The utility of 16S rRNA gene sequencing on intraoperative specimens from intracranial infections: an 8-year study in a regional UK neurosurgical unit

Optimal management of intracranial infections relies on microbiological diagnosis and antimicrobial choice, but conventional culture-based testing is limited by pathogen viability and pre-sampling antimicrobial exposure. Broad-range 16S rRNA gene sequencing has been reported in the management of culture-negative infections but its utility in intracranial infection is not well-described. We studied the efficacy of 16S rRNA gene sequencing to inform microbiological diagnosis and antimicrobial choice in intracranial infections. This was a retrospective study of all intraoperative neurosurgical specimens sent for 16S rRNA gene sequencing over an 8-year period at a regional neurosurgical centre in the UK. Specimen selection was performed using multidisciplinary approach, combining neurosurgical and infection specialist discussion. Twenty-five intraoperative specimens taken during neurosurgery from 24 patients were included in the study period. The most common reason for referral was pre-sampling antimicrobial exposure (68%). Bacterial rDNA was detected in 60% of specimens. 16S rRNA gene sequencing contributed to microbiological diagnosis in 15 patients and informed antimicrobial management in 10 of 24 patients with intracranial infection. These included targeted antibiotics after detection of a clinically-significant pathogen that had not been identified through other microbiological testing (3 cases), detection of commensal organisms in neurosurgical infection which justified continued broad cover (2 cases) and negative results from intracranial lesions with low clinical suspicion of bacterial infection which justified avoidance or cessation of antibiotics (5 cases). Overall, 16S rRNA gene sequencing represented an incremental improvement in diagnostic testing and was most appropriately used to complement, rather than replace, conventional culture-based testing for intracranial infection.