Diagnostic Challenges of Six-Pathogen Detected by mNGS in an Immunocompromised ICU Patient with Severe Community-Acquired Pneumonia-Induced Sepsis: A Case Report and Literature Review.

Abstract

Introduction: Severe community-acquired pneumonia (SCAP) in immunocompromised patients is often caused by rare atypical pathogens, which are difficult to detect using conventional microbiological tests (CMTs) and can progress to sepsis in severe cases. Metagenomic next-generation sequencing (mNGS), an emerging pathogen detection technique, enables rapid identification of mixed infections and provides valuable guidance for clinical treatment decisions. SCAP-induced sepsis caused by a six-pathogen co-infection has not been previously reported, but interpretation remains a challenge.

Case presentation: This report describes a case of SCAP-induced sepsis detected six pathogens by mNGS in a patient with IgA nephropathy who developed immunosuppression following long-term treatment with rituximab and corticosteroids. Bronchoalveolar lavage fluid (BALF) mNGS detected six pathogens, including Pneumocystis jirovecii, Klebsiella pneumoniae, Primate bocaparvovirus 1, Cytomegalovirus, Elizabethkingia anophelis, and Candida albicans. The patient was admitted to the intensive care unit (ICU) and received a combination of meropenem, trimethoprim-sulfamethoxazole, ganciclovir, piperacillin-tazobactam, and caspofungin. Following appropriate treatment, the patient recovered and was successfully discharged.

Conclusion: mNGS offers significant advantages for the diagnosis and identification of mixed infections in immunocompromised patients with SCAP-induced sepsis. It enables clinicians to initiate timely and targeted antimicrobial therapy, which facilitates early recovery, reduces the overuse of broad-spectrum antibiotics, and ultimately improves patient prognosis. Nevertheless, its interpretation requires caution, as distinguishing true pathogens from colonizers or contaminants still relies on clinical correlation and complementary diagnostic methods.