Genomic investigations of outbreaks were not first on the minds of the University of Münster's Dag Harmsen and his colleagues when they got their hands on a next-generation sequencer, but nature made its own plans.
In July, working with investigators at Life Technologies and elsewhere, the Münster team determined the strain responsible for the E. coli outbreak that began in northern Germany in May. Fueled by competition with investigators at BGI-Shenzhen, the German team worked to characterize the outbreak strain EHEC O104:H4 and make the data public.
Since then, Harmsen and his colleagues have put their E. coli experience to use, characterizing the antibiotic-resistant strain of Klebsiella pneumoniae Oxa-48 responsible for more than 80 infections at Maasstad Hospital in Rotterdam, the Netherlands.
"The EHEC outbreak could be regarded as a proof of principle that it is technically feasible, nearly in real-time, to sequence [outbreak strains]," Harmsen says. "However, we made no real good use [of that capability] for public health benefit from the EHEC data. It was more for scientific … modeling."
For this K. pneumoniae Oxa-48 outbreak, however, researchers at Münster and Life Tech, along with colleagues at the Wellcome Trust Sanger Institute, put the genomic data to use, creating a multiplex PCR-based rapid screening test, which has been distributed to all Dutch hospitals.
"Klebsiella was different in the sense that we really needed the sequence this time, for the development of a rapid screening test," Harmsen says, adding that now "several Dutch hospitals are using this test for screening patients that come in, especially those who were referred from this Rotterdam hospital."
Harmsen's team sequenced the outbreak strain using a single 316 chip on the Ion PGM. "If you would have asked me a year ago, I would have never believed that we are, from a technical point of view, really so far already," he says. "These smaller next-gen machines are exactly what we need; it's not only the Ion Torrent, [but also] the [Illumina] MiSeq, or the [Roche RS] Junior."
As more and more labs acquire these smaller, faster next-gen sequencers, Harmsen says he expects outbreak surveillance initiatives to improve along with detection practices. "[For EHEC] we competed with BGI and we are a really small laboratory compared to them. That wasn't possible a year ago, because you needed to invest so much money," he says. "What is now happening is basically democratizing next-gen sequencing, [so] that also smaller or mid-size laboratories are enabled. And the cool thing about the smaller machines is they are really fast, and that is exactly what you need for outbreaks."