Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR

Ju Chien Cheng, Chien Ling Huang, Chung Ching Lin, Chi Ching Chen, Yi Chih Chang, Shy Shin Chang, Ching Ping Tseng

Research output: Contribution to journalArticle

119 Citations (Scopus)

Abstract

Background: Broad-range PCR provides valuable information for detecting bacterial infections. This study assesses the combined use of broad-range real-time PCR and high-resolution melting analysis for rapid detection and identification of clinically important bacteria. Methods: We subjected 46 bacterial culture colonies representing 25 clinically important bacterial species to LightCycler real-time PCR amplification of the 16S rRNA gene in the presence of LCGreen I fluorescent dye. We performed high-resolution melting analysis of the PCR products with the HR-1 instrument and used melting profiles as molecular fingerprints for bacterial species identification. We validated this method via assessment of 54 consecutive bacteria culture colonies obtained from a clinical microbiology laboratory. Results: The 16S rRNA gene of all 25 bacterial species was amplifiable by this method, with PCR product lengths of 216 or 217 bp. Of the 25 bacterial species, we identified 11 via a 1-step post-PCR high-resolution melting analysis. The remaining bacterial species were identified via the high-resolution melting plots obtained by heteroduplex formation between the PCR products of the tested and reference bacterial species or by a 2nd real-time PCR targeting a different region of the 16S rRNA gene. A high-resolution melting database and a working protocol were established for identifying these 25 bacterial species. In the validation assay, a 94% accuracy rate was achieved when the bacterial species were in the high-resolution melting database. Conclusions: This assay requires no multiplexing or hybridization probes and provides a new approach for bacterial species identification in a molecular diagnostic laboratory.

Original languageEnglish
Pages (from-to)1997-2004
Number of pages8
JournalClinical Chemistry
Volume52
Issue number11
DOIs
Publication statusPublished - Nov 1 2006
Externally publishedYes

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Ribosomal RNA
Freezing
Real-Time Polymerase Chain Reaction
Bacteria
Melting
Polymerase Chain Reaction
rRNA Genes
Genes
Assays
Databases
Microbiology
Molecular Pathology
Dermatoglyphics
Fluorescent Dyes
Multiplexing
Bacterial Infections
Amplification

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR. / Cheng, Ju Chien; Huang, Chien Ling; Lin, Chung Ching; Chen, Chi Ching; Chang, Yi Chih; Chang, Shy Shin; Tseng, Ching Ping.

In: Clinical Chemistry, Vol. 52, No. 11, 01.11.2006, p. 1997-2004.

Research output: Contribution to journalArticle

Cheng, Ju Chien ; Huang, Chien Ling ; Lin, Chung Ching ; Chen, Chi Ching ; Chang, Yi Chih ; Chang, Shy Shin ; Tseng, Ching Ping. / Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR. In: Clinical Chemistry. 2006 ; Vol. 52, No. 11. pp. 1997-2004.
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abstract = "Background: Broad-range PCR provides valuable information for detecting bacterial infections. This study assesses the combined use of broad-range real-time PCR and high-resolution melting analysis for rapid detection and identification of clinically important bacteria. Methods: We subjected 46 bacterial culture colonies representing 25 clinically important bacterial species to LightCycler real-time PCR amplification of the 16S rRNA gene in the presence of LCGreen I fluorescent dye. We performed high-resolution melting analysis of the PCR products with the HR-1 instrument and used melting profiles as molecular fingerprints for bacterial species identification. We validated this method via assessment of 54 consecutive bacteria culture colonies obtained from a clinical microbiology laboratory. Results: The 16S rRNA gene of all 25 bacterial species was amplifiable by this method, with PCR product lengths of 216 or 217 bp. Of the 25 bacterial species, we identified 11 via a 1-step post-PCR high-resolution melting analysis. The remaining bacterial species were identified via the high-resolution melting plots obtained by heteroduplex formation between the PCR products of the tested and reference bacterial species or by a 2nd real-time PCR targeting a different region of the 16S rRNA gene. A high-resolution melting database and a working protocol were established for identifying these 25 bacterial species. In the validation assay, a 94{\%} accuracy rate was achieved when the bacterial species were in the high-resolution melting database. Conclusions: This assay requires no multiplexing or hybridization probes and provides a new approach for bacterial species identification in a molecular diagnostic laboratory.",
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