Current traditional culture methods can take up to three days to identify bacteria and test antimicrobial resistances from a urine sample.
Discerning whether an infection is viral or bacterial can be challenging. This uncertainty accounts for much of the overuse and over-prescribing of broad spectrum antibiotics. In many cases, illnesses such as respiratory infections, skin infections, and urinary tract infections (UTI) are viral or could be treated by antibiotics that are less likely to cause resistance.
Current traditional culture methods can take up to three days to identify bacteria and test for antimicrobial resistance in a urine sample. However, new technology undergoing evaluation through an early access program at the University of East Anglia (UEA), reportedly reduces the wait for laboratory results to less than four hours. This new technology, nanopore MinION technology, provides clinicians with more immediate results, allowing them to adjust prescriptions before the second dose is given.
The authors of a study published in the Journal of Antimicrobial Chemotherapy, explained, “Genome sequencing will be increasingly used in the clinical setting to tailor antimicrobial prescribing and inform infection control outbreaks. A recent technological innovation that could reduce the delay between pathogen sampling and data generation is single molecule sequencing. An example of this technology, which is undergoing evaluation through an early access programme, is the Oxford Nanopore MinION.”
A quicker way to determine whether a UTI is caused by an antibiotic-resistant pathogen will permit a precise and tailored treatment plan; it will also allow limited antibiotic resources to be better managed.
The authors state that rapid diagnosis will improve treatment as well as antibiotic stewardship, which is a major priority as the scientific and medical communities work to control antimicrobial resistance. If antimicrobial resistance is not addressed, by 2050 the death toll could amount to one person dying every three seconds from an antimicrobial-resistant infection.
For this study, the researchers used human cells removed from urine samples. Bacteria was recovered and sequenced by MinION. The results were then compared with standard culture and antibiotic susceptibility testing results.
In order to detect sub-variant chromosomal genes within a cluster and distinguish them between TEM-1 and TEM52, MinION must be able to identify mutations in relation to antimicrobial resistance. The researchers concluded that although MinION detects the presence of acquired resistance genes, in order for the results to accurately predict mutations in chromosomal genes, improvements to the technology are necessary.
It is also essential for laboratories and other publicly-funded institutions to be able to afford the technology. Current sequencing instruments approved for clinical use by the FDA retail at $125,000. Oxford Nanopore Technologies has proposed a pay-as-you-go model where approximately three hours of sequencing on the MinION would cost around $270. Portability and ease of use is also a factor, making it advantageous for remote laboratories to use sequencing when investigating emerging pathogens of unknown cause.