Genomic analysis of microbial infections

The genomic analysis of microbial infections entails the use of molecular methods to detect pathogen-specific genetic sequences to diagnose, monitor, or prognose infections (such as qualitative or quantitative nucleic acid amplification methods). Various molecular methods are utilized for the analysis of genetic sequences or arrangements in order to characterize pathogens or to differentiate often epidemiologically unrelated pathogens at the strain level. Molecular diagnostic methods have become the gold standard for diagnosing many infections because of their accuracy and rapid turnaround time compared to conventional methods, such as culture. Molecular strain typing and sequencing methods have become routine because of their accuracy, strain discrimination capability, and wide availability of reagents compared to serologic or phenotypic methods. This chapter provides an overview of molecular approaches to genomic analysis of pathogens in order to diagnose or monitor infections and to characterize the pathogens involved.