A new technology platform is set to transform the fight against infectious diseases, as we discover talking to Dr Bradley Perkins, CMO of Karius.
An infection called anaplasmosis is less well known than Lyme disease but it’s also tickborne, dangerous and on the rise.
It’s particularly worrying that while anaplasmosis – spread like Lyme by the same kinds of blacklegged ticks – can be treated with antibiotics, the symptoms can be confused with Covid, and failure to treat early can lead to severe disease or death.
Fortunately, Karius, a diagnostic company pioneering liquid biopsy for infectious diseases, has developed the Karius Test to detect the presence of more than 1,000 pathogens, including the Anaplasma bacteria. Hospitals can now use the Karius Test to detect microbial DNA from a single blood sample, guiding physicians to the right treatment path for tricky infections such as anaplasmosis.
The implications are potentially far-reaching.
Karius’ chief medical officer, Dr Bradley Perkins, says: “This technology platform, which Karius is really leading the world in, in developing and promulgating across a number of different hospitals and use cases in the United States, is really going to revolutionise the diagnosis and management of infectious diseases.”
The platform is built on intellectual property developed at Stanford University and, based on the research, Karius was founded in 2014, with the test being initially commercialised two years later.
Dr Perkins explains: “What it does is quite remarkable. It’s based on the new recognition that all of these different infectious diseases, leave ‘footprints’ in the body. In this case, those “footprints” are fragments of their DNA, in the case of DNA-based pathogens.”
Karius is exclusively focused on the microbial world that is based on DNA, which is the predominant structure for microbial agents. When these agents are infecting humans, they replicate and, as they replicate, they shed pieces of their DNA into the blood.
“What we do – and this is not trivial – is we get a single sample of blood and we process that blood in the laboratory, so that it’s enriched for these microbial fragments of DNA,’’ says Dr Perkins.
“That’s where this notion of cell-free DNA comes from. Then we sequence those using next generation sequencing technology, which is a critical technological advance that makes this possible.’’
The next key advance is simple raw computational power. Karius can take that simple sequence information – an enormous amount of data – and compare it to more than 1,000 different pathogens causing infectious diseases, that includes bacteria, DNA-based viruses, fungi, and parasites.
Dr Perkins explains: “Basically, this is like a police line-up. We line up thousands of microbial ‘suspects’ and then we look at these fragments of DNA, and match them using bioinformatics.
“It turns out, quite remarkably, and quite persuasively, that we can identify the presence of these important pathogens in ways that no other microbiology diagnostic test has ever identified them.”
This means that, within 24 hours, Karius’ platform can take a one blood sample, look for more than 1,000 pathogens and then report the likely pathogen causing an infection back to the physician immediately, so that the patient can receive the right therapy as soon as possible.
This is only the beginning.
“We expect the laboratory methods that are involved in doing this and the computational aspects to continue to improve,” says Dr Perkins.
“We expect – like other next generation sequencing methodologies – for the cost to come down and for the technology to be more widely distributed.
“Right now, we’re doing this from a single laboratory in Redwood City, California, serving hospitals all over the United States. We would expect the availability of this test will become more decentralised and less expensive as it becomes part of the practice of routine clinical medicine.”
Karius is working with over 200 hospitals, both paediatric and adult, and several transplant centres.
Dr Perkins points out that in the early use, the patients that Karius can help the most are the immunocompromised who are susceptible to the widest range of infections.
Apart from spreading the word in the medical world, the next stage is further R&D to further develop the test, so it not only provides physicians with the identity of microbial pathogens, but also its antimicrobial sensitivities when that’s relevant. Further work will extend beyond DNA to be able to detect RNA based infectious pathogens.
Diseases such as anaplasmosis are rare and difficult to diagnose, which is likely to make the test a useful tool worldwide and perhaps even prevent another global pandemic.
Dr Perkins says: “We’re in a position to identify not only single cases of these diseases, but potentially outbreaks that are occurring on a national level.
“We think that this platform is going to have a great deal of application in the forecasting, early recognition, and hopefully prevention of pandemic threats like SARS.
“We’re not currently working in animals, but there’s no reason that this technology can’t be used in animals, and, in particular, looking at this interface between the animals and humans in the emergence of new DNA and RNA-based pathogens.
“The Covid 19 pandemic is an example of how we must get better at doing this, to protect humanity when it’s possible to do so.”