In general, microorganisms can cause disease in two distinct ways. The first is through active infection: high-level replication in the host can lead to structural damage, toxicity, and dangerous hyperactivation of the immune system. The second is due to the fact that certain species of bacteria and fungi can produce toxins which can be ingested and cause disease even in the absence of viable bacterial or fungal cells. Toxin production itself requires robust replication; so although this disease mechanism does not require that microbial cells be alive or healthy at the point of ingestion, it does require that they were able to thrive on the food matrix at some prior point. It also requires that there be no processing step that removes or inactivates the toxin.
Here is a list of the Biological Species We Test For:Escherichia coli