An efficient strategy for broad-range detection of low abundance bacteria without DNA decontamination of PCR reagents

Shy Shin Chang, Hsung Ling Hsu, Ju Chien Cheng, Ching Ping Tseng

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Background: Bacterial DNA contamination in PCR reagents has been a long standing problem that hampers the adoption of broad-range PCR in clinical and applied microbiology, particularly in detection of low abundance bacteria. Although several DNA decontamination protocols have been reported, they all suffer from compromised PCR efficiency or detection limits. To date, no satisfactory solution has been found. Methodology/Principal Findings: We herein describe a method that solves this long standing problem by employing a broad-range primer extension-PCR (PE-PCR) strategy that obviates the need for DNA decontamination. In this method, we first devise a fusion probe having a 3′-end complementary to the template bacterial sequence and a 5′-end non-bacterial tag sequence. We then hybridize the probes to template DNA, carry out primer extension and remove the excess probes using an optimized enzyme mix of Klenow DNA polymerase and exonuclease I. This strategy allows the templates to be distinguished from the PCR reagent contaminants and selectively amplified by PCR. To prove the concept, we spiked the PCR reagents with Staphylococcus aureus genomic DNA and applied PE-PCR to amplify template bacterial DNA. The spiking DNA neither interfered with template DNA amplification nor caused false positive of the reaction. Broad-range PE-PCR amplification of the 16S rRNA gene was also validated and minute quantities of template DNA (10-100 fg) were detectable without false positives. When adapting to real-time and high-resolution melting (HRM) analytical platforms, the unique melting profiles for the PE-PCR product can be used as the molecular fingerprints to further identify individual bacterial species. Conclusions/Significance: Broad-range PE-PCR is simple, efficient, and completely obviates the need to decontaminate PCR reagents. When coupling with real-time and HRM analyses, it offers a new avenue for bacterial species identification with a limited source of bacterial DNA, making it suitable for use in clinical and applied microbiology laboratories.

Original languageEnglish
Article numbere20303
JournalPLoS One
Volume6
Issue number5
DOIs
Publication statusPublished - May 31 2011
Externally publishedYes

Fingerprint

Decontamination
decontamination
Bacteria
Bacterial DNA
Polymerase Chain Reaction
DNA
bacteria
Microbiology
Melting
melting
Amplification
probes (equipment)
Exodeoxyribonucleases
Freezing
DNA Polymerase I
microbiology
DNA Primers
Contamination
Fusion reactions
DNA Contamination

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

An efficient strategy for broad-range detection of low abundance bacteria without DNA decontamination of PCR reagents. / Chang, Shy Shin; Hsu, Hsung Ling; Cheng, Ju Chien; Tseng, Ching Ping.

In: PLoS One, Vol. 6, No. 5, e20303, 31.05.2011.

Research output: Contribution to journalArticle

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