A key landmark in molecular microbiology was the publication,
in 1995, of the complete genome sequences of
H. influenzae [19] and Mycoplasma genitalium [20], by use
of the sequencing technology developed by Sanger [21]. The
innovative aspect of this work was to sequence random fragments
of genomic DNA and to use computers to assemble
the resulting sequences into increasingly larger contiguous
sequence reads (so-called ‘contigs’). Microbial genome
sequencing, which originally cost greatly in excess of
$1 million per genome and which could take years to complete,
can now be done in a few days for a fraction of the
cost by means of next-generation sequencing techniques
[22]. The rapid progress in this field is such that it is predicted
that genome sequencing will become routine in diagnostic
microbiology laboratories. This will provide clinicians
with unprecedented information about a given infective
microorganism, including its precise identification, antibiotic
resistance profile, toxin production and other potential virulence
factors that may affect therapy and thereby treatment
outcomes [23]. Already, multiple whole-genome sequences
are available for the majority of known human microbial
pathogens and the number of sequences is currently increasing
exponentially.