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Article: Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: A proof-of-concept study

TitleNovel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: A proof-of-concept study
Authors
Issue Date2011
PublisherAmerican Society for Microbiology.
Citation
Journal Of Clinical Microbiology, 2011, v. 49 n. 3, p. 814-821 How to Cite?
AbstractBurkholderia pseudomallei, Burkholderia thailandensis, and the Burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. Yet, they are occasionally misidentified by biochemical profiling, and even 16S rRNA gene sequencing may not offer adequate discrimination between certain species groups. Using the 23 B. pseudomallei, four B. thailandensis, and 16 B. cepacia complex genome sequences available, we identified gene targets specific to each of them (a Tat domain protein, a 70-kDa protein, and a 12-kDa protein for B. pseudomallei, B. thailandensis, and the B. cepacia complex, respectively), with an in-house developed algorithm. Using these targets, we designed a robust multiplex PCR assay useful for their identification and detection from soil and simulated sputum samples. For all 43 B. pseudomallei, seven B. thailandensis, and 20 B. cepacia complex (B. multivorans, n = 6; B. cenocepacia, n = 3; B. cepacia, n = 4; B. arboris, n = 2; B. contaminans, B. anthina, and B. pyrrocinia, n = 1 each; other unnamed members, n = 2) isolates, the assay produced specific products of predicted size without false positives or negatives. Of the 60 soil samples screened, 19 (31.6%) and 29 (48.3%) were positive for B. pseudomallei and the B. cepacia complex, respectively, and in four (6.7%) soil samples, the organisms were codetected. DNA sequencing confirmed that all PCR products originated from their targeted loci. This novel pan-genomic analysis approach in target selection is simple, computationally efficient, and potentially applicable to any species that harbors species-specific genes. A multiplex PCR assay for rapid and accurate identification and detection of B. pseudomallei, B. thailandensis, and the B. cepacia complex was developed and verified. Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Persistent Identifierhttp://hdl.handle.net/10722/135261
ISSN
2015 Impact Factor: 3.631
2015 SCImago Journal Rankings: 2.151
PubMed Central ID
ISI Accession Number ID
Funding AgencyGrant Number
Committee of Research and Conference Grants
University of Hong Kong
Croucher Foundation
Funding Information:

This work was partly supported by the Committee of Research and Conference Grants, The University of Hong Kong, and the Croucher Foundation.

References

 

DC FieldValueLanguage
dc.contributor.authorHo, CCen_HK
dc.contributor.authorLau, CCYen_HK
dc.contributor.authorMartelli, Pen_HK
dc.contributor.authorChan, SYen_HK
dc.contributor.authorTse, CWSen_HK
dc.contributor.authorWu, AKLen_HK
dc.contributor.authorYuen, KYen_HK
dc.contributor.authorLau, SKPen_HK
dc.contributor.authorWoo, PCYen_HK
dc.date.accessioned2011-07-27T01:30:51Z-
dc.date.available2011-07-27T01:30:51Z-
dc.date.issued2011en_HK
dc.identifier.citationJournal Of Clinical Microbiology, 2011, v. 49 n. 3, p. 814-821en_HK
dc.identifier.issn0095-1137en_HK
dc.identifier.urihttp://hdl.handle.net/10722/135261-
dc.description.abstractBurkholderia pseudomallei, Burkholderia thailandensis, and the Burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. Yet, they are occasionally misidentified by biochemical profiling, and even 16S rRNA gene sequencing may not offer adequate discrimination between certain species groups. Using the 23 B. pseudomallei, four B. thailandensis, and 16 B. cepacia complex genome sequences available, we identified gene targets specific to each of them (a Tat domain protein, a 70-kDa protein, and a 12-kDa protein for B. pseudomallei, B. thailandensis, and the B. cepacia complex, respectively), with an in-house developed algorithm. Using these targets, we designed a robust multiplex PCR assay useful for their identification and detection from soil and simulated sputum samples. For all 43 B. pseudomallei, seven B. thailandensis, and 20 B. cepacia complex (B. multivorans, n = 6; B. cenocepacia, n = 3; B. cepacia, n = 4; B. arboris, n = 2; B. contaminans, B. anthina, and B. pyrrocinia, n = 1 each; other unnamed members, n = 2) isolates, the assay produced specific products of predicted size without false positives or negatives. Of the 60 soil samples screened, 19 (31.6%) and 29 (48.3%) were positive for B. pseudomallei and the B. cepacia complex, respectively, and in four (6.7%) soil samples, the organisms were codetected. DNA sequencing confirmed that all PCR products originated from their targeted loci. This novel pan-genomic analysis approach in target selection is simple, computationally efficient, and potentially applicable to any species that harbors species-specific genes. A multiplex PCR assay for rapid and accurate identification and detection of B. pseudomallei, B. thailandensis, and the B. cepacia complex was developed and verified. Copyright © 2011, American Society for Microbiology. All Rights Reserved.en_HK
dc.languageengen_US
dc.publisherAmerican Society for Microbiology.-
dc.relation.ispartofJournal of Clinical Microbiologyen_HK
dc.rightsJournal of Clinical Microbiology. Copyright © American Society for Microbiology.-
dc.rightsCopyright © American Society for Microbiology, [Journal of Clinical Microbiology, volume 49, 814-821, 2011]-
dc.subject.meshAnimals-
dc.subject.meshBacteriological Techniques - methods-
dc.subject.meshBurkholderia - classification - genetics - isolation and purification-
dc.subject.meshBurkholderia Infections - diagnosis - microbiology-
dc.subject.meshPolymerase Chain Reaction - methods-
dc.titleNovel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: A proof-of-concept studyen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0095-1137&volume=49&issue=3&spage=814&epage=821&date=2011&atitle=Novel+pan-genomic+analysis+approach+in+target+selection+for+multiplex+PCR+identification+and+detection+of+Burkholderia+pseudomallei,+Burkholderia+thailandensis+and+Burkholderia+cepacia+complex+species:+a+proof-of-concept+study-
dc.identifier.emailYuen, KY:kyyuen@hkucc.hku.hken_HK
dc.identifier.emailLau, SKP:skplau@hkucc.hku.hken_HK
dc.identifier.emailWoo, PCY:pcywoo@hkucc.hku.hken_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.identifier.authorityLau, SKP=rp00486en_HK
dc.identifier.authorityWoo, PCY=rp00430en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1128/JCM.01702-10en_HK
dc.identifier.pmid21177905-
dc.identifier.pmcidPMC3067743-
dc.identifier.scopuseid_2-s2.0-79952329442en_HK
dc.identifier.hkuros195242en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79952329442&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume49en_HK
dc.identifier.issue3en_HK
dc.identifier.spage814en_HK
dc.identifier.epage821en_HK
dc.identifier.isiWOS:000287967100009-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridHo, CC=42061526500en_HK
dc.identifier.scopusauthoridLau, CCY=8398162900en_HK
dc.identifier.scopusauthoridMartelli, P=24067396100en_HK
dc.identifier.scopusauthoridChan, SY=36901190200en_HK
dc.identifier.scopusauthoridTse, CWS=7103295064en_HK
dc.identifier.scopusauthoridWu, AKL=7402998681en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK
dc.identifier.scopusauthoridLau, SKP=7401596211en_HK
dc.identifier.scopusauthoridWoo, PCY=7201801340en_HK

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