L2. New diagnostics
Oral Abstract Submission
Muhammad R. Sohail, MD
Disclosure: Boston Scientific Corporation : Consultant, Honoraria
Mayo Foundation : Other Financial or Material Support, Prior research unrelated to this study
Medtronic: Consultant, Honoraria
Medtronic: Other Financial or Material Support, Prior research unrelated to this study
Spectranetics : Consultant, Honoraria
TyRx.: Other Financial or Material Support, Prior research unrelated to this study
Robin Patel, MD
Disclosure: ASM and IDSA: Other Financial or Material Support, Travel reimbursement, editor's stipends
CD Diagnostics, Merck, Hutchison Biofilm Medical Solutions, Accelerate Diagnostics, ContraFect, TenNor Therapeutics Limited, Shionogi: Grant/Research Support
Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, Qvella: Consultant
NBME, Up-to-Date, the Infectious Diseases Board Review Course: Honorarium recipient, Other Financial or Material Support
Patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and a patent on an anti-biofilm substance issued: Other Financial or Material Support, Patents
Polymerase chain reaction (PCR)/sequencing targeting the 16S ribosomal RNA (rRNA) gene to detect bacteria in normally sterile tissues and fluids has become increasingly popular in clinical medicine. This culture-independent technique can detect bacteria that are non-viable or difficult to cultivate using conventional methods. The clinical value of this type of testing is not well-defined. We aimed to assess the diagnostic value of 16S rRNA PCR/Sanger sequencing as a clinical diagnostic assay at Mayo Clinic.
This is an interim analysis of the first 173 of 478 patients who had 16S rRNA PCR/Sanger sequencing done on sterile tissues or fluids at our institution from April, 2017 to November, 2018 as part of routine clinical practice. Medical records are being retrospectively reviewed, with results compared to those of culture.
We reviewed 207 specimens from 173 patients (musculoskeletal 79%, cardiovascular 7%, central nervous system 4%, other 9%) that underwent 16S rRNA PCR/Sanger sequencing by clinical request (Table 1). In 90% of these specimens, the test was pre-planned rather than added-on. Nine specimens were excluded from analysis, as cultures were not performed. Overall concordance of culture with PCR/sequencing was 81% (160/197; p < .0001). Of 44 culture positive specimens, PCR detected the same bacterium in 21 (48%) (Table 2). 45% (20/44) of those with positive cultures and 46% of those with positive PCR/sequencing results had received prior antimicrobial therapy (Table 3). PCR was negative in 139/144 specimens that were culture-negative (97%). PCR/sequencing was helpful in detecting a putative bacterial pathogen in 4 patients with negative cultures (Table 4).
Overall, 16S rRNA PCR/Sanger sequencing improved diagnostic yield compared to culture in a minority of cases. The described assay is limited by its inability to detect polymicrobial infections, a technical limitation that could possibly be addressed using massive parallel sequencing. Careful selection of cases and a save and add-on approach may be more cost-effective than up front testing, although this was requested in a minority of cases.