Mycobacterium mageritense submandibular lymphadenitis in children: diagnostic challenges and the role of metagenomic next-generation sequencing: two case reports and literature review

Mycobacterium mageritense is an extremely rare, rapidly growing nontuberculous mycobacterium (NTM). Pediatric cases are rarely reported worldwide, and the non-specific clinical manifestations, low sensitivity of conventional microbiological tests, and limited specimen volume from children often lead to diagnostic delays. We describe the clinical data of two immunocompetent children with submandibular lymphadenitis caused by Mycobacterium mageritense, both diagnosed by metagenomic next-generation sequencing (mNGS). We also systematically reviewed the relevant literature and performed a pooled analysis of 36 eligible cases (the two new paediatric cases from the present study included). Case 1 involved a 6-year-old girl with dental caries and acute fever who was initially misdiagnosed with common bacterial infection and received ineffective empirical antibiotics for over two weeks; mNGS of aspirated pus confirmed the diagnosis. Case 2 involved a 9-year-old girl with dental caries who presented only with submandibular lymphadenopathy and normal laboratory findings, with a diagnostic delay of up to two months; mNGS of lymph node tissue identified the pathogen. Literature-pooled analysis of 36 patients revealed a mean diagnostic delay of 4.69 months (median 2.00 months, IQR: 0.81–5.75 months). Conventional culture had low sensitivity, often requiring prolonged incubation (≥96 h) or special media to obtain positive results. Initial misdiagnosis occurred in 17.6% of cases. Patients diagnosed by NGS achieved more rapid and accurate pathogen identification. This report suggests that mNGS, as a culture-independent, unbiased pan-pathogen detection technique, shows clear advantages in identifying rare and fastidious pathogens such as M. mageritense. For pediatric patients with dental caries, fever, and cervical lymphadenopathy unresponsive to conventional therapy, clinicians should suspect Mycobacterium mageritense infection, and mNGS is an effective tool for its rapid and accurate diagnosis.