Source: SD News
SHENZHEN scientists released a third version of the assembled genome of the deadly new E. coli strain and diagnostic kits for rapid identification of the highly infectious bacterium Tuesday.
The new assembly, developed by the Beijing Genomics Institute (BGI) Shenzhen and researchers at the University Medical Center Hamburg-Eppendorf, provides a more complete genome map and corrects any assembly errors in the previous version. More importantly, the new version is a completely de novo assembly, whereas the previous versions by BGI used a reference-based assembly method to obtain a consensus sequence.
The new assembly continues to support the finding that the infectious strain carries disease-causing genes from two types of pathogenic E. coli: enteroaggregative E. coli (EAEC) and enterohemorrhagic E. coli (EHEC).
Taking advantage of this genomic feature, BGI and the Beijing Institute of Microbiology and Epidemiology researchers have developed a straightforward PCR diagnostic protocol for rapid identification of the strain. Diagnostic results can be obtained within two to three hours of receiving the sample and will be extremely useful for epidemic surveillance.
BGI has assessed the specificity and sensitivity of this kit and protocol through computational analyses of 4,547 strains using publicly available whole-genome sequences and by experimental analyses of 323 DNA samples. The findings demonstrated that the kit and protocol have high specificity: No bacterial strain other than E. coli O104 had positive amplification results of both target regions. Sensitivity testing indicated that the kit and protocol could detect the bacterium using a DNA concentration as low as 10-12 g in the PCR. Additional validation tests on more patient isolates will be conducted within the week.
