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Tracing the source of an infectious human disease can save lives. It allows for measures to be taken to prevent further spread of the disease. Although the mode of transmission for many human pathogens is known, it often remains difficult to trace the exact source of an outbreak of a disease with laboratory methods. Viruses, bacteria, fungi, parasites and protozoa can cause human diseases, but here we focus on bacterial pathogens. The currently used techniques to obtain DNA fingerprints of bacterial agents of infectious diseases frequently cannot discriminate between all bacterial strains of the same outbreak, making it impossible to follow the spread of the disease. A recent solution to this problem is the application of next‐generation whole‐genome sequencing techniques, which allows all available genetic information of each clinical isolate to be determined.
Trends in bacterial typing
Historically, identification and classification of bacterial pathogens have been accomplished with phenotypic analyses, such as bacteriophage typing or drug susceptibility testing. Nowadays, molecular biology techniques such as restriction‐fragment length polymorphism typing [RFLP (Todd et al., 2001)] or pulsed‐field gel electrophoresis are used to assign a ‘type’ to a bacterial isolate, together with techniques that rely on variations in sequence repeat lengths [variable numbers of tandem repeats, VNTR (van Belkum, 1999)], or on sequencing of one or several housekeeping genes, for example spa typing (Frenay et al., 1996) or multilocus sequencing typing [MLST (Maiden, 2006)]. Although these methods are often well established, fast and comparatively cheap, their main drawback is lack of discriminatory power when it comes to typing of closely related isolates, for example isolates from a single outbreak of a bacterial pathogen. Many isolates, especially within a high‐incidence setting, show an identical result with the fingerprinting methods, and have the same ‘type’ assigned. This prevents the definition of precise relationships between these isolates, and prohibits the identification of source cases or environmental sources, and an understanding of the detailed molecular architecture of bacterial epidemics.
The advent of comparatively cheap whole‐genome sequencing technologies (next‐generation sequencing) in the last few years seems to offer an easy solution, as these techniques monitor all changes in a bacterial genome, and therefore provide the maximum possible discriminatory power between two isolates. Such changes include...