Handheld cancer detection: Microfluidics meets NMR

Adaptation

A handheld device first developed for cancer diagnosis has been adapted to rapidly diagnose tuberculosis (TB) and other bacterial infections. Two papers appearing in the journals Nature Communications and Nature Nanotechnology describe the portable systems that bring together microfluidics technology and NMR relaxometry. The system is also able to determine whether or not resistant strains of any given microbe are present in a sample.

The team has previously developed portable devices that can detect cancer biomarkers in the blood or in very small tissue samples. In those tests, target cells or molecules are first labelled with magnetic nanoparticles, and the sample is then passed through a micro-NMR system that can detect and quantify amounts of the target substance. However, that preliminary work was not amenable to adaptation for bacterial diagnosis because of a dearth of suitable antibodies for labelling. The team thus switched to targeting specific nucleic acid sequences rather than proteins to open up their cancer-detection system to bacterial infection.

DNA labelling

Writing in Nature Communications, the team explains how their system can detect DNA from the tuberculosis bacterium present in small sputum samples. After DNA is extracted from the sample, any of the target sequence that is present is amplified using standard molecular biology procedures, then captured by polymer beads containing complementary nucleic acid sequences. It is only these conjugated species that are labelled by the magnetic nanoparticles bearing sequences appropriate for binding to other portions of the target DNA. The micro-NMR coil incorporated into the device - which is not much bigger than a standard laboratory microscope slide - then reveals the presence of bacterial DNA present in the sputum sample.

The researchers have tested their device on samples from patients known to have tuberculosis and from healthy controls. The device identified all positive samples with no false positives and took less than three hours to do so. Existing diagnostic procedures are much slower and can produce false negatives in 2 of every 5 patients that are subsequently observed to be infected. The team adds that test results for patients infected with TB and human immunodeficiency virus (HIV). The co-infection gives even stronger results because HIV/AIDS leads to a higher TB burden in those patients. The researchers add that their specialized nucleic acid probes could also distinguish between treatment-resistant bacterial strains and non-resistant strains.

rRNA labelling

In parallel work, the team has also turned to ribosomal RNA (rRNA), which has been used as a bacterial biomarker for some time. They have now developed a universal nucleic acid probe that detects a specific rRNA region common to many bacterial species and a set of probes that target sequences specific to thirteen clinically important pathogens, including Streptococcus pneumoniae, Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA). They report that the device was sensitive enough to detect as few as one or two bacteria in a 10 millilitre sample of blood and to provide an accurate measure of bacterial load. Tests showed that the rRNA approach could identify particular bacterial strains in less than two hours in samples from infected patients. Moreover, the technology revealed the existence of two strains that had not been identified with standard culture techniques.

There is work yet to be done in making the systems self-contained and commercially viable as standalone devices. However, once that work has been done the small size and ease of use of these devices will make them amenable to use in hospitals and clinics in the developing world. "The magnetic interactions that pathogen detection is based on are very reliable, regardless of the quality of the sample, meaning that extensive purification - which would be difficult in a resource-limited setting - is not necessary," explains Ralph Weissleder, director of the MGH Center for Systems Biology (CSB). "The ability to diagnose TB in a matter of hours could allow testing and treatment decisions within the same clinic visit, which can be crucial to controlling the spread of TB in developing countries," he adds.

In the work supported by the National Institutes of Health, Weissleder, explains that, "Rapidly identifying the pathogen responsible for an infection and testing for the presence of resistance are critical not only for diagnosis but also for deciding which antibiotics to give a patient." The new technology would allow medics to make a decision within two to three hours, which represents a significant reduction in waiting times over standard bacterial culture methods some of which might take as long as a week or even a fortnight to generate sufficient evidence to make a diagnosis. Co-senior author on the papers Hakho Lee adds that the system will be particularly useful in developed countries. "The capacity of the system not only to identify bacterial species but also to differentiate factors such as antibiotic resistance will help clinicians treat patients with the 'right' drugs from the start, which also helps reduce the emergence of treatment-resistant strains," he says. "The fact that this device requires only a tiny drop of the sample to be tested will be helpful in instances when specimens can be hard to obtain, such as treating children or seniors."

Monty Liong and Anh Hoang were co-authors on the Nature Communications paper along with colleagues at Harvard School of Public Health and the Broad Institute, while Hyun Jung Chung is a lead author on the strand of the research published in the journal Nature Nanotechnology.