Microbial identification and monitoring

Rapid microbial characterization and identification to support environmental monitoring

Microbial control within biopharmaceutical manufacturing is a critical quality control to help ensure drug products are free from viable microorganisms. Per regulatory guidelines, the implementation of an environmental monitoring program is required to comply with good manufacturing practices and identification of microorganisms to species level is a minimal requirement. Regulatory agencies consider genotypic identification to be more reliable than phenotypic methods.

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MicroSEQ Microbial Identification System

Used in top pharmaceutical companies worldwide, the Applied Biosystems MicroSEQ Rapid Microbial Identification System is ideal for environmental monitoring, contamination investigation, root cause analysis, raw materials testing, and microbial identification in small-molecule and biopharmaceutical manufacturing, and service laboratories. The MicroSEQ Rapid Microbial ID System combines the benefits of PCR and DNA sequencing technologies to enable highly accurate results.

Benefits of the MicroSEQ Rapid Microbial ID System

  • Accurate and specific: phylogenetic approach, based on the sequencing of the 16S rRNA gene for bacteria or the D2 region of the large subunit ribosomal DNA for fungi, delivers high discrimination power.
  • Regulatory compliant: complies with approaches recommended by regulatory agencies such as ICH, USP, EUP, and JP, for accurate contamination identification.
  • Rapid time to results: ~5 hrs from colony to identification, allowing in-process testing.
  • Wide range of organisms: software using largest and most comprehensive validated libraries for bacteria and fungi.
  • Streamlined workflow: standardized, simple and easy-to-validate workflow.
  • Support network: worldwide technical and validation support, detailed training and implementation guidance.


“Genotypic methods have been shown to be more accurate and precise than traditional biochemical and phenotypic techniques. These methods are especially valuable for investigations into failures (e.g., sterility test; media fill contamination).”

U.S. Food and Drug Administration. Sterile Drug Products Produced by Aseptic Processing — Current Good Manufacturing Practice. U.S. Food and Drug Administration. FDA, October 2004.

Integrated platform solution generating actionable results, the first time

The MicroSEQ Rapid Microbial Identification System, based on comparative rDNA sequencing of the 16S region (for bacteria) or the LSU D2 region (for fungi), is a proven genotypic method for rapid and accurate microbial identification.

With the MicroSEQ System, right-the-first-time results can be obtained rapidly, using a logical workflow that requires minimum hands-on time. A single, standardized procedure is used for identifying both bacterial and fungal isolates, giving you results from colony to identification in less than 5 hours.

The MicroSEQ Rapid Microbial ID System includes PCR and sequencing kits, a PCR thermal cycler, and a genetic analyzer, the MicroSEQ ID software, and gene libraries. Choose your desired genetic analyzer based on your throughput requirements—no matter the number of samples you need to process, we have you covered.

Our kits, instruments, and software offer an integrated platform solution for your microbial identification needs. Everything you needincluding technical assistance and implementation supportavailable from one source.

Simple workflow

After growing the culture, DNA from the culture is extracted. Next, a PCR is performed to obtain template for the sequencing step. Purification kits are used to clean up templates after PCR and sequencing. After sequencing, the organism is identified using MicroSEQ ID library and software.

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No matter your questions, we are here to help. Our experienced team of scientists and technical specialists is ready to assist you in choosing the right MicroSEQ ID solutions and products. Complete this form to start the conversation.

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Bioprocessing resources

Access a targeted collection of scientific application notes, case studies, posters, white papers and more for bioprocessing:

For Research Use Only. Not for use in diagnostic procedures.