Concurrent Burkholderia cepacia detected by plasma mcfDNA sequencing in a child with MRSA liver abscess and chronic granulomatous disease: a case report

BACKGROUND: Chronic granulomatous disease (CGD) is a primary immunodeficiency marked by defective phagocyte function, predisposing patients to recurrent infections, granuloma formation, and hyperinflammation. Initial diagnosis can be delayed due to nonspecific clinical features, incomplete pathogen detection, and common outpatient antimicrobial use. Plasma microbial cell-free DNA next-generation sequencing (mcfDNA-Seq) is an emerging non-invasive diagnostic tool, but its sensitivity and specificity vary by infection type and host. We report a case of CGD first presenting with concurrent Staphylococcus aureus liver abscess and disseminated Burkholderia cepacia infection, where mcfDNA-Seq contributed to diagnosis and management. CASE PRESENTATION: An 11-month-old male presented with 17 days of fever, irritability, and bulky cervical lymphadenopathy unresponsive to outpatient antibiotics. Physical exam demonstrated extremity rash, oral ulcers, and bilateral cervical lymphadenopathy. Initial infectious workup was negative including blood and urine cultures, chest radiograph, CMV and EBV serology. Abdominal imaging demonstrated a hepatic abscess, and multiple splenic and hepatic lesions interpreted as granulomas. Culture of liver abscess drainage grew methicillin-resistant S. aureus (MRSA). Fevers and lymphadenopathy continued despite vancomycin, with no evidence of spread or recurrence of MRSA. Rapid resolution of symptoms was achieved after initiating intravenous trimethoprim-sulfamethoxazole and plasma mcfDNA-Seq confirmed presence of Burkholderia cepacia. Subsequent genetic and dihydrorhodamine flow cytometric testing confirmed the suspected diagnosis of CGD. CONCLUSIONS: This case highlights the diagnostic challenges associated with CGD and the potential utility of plasma mcfDNA-Seq in this immunocompromised population. It may serve as a less invasive alternative to tissue specimens, particularly when conventional diagnostics are unrevealing. Concurrent infections should be considered during febrile illness in patients with CGD, especially with failure to respond to therapy.