FAQ Diagnostics
Which organisms have been detected using SepsiTest™-UMD or Micro-Dx™?
List of microorganisms To date, there are more than 1,300 microbes successfully identified in clinical and other specimens. The complete list you can find here. Bacteria Fungi Acinetobacter baumannii*+ Mycobacterium spp. Aspergillus fumigatus ...
Can molds be isolated and detected with SepsiTest™-UMD or Micro-Dx™?
Mold? Yes, some genera belonging to molds have been successfully isolated and detected (18S PCR), for example, Aspergillus, Fusarium, and Cladosporium. See List of Microorganisms/Fungi
What IT infrastructure is required for SepsiTest™-UMD and Micro-Dx™?
IT infrastructure The required IT infrastructure is quite small: a software to view (and if required edit) sequences, e.g., Chromas internet access for the BLAST search space on the server is quite small, sequencing files are between 200 and 300 kb ...
Will SepsiTest™-UMD and Micro-Dx™ transit to IVDR?
CE IVD Yes, both kits will be transferred to IVDR, at the latest in May 2026. Please find Molzym’s statement on the transition to IVDR here.
Which part of SepsiTest™-UMD or Micro-Dx™ is CE IVD marked?
CE IVD In brief, from sample to PCR result which resembles the pathogen detection is marked CE IVD. The identification of the pathogens is not included.
How much does a RipSeq® analysis cost for a mixed sequence?
Please inquire about pricing from Pathogenomix directly as availability and price may differ from country to country.
Can pathogens be identified in mixed infections? What to do with overlapping sequences?
Polymicrobial infection Yes, for a fee, there is an online tool available from Pathogenomix called RipSeq® which can identify up to three bacterial species from a sequence depending on the sequence quality. With the two sequencing primers, SeqGN16 ...
What are the benefits of SepsiTest™ BLAST?
SepsiTest BLAST SepsiTest™ BLAST is a quality-controlled database with: 7,042 full-length 16S rRNA gene sequences, exclusively from cultivated reference strains of the described species of the domains Bacteria and Archaea 342 selected 18S rRNA gene ...
What is the approximate cost that 3rd party would charge to provide Sequencing services?
Sanger Sequencing Service The cost for Sanger sequencing at a 3rd party is significantly below 10€ in Germany but might differ between countries and providers.
Approximately what % of samples require sequencing once they go through the PCR test?
Positivity rate The positivity rate of samples in PCR depends immensely on the sample material and may range between 20-50%.
How many sequencing reactions are needed per sample?
Sequencing For every sample with a positive 16S PCR, there are two sequencing reactions based on two sequencing primers, SeqGN16 and SeqGP16. This allows the identification of up to two pathogens, mainly separated into Gram-negative and Gram-positive ...
How shall PCR products be purified?
We recommend the Qiagen QIAquick PCR purification kit (Qiagen, Germany) with an elution volume of 30µl. Especially for samples with low microbial load, we achieved the best results with this kit. We cannot recommend enzymatic purification methods or ...
The melt curve analysis shows high primer dimer formation: why and what can I do?
Primer Dimer Primer dimer formations are non-specific products and can be minimized by constant cooling during PCR setup. It is completely normal that in negative samples, for example, the negative control (NC), the primer dimer can be higher ...
How to interpret the PCR results?
PCR results Interpretation Amplicons can either be analyzed by conventional gel electrophoresis with bands displaying the size of the amplicons (460bp for the MA Bac and 310bp for the MA Yeasts). Alternatively, a real-time PCR cycler can be used, and ...
Which real-time PCR cyclers are validated for SepsiTest™-UMD and Micro-Dx™?
PCR Cyclers The following cyclers are validated: LightCycler® 1.5, 2.0, 96, 480 and Nano, Roche DNA Engine Opticon®, CFX96™, BioRad Mx3000P®, Mx3005P®, Stratagene ABI 7500 Fast®, Life Technologies Rotor-Gene®, Qiagen peqStar 96Q, peqlab Not suitable ...
How long are the amplicons of the 16S and 18S assays?
16S/18S PCR assays The amplicon of the bacteria assay MA Bac covers the V3-V4 region of the 16S rRNA gene and is approximately 460bp long. The amplicon of the yeast assay MA Yeasts covers the V8-V9 region of the 18S rRNA gene and is approximately ...
How many PCR reactions are needed per patient?
PCR Setup / PCR reactions per sample Every sample is applied to 3 (three) master mixes: MA Bac for 16S, MA Yeasts for 18S, and MA Control for the extraction control. All master mixes need at least one negative control and MA Bac and MA Yeasts have ...
Does a small number of samples per extraction (manual or automated in the SelectNA™plus instrument) reduce the total amount of reactions per kit?
Number of reaction / extraction The number of reactions indicated in the kit size refers to the number of extractions e.g. a kit with 48 reactions = 48 extractions. The limitation arises concerning the reactions in the master mixes: Since every PCR ...
Can primary sample tubes be used for the Micro-Dx™/SelectNA™plus?
Sample Tubes No, there are specific sample tubes (Plus SV – Plus Sample Vials) included in the kit which need to be used in the SelectNA™plus instrument.
Can FFPE samples be analyzed with SepsiTest™-UMD or Micro-Dx™?
FFPE samples Yes, FFPE samples can be processed by simply following the tissue protocol of the kit. There are no additional steps like a deparaffinization required.
How to process tissue?
Tissue Pre-treatment Tissue is pre-treated with a 10-minute enzymatic approach followed by the normal protocol of host DNA depletion for SepsiTest™-UMD or placed into the SelectNA™plus instrument with Micro-Dx™. Other tissue treatments like bead ...
How is the human DNA depleted?
MolYsis Technology for human DNA depletion Samples are treated with a buffer lysing the human cells, while bacterial and fungal cells stay intact. The released human DNA and other free DNA are enzymatically degraded. Afterward, the microbial cells ...
Which sample sizes can be used?
Clinical Sample Size & Volume For SepsiTest™-UMD and Micro-Dx™: Fluid samples: 1 ml. We recommend using as much sample volume as possible. For samples with smaller volumes, a buffer for volume adjustment to 1 ml is included in the kits. Tissue ...
Which swabs can be used for diagnostic workflow and which to avoid?
Swabs compatibility Dry swabs, swabs within some aspirate collected at the same site as the swab, or swabs in NaCl can be used. Swabs in a medium containing agar can be difficult because the agar might lead to clogged columns. Commercially available ...
Can blood culture samples be used?
Blood culture samples Yes, blood culture samples can be used but they first need to be diluted for use with SepsiTest™-UMD and Micro-Dx™. Please use 100 µl blood culture and 900 µl SU buffer for both kits. For Micro-Dx™, please ensure that the medium ...
Which samples can be used for Micro-Dx™?
Micro-Dx & Clinical sample For Micro-Dx™ the following clinical samples are applicable: Body fluids: e.g., whole blood (EDTA- or citrate-stabilized), pleural fluid, cerebrospinal fluid, ascites aspirates, broncho-alveolar lavage, blood cultures, ...
Which samples can be used for SepsiTest™-UMD?
SepsiTest-UMD & Clinical samples For SepsiTest™-UMD the following clinical samples are applicable: Body fluids: e.g., ascites, broncho-alveolar lavage, whole blood (EDTA- or citrate-stabilized), CSF, pleural fluid, pus, synovial fluid Tissues: e.g., ...
What are the sample requirements? How shall samples be stored after sample collection? How fresh or old can samples be?
Please note: For any MolYsis™-based kits the microbial cells need to be intact! After taking the samples, please cool the samples in the fridge at ~8°C for short-term storage. Optimally, fresh samples are used for SepsiTest™-UMD and Micro-Dx™ for the ...
Which consumables and instruments are necessary to work with Micro-Dx™?
In addition to the SelectNA™plus instrument, mainly standard laboratory equipment is needed. Please find the list here.
Which consumables and instruments are necessary to work with SepsiTest™-UMD?
For SepsiTest™-UMD mainly standard laboratory equipment is needed. Please find the list here.
What is included in the kits SepsiTest™-UMD and Micro-Dx™?
SepsiTest(tm)-UMD Micro-Dx(tm) Manual and short manual Yes Yes Reagents for sample pre-treatment e.g. tissue biopsies Yes Yes Reagents for host DNA depletion and microbial DNA isolation Buffers and enzymes Prefilled buffer cartridges and enzyme vials ...
What are the differences between SepsiTest™-UMD and Micro-Dx™?
Both are culture-independent diagnostic kits for the detection and identification of bacteria and fungi from clinical samples by 16S and 18S rRNA amplification and subsequent Sanger sequencing. The difference between both kits is that the host DNA ...
What benefit has human DNA depletion before a PCR assay of bacteria and fungi?
A high proportion of human DNA can lead to non-specific primer binding to human DNA, which can result in false-positive PCR signals. In addition, an excess of human DNA limits the accessibility of primers to specific sites on the 16S/18S rRNA target ...