B-245 Applicability of metagenomic Next-Generation Sequencing (mNGS) in challenging infectious diseases in a tertiary hospital
Authors: Chebabo L F , Conti F M , Bandeira S P , Castelo M C , Lopes A C 
Published: September 2023

Abstract

Background
Infectious diseases caused by rare pathogens or with unusual presentations pose a diagnostic challenge. Traditional microbiologic tests can be time-consuming, labor-intensive and have limited sensitivity for some organisms. Plasma metagenomic Next-Generation Sequencing (mNGS) detects whole microbial genetic material and detects even unsuspected organisms. We present three cases of challenging infectious diseases and discuss the applicability of mNGS in different scenarios.

Methods
Plasma NGS was performed at Karius, Inc. (Redwood City, CA, USA). Patient data was collected from hospital and laboratory electronic records.

Results
Case 1: An 8-year-old female with sickle-cell anemia developed a persistent daily fever two weeks after recovery from sepsis due to Streptococcus pyogenes. Clinical exam was normal and investigation was negative (blood cultures, echocardiogram, thoracic and abdominal CT scans and bone scintigraphy). Two weeks later mNGS was performed, which came out positive for Cytomegalovirus. As patient became afebrile in 48 h and the viral burden was low, she could be safely discharged. Case 2: A 43-year-old male with prosthetic aortic valve and an intraluminal aortic ring had a year-long history of fatigue, weight loss and hypoalbuminemia. CT scans showed ground-glass infiltrates and enlarged mediastinal lymph nodes. Empirical treatment for tuberculosis was ineffective. A year later, he developed hepatosplenomegaly, fever and pancytopenia. Blood cultures, bone marrow biopsy and serologies (HIV, hepatitis B/C, syphilis, brucellosis, bartonellosis, leishmaniasis) were negative. Cardiac surgery found no apparent signs of endocarditis and the prosthetic aortic valve biopsy revealed only an inflammatory infiltrate. A new CT scan showed thickened intraluminal aortic ring with aortic pseudoaneurysms and splenomegaly with splenic infarction. A blood sample was then collected for mNGS and liver biopsy and splenectomy were performed. However, surgery complicated with hemodynamic instability, renal and liver failure and the patient died in less than 24 h. Two days later, mNGS came out positive for Coxiella burnetti. Case 3: A 45-year-old female with relapsed AML treating a chronic disseminated candidiasis with micafungin for 3 months had persistent liver and splenic nodules and new pulmonary nodules on the CT scan. In the following three months after chemotherapy (Gilteritinib), she developed multiple episodes of febrile neutropenia, some without microbiological documentation, leading to multiple courses of antibiotic treatment and a shift to liposomal amphotericin B. After clinical improvement and bone marrow recovery, liposomal amphotericin B was replaced by isavuconazole. A negative mNGS result allowed antifungal treatment to be safely discontinued, avoiding six months of unnecessary antifungal treatment.

Conclusion
We summarize three different scenarios of mNGS applications. In common, patients were submitted to multiple laboratory and image testing and received large doses of empirical antimicrobials due to lack of a precise diagnosis. In two cases, mNGS was diagnostic, shortened hospital stay and reduced overall costs. In case 2, the patient’s death might have been prevented if mNGS had been performed earlier. Vulnerable hospitalized patients with a broad spectrum of diagnostic possibilities, in whom sequential diagnostic tests could delay adequate therapy and cause significant adverse effects, could greatly benefit from mNGS when performed in a timely manner.