Microbial DNA qPCR Multi-Assay Kits

For real-time PCR-based, application-specific microbial identification or profiling; includes 3–6 assay tubes in one box for 20 reactions
  • Complete kit for microbial profiling with assays, controls, and reagents 
  • Includes a panel of experimentally verified Microbial DNA qPCR Assays
  • Uses 5' hydrolysis probe detection for high sensitivity and specificity
Microbial DNA qPCR Multi-Assay Kits are a complete solution for real-time PCR-based microbial detection. Microbial DNA qPCR Multi-Assay Kits contain a panel of Microbial DNA qPCR Assays, which are a mix of two PCR primers (10 µM each) and one 5′-hydrolysis probe (5 µM) that enable quantitative real-time PCR. The kit also contains everything required for a successful qPCR run, including Microbial DNA Positive Control, Positive PCR Control, Microbial DNA-Free Water and Microbial qPCR Mastermix.

What is the difference between microbial identification and profiling? Identification is determining the microbe’s presence or absence in your sample which requires running a No Template Control during your analysis. Profiling is determining the microbe’s relative expression in two or more experimental conditions for which you will need to run a reference sample and a normalizer (provided by QIAGEN).
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1501Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1502Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1503Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1504Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1505Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1506Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1507Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1508Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1509Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1510Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1511Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1512Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1513Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1514Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1515Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1516Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1517Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1518Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1519Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1520Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1521Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1522Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1523Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1524Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1525Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1526Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1551Z
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One 20 µl tube for each Microbial DNA qPCR Assay, 1 tube Positive PCR Control (20 µl), 1 tube Microbial DNA Positive Control (50 µl), 1 or 2 tubes Microbial DNA-Free Water (1.35 ml each), 1 or 2 tubes Microbial qPCR Mastermix (1.35 ml each)
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330043 BBID-1552Z
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Microbial DNA qPCR Multi-Assay Kits are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.


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Limit of detection versus lower limit of quantification.|The lower limit of quantification (LLOQ) for all Microbial DNA qPCR Assays reveals high sensitivity.|The lower limit of quantification (LLOQ) for microbial identification Microbial DNA qPCR Assays reveals high sensitivity.|The lower limit of quantification (LLOQ) for virulence factor gene detection Microbial DNA qPCR Assays reveals high sensitivity.|The lower limit of quantification (LLOQ) for antibiotic resistance gene detection Microbial DNA qPCR Assays reveals high sensitivity.|Microbial DNA qPCR Assays are highly specific.|Microbial DNA qPCR Assays display high sensitivity even in complex metagenomic samples.|
This chart demonstrates the difference between the limit of detection (LOD) and the lower limit of quantification (LLOQ). The LOD is defined as the lowest concentration at which 95% of the positive samples are detected, whereas the LLOQ is the lowest concentration that falls within the linear range of a standard curve. LOD depends upon the precision of the assay, and requires at least 40 replicates for determination of a positive sample. For the Microbial DNA qPCR Assays, LLOQ is sufficient to determine assay sensitivity.|This chart shows the distribution of LLOQ for all Microbial DNA qPCR Assays. 93% of all Microbial DNA qPCR Assays have a LLOQ of <100 gene copies.
|This chart shows the distribution of LLOQ for microbial identification Microbial DNA qPCR Assays. 92% of all microbial identification assays have a LLOQ of <100 gene copies.|This chart shows the distribution of LLOQ for Microbial DNA qPCR Assays for virulence factor gene detection. 97% of all virulence factor gene assays have a LLOQ of <100 gene copies.|This chart shows the distribution of LLOQ for Microbial DNA qPCR Assays for antibiotic resistance gene detection. 95% of all antibiotic resistance gene assays have a LLOQ of <100 gene copies.|To determine the specificity of Microbial DNA qPCR Assays, each assay was tested against 119 genomic DNA samples from different bacteria and fungi. To facilitate testing, genomic DNA from different microbial species was pooled (10 different genomic DNA samples per pool) and each assay was tested against the different pools. None of the pools contained DNA from the same genus, to facilitate identification of cross-reacting species. Each pool contained the equivalent of 2000 genome copies for each microbial species. In addition, each assay was tested against human, mouse, and rat genomic DNA. A representative example for Streptococcus pyogenes is shown. The assay for Streptococcus pyogenes gave a CT of 26.9 and 26.6 for the Staphylococcus/Streptococcus pool and complete pool [A]. Both pools contained genomic DNA for Streptococcus pyogenes. To determine which genomic DNA was detected by the Streptococcus pyogenes assay, each individual genomic DNA comprising the Staphylococcus/Streptococcus pool was tested separately [B]. Only Streptococcus pyogenes genomic DNA gave an acceptable CT call (26.8) while the others gave a CT>35. Most of the assays were specific as they did not detect unintended targets. For assays that detected other species, the list of detected targets along with in silico predictions are given in the specifications sheet.
|To ensure that Microbial DNA qPCR Assays performed comparably in a complex sample, where there may be up to a thousand different microbial species, each assay was tested using stool, tooth plaque, and sputum samples. For each sample, synthetic template targets were spiked in and the CT was compared to synthetic template alone. PCR was performed using several sample types, which included pooled synthetic template targets alone, stool, stool plus pooled synthetic template targets, plaque, plaque plus pooled synthetic template targets, sputum, and sputum plus pooled synthetic template targets. If the CT<35 in stool, plaque, or sputum samples alone, then ΔCT was calculated (i.e., CTstool – CTpooled synthetic template targets). This calculation was performed for all the assays. For each assay, the ΔCT<3, indicating that a complex metagenomic background does not affect the performance of each Microbial DNA qPCR Assay.|
Performance
Lower limit of quantification (LLOQ)
The LLOQ is the lowest concentration of template that still falls into the linear range of the standard curve (see figure, Limit of detection versus lower limit of quantification). Across all Microbial DNA qPCR Assays, 93% have an LLOQ of <100 gene copies (see figure, The LLOQ for all Microbial DNA qPCR Assays reveals high sensitivity). 92% of microbial identification assays meet this LLOQ, as do 95% of virulence factor gene assays and 97% of antibiotic resistance gene assays (see figures, The LLOQ for microbial identification Microbial DNA qPCR Assays reveals high sensitivityThe LLOQ for virulence factor genes Microbial DNA qPCR Assays reveals high sensitivity, and The LLOQ for antibiotic resistance genes Microbial DNA qPCR Assays reveals high sensitivity).

Specificity
Each Microbial DNA qPCR Assay is stringently tested to ensure that it detects only one target species or gene (see figure, Microbial DNA qPCR Assays are highly specific). For assays that do detect more than one target, a list of detected targets and in silico predictions is included on the product sheet.

This specificity is maintained even when samples have high species complexity, such as in stool, sputum, and plaque (see figure, Microbial DNA qPCR Assays display high sensitivity even in complex metagenomic samples).
Principle
Microbial DNA qPCR Assays are designed to detect bacterial 16S rRNA gene and fungal ribosomal rRNA gene sequences for species identification, as well as detecting virulence factor genes and antibiotic resistance genes using PCR amplification primers and hydrolysis-probe detection.
Procedure
The procedure for Microbial DNA qPCR Multi-Assay Kits is simple, and can be performed in any laboratory with a real-time PCR instrument. DNA is isolated from the sample using the appropriate QIAamp kit, and PCR reactions are set up using the appropriate Microbial qPCR Mastermix for the PCR instrument. Three control reactions are prepared for each sample, including Positive PCR Control, No Template Control, and the Microbial DNA Positive Control, as well as the Microbial DNA qPCR Assays. Real-time PCR is performed and data is analyzed using web-based data analysis software or Excel templates.
Applications
Microbial DNA qPCR Multi-Assay Kits are highly suited for the detection of related bacterial or fungal species, or microbial genes for antibiotic resistance or virulence factors, from a variety of samples.

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For application-specific microbial identification and profiling by real-time PCR
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Kit Handbooks
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New version – For real-time PCR-based profiling/detection of microbial species, antibiotic resistance genes or virulence factor genes
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