Roach et al. performed prospective whole-genome sequencing of almost all bacterial isolates collected from a hospital's intensive care units over the course of a year: 12% of isolates that had been assigned a species-level classification via traditional microbiological methods were identified as novel genomospecies, on the basis of de novo genome assemblies. Interestingly, pangenome analysis revealed significant variation in pangenome size between species, reflecting differences in genome flexibility. Exploring the infection dynamics of individual patients, the authors detected a high incidence of co-infection with multiple strains of the same species (polyclonal infection). Analysis of clonal lineages across multiple patients suggested the inter-patient transmission of several opportunistic pathogens, including Staphylococcus epidermidis and Pseudomonas aeruginosa. This study demonstrates the value of routine genomic surveillance of bacterial isolates in providing useful information that has the potential to improve patient treatment and infection control practices.
Roach, D. J. et al. A year of infection in the intensive care unit: prospective whole genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel microbiota. PLoS Genet. http://dx.doi.org/10.1371/journal.pgen.1005413 (2015)
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Waldron, D. Sequencing of clinical bacterial isolates. Nat Rev Genet 16, 499 (2015). https://doi.org/10.1038/nrg4002