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This month we feature a very interesting new article from the open-access journal PLoS Pathogens by Köser et al from Cambridge, UK entitled “Routine Use of Microbial Whole Genome Sequencing in
Diagnostic and Public Health Microbiology”. You can download it here:
http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002824
Microbiology laboratories around the world follow the steps of pathogen isolation followed by identification, susceptibility testing, and epidemiological typing as required. We are now entering an unheralded era where all these steps could be combined into one with whole genome sequencing in routine diagnostic laboratories in well-resourced settings. This is a particularly attractive approach for pathogens of high public health importance which are slow to culture (for example Mycobacterium tuberculosis) or where early detection of resistance mutations in a genetically mixed pathogen population is beneficial (for example HIV). Whole genome sequencing is already a powerful tool in the international setting to source and track outbreaks, for example the Haitian cholera outbreak http://www.nejm.org/doi/full/10.1056/NEJMoa1012928.
While the cost, time and expertise required for whole genome sequencing continues to decrease, at £40 per sample it is clearly beyond the means of most jobbing laboratories internationally. Further work is needed on the relationship between genotype and phenotype for susceptibility testing, and in establishing robust and updated software platforms to deal with the data output from sequencing. It seems amazing where we are up to with technology applications now, but meanwhile for most of us in the tropics it’s on with our agar plates!