TY - JOUR

T1 - Next generation microbiology and cystic fibrosis diagnostics: are we there yet?

AU - Moser, Claus

AU - Thomsen, Trine Rolighed

AU - Hoiby, Niels

PY - 2018

Y1 - 2018

N2 - Purpose of reviewThe 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 findingsThis 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.SummaryMore 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.

AB - Purpose of reviewThe 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 findingsThis 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.SummaryMore 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.

KW - clinical diagnostics

KW - lung microbiota

KW - molecular diagnostics

KW - next-generation sequencing

KW - whole-genome sequencing

U2 - 10.1097/MCP.0000000000000516

DO - 10.1097/MCP.0000000000000516

M3 - Review

C2 - 30074508

VL - 24

SP - 599

EP - 605

JO - Current Opinion in Pulmonary Medicine

JF - Current Opinion in Pulmonary Medicine

SN - 1070-5287

IS - 6

ER -