A reliable and accurate identification is immediately needed. However, an identification even to the species level may not be enough to establish root cause. To identify if the microorganism came from the same or different sources, you may need to utilise strain typing methods.
Strain Typing is a microbial characterisation process used to distinguish closely related microorganisms to the strain level by utilising well-established, highly accurate DNA sequencing methods. For example, a company identifies a microorganism of the same species but different strains, one was sampled from the HVAC system through environmental monitoring and the other was recovered from routine quality testing of a new raw material.
If the microbes are determined to be identical by strain typing that means that their DNA is identical and that they could have come from the same source.
That means the same microorganism contaminating the raw material could be the same one you’re finding in your HVAC, the source could be in the air. This is the reason why strain typing is critical to resolving and remediating contamination events. Strain typing has been traditionally done by analysing multiple coding genes in independent steps using Multi-Locus Strain Typing (MLST).
Now, there is a technology that is being utilised called Next Generation Sequencing (NGS) that can analyse the entire DNA genome in one test producing the same results in less steps.