Purpose of review
The major problem for cystic fibrosis patients is the recurrent and chronic infections of the lungs, determining their prognosis. The challenge from biofilm-growing bacteria and emerging viruses urge the microbiological laboratories to develop better and faster diagnostic tools. Of these, molecular diagnostics are rapidly developing. However, beyond detecting many microorganisms, the task is to evaluate their clinical significance. This has always been a problem resulting in Koch's postulates. Then, the task was to distinguish the offending pathogens from the normal flora, as today, however, the normal flora is renamed microbiota.

Recent findings
This review includes the most recent studies on molecular diagnostics of viral and bacterial infections in cystic fibrosis. Generally, molecular methods have revolutionized virus and bacterial detection, and species-specific and multiplex molecular methods are valuable. However, the large amount of data obtained from new sequencing techniques challenge the interpretation and evaluation of clinical relevance.

Summary
More research is needed to discriminate offending pathogens from contaminating microbiota and to be able to identify the anatomical origin of the many detected microbes. Furthermore, the sequencing techniques must report all the detected microbes to the species level to allow the clinician to evaluate the properties of the microbes being relevant for the infection.