Pritt, Bobbi S.

Shotgun metagenomic sequencing can detect nucleic acids from bacteria, fungi, viruses, and/or parasites in clinical specimens; however, little data exist to guide its optimal application to clinical practice. We retrospectively reviewed results of shotgun metagenomic sequencing testing requested on cerebrospinal fluid samples submitted to an outside reference laboratory from December 2017 through December 2019. Of the 53 samples from Mayo Clinic patients, 47 were requested by neurologists, with infectious diseases consultation in 23 cases.

Tick-borne diseases, due to a diversity of bacterial pathogens, represent a significant and increasing public health threat throughout the Northern Hemisphere. A high-throughput 16S V1-V2 rRNA gene-based metagenomics assay was developed and evaluated using >13,000 residual samples from patients suspected of having tick-borne illness and >1,000 controls. Taxonomic predictions for tick-borne bacteria were exceptionally accurate, as independently validated by secondary testing. Overall, 881 specimens were positive for bacterial tick-borne agents.

A 38‐year‐old woman, status‐post renal transplant on immunosuppressive therapy, presented with fever, hypotension, and painful erythematous nodules on her chest, abdomen, and back. Skin biopsy revealed panniculitis with fat necrosis, and corresponding cultures showed no growth. Over the next 5 days, she became obtunded and developed a left hemiparesis. MRI showed non‐enhancing bilateral lesions in the cerebral cortex. She deteriorated and died. At autopsy, the 954 gram brain demonstrated flattened gyri and multiple disseminated necrotic foci. Microscopically, numerous cysts and trophozoites were identified within necrotic foci, consistent with Acanthamoeba spp. Review of the skin biopsy revealed similar organisms. Unlike primary amebic meningoencephalitis in healthy children and young adults caused by Naglearia fowlerii, encephalitis due to Acanthamoeba spp. is a subacute, progressive disease of immunocompromised patients. The double‐walled, cysts of Acanthamoeba spp. stain with H&E and Gomori Methenamine Silver, and may be mistaken for a fungus. Knowledge of the epidemiology and microscopic appearance of Acanthamoeba spp. is essential for accurate and timely diagnosis of this serious and potentially treatable infection.