Previously, it took days to obtain the results of bacterial culture for the detection of respiratory infection. In the future, the result will probably be available after just six hours: Metagenomic sequencing is making this possible.
In order to be able to diagnose bacterial infections of the lower respiratory tract, sputum samples had to be taken in order to grow cultures. However, this detection procedure is much too slow with a duration of a few days. New technologies could enable faster diagnoses in the future. One of them, metagenomic sequencing, involves the simultaneous analysis of the entire microbial genome in a sputum sample. But one problem still remains: how to remove the immense excess of human genes from these samples?
In a recent paper, scientists presented for the first time results on their development of a metagenomic diagnostic method for bacterial infections of the lower respiratory tract. The human cells abundantly contained in the sample material were destroyed with the help of saponins. Following this, the bacterial DNA was further enriched. The researchers then analyzed the bacterial DNA fragments and compared them with a reference library of microbial DNA sequences. This ultimately made it possible to identify individual bacterial species.
The small pilot study with 40 patients with respiratory infections showed a sensitivity of 91.4% and a specificity of 100% after eight hours compared to the culture standard.
It was also interesting that the new diagnostic method even detected pathogenic bacteria in 5 of the 40 samples, which had escaped the culture technique. These included Moraxella catarrhalis, E. coli, H. influenzae, and Klebsiella pneumoniae. On the other hand, metagenome analysis also failed to detect three bacterial species that the culture was certain to recognize: S. pneumoniae, H. influenzae, and S. aureus.
Overall, the new method achieved a sensitivity of 96.6% and a specificity of 100% within six hours after further optimization of the sample preparation.
Charalampous T et al., Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol 2019; 37(7):783-792