Lower Respiratory Infections; Scientists at the Quadram Institute and the University of East Anglia (UEA) have developed a new, rapid way of diagnosing bacterial lower respiratory tract infections in hours rather than days, that could improve patient care and slow the spread of antimicrobial resistance. The method is published today in the journal Nature Biotechnology.
Lower respiratory infections, such as pneumonia, account for around 3 million deaths worldwide each year. Current diagnostic methods rely on growing bacteria from patient samples; but this takes two to three days and may still not identify the cause. During this time, patients are given broad-spectrum antibiotics; which may not work if the infection is cause by a resistant pathogen and could trigger side effects.
Lower respiratory infections
Over utilization of broad-spectrum antibiotics is also a know driver; so for the development of antimicrobial resistance. Dr Justin O’Grady and his team have successfully develop a clinical meta genomics test (genomic analysis of multiple organisms obtaine from a single sample); so to precisely identify the bacterial causes of lower respiratory infections within 6 hours. It can also determine if the pathogens are resistant to any of the antibiotics use to treat these infections.
This allows rapid treatment with target antibiotics; so resulting in improve patient outcomes whilst reducing the use of broad-spectrum antibiotics; also helping in the fight against antimicrobial resistance. The study overcomes some of the hurdles that have, to date, held back the widespread deployment of clinical metagenomics.
The new method incorporates a step that rapidly and efficiently removes human genetic material; so from the sample provide by the patient, thereby leaving mainly pathogen DNA for sequencing. Respiratory samples are difficult to work with because they are mainly comprise of human genetic material. Removing this makes detecting the pathogens easier and reduces the sequencing cost and time. said Themoula Charalampous, a researcher on the study.
The data generation
The new method was develop with colleagues on the Norwich Research Park; so at the Norfolk and Norwich University Hospital and the Earlham Institute. Funding for the study came from the Biotechnology and Biological Sciences Research Council, the Medical Research Council and the National Institute for Health Research.
The researchers use Oxford Nanopore’s portable MinION sequencing device to facilitate real-time sequencing, data generation and analysis. This help reduce time-to-result from days to hours. The portability of this sequencing device means that it could be use closer to the patient, reducing the time spent sending samples to a central laboratory.
The pipeline that we’ve develop in this study produces data that can be use not only for clinical diagnostics but for public health applications such as outbreak detection and hospital infection control said Dr Gemma Kay. The protocol is now asses in a larger multi-site clinical trial to evaluate its performance for the diagnosis of hospital-acquired pneumonia.