In 2011, University of Münster researchers reported their sequencing of an Escherichia coli strain behind an outbreak in Germany, showing that real-time sequencing was feasible. Then they characterized a K. pneumoniae strain that infected patients in a Dutch hospital. This information was used to develop a multiplex PCR-based assay for the disease.
For the K. pneumoniae outbreak at the US National Institutes of Health’s Clinical Center, Julie Segre and her colleagues sequenced isolates from the 18 infected patients using a 454/Roche machine. From their Newbler assembly and subsequent analysis, they found that isolates from patient 1 and patient 2 differed by two SNPs out of the 6 megabase K. pneumoniae genome, indicating they were infected with the same strain. …
As the cost of sequencing is dropping, major medical centers could soon implement whole genome sequencing to monitor disease exposure of patients. “If the analysis is that you are spending $100,000 to have an organ transplant or go through some very intensive cancer treatment that involves a few nights’ stay in the ICU,” Segre says, “at that point, putting up $500 to sequence an organism that may be affecting another patient in the ICU. … I could imagine in the future that that becomes part of the economic model.”
Read the whole GenomeWeb article at http://bit.ly/Qu3tRX