Primer and probe for detection of mycobacterium avium and method for detection of mycobacterium avium by using the primer or probe

Abstract

The object of the present invention is to provide a novel primer for use in the detection of Mycobacterium avium (M. avium), and a method for detection of M. avium conveniently, rapidly and with high precision by using the primer. More specifically, disclosed are an oligonucleotide which comprises a part or an entire of the nucleotide sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:132, SEQ ID NO:133, SEQ ID NO:134, SEQ ID NO:135 and SEQ ID NO:136, or a part or an entire of the sequence complementary to the nucleotide sequence, and which is capable of hybridizing with the nucleotide sequence for a Mycobacterium avium gene; a primer and a probe for use in the detection of M. avium, which comprises the oligonucleotide; and a method for detection of M. avium using the primer and / or probe.

Description

RELATED APPLICATIONS[0001]This is a division of application Ser. No. 15 / 386,409, filed Dec. 21, 2016, which is a division of application Ser. No. 12 / 519,141, filed Jun. 12, 2009, which is a national phase filing of International Application No. PCT / JP2007 / 072324, filed on Nov. 16, 2007, which claims priority from Japanese Patent Application No. 2006-339884, filed Dec. 18, 2016, and Japanese Patent Application No. 2006-356189, filed Dec. 28, 2006. Each of these applications are incorporated herein by reference for all purposes.TECHNICAL FIELD[0002]The present invention relates to a method for detection and / or identification of Mycobacterium avium (hereinafter, described as M. avium) in clinical laboratory testing through the use of nucleic acid amplification and detection system.BACKGROUND ART[0003]Nontuberculous Mycobacterium is a gram positive Bacillus having acid-fast characteristics classified into genus Mycobacterium (hereinafter, optionally abbreviated simply as M.), and is a k...

AI Technical Summary

Benefits of technology

[0028]According to the method for detection of M. avium using the primer and / or probe of the present invention, M. avium can be detect and diagnosed more rapidly and with high precision as compared to the conventional bacterium identification method by bacterial cell culture examination and the like. In addition, by performing the detection using the method of the present invention, any false-positive result in diagnosis can be eliminated as compared with the diagnostic method by the PCR using a conventional primer and / or a probe, and as the results, M. avium can be detected and diagnosed with higher accuracy and preciseness in a specific manner. In addition, by the use of the detection method of the present invention, M. avium cell can also be quantified.

[0029]In addition, according to the method for detection of M. avium using the primer and / or probe which comprises a sequence derived from the sequence shown in SEQ ID NO:130 to 136 of the present invention, namely the sequence shown in SEQ ID NO:130 to 205, the plural number of M. avium with various serotypes can be detected specifically and efficiently in distinction from other Mycobacterium genus by a single measurement. In addition, this may make detection procedure simple and also may provide such a beneficial effect that the time necessary for the diagnosis will be reduced.

Problems solved by technology

However, on rare occasions, they may exert infectivity to human.

However, nontuberculous Mycobacterium diseases do not show any specific clinical symptom.

Therefore, it is quite difficult to differentiate tuberculosis from nontuberculous Mycobacterium disease by clinical observation and histopathological manifestation, and to specify the species of the nontuberculous Mycobacterium.

However, by this test, what can be figured out is only whether the pathogenic bacterium is “positive for acid-fast bacterium” or not and whether the pathogenic bacterium is tuberculosis bacterium or nontuberculous Mycobacterium cannot be differentiated.

However, in general, growth of bacterium belonging to genus Mycobacterium is slow; for example, it takes 3 to 4 weeks only for its isolation culture.

Accordingly, the conventional basic method, in which a diagnostic outcome on whether the disease is tuberculosis or not is obtained by conducting the above described smear examination and a cell culture examination, is a considerably time-consuming method.

However, in the usual PCR method, the number of bacterial count cannot be determined.

Therefore, by the PCR method, diagnosis on whether the bacteria detected in a patient are infectious or not will be uncertain.

Furthermore, the method has a problem such as providing a frequent false positive judgment due to its too high sensitivity.

1). However, by this method, discrimination between M. avium and M. intracellulare cannot be ach

vium. However, even by the detection method using these probe and primer, there also disclosed some cases where M. avium can not be identified clearly as M. avium depending on the typ

e of strain. That is, the specificity of these probe and primer for M. avium is far from

However, in the PCR using aforementioned primer, the primer extension product can be obtained in either the case where the sample is avian tuberculosis bacterium (M. avium) and the case of M. intracellulare, and therefore, this determination method can not be said as a specific method for M. avium< /

i>. In addition, the method, whereby the discrimination between both bacterial strains is carried out based on the chain length of the primer extension product is cumbersome; and it is conceivable that different determination may be made by different judge; and in consequence, it cannot be said that the method is a reliable determination met

Because of that, MAC can be detected by this method; however, it is impossible to detect M. avium specifically.

In addition, even when MAC is detected, there can be an instance where false-positive result is provided.

However, specific detection of M. avium is impossible to achieve without detection of M. intracellulare.

However, in the LAMP method, there are some problems, for example, the nucleotide sequence of amplified DNA cannot be determined; efficient length of DNA to be amplified is limited; and the method provides false-positive result occasionally.

Therefore, it is difficult to find out a consensus sequence between strains.

In consequence, it is difficult to detect all the M. avium having various serotypes by PCR using single primer set.

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