Diagnostics
Metagenomics is the study of microbial communities by
analysing their collective genetic material.
target treatment to specific microbes, understanding the root causes of infections lessens our reliance on broad-spectrum antibiotics, along the way stifling microbial resistance. That outcomes improve dramatically is obviously another advantage. Whatever the sector’s financial strengths, however, the sector continues to face challenges. Though doctors now boast plenty of tools to identify common infections, like staphylococcus or the common flu, new or unusual pathogens have typically been far tougher to spot. That inevitably makes successful treatment much harder, even as time and money are spent on less effective alternatives. Yet, as so often in the clinical care space, new technology could soon consign these challenges to the same dustbin as Nicolas Andry’s ‘worms’. Known as clinical metagenomic next-generation sequencing (mNGS), this groundbreaking approach allows researchers to rapidly determine the microbe responsible for a particular illness, a godsend for patients and medical administrators alike. Not, of course, that the machines can do it all themselves – metagenomics can only really succeed if used in coordination with the human expertise of doctors and nurses.
Give it to me straight?
The medical calendar has regular rhythms. Every autumn, the flu rears its yearly head. Strep throat, for its part, tends to be more common in the winter and spring. While dispiriting from a medical perspective, this seasonality does have its uses. When it comes to common illnesses, after all, doctors can dovetail past experience and current symptoms to guess at a cause. That’s echoed by a plethora of diagnostic tests. When it comes to influenza, for example, some molecular tests offer results in as little as 15 minutes, even as accuracy hovers around the 95% mark.
But what happens if a patient arrives with unusual symptoms, ones that can’t easily be explained by flu or strep throat? For Dr Anne Jamet – head of mNGS at the Necker-Enfants Malades Hospital (AP-HP) in Paris, and a researcher at the Institut Necker-Enfants Malades –
Practical Patient Care /
www.practical-patient-care.com
this can quickly cause difficulties. “Targeted research is limited by prior knowledge,” Jamet says, “making it unusable for emerging infectious diseases with new pathogens, which can also evolve rapidly.” Fair enough: if they don’t know what they’re looking for, researchers obviously can’t develop tests for specific pathogens. And even when they do have more information, traditional detection methods come with other problems. One tactic involves isolating and cultivating microorganisms, before testing for pathogens. But this process can sometimes take weeks, even as prior exposure to antibiotics can impair results.
“Targeted research is limited by prior knowledge, making it unusable for emerging infectious diseases with new pathogens, which can also evolve rapidly.” Dr Anne Jamet
These technical irritations can lead to serious practical consequences. As Jamet explains, not knowing the specific cause of a disease can force doctors to “open the umbrella” – and ply patients with various drugs hoping they stick. Though this can succeed in the short term, it can make the pathogen more resistant to drugs later, even as they become more transmittable. There are other consequences too. “If infection is not properly treated, it is likely to be associated with prolonged illness and increased mortality rates,” Jamet warns, adding that longer hospital stays also mean more costs. Dr Jessica Galloway-Peña makes a similar point. Though she concedes the price of misdiagnosed infections is hard to quantify, the Texas A&M University professor stresses that misidentification of illnesses such as sepsis can be fatal. It hardly helps that antimicrobial resistance costs $55bn a year in the US alone.
Next (patho)gen
Over the past few years, a solution to these varied frustrations has emerged. As the name implies,
$55bn
The annual cost of antimicrobial resistance in the US.
NIH 9
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