Contamination of Qiagen DNA Extraction Kits with
            <i>Legionella</i>
            DNA

Evans, Gloria; Murdoch, David R.; Anderson, Trevor P.; Potter, Howard; George, Peter M.; Chambers, Stephen T.

doi:10.1128/jcm.41.7.3452-3453.2003

Cited by 54 publications

(28 citation statements)

References 5 publications

(3 reference statements)

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“…Casjens, 2003). While columns and reagents can be contaminated with low levels of bacteria and mouse sequences (van der Zee et al ., 2002; Evans et al ., 2003; Shen et al ., 2006; Erlwein et al ., 2011), non‐uniform contamination across treatments and replicates argues against kit‐based contamination being responsible. Further, it is unlikely that contaminating DNA would have survived myriad purification methods across triplicate samples, which suggests that GTAs are the probable largest contributor to the ‘bacterial’ signal in these data.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Hurwitz

Deng

Poulos

et al. 2012

Environmental Microbiology

167

177

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Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF-concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3-precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k-mers (100% of reads) showed 50–53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF-concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k-mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for ‘rare’ reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture-independent viral ecology studies.

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Section: Discussionmentioning

confidence: 99%

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Hurwitz

Deng

Poulos

et al. 2012

Environmental Microbiology

167

177

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“…Total DNA from blood samples was extracted using a commercial kit (DNeasy blood and tissue kit; Qiagen), following the pretreatment steps for bacteria. A further pretreatment of Qiagen columns was performed to wash away contaminating bacterial DNA [2,3].…”

Section: Plasma Levels Of Bacterial Dna In Hiv Infection: the Limits mentioning

confidence: 99%

Plasma Levels of Bacterial DNA in HIV Infection: The Limits of Quantitative Polymerase Chain Reaction

et al. 2010

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“…The Taq DNA polymerase can be contaminated with bacterial DNA, creating technical dilemmas when developing universal 16S rRNA gene-based tests [14]. Legionella and other microbial contaminants have been detected in DNA extraction kits [15,16]. Additionally, technical error can lead to false positives.…”

Section: Sources Of False-positive Resultsmentioning

confidence: 99%

False positives and false negatives encountered in diagnostic molecular microbiology

Sefers

Pei

Tang

2005

Reviews in Medical Microbiology

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Nucleic acid-based tests are rapidly expanding in the field of diagnostic microbiology, due to their unique high sensitivity and specificity as well as rapid assay turnaround time. However, the potential of false positives and false negatives can hinder the wide application of these novel techniques. This mini-review article summarizes common causes and potential solutions for false-positives and false-negatives encountered in the field of diagnostic molecular microbiology.

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Contamination of Qiagen DNA Extraction Kits with Legionella DNA

Cited by 54 publications

References 5 publications

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

Plasma Levels of Bacterial DNA in HIV Infection: The Limits of Quantitative Polymerase Chain Reaction

False positives and false negatives encountered in diagnostic molecular microbiology

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