British scientists propose new scheme to accurately identify lower respiratory pathogens within six hours

Recently, Dr Justin O'Grady of the University of East Anglia in the UK and scientists at the Earlham Institute have successfully developed a research method for macrogenomics detectionThe optimized solution is for bacterial lower respiratory tract infections, which removeup up to 99.99% of host nucleic acids from clinical respiratory samples and accurately identify pathogens and antibiotic resistance genes within 6 hours using real-time detection of nanoporous sequencingThe study was published in a cover article in July by Nature Biotechnologythe threat of bacterial lower respiratory tract infections and macrogenomic challenges
about 3 million people worldwide die each year from lower respiratory infections such as pneumoniaAt present, the gold standard of clinical diagnosis of bacterial lower respiratory tract infection (LRIs) mainly relies on collecting patient samples for bacterial culture, but its cycle is slow and sensitiveDuring this time, patients are usually treated with broad-spectrum antibioticsIf the infection is caused by a resistant pathogen, treatment may not only be ineffective, but may also cause side effectsOveruse of broad-spectrum antibiotics is also one of the main factors driving the development of antimicrobial resistanceclinical macrogenomic sequencing is a genome analysis of a variety of organisms obtained from a single sampleMacro genome sequencing can identify bacterial lower respiratory tract infection pathogens more quickly than bacterial cultureThere is a large amount of human genetic material (host DNA) in respiratory samples that needs to be removed in a specific way, making it difficult to deal with itThe study overcomes some of the obstacles that have so far prevented the widespread use of clinical macrogenomics, including the method of quickly and effectively removing human DNA from samples provided by patients, leaving only pathogen DNA for sequencingreal-time nano-porous macro genome sequencing within 6 hours of accurate identification of pathogens
DrJustin O'Grady's team developed a macrogenomics method for the study of bacterial lower respiratory tract infections that combines the characteristics of effective host DNA removal and real-time nanoporous sequencing detection using saponinThe method began with a feasibility study of 40 samples from patients with suspected lower respiratory tract infections After the method was optimized and optimized, an additional 41 respiratory samples were tested researchers use Oxford Nanopore's portable MinION sequencing device to facilitate real-time sequencing, data generation and analysis, and to reduce the time it takes for samples to arrive at results to six hours The portability of the sequencing device means it can be used closer to the patient, reducing the time it takes to deliver samples to a central laboratory compared with the culture method, the optimized method has a sensitivity of 96.6% to pathogen detection and 41.7% specificity, and can accurately detect antibiotic resistance genes After quantitative PCR and pathobiont specific genetic analysis was confirmed, specificity and sensitivity increased to 100% This suggests that nanoporous macro genomics can quickly and accurately identify pathogens in bacterial lower respiratory infection studies and may help reduce the use of broad-spectrum antibiotics MARA and E coli after 48 hours of sequencing conclusion " clinical macrogenomics has the prospect of revolutionary infectious disease diagnosis Our study describes the first rapid, cost-effective, and accurate clinical macro genome testing that can be used quickly in general clinical settings Dr O'Grady, a project leader at the Quadram Institute and an associate professor at the University of East Anglia, said Dr Richard Leggett, another leader of the project, said: "Nanoporous sequencing is an attractive technique in clinical diagnosis and this work is just one of many scenarios in which we tried it the protocol is currently being evaluated in a larger multisite clinical trial to evaluate its performance in diagnostic studies of acquired pneumonia in hospitals references: Charalampous etal., Nanopore metagenomics enables rapid clinical diagnosis of the lower lyce Nature Biotechnology volume 37, pages783-792 (2019) original title: Nature Sub-Journal Cover , Fast Economy, British Scientists Propose first new solution to accurately identify lower respiratory pathogens in 6 hours