11: Molecular Microbial Diagnostics^†

The suffering and deaths caused by infections and epidemics remain unsurpassed by any other malady afflicting the human species. Fortunately, a revolution has happened and is ongoing concerning laboratory diagnosis of infectious agents, including viruses, bacteria, fungi and parasites. Foremost amongst the new methods are tests based on analyses of nucleic acids – including DNA and RNA – from the causative microbial agents. Not only are these techniques orders of magnitude faster than the older techniques, they are also more sensitive and specific, and enable the detection of non-cultivable microbes. This chapter reviews the methodological basis of nucleic acid amplification, hybridization and sequencing methods that have now become established in modern diagnostic microbiology laboratories. The new molecular methods assist the medical doctor in agent identification, choice of correct therapy, monitoring of therapeutic effect and discovery of drug resistance. The new methods are used to discover and monitor epidemics. The future potential is great for automation, miniaturization, increased capacity, speed, reliability and user friendliness, whilst relative roles of nucleic acid amplification, next-generation sequencing and novel innovations remain undetermined. What is certain is that nucleic-acid-based techniques will continue to revolutionize the way we diagnose and treat infections.