A Case for NGS
NGS identifies Kocuria missed by MALDI-TOF in joint infection
A 77-year-old male with history of type 2 diabetes mellitus, hypertension, and hyperlipidemia presented to clinic with pain and stiffness to his right knee. Surgical history included a right TKA and subsequent revision surgery. Biomarkers from synovial fluid and serum were consistent with infection.
Synovial fluid and intraoperative samples were sent for culture MALDI-TOF and MicroGenDX NGS identification. Culture MALDI-TOF isolated very light growth Staphylococcus spp. and gram positive cocci. However, MicroGenDx NGS identified Kocuria ocularis to be the main culprit. A research MALDI-TOF database confirmed NGS identification of Kocuria ocularis. Patient treatment changed from vancomycin to penicillin, and patient was recovering well at 6-month follow-up.
The reference database used for MALDI-TOF did not contain Kocuria ocularis. An inability to identify an organism in this manner, along with the morphologic similarity to some coagulase-negative Staphylococcus (CoNS) species, led to the inaccurate reporting of the sample and initial implementation of incorrect antibiotic treatment.
NGS quickly identifies Mycobacterium smegmatis in spine implant infection
A 62-year-old female with history of osteoarthritis, hyperlipidemia, depression, and anxiety initially presented to clinic with approximately two years of frequent falls and progressively worsening issues with balance and coordination. She denied any neck or back pain, but did note weakness, numbness, and tingling to upper extremities, with symptoms worse on the right side. She had begun to require the use of a walker for ambulation, and saw no relief with multiple epidural injections or aqua therapy. Physical exam revealed decreased range of motion of her cervical spine, and decreased strength to bilateral triceps, wrist flexors, and intrinsics. CT and MRI of the cervical spine demonstrated myelopathy and destructive changes consistent with advanced osteoarthritis at C1-C2, and the patient subsequently underwent a C1 to C3 laminectomy and occiput to C5 posterior fusion.
At one-month follow-up, the patient reported intermittent posterior neck pain and frontal headaches, but overall her symptoms had improved. However, at 42 days status-post her initial surgery, she presented to clinic with a week of shooting pain up her posterior head, and radiographic imaging revealed two occipital screws displaced and migrated from the plate. As the patient showed no constitutional signs or symptoms of infection, she was indicated for a revision surgery with placement of new instrumentation. However, during the procedure, there was noted to be a large amount of inflammatory tissue surrounding the disengaged screws, and three samples of this tissue were sent for analysis with culture.
Culture of tissue grew a nontuberculous mycobacteria (NTM) in five days, but a specific species was not identified using culture until five weeks following sample collection. In contrast, next-generation sequencing (NGS) analysis performed on samples obtained during a subsequent irrigation and debridement confirmed the presence of Mycobacterium smegmatis within one week. Although traditional culture identified a rapidly growing NTM in this case of spine implant infection (SII), the species was not identified in a timely manner. Accurate and rapid species-level pathogen identification is imperative in the targeted treatment of spinal infections including those caused by NTM. The use of molecular testing such as NGS is helpful in identifying infecting organisms and guiding antimicrobial treatment.