title: Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review.
abstract: BACKGROUND
  The study aimed to explore the sensitivity and specificity of a novel fast 16S rDNA PCR and sequencing assay for the improved diagnosis of infective endocarditis (IE) in patients with suspected native or prosthetic heart valve (HV) infection over a multi-year period at our cardiovascular center.
  
  
  METHODS
  Sixty-eight patients were prospectively enrolled who underwent HV replacement for suspected or confirmed IE between February 1, 2009 and September 1, 2014. Patient demographics, medical co-morbidities, Duke's criteria, culture results, and antibiotic therapy were collected by detailed chart reviews. Dual-priming oligonucleotide primers targeted to 500 bps of the V1-V3 region of the 16S rRNA gene were used to perform fast broad-range 16S rDNA PCR and Sanger sequencing on ribosomal DNA extracted from HV tissues. The performance/diagnostic efficiency of the molecular test was evaluated against blood cultures and Gram stain and culture of HV tissue in patients' with definite IE according to Duke's criteria.
  
  
  RESULTS
  Fifty patients (73.5%) had definite IE and another 8 (11.8%) had possible IE according to Duke's criteria. Cardiac surgery was delayed an average of 15.4 days from the time of the patient's last positive blood culture, and appropriate antibiotic therapy was given in the pre-operative period. While 44/50 (88%) patients had a positive blood culture, HV tissue culture was only positive in 23 (46%) of them. Molecular testing of all HV tissues had sensitivity, specificity, NPV and PPV of 92, 77.8, 77.8 and 92% compared to 44, 100, 39.1 and 100% respectively for culture for diagnosis of definite IE. For prosthetic HV tissue, 16S rDNA PCR had sensitivity of 93% and specificity of 83% compared to 35 and 100% respectively for culture. A literature review showed that the diagnostic accuracy of our novel fast broad-range 16S rDNA PCR assay was similar or better than that of previously published studies.
  
  
  CONCLUSIONS
  This novel fast broad-range 16S rDNA PCR/sequencing test had superior sensitivity compared to tissue Gram stain and culture for identifying underlying bacterial pathogen in both native and prosthetic valve endocarditis.
authors.affiliation: Department of Cardiac Sciences, University of Calgary, Calgary, Alberta, T2N 2T9, Canada.
authors.forename: Robert J H
authors.initials: RJ
authors.lastname: Miller
authors.affiliation: Calgary Laboratory Services, Calgary, Alberta, T2L 2K8, Canada.
authors.forename: Barbara
authors.initials: B
authors.lastname: Chow
authors.affiliation: Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Calgary Laboratory Services, 9-3535 Research Rd. NW, Calgary, Alberta, T2L 2K8, Canada.
authors.forename: Dylan
authors.initials: D
authors.lastname: Pillai
authors.affiliation: Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Calgary Laboratory Services, 9-3535 Research Rd. NW, Calgary, Alberta, T2L 2K8, Canada. Deirdre.Church@cls.ab.ca.
authors.forename: Deirdre
authors.initials: D
authors.lastname: Church
mesh_terms: D000328:Adult; D000368:Aged; D002170:Canada / Q000453:epidemiology; D004697:Endocarditis, Bacterial / Q000175:diagnosis* / Q000453:epidemiology / Q000382:microbiology; D004926:Escherichia coli / Q000235:genetics; D005260:Female; D006351:Heart Valves / Q000382:microbiology; D006801:Humans; D008297:Male; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D011424:Propionibacterium / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D013210:Staphylococcus / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Bacterial pathogen; Broad-range 16S rDNA PCR; Endocarditis; Molecular diagnosis