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Diagnostics Microbiology and immunology, Genetics and epigenetics, Omics

Rooting out Resistance

Antimicrobial resistance is a huge and ever-growing problem, and it’s a known fact that, if doctors and researchers want to stay one step ahead of the superbugs, new antibiotics and diagnostic tools are needed. One such potential weapon is Mykrobe Predictor, a computer program that can provide drug resistance information in a few minutes using gene sequencing data from a bacterial infection, according to its developers.

Traditionally, drug susceptibility testing is used to find out which drugs an infection is resistant to, and involves introducing different antibiotics to a culture of the bacteria, but this process can take days, or potentially even longer for slow-growing pathogens like tuberculosis (TB). The Mykrobe program looks directly at the bacterial DNA and quickly analyzes it, presenting the results in a format that does not require specialist interpretation (see Figure 1).

Figure 1. A screenshot from the Mykrobe Predictor for Staphylococcus aureus, showing the easily interpreted results screen.

A retrospective study of over 4,500 patients found the prediction software accurately detected antibiotic resistance in Staphylococcus aureus and TB – detecting resistance to five antibiotics in over 99 percent of S. aureus cases, comparable to the performance of drug sensitivity testing. For TB, sensitivity was lower (82.6 percent), presumably because the genetic basis of resistance in TB is not as well understood – but the test matched the performance of current DNA tests, and returned a result in just three minutes; weeks faster than a drug susceptibility test can. According to the study authors, the software can also identify mixtures of drug-resistant and drug-susceptible microbes.

But the technology isn’t just aimed at the diagnosis and treatment of individual patients. “The key is this,” says senior author of the associated paper (1), Zamin Iqbal, “Current mix-bug-and-drug methods are all about the patient. Get a result for the patient, treat them, then throw the data in the bin. Maybe not literally, but currently the information that patient X had an infection that was resistant to A, B, or C drugs is useless to anyone else. But using genome sequencing, we can get the resistance information for the patient and detailed information on the ancestry of the sample – i.e., which strain it is. We can then share this digitized information globally, because bacterial DNA contains no patient information, and contribute to global tracking of bacterial strains, and of drug resistance.”

The software is now being evaluated for clinical use in three UK hospitals, with the aim of testing the technology on real clinical samples, resolving any issues that arise for the microbiologists using Mykrobe, and collecting more data on rare mutations. The complex data that arises from whole genome sequencing is a major barrier to its adoption by the National Health Service, adds Iqbal. The developers hope that programs like Mykrobe could help to overcome this problem and provide fast genetic information to better treat patients, and better understand antibiotic resistance.

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  1. P Bradley at al., “Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis”, Nature Commun, 6, 10063 (2015). PMID: 26686880.
About the Author
Roisin McGuigan

I have an extensive academic background in the life sciences, having studied forensic biology and human medical genetics in my time at Strathclyde and Glasgow Universities. My research, data presentation and bioinformatics skills plus my ‘wet lab’ experience have been a superb grounding for my role as an Associate Editor at Texere Publishing. The job allows me to utilize my hard-learned academic skills and experience in my current position within an exciting and contemporary publishing company.

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