ers were well prepared to confront the outbreak, communication with the public was not handled as well. For example, an accusation made early in the outbreak implicating Spanish cucumbers came from a local food agency in Hamburg. This agency used screening tests that were not specific for the O104 strain and the Spanish cucumbers were wrongly implicated as the source. Spain sustained substantial economic losses and sought compensation. Communication among the national, state, and local authorities was not always consistent, nor was there agreement between public health and food communications groups. Intense media attention is common in such situations and is not always helpful. Harmsen noted that he himself was misquoted during interviews. He suggests that there should be centralization of information for these kinds of communication.
The E. coli case demonstrated that rapid NGS can be used almost in real time during outbreaks, and Harmsen described a second example that proved the usefulness of NGS for diagnostics during an outbreak. Only a month after the German E. coli case in June 2011, there was an outbreak of K. pneumoniae at Dutch Maasstad Hospital in Rotterdam. The strain was multidrug-resistant K. pneumoniae OXA-48. The outbreak did not receive the global attention that the German outbreak had, but it was an enormous public health issue in the Netherlands.
The Dutch National Institute for Public Health and the Environment (RIVM) sent K. pneumoniae strains to the University of Münster to sequence. A draft genome of the K. pneumoniae OXA-48 outbreak strain was developed and compared with other publicly available Klebsiella genomes. Scientists identified 36 candidate regions to use in developing a strain-specific multiplex PCR test. They enlisted the help of the Wellcome Trust Sanger Institute in Cambridge in the United Kingdom, which was conducting a global surveillance of Klebsiella. By comparing the candidate signature sequences against Sanger’s additional 200 Klebsiella genomes, they identified two candidate regions that were specific for the Dutch outbreak (Netherlands National Institute for Public Health and the Environment, 2013). This information was given to RIVM, and a multiplex molecular diagnostic test assay that targeted one of the two signatures as well as antibiotic resistance genes was developed. This test assay was supplied to every Dutch hospital and is still used today for screening patients, mainly for exclusion purposes. The case is an excellent example of the important role of genomics in diagnostics as well as microbial forensics.
As detailed in Box 3-2, clinical microbiologists see many potential applications for NGS that can be broadly organized under these categories: (1) ad hoc epidemiology; (2) diagnostics; (3) therapeutics; and (4) global surveillance, early warning, and outbreak detection. Benchtop NGS is a democratizing force, enabling small- and medium-sized labora-