mycoplasma detection diagram

Why is mycoplasma testing necessary for GMP manufacturing?

Mycoplasmas, the smallest known free living organisms, are relatively common and difficult to detect bacterial contaminants of mammalian cell cultures. In therapeutic applications, an undetected mycoplasma contamination can negatively impact product quality and patient safety. GMP manufacturers develop stringent risk mitigation plans to ensure early detection of mycoplasmas to avoid costly manufacturing delay or remediation activities. For lot-release testing, regulatory guidance requires that all products derived from cell culture be tested for the presence of mycoplasma.

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Proven, regulatory-accepted method for mycoplasma detection

The Applied Biosystems MycoSEQ Mycoplasma Detection Assay has been accepted world-wide to meet existing regulation and guidance for the detection of mycoplasmas across multiple therapeutic modalities.

Regulatory acceptance track-record for the MycoSEQ Detection System used for lot-release testing as of 2021

Therapeutic drug category

Number of commercially released drugs

Number of drugs pending approval

Regulatory agencies granting approval

Cell/Gene therapy



  • EMA (EU)
  • FDA (US)
  • PMDA (Japan)
  • Local agencies

Tissue therapy



  • EMA (EU)
  • FDA (US)
  • Local agencies

Recombinant protein



  • EMA (EU)
  • FDA (US)

Monoclonal antibodies



  • EMA (EU)
  • FDA (US)




  • MFDS (Korea)
  • Local agencies

Contract services/Others



  • Local agencies





*EMA - European Medicines Agency; FDA - United States Food and Drug Administration; PMDA - Pharmaceuticals and Medical Devices Agency, Japan; MFDS - Ministry of Food and Drug Safety, Korea)

Requirements for regulatory acceptance

For mycoplasma detection assays, regulatory agencies require validation studies to confirm the sensitivity, specificity, and robustness of the method to meet their standards. The MycoSEQ detection assay has achieved such success through demonstrating these parameters:

Proven specificity of the MycoSEQ Detection Assay:

The MycoSEQ kit has been validated in numerous independent studies to specifically detect a wide variety of Mycoplasma, Acholeplasma, and Spiroplasma species with no known cross-reactivity with closely related bacterial species. Specificity testing results and bioinformatics analysis are detailed in the Drug Master File (DMF) which is filed with the United States Food and Drug Administration (FDA) and Health Canada.

High sensitivity of the MycoSEQ Detection Assay:

Internal and external validation methods have demonstrated limit of detection (LOD) to meet or exceed the recommended regulatory guidance of 10 CFU/mL, or the genomic equivalent of 10 genome copies (GC)/mL for a vast panel of mycoplasma species including those known to contaminant bioprocessing cultures.

Robustness of the MycoSEQ Detection Assay:

Deliberate variations in the method parameters have been extensively evaluated by Thermo Fisher Scientific as part of the assay development process and validated by independent studies.

Read the press release

Press release: Rapid Mycoplasma Testing Method Now Accepted by Regulators

Learn the history of how The Applied Biosystems MycoSEQ Mycoplasma Detection Kit was accepted by regulators for QA/QC and lot release.

Read the press release ›

Read the e-book

E-book: Rapid Mycoplasma Testing Method for Lot-Release

Learn how the MycoSEQ Drug Master File with the US FDA and Health Canada can assist in regulatory acceptance of the method.

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Read the fast facts poster/video

Webinar: Mycoplasma detection in cell therapy products: GMP-compliant implementation and validation

Explore a case study of the implementation and validation of the MycoSEQ mycoplasma detection system for routine quality control and lot release testing for a mesenchymal cell therapy ATMP.

Watch video or read poster ›

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.

  • Method accepted by regulatory agencies for Mycoplasma detection in a cGMP environment
  • Proven sensitivity to less than 10 copies/reaction with no known cross-reactivity to closely related non-mycoplasma species
  • Total workflow solution, from sample prep to analysis with SAE compatible software
  • Detection of more than >90 Mycoplasma species
  • Supported throughout the validation process with our regulatory specialists and our Field Application Specialists
Test kits for MycoSEQ Mycoplasma Detection system for biologics

Total mycoplasma workflow from sample prep to analysis

Streamlined workflow with results in less than five hours

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

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.

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 five minutes of hands-on time.

QuantStudio 5 system for qPCR Mycoplasma Detection testing with MycoSEQ

Powerful platform

The Applied Biosystems Pharmaceutical Analytics QuantStudio 5 Real-Time PCR System is designed for both new and experienced users who need a simple and affordable real-time PCR system without compromising performance and quality. The QuantStudio 5 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 QuantStudio 5

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

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 third generation platform features an innovative optical system that enhances sensitivity.

Learn more about our 7500 system

AccuSEQ software, QuantStudio 5, MycoSEQ mycoplasma detection qPCR testing

Software to help enable 21 CFR Part 11 compliance

The Applied Biosystem AccuSEQ Real-Time Detection Software is designed to work with the QuantStudio 5 Real-Time PCR instrument or the 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

The AccuSEQ software features an intuitive interface that provides an easy way to identify presence or absence of mycoplasma. The software demonstrates one of the key parameters.

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.

Mycoplasma detection sensitivity and specificity


Highly sensitive 1–3 genome copies/PCR detection

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.

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

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.


Detection of more than 90 bacterial species and contaminants

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

View the Partial Inclusion Panel based on 10 ng purified DNA/reaction

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

Implementation and technical support

Our mission is to support your MycoSEQ Detection 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, which could include instrument installation with IQ/OQ and Computer System Validation, 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

For decades, Thermo Fisher Scientific’s extensive network of Field Application Specialists around the world have helped customers establish analytical assays that have satisfied regulatory guidelines, and our Regulatory Consulting Services specialists have offered customers needed support when working with regulatory agencies.

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
  • National Institute of Standards and Technology (NIST), Standards Coordinating Body (SCB)
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:

Accessing a webinar on a laptop

Bringing Rapid Mycoplasma Testing In-House to Expedite Lot Release of Recombinant Protein Product

This presentation will give an overview of one customer’s journey to replace an out-sourced mycoplasma test with an in-house mycoplasma qPCR assay. Octapharma received regulatory approval for the assay in October 2019 and now use in-house mycoplasma testing for lot release, saving lead time for their recombinant production.

Watch our webinars now

Take advantage of knowledge sharing sessions with industry thought leaders

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.

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.

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.

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Bioprocessing resources

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