Link to Pubmed [PMID] – 28192237
Clin. Microbiol. Infect. 2017 Feb;
OBJECTIVE: Infections are the major cause of morbidity and mortality in immunocompromised patients. Improving microbiological diagnosis in these patients is of paramount clinical importance.
METHODS: We performed this multicentre, blinded, prospective, proof-of-concept study, to compare untargeted next-generation sequencing with conventional microbiological methods for first-line diagnosis of infection in 101 immunocompromised adults. Patients were followed for 30 days and their blood samples, and in some cases nasopharyngeal swabs and/or biological fluids, were analysed. At the end of the study, expert clinicians evaluated the results of both methods. The primary outcome measure was the detection rate of clinically-relevant viruses and bacteria at inclusion.
RESULTS: Clinically-relevant viruses and bacteria identified by untargeted next-generation sequencing and conventional methods were concordant for 72 of 101 patients in samples taken at inclusion (Kappa test=0.2 [95% confidence interval, 0.03 to 0.48]). However, clinically-relevant viruses and bacteria were detected in a significantly higher proportion of patients with untargeted next-generation sequencing than conventional methods at inclusion (36/101 (36%) vs. 11/101 (11%), respectively, P<0.001), and even when the latter were continued over 30 days (19/101 (19%), P=0.003). Untargeted next-generation sequencing had a high negative predictive value compared with conventional methods (64/65, confidence interval 95%: 0.95-1).).
CONCLUSIONS: Untargeted next-generation sequencing has a high negative predictive value and detects more clinically-relevant viruses and bacteria than conventional microbiological methods. Untargeted next-generation sequencing is therefore a promising method for microbiological diagnosis in immunocompromised adults.https://www.ncbi.nlm.nih.gov/pubmed/28192237