Microorganism Identification

Accurate microorganism species identification is critical to any contamination control plan. Manufacturers should be aware of the risks to their products and processes, and be able to accurately assess these risks upon completion of identification.

In GMP regulated manufacturing facilities, it is essential to understand the microorganisms found in your cleanrooms. ​The presence of microorganisms in a controlled cleanroom can significantly impact the release of a finished product or intermediates.

Annex 1 states that species identification is required:

• “Microorganisms detected in Grade A zone and Grade B area should be identified to species level and the potential impact of such microorganisms on product quality (for each batch implicated) and overall state of control should be evaluated".
• “Consideration should also be given to the identification of microorganisms detected in Grade C and D areas (for example where action limits or alert levels are exceeded or where atypical or potentially objectionable microorganisms are recovered).”

After identifying microorganisms, it is important to conduct risk assessments to evaluate the threat to both the product and process, which allows you to determine possible sources of contamination.

Identification also allows you to determine a possible route of entry to critical areas – if organisms found in the critical areas have also been seen previously in non-critical areas or surrounding rooms, the organism could have been tracked into the critical areas by equipment or personnel. It is therefore important to track not only the flora within your critical areas, but also in surrounding preparation and support areas.

Species identification can be useful in many industries:

• Pharmaceutical Microbiology
• Medical Device Testing
• Environmental Microbiology
• Research and Development
• Food Microbiology

Traditional microorganism identification analysing phenotypic characteristics (such as APIs) can be challenging and time-consuming. Results often aren’t available for several days after receipt of samples. Results are often obtained more than 24 hours after isolation and testing. This can often lead to delays in receiving critical results.

Eurofins MGS Laboratories are now able to offer a new MALDI-TOF service which allows for rapid species-level identification using mass spectrometry.

• Genus and species level identification
• Rapid identification testing for bacterial and fungal species
• Cost effective solution

MALDI-TOF stands for Matrix-assisted laser desorption ionisation (MALDI) time of flight (TOF). This means that the MALDI uses a laser to irradiate samples, and then measures the time of flight for these particles as they pass through the equipment.

Different proteins and peptides will travel at different speeds depending on their size and mass, allowing the machine to generate a unique fingerprint from the time of flight measured for the particles generated. As with gene sequencing and chemical characterisation, different species have different fingerprints produced by this process. These fingerprints are analysed against the instrument library, matching the patterns to the microorganisms stored within this library. This analysis takes minutes, rather than hours, and therefore a result can be obtained on the same day as the test is run.

Analysis is also straightforward, allowing hundreds of samples to be analysed each day:

• Gram-positive and gram-negative bacteria
• Moulds
• Mycobacteria
• Anaerobic Microorganisms
• Customer-Specific Microorganisms

Should our MALDI-TOF library not contain the microorganism fingerprint of a specific microorganism sent to us for identification, we can send samples for additional genotypic identification to our site in Dungarvan. Here, we can use PCR to compare samples to our validated, proprietary database for further identification.

These identifications can then be added to our MALDI-TOF library, so we can identify the microorganism the next time it is recovered and sent to us.