This editorial in Eurosurveillance gives a nice overview of the microbiological side of the German E. coli outbreak investigation, including applauding the public data release & analysis efforts:
The data sets from these sequencing initiatives were instantly released for public access, resulting in data analysis among bioinformaticians and other researchers around the world. Results from these preliminary analyses have been rapidly communicated via blogs, Twitter and private web pages, outside the standard peer-reviewed scientific publication route. These initiatives have confirmed the microbiological characterisation of the outbreak strain made in the public health laboratories by targeted genotyping and phenotyping of facultative E. coli virulence genes. Most importantly, among compared E. coli genome sequences, the genome of the 2011 outbreak strain clustered closest to an EAggEC strain isolated in 2002, with the addition of stx2 and antibiotic resistance genes.
The details of findings to date are outlined in this article in the same issue, including details of Shiga toxin-producing enteroaggregative E. coli O104:H4 from an outbreak in Georgia in 2009 (main difference seems to be that it was ESBL negative, unlike the current strain which has acquired an IncI plasmid carrying the ESBL gene blaCTX-M). They also discuss a rapid PCR test for the outbreak strain direct from food samples, involving enrichment+incubation (18-24h) followed by PCR for stx2 gene from extracted DNA, followed by PCR for O104 and then confirmation from pure cultures.
There are now reports of E. coli O104 from a stream in Germany, located downstream from a sewage plant… although this is more likely to be caused by the outbreak than a cause of it, it highlights that even highly industrialized countries need to be vigilant with sanitation and hygiene to prevent the spread of dangerous human pathogens [sourced from ProMed].