Enterococcus faecium pneumonia diagnosed by metagenomic next-generation sequencing in a patient with chronic...

Enterococcus faecium is a rare pathogen in community-acquired pneumonia (CAP), and its diagnosis is challenging, particularly when prior antibiotic therapy hampers isolation by conventional culture. We report a 72-year-old man with a 6-year history of chronic obstructive pulmonary disease (COPD) who presented with fever, cough, and progressive dyspnea. Despite empirical broad-spectrum antibiotics (piperacillin-tazobactam followed by imipenem-cilastatin), his condition deteriorated into acute respiratory distress syndrome (ARDS) requiring invasive mechanical ventilation. All routine cultures of blood, sputum, and throat swabs were negative, and extensive atypical pathogen screening was unrevealing. Metagenomic next-generation sequencing (mNGS) of sputum and subsequently bronchoalveolar lavage (BAL) fluid, performed at the ISO 15189-accredited central laboratory of Qujing Central Hospital of Yunnan Province, detected high read counts of E. faecium (sputum: 22,710 reads; BAL: 7921 reads; opportunistic pathogen, classification B), with simultaneous routine screening for 31 resistance genes, 4 resistance loci, and virulence genes, all negative. Additionally, sputum mNGS detected Epstein-Barr virus (Human gammaherpesvirus 4, 6715 reads, normal microbiota, classification C), and BAL fluid mNGS detected HSV-1 (Human alphaherpesvirus 1, 407 reads, normal microbiota, classification C). Both herpesviruses had classification C and were interpreted as non-pathogenic "bystanders"; no antiviral therapy was administered. The patient gradually improved on imipenem-cilastatin plus moxifloxacin and was successfully extubated and discharged. This case suggests that E. faecium can cause severe CAP in COPD patients, and mNGS is a valuable diagnostic tool when conventional cultures are negative; herpesviruses with classification C detected by mNGS should not be overinterpreted.