogens (Listeria sp, Staphylococcus aureus, Campylobacter jejuni and/or Escherichia coli O157:H7) simultaneously in samples of cold meats, dairy and atmosphere, using only one device with a single mixture of reagents and four specific oligonucleotides for different pathogens to a single condition of temperatures and mixing for their amplification. Also, the
Staphylo-
Campylo-
Listeria
coccus
bacter
Escherichia
aureus
jejuni
coli O157: H7
Staphylococcus
Campylobacter
Escherichia coli
Listeria sp
aureus
jejuni
The method of the present invention does not require a pre-enrichment, therefore, the process time is much shorter, approximately 2.5 hours, and has the capacity to detect and quantify possible pathogens cultivable, apart from possible pathogens non-cultivable in a simultaneous manner.
In general, the diagnostics sets of the invention contain each of the pairs of oligonucleotide primers corresponding to each of the pathogens to be detected (Listeria sp, Staphylococcus aureus, Campylobacter jejuni and/or Escherichia coli O157:H7), just as each of the probes marked for each of said pathogens, in order to be able to make a choice between performing the detection of a single pathogen (using only the pair of oligonucleotide primers and its probe marked), or for the simultaneous or combined detection of the four pathogens mentioned, depending on the necessities.
The diagnostics kits provided by this invention may be presented in the form of a box containing, in addition to some containers with the pairs of oligonucleotide primers and/or marked probes mentioned previously, some containers with the totality or part of the rest of the reagents needed to perform said method, for example, ultrapure water, dNTPs (dATP, dCTP, dGTP, and dTTP), an appropriate buffer for the enzymatic amplification reaction, a thermostable DNA polymerase (e.g., Taq DNA polymerase), a magnesium salts (for example, MgCl2), among others. Additionally and optionally, the diagnostics sets provided by this invention may include some containers with DNA from Listeria sp, Staphylococcus aureus, Campylobacter jejuni and/or Escherichia coli O157:H7 for their use as positive controls.
Based on the embodiments described above, it is considered that the modifications to the environments of the described embodiment, as well as to the environments of alternate embodiments will be considered evident for an expert in the state of the art under the present description. Therefore, it is considered that the claims cover those modifications and alternatives that are within the scope of the present invention or its equivalents.
| Number | Date | Country | Kind |
|---|---|---|---|
| NL/A/2006/000028 | Apr 2006 | MX | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/MX2007/000052 | 4/19/2007 | WO | 00 | 10/23/2008 |
