This comes from understanding the pathogenesis of the identified fungal species in relation to commensal fungal species. Usually through advanced training through programs such as ASCP that train MLT, MT, CLS,etc can obtain a key insight is a species is pathogenic or a contaminate. Factors that one has to consider is the site of origin in relation to species recovery i.e. blood vs CSF vs SKIN, etc; knowledge of the typical commensal species that are typically seen in that tissue; susceptibility patterns to various anti microbial medications all in relation to actual patient observed symptoms i.e. fever, rash, blood pressure, oxygen in take etc, and immunological status amongst other factors. Ironically it is still extremely difficult to determine solely on if an species is truly causing the source of infection but mostly relies on the Pathologist medical background if everything makes clinically makes sense (this is hard because numerous factors can be causing the pathogenesis seen like toxins, other bacteria etc). Usually one can get an ideal sense of a pathogen species if culture bottles only grow one species in one condition rather then the other i.e. aerobic vs anaerobic.