Clinical Metagenomics for the Diagnosis of Hospital-acquired Infections: Promises and Hurdles/Reply

[...]when not applying a DNA extraction method aimed at reducing the load of human DNA, the vast majority of sequenced reads may be of human origin. [...]a proxy is required to translate percentages into colony-forming units/ml. [...]the authors reported a short turnaround time (9 h for the first case), which could allow a rapid optimization of the antibiotic treatment under three conditions: (1) the sequencer would be available 24 hours a day and the results rapidly sent to the physician, (2) the output of the sequencer would be actionable for the physician, and (3) the resistance pattern of the pathogen(s) would be inferred. [...]we acknowledge that the article by Pendleton and colleagues is an important contribution that supports the use of CMg in the context of hospital-acquired pneumonia but note that several limitations need to be addressed before CMg can eventually be used in the routine setting.