In June 2014, Heartlands Hospital in Birmingham reported an outbreak of Salmonella infection. It affected 30 patients and staff in two wards and spread to long-term in-patients on two adjoining wards. Salmonella food poisoning is associated with eggs and undercooked poultry, and although outbreaks are common, they are rare in hospitals.
On June 12, the infection-control team sent 16 strains of the bacteria from patients’ faeces to Nick Loman, an expert in infectious diseases at the University of Birmingham. It wanted results ready for a meeting the following morning. “The hospital wanted to understand quickly what was happening,” Loman says. “But routine genome sequencing is quite slow. It usually takes weeks or even months to get information back.”
However, Loman had a new type of DNA sequencer that was, in theory, suited to the task. Called MinION, it was made by a British company called Oxford Nanopore and was based on a new technology called nanopore sequencing. “It was announced two years ago as the first portable device that could do rapid DNA sequencing in real time,” Loman says. “Everybody was excited. Then for a long period nothing happened. We started to worry. Some people were even saying it was never going to happen because the technology they used defied the laws of physics.”
Loman used MinION to detect Salmonella in some of the samples sent from Heartlands, obtaining results in less than 15 minutes. Two hours later, he concluded that the majority of the Salmonella strains were part of the same outbreak, except for a second smaller outbreak linked to children who had been to Egypt. When the genome sequence of the Salmonella was compared with other strains in the public-health databases, the results suggested a link with cases not only in London, Bedford and Northampton but also in Germany, France and Austria. The source was a German egg supplier.
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