The low cost and ease with which the genomes of
microbial strains can be sequenced has opened up technology
platforms for the analysis of microorganisms in
ways that were unimaginable even a few years ago. For
example, the comparative analysis of the genomes of
related organisms provides insights into their evolution
and particularly their acquisition of genes and groups of
genes, such as antibiotic resistance genes and pathogenicity
islands, by horizontal transfer. For example, in a
ground-breaking study, the ancient genome sequence of
Yersinia pestis, responsible for the Black Death that ravaged
Europe in the Middle Ages, was reconstructed after
the sequencing of DNA extracted from the teeth of victims
interred in a burial ground in East Smithfield,
London [24]. Phylogenetic analysis indicated this ancient
strain is an ancestor of most extant strains of Y. pestis.
Unexpectedly, its perceived enhanced virulence was
found not to be due to phenotypic differences, but probably
the result of prevailing social and environmental
factors. In a more contemporary analysis of the genomes
of 151 strains of Clostridium difficile, it has been possible
to monitor retrospectively the emergence and global
spread of the epidemic strain C. difficile 027/BI/NAP1
and show the existence of two epidemic lineages and a
relationship with rare fluoroquinolone resistance [25].