JMM Editor's Choice: Shotgun sequencing to detect respiratory disease

Posted on July 4, 2019   by Microbiology Society

The Journal of Medical Microbiology (JMM) is a journal published by the Microbiology Society, focused on providing a comprehensive coverage of medical, dental and veterinary microbiology and infectious diseases, including bacteriology, virology, mycology and parasitology. This month, Professor Roberto La Ragione has selected an outstanding paper from the July issue to highlight as Editor's Choice. The paper, titled 'Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing,' discusses a pilot study to assess whether metagenomic sequencing could be a useful alternative to PCR to detect respiratory pathogens.

Professor Roberto La Ragione: The detection and quantification of non-culturable organisms implicated in respiratory disease remains a clinical challenge for both human and veterinary medicine. Culture-independent approaches offer a potential solution for the rapid and sensitive detection of respiratory pathogens from clinical samples. 

This article describes a shotgun metagenomics sequencing (SMS) approach that could be utilised for the rapid and accurate detection of pathogens present in clinical samples from respiratory disease. This publication has significant implications for improving the diagnosis of respiratory disease and thus improving patient outcome. This approach may also potentially reduce antibiotic use and the development of AMR.

Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing

With the standard of care cultivation approaches and targeted PCR, an etiologic agent could not be identified in approximately 46% of cases of community-acquired pneumonia. Cultivation-independent molecular approaches offer a potential solution. Our study demonstrates that shotgun metagenome sequencing strategy is able to detect bacterial, fungal, and viral organisms in bronchoalveolar lavage samples, including in cases which were negative in culture.