Use in clinical context
Infectious diseases are caused by pathogenic bacteria, viruses, parasites or fungi. The route of infection can be direct, for example by a sneeze, or indirect, for example by parasites transmitted via an insect vector, or bacteria ingested on contaminated food.
Genomic information from the infectious organism can help to accurately diagnose and treat the disease. This can be particularly helpful when different infectious diseases have symptoms that overlap each other, making diagnosis difficult. Genomic information can also be useful when different strains of an infectious organism have different properties, for example if one strain responds to different drugs to another.
An additional use of genomic information is to aid in identifying clusters of infections or the source of an outbreak.