Direct identification of mycobacteria from clinical specimens by multiplex real‐time PCR

AIMS: To directly identify clinically relevant mycobacteria from clinical specimens, we have developed a multiplex real‐time PCR assay with hydrolysis probes that can identify 20 mycobacterial species. METHODS AND RESULTS: The assay was initially evaluated using 248 strains, including both reference...

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Published in:Journal of applied microbiology 2015-06, Vol.118 (6), p.1498-1506
Main Authors: Kim, J.‐U, Cha, C.H, An, H.K
Format: Article
Language:English
Subjects:
Bacteria
clinical specimen
Humans
hydrolysis
identification
Microbiology
Multiplex Polymerase Chain Reaction - methods
mycobacteria
Mycobacterium - classification
Mycobacterium - genetics
Mycobacterium - isolation & purification
Mycobacterium Infections - diagnosis
Mycobacterium Infections - microbiology
Mycobacterium tuberculosis
Mycobacterium tuberculosis complex
Polymerase chain reaction
quantitative polymerase chain reaction
rapid methods
Real-Time Polymerase Chain Reaction - methods
real‐time PCR
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creator Kim, J.‐U
Cha, C.H
An, H.K
description AIMS: To directly identify clinically relevant mycobacteria from clinical specimens, we have developed a multiplex real‐time PCR assay with hydrolysis probes that can identify 20 mycobacterial species. METHODS AND RESULTS: The assay was initially evaluated using 248 strains, including both reference strains and clinical isolates. Then, the assay was implemented according to a scheme in our laboratory. The scheme based on the clinical differences between the Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) consisted of three stepwise PCRs. MTC and NTM were differentially detected in the step 1 PCR, and the NTM species were identified in the step 2 and step 3 PCRs. During a 2·5‐year period, 1877 isolates of MTC (1142 directly recovered from clinical specimens) and 596 isolates of NTM (143 directly recovered from clinical specimens) were detected, and the species of 590 (99·0%) of the 596 NTM isolates were identified. CONCLUSIONS: Our experience shows that this is a new paradigm for rapidly and accurately identifying clinically relevant mycobacteria, in which a multiplex real‐time PCR assay is directly applied to clinical specimens in a stepwise fashion. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is the first report of a multiplex real‐time PCR assay for identifying clinically important mycobacterial species directly from clinical specimens and its application in a clinical microbiology laboratory.
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SIGNIFICANCE AND IMPACT OF THE STUDY: This study is the first report of a multiplex real‐time PCR assay for identifying clinically important mycobacterial species directly from clinical specimens and its application in a clinical microbiology laboratory.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/jam.12780</identifier><identifier>PMID: 25715744</identifier><identifier>CODEN: JAMIFK</identifier><language>eng</language><publisher>England: Published for the Society for Applied Bacteriology by Blackwell Science</publisher><subject>Bacteria ; clinical specimen ; Humans ; hydrolysis ; identification ; Microbiology ; Multiplex Polymerase Chain Reaction - methods ; mycobacteria ; Mycobacterium - classification ; Mycobacterium - genetics ; Mycobacterium - isolation &amp; purification ; Mycobacterium Infections - diagnosis ; Mycobacterium Infections - microbiology ; Mycobacterium tuberculosis ; Mycobacterium tuberculosis complex ; Polymerase chain reaction ; quantitative polymerase chain reaction ; rapid methods ; Real-Time Polymerase Chain Reaction - methods ; real‐time PCR</subject><ispartof>Journal of applied microbiology, 2015-06, Vol.118 (6), p.1498-1506</ispartof><rights>2015 The Society for Applied Microbiology</rights><rights>2015 The Society for Applied Microbiology.</rights><rights>Copyright © 2015 The Society for Applied Microbiology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5150-db3419a884c001048fc3de8876111e8484cae81db58f9804791002366663d3be3</citedby><cites>FETCH-LOGICAL-c5150-db3419a884c001048fc3de8876111e8484cae81db58f9804791002366663d3be3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjam.12780$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjam.12780$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>315,786,790,27957,27958,50923,51032</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25715744$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kim, J.‐U</creatorcontrib><creatorcontrib>Cha, C.H</creatorcontrib><creatorcontrib>An, H.K</creatorcontrib><title>Direct identification of mycobacteria from clinical specimens by multiplex real‐time PCR</title><title>Journal of applied microbiology</title><addtitle>J Appl Microbiol</addtitle><description>AIMS: To directly identify clinically relevant mycobacteria from clinical specimens, we have developed a multiplex real‐time PCR assay with hydrolysis probes that can identify 20 mycobacterial species. METHODS AND RESULTS: The assay was initially evaluated using 248 strains, including both reference strains and clinical isolates. Then, the assay was implemented according to a scheme in our laboratory. The scheme based on the clinical differences between the Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) consisted of three stepwise PCRs. MTC and NTM were differentially detected in the step 1 PCR, and the NTM species were identified in the step 2 and step 3 PCRs. During a 2·5‐year period, 1877 isolates of MTC (1142 directly recovered from clinical specimens) and 596 isolates of NTM (143 directly recovered from clinical specimens) were detected, and the species of 590 (99·0%) of the 596 NTM isolates were identified. CONCLUSIONS: Our experience shows that this is a new paradigm for rapidly and accurately identifying clinically relevant mycobacteria, in which a multiplex real‐time PCR assay is directly applied to clinical specimens in a stepwise fashion. 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source Wiley; Oxford Journals Online; Alma/SFX Local Collection
subjects Bacteria
clinical specimen
Humans
hydrolysis
identification
Microbiology
Multiplex Polymerase Chain Reaction - methods
mycobacteria
Mycobacterium - classification
Mycobacterium - genetics
Mycobacterium - isolation & purification
Mycobacterium Infections - diagnosis
Mycobacterium Infections - microbiology
Mycobacterium tuberculosis
Mycobacterium tuberculosis complex
Polymerase chain reaction
quantitative polymerase chain reaction
rapid methods
Real-Time Polymerase Chain Reaction - methods
real‐time PCR
title Direct identification of mycobacteria from clinical specimens by multiplex real‐time PCR
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