mycoplasma detection diagram

Why Mycoplasma testing is required

Mycoplasmas, the smallest known free living organisms, are relatively common bacterial contaminants of mammalian cell cultures. Regulatory guidance requires that all products derived from mammalian cell culture undergo mycoplasma testing. Mycoplasma detection is difficult, sometimes impossible, when using a traditional 28-day culture-based test. Regulatory agencies have expanded acceptance of nucleic acid tests, such as real-time PCR, as an alternative method to traditional Mycoplasma detection after appropriate validation and regulatory review. Over 40 major global biotechnology companies have implemented, validated, and received regulatory approval to use the MycoSEQ system as their mycoplasma lot release test.

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MycoSEQ mycoplasma detection system

The MycoSEQ Mycoplasma Detection System is a real-time PCR based mycoplasma detection assay, providing sensitivity that meets or exceeds the regulatory guidance for mycoplasma detection and same-day actionable results to enable early detection of mycoplasma contamination. The MycoSEQ Mycoplasma Detection System integrates real-time PCR assays, instruments, and software with optimized PrepSEQ sample preparation reagents—delivering results in hours, not days. This enables you to test at multiple points in cell line and cell bank production and media harvest, to help increase your productivity and reduce the risk of downstream contamination.

MycoSEQ Mycoplasma Detection system for biologics lot release and in process testing

Following validation, regulatory review, and acceptance, the MycoSEQ assay can be used as a preferred same-day mycoplasma lot release test, replacing the 28-day culture-based test.

Highly sensitive detection across species with demonstrated sensitivity down 1–3 genome copies/PCR

Detection of more than 90 Mycoplasma, Acholeplasma, and Spiroplasma species, including commonly known contaminants within bioprocessing facilities with no cross reactivity with non-mycoplasma DNA

Streamlined workflow with results in less than 5 hours

The MycoSEQ Mycoplasma Detection System’s easy workflow delivers actionable results in less than 5 hours—enabling you to detect contamination quickly in process development, equipment, raw materials, harvest, helping to expedite the release of your product.

MycoSEQ Validated Workflow

Designed for purpose using a multi-parameter analysis

Three distinct assay acceptance criteria provide confidence in the determination of the presence or absence of mycoplasma. The cycle threshold (Ct) value indicates that amplification has occurred, while melting temperature (Tm) and derivative value (DV) confirm that amplification was due to mycoplasma DNA. All three criteria must meet specific values established during validation for a test sample to be positive for the presence of mycoplasma DNA.

A measure of target DNA level at the beginning of the PCR reaction

A measure of target DNA level at the beginning of the PCR reaction

A measure of amplicon size and base composition (known for mycoplasma using this assay)

A measure of amplicon size and base composition (known for mycoplasma using this assay) 

A measure of specific amplicon quantity generated during the PCR reaction

A measure of specific amplicon quantity generated during the PCR reaction


Assay sensitivity is critical to meet regulatory expectations and provide results for early detection of mycoplasma contamination. The MycoSEQ assay consistently detects between 1 to 10 genome copies of mycoplasma target DNA. This highly sensitive method meets the rigorous expectations of regulatory agencies.

Amplification plot of a 10-fold dilution series of purified M. arginini DNA performed in triplicate

Amplification plot of a 10-fold dilution series of purified M. arginini DNA performed in triplicate. The MycoSEQ assay provides highly reproducible detection of mycoplasma DNA down to 1 genome copy per PCR reaction.

Positive means positive

Our proprietary Discriminatory Positive/Extraction Control gives you the confidence in your results.

  • Our positive control DNA is made with mycoplasma amplicon modified to have a melting temperature (Tm) outside the range of mycoplasma amplicons, providing an additional level of confirmation of positive test results.
  • Higher Tm allows discrimination between true mycoplasma and accidental contamination of test sample with positive control.
  • This helps enable simple extraction control spiking of test samples.
  • This can be used as a surrogate for mycoplasma DNA during method qualification.
Amplification plot showing distinction between discriminatory control amplicon versus mycoplasma


Equally important is specificity to demonstrate that only the target species are detected. The MycoSEQ assay provides highly sensitive detection of more than 90 Mycoplasma, Sprioplasma, and Acholeplasma species with no detection of non-related bacteria. The assay detects all species required by European Pharmacoepia <2.6.7>.

Broad detection of Mycoplasmas

Below you can see a partial listing of the >90 species inclusion panel*, designed to detect the most common isolated species recommended for testing and validation of mammalian cell cultured biologics.

Partial inclusion panel

Acholeplasma granularum

Mycoplasma genitalium

Mycoplasma testudinis

Acholeplasma laidlawii

Mycoplasma gypis

Mycoplasma timone

Acholeplasma pleciae

Mycoplasma hominis

Spiroplasma citri

Mycoplasma alkalescens

Mycoplasma hyorhinis

Spiroplasma endosymbionts

Mycoplasma alvi

Mycoplasma imitans

Spiroplasma insolitum

Mycoplasma anseris

Mycoplasma indiense

Spiroplasma kunkelii

Mycoplasma arginini

Mycoplasma lagogenitalium

Spiroplasma melliferum

Mycoplasma auris

Mycoplasma lipofaciens

Spiroplasma mirum

Mycoplasma buccale

Mycoplasma mobile

Spiroplasma phoeniceum

Mycoplasma californicum

Mycoplasma molare

Spiroplasma poulsonii

Mycoplasma canadense

Mycoplasma mycoides

Mycoplasma bovirhinis

Mycoplasma capricolum

Mycoplasma neurolyticum

Mycoplasma bovis

Mycoplasma caviae

Mycoplasma orale

Mycoplasma bovigenitalium

Mycoplasma collis

Mycoplasma phocidae

Mycoplasma canis

Mycoplasma cricetuli

Mycoplasma pirum

Mycoplasma felis

Mycoplasma equirhinis

Mycoplasma pneumoniae

Mycoplasma fastidiosum

Mycoplasma fermentans

Mycoplasma salivarium

Mycoplasma muris

Mycoplasma gallinaceum

Mycoplasma simbae

Mycoplasma pulmonis

Mycoplasma gallisepticum

Mycoplasma spumans


Mycoplasma gateae

Mycoplasma synoviae


*Common isolated species recommended for use in qualification and validation are listed in bold.

No cross reactivity with non-mycoplasma DNA

Multiple non-mycoplasma species have been tested and confirmed to not be detected by the assay, including but not limited to Bacillus spp., Enterobacter spp., E. coli, Pseudomonas spp., Staphylococcus spp., and Streptococcus spp. Additionally, the assay has no cross-reactivity with chicken, chimpanzee, CHO, HeLa, mouse, rat, and many others.

Partial Exclusion Panel based on 10 ng purified DNA/reaction

















Bacillus cereus




Bacillus subtilis




Candida albicans




Clostridium perfringens




Clostridium sporogenes




Escherichia coli




Lactobacillus delbrueckii




Micrococcus luteus




Staphylococcus aureus




Staphylococcus epidermidis




Steptococcus faecalis




Support throughout the validation process

Implementations and technical support

  • Our mission is to support your MycoSEQ system implementation, from the decision stage through validation and routine use. Our experienced field application scientists are dedicated to facilitating seamless implementation into your process and will train the lab on the appropriate protocols. We know it’s not easy. We’ve helped many companies and will collaborate with your team to develop a comprehensive implementation plan, including instrument installation with IQ/OQ and CSV services, team training, method/protocol optimization, and regulatory support.

Regulatory consulting support

Our team of regulatory consultants provide support to address your bioprocessing and regulatory compliance challenges. We can:

  • Advise customers on the features of our products that enable alignment with regulatory guidance.
  • Support evaluation, implementation, and validation of bioproduction solutions.
  • Provide guidance on regulatory strategy during implementation and qualification of bioproduction solutions.
  • Provide consultation to support deviation or nonconformance investigations, including guidance on development of CAPA.
Validation guidance icon

Validation guidance

  • Consultation on validation, strategy, and approach
  • Assist in alignment with current industry guidance documents: International Committee for Harmonization (ICH), regional pharmacopeias (USP, EP, JP, CP), FDA Guidance for Industry, World Health Organization (WHO)
  • Review validation protocols, acceptance criteria, and reports
  • Validation support at Customer Experience Centers
Regulatory support icon

Regulatory support

  • Consult on regulatory strategy: Prior Approval Supplement (PAS), Type C, Chemistry, Manufacturing, and Controls (CMC) update
  • Review briefing documents and presentations
  • Organization of informational meetings with key regulatory thought leaders
Regulatory documentation icon

Regulatory documentation

  • Regulatory submissions support documentation is available to support regulatory filings in multiple jurisdictions
  • MycoSEQ Drug Master File (DMF) on file with FDA and Canada
  • Validation and comparability reports
Industry organization icon

Industry organizations: active engagement

  • Parenteral Drug Association (PDA)
  • BioPhorum Operations Group (BPOG)
  • Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB)
  • Advanced Virus Detection Technologies Interest Group (AVDTIG)
  • NSF Center for Cell Manufacturing Technologies (CMaT)
  • National Institute of Standards and Technology (NIST), Standards Coordinating Body (SCB)

Webinar spotlight: Making the Switch–The Evaluation, Implementation, and Validation of Bringing Rapid Mycoplasma Testing In-House to Expedite Lot Release of Recombinant Protein Product

Accessing a webinar on a laptop

Octapharma AB in Stockholm, Sweden is the manufacturing site for NUWIQ®, a recombinant human FVIII produced in human cells. Regulatory guidelines state that recombinant bulk harvest must be tested for mycoplasma prior to further processing. This presentation will give an overview of Octapharma’s journey on replacing an out-sourced mycoplasma test with an in-house mycoplasma qPCR assay. Octapharma received regulatory approval for the assay in October 2019 and plan to run in-house mycoplasma testing as an alternative to the traditional growth-based mycoplasma testing and the process of laboratory set-up and instrument qualifications and software requirements. This webinar also presents a summary of the method development and validation, as well as how to help provide assay sensitivity meets regulatory requirements.

Automated sample preparation

Superior sample prep for consistent detection across multiple matrices

Efficient sample preparation and DNA extraction are the base for a high sensitivity assay. Our Applied Biosystems PrepSEQ nucleic acid extraction kits utilize magnetic bead-based technology to provide quantitative recovery of nucleic acids from a variety of complex sample matrices. Our MycoSEQ system is optimized with sample preparation protocols for use with either automated or manual workflows.

PrepSEQ Mycoplasma Nucleic Acid Extraction kit to be used with MycoSEQ for mycoplasma detection
Automate Express Nucleic Acid

Reduce hands-on time with automation

The Applied Biosystems AutoMate Express Nucleic Acid Extraction System delivers the power of efficient extraction in a fully automated system. Implementing the same PrepSEQ chemistry in preloaded cartridges, the AutoMate Express provides complete extraction of up to 13 samples in under two hours with only 5 minutes of hands on time.

PrepSEQ Express kit for automated sample preparation.

Powerful platform

QuantStudio 5 system for qPCR Mycoplasma Detection testing with MycoSEQ

The Applied Biosystems QuantStudio 5 (QS5) system is designed for both new and experienced users who need simple and affordable real-time PCR systems without compromising performance and quality. The QuantStudio 5 Real-Time PCR System detects differences in target quantity as small as 1.5-fold in singleplex reactions and provides 10 logs of linear dynamic range.

Learn more about our QS5

The Applied Biosystems 7500 Real-Time PCR System is a powerful platform for labs requiring superior performance and maximum dye versatility. It is a sophisticated platform for users who require extended capabilities and maximum versatility. The 3rd generation platform features an innovative optical system that enhances sensitivity.

Learn more about our 7500 system

7500 Real-time PCR system for Mycoplasma Detection testing using MycoSEQ

Dedicated software for easy interpretation

The Applied Biosystem AccuSEQ Real-Time Detection Software is designed to work with the Applied Biosystems QuantStudio 5 Real-Time PCR instrument or the Applied Biosystems 7500 Fast Real-Time PCR instrument. Dedicated templates and data analysis algorithms allow for easy plate set up and automated mycoplasma presence-absence calling. Security, audit, and e-signature features enable 21 CFR Part 11 compliance.


  • Optimized and validated for the MycoSEQ Mycoplasma Detection assay
  • Easy visual result summary provides immediate understanding of presence or absence of mycoplasma in your samples
  • Confidence in positive results with automated detection of discriminatory positive control (DPC)
  • Robust data analysis parameters for the MycoSEQ Mycoplasma Detection assay (Ct, Tm, and DV values)
  • Security, audit, and signature capabilities to enable 21 CFR Part 11 compliance
AccuSEQ software, QuantStudio 5, MycoSEQ mycoplasma detection qPCR testing
AccuSEQ 3.1, mycoplasma detection qPCR testing software, automated presence or absence calls

The AccuSEQ software features an intuitive interface that provides an easy way to identify presence or absence of mycoplasma.

AccuSEQ 3.1, mycoplasma detection qPCR testing software, amplification plot

The AccuSEQ software demonstrates one of the key parameters (Ct value) to show the amplification which indicates the presence of DNA.

AccuSEQ 3.1, mycoplasma detection qPCR testing software, melt curve and derivative reporter

The specificity of the qPCR reaction can be confirmed using melting curve analysis. The melting curve shows what you amplified based on Tm, while the derivative shows how much of the product/target we have.

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Take advantage of knowledge sharing sessions with industry experts

Educational programs


A journey to cell therapy manufacturing: From R&D to lot-release

This webinar discusses three key areas to consider when commercializing a cell therapy—starting/raw materials, controlled manufacturing processes, and testing safety and quality. The starting and raw materials you choose at discovery can ultimately define the success of your development and GMP manufacturing process. We highlight some key watch outs and review essential tests that are required for lot release and regulatory filing and present solutions that save time and are accepted by regulators for lot release testing.

Accelerating Vaccine Development by Innovative Purification Solutions and State of the Art Quality Testing

This webinar addresses regulatory requirements for safety and purity testing during the vaccine production process and highlights the benefits of implementing automated systems to save time and demonstrate product quality and safety.

Business of regenerative medicine III: An expert panel discussion

Six industry leaders discuss their pain points and the business landscape of advanced therapies, bringing expertise from around the regenerative medicine ecosystem, real-world evidence on accelerating approval, obstacles and aids to translation, and looking into the future of manufacturing and quality control.

Combining state-of-the-art production, purification, and analytics to optimize AAV manufacturing for clinical and commercial gene therapies

In this webinar, Thermo Fisher Scientific describes how they are mobilizing to meet rapidly growing demands for AAV vector manufacturing from both technology development and manufacturing strategy viewpoints.

Developing a risk mitigation plan for gene therapy manufacturing

This interview with gene therapy industry-leading scientists discusses strategies for risk mitigation, including greatest risks, key do's and don'ts, critical steps to risk mitigation, and much more.

Enabling cell & gene therapy raw materials standardisation and regulatory compliance

We surveyed readers on their understanding of the current regulatory guidelines for cell and gene therapy. Our regulatory consultants discuss the results and provide guidance for readers on raw material and quality testing.

Expert Roundtable: Getting a gene therapy product to market: Pitfalls and how to prevent them

This expert roundtable discussion covers some of the major pitfalls when scaling up a gene therapy effort and how to prevent them, focusing on the preparation needed for scaling up to clinical and commercial scale.

Global Regulators' FAQs on CMC in IND/BLA Filing: A Retrospective Look at Past Mycoplasma Validation Queries and Responses

Every IND or BLA is different, as is every therapy being considered for regulatory approval. The CMC validation is a significant part of the regulatory filing, and interpretation of regulatory guidance is not always easy, with variability depending on the product. Thermo Fisher’s team takes a retrospective look at some of the commonly asked regulator’s questions regarding mycoplasma testing and validation.

Making the Switch: The Evaluation, Implementation, and Validation of Bringing Rapid Mycoplasma Testing In-House to Expedite Lot Release of Recombinant Protein Product

This presentation provides an overview of Octapharma’s journey on replacing an outsourced mycoplasma test with an in-house mycoplasma qPCR assay. Octapharma received regulatory approval for the assay in October 2019 and plan to run in-house mycoplasma testing for lot release, saving lead time for their recombinant production.

Mycoplasma Matters–Live Q&A

Our panel of experts answered questions regarding implementation and validation of a rapid mycoplasma system, covering topics including regulatory requirements, lot release, in-process testing, risk mitigation, live mycoplasma requirements, sensitivity, specificity, validation considerations, 28-day vs. same day, and compendial vs. rapid microbial method.

Regulatory FAQs & common concerns for cell & gene therapy raw & starting materials

In cell and gene therapy, materials matter. However, misconceptions abound, exacerbating a lack of harmonization and standardization in key areas. This presentation aims to debunk some popular myths, provide practical guidance based upon long experience in the field, and clarify key regulatory considerations and requirements across the cell and gene therapy raw and starting materials area.

Scalable AAV manufacturing–Addressing challenges across the workflow

This webinar addresses regulatory requirements for safety and purity testing during the AAV production process and discusses the benefits of implementing automated systems to save time and demonstrate product quality and safety.

Setting up for Success: Raw Materials Roundtable Discussion & Webinar

Cell and gene therapy industry leaders discuss the critical issues to consider when developing your raw material sourcing strategy. They share their thoughts on sourcing, supply, and regulatory documentation that should be taken into consideration at such a key step in the manufacturing of therapies.

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Bioprocessing resources

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