Considerations in Molecular Strain Typing for Bacteria, Fungi, and Viruses

Strain typing has traditionally been used for a variety of purposes, including molecular epidemiology, disease surveillance, and outbreak investigations. Species diversity is another characteristic of importance to strain typing that must be considered when devising a scheme or studying a population of bacteria. Mixed infections can present challenges for typing. Fungal genomes are much larger and an order of magnitude more complex than bacterial genomes. Heterokaryosis and parasexuality are two issues in fungi that require specific attention when attempting to perform fungal strain typing. RNA and DNA viruses each have unique challenges for typing, due to differences in mutation rates, genome stability, and replication. Next-generation DNA sequencing of RNA viruses requires a reverse transcription step prior to typing which may have a possibility of introducing error.