Transforming clinical microbiology with bacterial genome sequencing

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Abstract
Whole-genome sequencing of bacterial isolates is becoming more and more widespread, paving the way for a transformation of many current procedures in clinical microbiology. Identifying the species of an isolate is currently a complex laboratory process. A few methods have already been proposed for doing this using the genome sequence, which could result in a re-evaluation of the bacterial species concept. Testing antibiotic resistance properties is often crucial for determining the appropriate treatment. As resistance is encoded by specific genes, this susceptibility assessment could be performed in silico using the genome sequence. The same is true for determining virulence properties of a strain, but with the difference that correlations between the genotype and phenotype is often more complex (involving several genes) than for resistance. However, association-mapping techniques can be used to detect such complex correlations, leading to a better understanding of pathogenicity. Several studies have already demonstrated the great potential of whole-genome sequencing in epidemiological investigations. These have so far been carried out after the course of an outbreak. In the future, with improving technology, this could be carried on an ongoing basis to detect epidemiological risks as they arise and react accordingly. Bacteria culturing is a pre-requirement even for whole-genome sequencing as it is currently carried out. This represents an important bottleneck as some bacteria are slow-growing and others cannot be cultured. Metagenomics approaches could provide a solution to this long-standing issue.