Machine learning flags emerging pathogens: A new machine learning tool could flag dangerous bacteria before they cause an outbreak, from hospital wards to a global scale

Reported today (8 May) in PLOS Genetics, the machine learning tool could be useful for flagging dangerous bacteria before they cause an outbreak, from hospital wards to a global scale. As the cost of genomic sequencing falls, scientists around the world are using genetics to better understand the bacteria causing infections, how diseases spread, how bacteria gain resistance to drugs, and which strains of bacteria may cause outbreaks. However, current methods to identify the genetic adaptations in emerging strains of bacteria behind an outbreak are time-consuming and often involve manually comparing the new strain to an older reference collection. The group of bacteria known as Salmonella includes many different types that vary in the severity of the disease they cause. Some types cause food poisoning, known as gastrointestinal Salmonella, whereas others cause severe disease by spreading beyond the gut, for example Salmonella Typhi which causes typhoid fever.