The 5PSeq method, described Monday in the journal Nature Microbiology, is based on sequencing the messenger RNA (mRNA) that the bacteria break down as they synthesize proteins.

Since treatment for very ill patients with bacterial infections often needs to be given promptly to avoid serious health consequences, it is important that doctors quickly find the right antibiotic for the patient. However, current methods of testing antibiotic resistance can take hours or even days. Because of this, broad-spectrum antibiotics are often prescribed, which increases the risk of antibiotic resistance.

The researchers sought to reduce unnecessary antibiotic use by finding a way to quickly measure how bacteria are affected by different environmental factors, including antibiotic treatments.

They investigated mRNA degradation intermediates in isolated species and complex microbiomes using the 5PSeq method. They tested the method on a total of 96 bacterial species from different phyla in complex clinical samples, including fecal, gut, and vaginal samples, as well as compost samples. Within minutes, they were able to assess whether the bacteria were responding to antibiotic treatment; the effect was most significant after about 30 minutes.

Using metadegradome sequencing -- parallel analysis of RNA ends -- the researchers characterized 5′P mRNA decay intermediates in all 96 species, including Bacillus subtilis, Escherichia coli, Synechocystis spp., and Prevotella copri. They found co-translational mRNA degradation to be widespread among bacteria, and produced a degradome atlas for the 96 species to enable further analysis of RNA degradation mechanisms in bacteria.

Apart from measuring antibiotic resistance, the method can be used to help researchers understand how bacteria handle various environmental stressors, and how they interact with one another and with their hosts. The researchers will continue to study complex intestinal samples in order to better understand how bacterial communities interact in the gut and impact human health.

Researchers started up the 3N Bio company in the KI Innovations incubator to develop the method and create a rapid molecular test for clinical use. They recently received financing from the Swedish Research Council to demonstrate proof of concept for such a test in collaboration with Karolinska University Hospital.

"We demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations," the researchers wrote. "Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities."

Bioengineered drug fights Staphylococcus infection
Early tests show that a bioengineered drug can counter infection with Staphylococcus aureus, a major cause of death in hospital patients. The...

Shape-shifting antibiotic in study fights resistant infections
Researchers at Cold Spring Harbor Laboratory have created a new weapon against drug-resistant bacteria: an antibiotic that can shape-shift by rearranging...

Discovery of first steps in drug resistance process reveals new targets for antibiotics
Scientists have revealed the initial mechanisms that give rise to drug-resistant Escherichia coli, pointing to potential targets for antibiotics...

Multidrug-resistant bacteria cooperate to reduce the impact of antibiotics: study
Two of the most dangerous multidrug-resistant pathogens work together to nullify antibiotics, suggesting physicians need to determine if both bacteria...

Researchers discover new form of undetectable antimicrobial resistance
Australian researchers have discovered a new form of antimicrobial resistance that is undetectable using traditional testing methods. Their findings may...

COVID-19 virus disrupts gut bacteria, increasing secondary infection risk
New research, led by New York University Grossman School of Medicine researchers, shows that SARS-CoV-2 infection reduces bacterial diversity in a patient's...

Pain-sensing neurons protect against gut inflammation in mice
Weill Cornell Medicine researchers discovered that pain-sensing neurons protect the gut from inflammation and associated tissue damage by regulating the...

Stanford scientists create synthetic microbiome
Stanford University researchers built a complex and well-defined synthetic microbiome with 100 bacterial species that they successfully transplanted into...

New sensor-based test could lead to fast, cheap antibiotic susceptibility testing
Scientists have developed a new method for monitoring bacterial responses to antibiotics that could enable personalized antibiotic therapies. The test...