title: Identification of bacterial pathogens from formalin-fixed, paraffin-embedded tissues by using 16S sequencing: retrospective correlation of results to clinicians' responses.
abstract: 16S sequencing on formalin-fixed, paraffin-embedded (FFPE) material has been used to identify bacteria when culture-based phenotyping techniques have not worked. The objective of this study was to determine how frequently 16S sequencing used in FFPE material was helpful to clinicians in the diagnosis and treatment of infectious diseases. Requests for testing occurred upon consultation between an infectious disease pathologist and a surgical pathologist or an infectious disease physician. A selected paraffin block from each case was referred for 16S sequencing. Retrospectively, we correlated clinical history and management decisions on 27 cases that were tested by paneubacterial 16S sequencing. Samples included 24 surgical specimens, 1 autopsy, and 2 cytology blocks. Seventeen (63%) of the 27 cases had a positive 16S sequencing. Acute inflammation was present in 10 of these cases, and organisms were observed using special stains in 3. In 11 (65%) of the 17 cases, clinicians considered the organism identified by 16S sequencing to be the cause or possible cause of the infectious process. Organisms included common (Citrobacter) and fastidious bacteria (Haemophilus, Fusobacterium). In 3 cases, clinicians changed antibiotic treatment based on the bacteria identified, whereas in 8 (including 2 where no organism was found), clinicians continued the antibiotic treatment. The use of 16S sequencing on FFPE identified specific bacteria even when organisms were not observed histopathologically. 16S results had an impact in infectious disease management decisions.
authors.affiliation: Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322;. Electronic address: Ldracsa@gmail.com.
authors.forename: Lori D
authors.initials: LD
authors.lastname: Racsa
authors.affiliation: Infectious Disease Pathology Branch, Centers for Disease Control and Prevention, Atlanta, GA 30303. Electronic address: mld7@cdc.gov.
authors.forename: Marlene
authors.initials: M
authors.lastname: DeLeon-Carnes
authors.affiliation: Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322;. Electronic address: matthew.hiskey@emory.edu.
authors.forename: Matthew
authors.initials: M
authors.lastname: Hiskey
authors.affiliation: Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322;. Electronic address: jguarne@emory.edu.
authors.forename: Jeannette
authors.initials: J
authors.lastname: Guarner
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D001419:Bacteria / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000472:pathogenicity; D001424:Bacterial Infections / Q000175:diagnosis / Q000188:drug therapy / Q000382:microbiology*; D000066491:Clinical Decision-Making; D004269:DNA, Bacterial / Q000235:genetics*; D005260:Female; D005404:Fixatives; D005557:Formaldehyde; D006801:Humans; D008297:Male; D008875:Middle Aged; D016612:Paraffin Embedding; D011237:Predictive Value of Tests; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D015203:Reproducibility of Results; D012189:Retrospective Studies; D021521:Ribotyping / Q000379:methods*; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D005404:Fixatives; D012336:RNA, Ribosomal, 16S; D005557:Formaldehyde
keywords: 16S; Bacteria; Bacterial sequencing; Infection; Paraffin samples