Characterising the microbial and antimicrobial resistance signatures of hospital-acquired pneumonia using nanopore metagenomic sequencing

Hospital-acquired pneumonia (HAP) is a serious infection, but its microbial causes are not fully understood. In a UK study of 250 HAP patients, researchers used advanced nanopore sequencing to analyse respiratory microbiomes, confirming results with PCR and culture tests. Sequencing detected key pathogens and even identified likely microbes in nearly 50 cases missed by standard tests.

Notably, fungi were found in one-third of patients, often undetected by routine methods, highlighting their overlooked role in HAP. The study also revealed high levels of multidrug resistance: 21% of bacterial genomes carried genes for resistance to at least three antibiotic classes, including in Staphylococcus epidermidis, usually seen as harmless but here acting as a reservoir for resistance.

Conclusion: Metagenomic sequencing provides a powerful tool to uncover the complex causes of HAP, detect hidden pathogens, and guide more effective treatment by identifying antimicrobial resistance.