| FEATURES & INNOVATIONS |
A FISHY INFECTION In early 2015, a mysterious outbreak of group B streptococcus appeared in Singapore. Streptococcus typically lines the intestines and urinary tracts of one-third of healthy adults, and is mostly considered harmless. The only doctors who really worry about the disease are obstetricians, because of the risk it poses to newborns. But here were strong and fit adults succumbing to the infection, arriving at emergency wards feeling feverish and confused, with severe headaches. Between January and July, 238 strep-
tococcus cases were detected in Singapore, compared to an annual average of 150. Government officials soon traced these cases to a popular dish of raw freshwater fish called yusheng, which is served with rice porridge at hawker stalls. “Group B streptococcus was not known to be a food-borne illness until this outbreak,” says Swaine Chen at the National University of Singapore and GIS. Chen and his colleagues used genomic
sleuthing to further investigate the source of the outbreak. “We found that more than 90 per cent of the group B streptococcus cases during that period were infected by the exact same strain,” he says. “It was a total slam dunk.” Genomics offers a level of precision that
other detective tools cannot, and has become common practice in outbreak surveillance. It was used to assess the 2014 Ebola epidemic, and is regularly used to monitor listeria and salmonella contamination in food. As part of ROUTES, Chen is trying to increase the scale and speed of such analyses for almost any bacteria.
Influenza virus sequencing has shown that even penguins can catch the flu. Driving the initiative is the proliferation of
genomic bacterial data. He now has access to 2,000 strains of group B streptococcus, with close to 50,000 strains of Escherichia coli and 130,000 strains of Streptococcus pneumoniae becoming publically available in the next year. Once the system is in place, Chen’s team could analyse the raw bacterial data of an emerging outbreak within six hours, instead of the week it took them in 2015. Eventually, the system will be so easy to use that physicians could do the detective work themselves. “We want clinicians to be able to manage the deluge of data without needing to know much about the low-level processing.”
PENGUIN FLU What Chen is doing for bacteria, Sebastian Maurer-Stroh at the BII is doing for viruses. In the midst of the swine flu pandemic in 2009, he developed FluSurver, a public online tool for analyzing sequences of the influenza virus to identify mutations and determine how those changes affect the structure of the virus. The World Health Organization’s national
Data detectives confirmed the food source of a spike in group B streptococcus infections in Singapore in 2015.
www.astar-research.com
influenza centers based in 113 countries use FluSurver for their surveillance, connected to the virus database of the Global Initiative for Sharing All Influenza Data (GISAID), which amounts to up to 20,000 sequences of influenza analyzed every year. The tool has been used to spot where and when new
mutations emerge in distant reaches of the world, including antiviral resistant swine flu variants in Singapore and Australia, as well as highly pathogenic strains of the avian influenza virus in Mexican chicken farms and in live poultry markets in eastern China. In 2014, a large collaborative team including Maurer-Stroh confirmed for the first time that even penguins catch the flu, and that their flu type is not dangerous to humans. Beyond FluSurver, the BII has applied
genomic analysis tools to outbreaks of norovirus, adenovirus, dengue, hepatitis C, and even the Zika virus in Singapore. In 2016 for example, the BII team, together with the National Public Health Laboratory of the Ministry of Health, rapidly characterized the local Zika strain linked to a large cluster of cases in Singapore. Under c-BIG, Maurer-Stroh also plans to work with colleagues at the I2
R to map the genetic diversity
of dengue against the movement of commuters through the public transport system. Eventually, c-BIG expects to take such
analyses into our everyday lives. “In the future, genomics will be just as ubiquitous as computing — everyone will have sequencers in their hands, their homes and various devices, essentially serving as sensors for life,” says Nagarajan. “We need to develop algorithms and robust systems that can aggregate data, make inferences and provide useful informa- tion about our environment in real-time.”
A*STAR RESEARCH 37
Courtesy of CDC/ James Archer
© Simon Bottomley/DigitalVision/Getty
Page 1 |
Page 2 |
Page 3 |
Page 4 |
Page 5 |
Page 6 |
Page 7 |
Page 8 |
Page 9 |
Page 10 |
Page 11 |
Page 12 |
Page 13 |
Page 14 |
Page 15 |
Page 16 |
Page 17 |
Page 18 |
Page 19 |
Page 20 |
Page 21 |
Page 22 |
Page 23 |
Page 24 |
Page 25 |
Page 26 |
Page 27 |
Page 28 |
Page 29 |
Page 30 |
Page 31 |
Page 32 |
Page 33 |
Page 34 |
Page 35 |
Page 36 |
Page 37 |
Page 38 |
Page 39 |
Page 40 |
Page 41 |
Page 42 |
Page 43 |
Page 44 |
Page 45 |
Page 46 |
Page 47 |
Page 48 |
Page 49 |
Page 50 |
Page 51 |
Page 52