Pathogenomics - History

History

In the early investigation of microbial genomics, it was difficult and costly to obtain sequence information for any pathogen. In 1995, the first pathogen genome, that of Haemophilus influenza was sequenced by traditional Sanger methods. Sanger methods, however, were slow and costly. The emergence of second generation high through-put sequencing technologies have allowed for microbial sequence information to be obtained much more quickly and at a considerably lower cost. Largely thanks to second generation sequencing methods, hundreds of pathogen genomes have been sequenced since 1995. The emergence of second generation high through-put sequencing technologies have allowed for microbial sequence information to be obtained much more quickly and at a considerably lower cost. This influx of information is also due to the capacity of sequencing platforms to evaluate the sequences of many organisms in parallel.

With the sequences of many organisms available for analysis, scientists, through their investigations, began to challenge some of the earlier tenants of bacterial genome structure. Older paradigms of microbial genomics believed that only a few strains were sufficient to represent a specific bacterial species.

It was thought that bacterial genomes, like eukaryotes, were relatively stable. In 2001, however, the sequences of Escherichia coli 0157:H7 was obtained in a study by Perna and her colleagues; the study showed that two members of the same bacterial species can differ as much as 30% in genomic content. It became evident that sequencing multiple strains for a species, rather than a few selectively chosen ones, was necessary to understand the diversity in a microbial species gene pool. It was also increasingly important to understand how to account for these differences in genomic content across a species strains and how it may contribute to pathogenic behaviour or prevent the formation of pathogens.

More recently, the sequenced genomic data has been catalogued in databases and made publicly available online (there do also exist non-publicly available databases in the private sector). The availability and influx of this information presses upon those who conduct pathogenomics research to come up with a way of drawing meaningful conclusions from this data. In addition, the availability of such data on the internet encourages global collaboration of labs.