Taking antibiotics to fight an infection will not necessarily solve your problems. Naturally occurring bacteria in the gut often harbor several resistance genes. These bacteria could exchange their resistance genes with infectious bacteria that invade our bodies and result in antibiotic resistance. Knowing the pool of resistance genes — the resistome — present in the gut is therefore very important in improving treatment.
Today, getting resistome-data from a patient takes weeks. In the meantime, the resistome profile might change dramatically, and the patient will suffer from failing health. Every year 700,000 people die of resistant infections, in particular hospitalized patients; and the problem seems to be growing. For many patients, a quick assessment of their personal pool of resistance genes in their feces can be lifesaving.
Now researchers in Denmark have developed a super-fast and cheap method called poreFUME that can quickly shed light on the pool of resistance genes in the gut. "With this method, you will get an overview of the resistome in 1-2 days, and, hence, be able to start the treatment of the infection sooner and with better results than before," says Eric van der Helm, Postdoc at the Technical University of Denmark.
The poreFUME method using a new gene sequencing method is very rapid compared to current methods, because it does not require growth of the fecal bacteria, which takes time and can be difficult. Also, the data from the device is streamed in real time, so the user does not have to wait until the end of a 'run' to access information about the experiment. The researchers believe that their rapid resistome profiling could lead to personalized antibiotic treatment in high risk patients.
The results from the study showed that the poreFUME method was 97 percent accurate, when compared to standardized resistome profiling methods. This percentage is sufficient when measuring the resistome.
Furthermore, the poreFUME method is much cheaper than current methods, primarily due to the low cost of the so-called MinION; a small handheld DNA-sequencing device, which scientists can start to use for around US$1,000. In comparison, conventional so-called next generation sequencing devices are priced at between $50,000 and $10 million.
"If hospitals can purchase equipment for resistome profiling cheaper than today, it opens up for better profiling of more patients and hopefully fewer cases of bacterial resistance," says the research team.