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Table 1 Patient characteristics and results of culture/sequencing

From: Evaluation of multi-sample 16S ribosomal DNA sequencing for the diagnosis of postoperative bone and joint infections during antimicrobial treatment

Case no. Infection Antibiotic treatment Days on antibiotic treatment when sampled No. biopsies for sequencing/cultured 16S ribosomal DNA findingsa,b Culture findingsa
16S rDNA sequencing yielded the full etiology of the infection opposed to culture
 7 = 9 PJI hip Cloxacillin 11 4/6 Staphylococcus aureus + Bacillus spp.d Culture negativec
 9 = 7 PJI hip Cloxacillin 19 4/4 S. aureus + Bacillus spp. S. aureuse
 21 PJI knee Cloxacillin + Rifampicin 10 3/7 S. aureus Culture negative
 22 = 19 FRI upper limb Clindamycin + Trimethoprim-sulfamethoxazole 12 4/4 Enterobacterales Culture negative
 25 FRI pelvis Linezolid 60 2/2 Enterobacterales Culture negative
16S rDNA sequencing equal to conventional culture in deciding the causative agent of the infection
 1 FRI hip Imipenem 7 2/2 Escherichia. coli E. coli
 5 Postop arthritis Cloxacillin 4 3/3 Not detectedf Culture negative
 4 Postop arthritis Cloxacillin 1 6/9 Not detectedg Culture negativeg
 2 Postop arthritis Cefotaxime 8 1/1 E. coli E. coli
 6 FRI hip Isoxazolyl-penicillin 7 − 2/2 Not detected Culture negative
 12 FRI lower limb Clindamycin 1 1/1 S. aureus S. aureus
 13 PJI hip Cefuroxime 3 7/7 S. aureus S. aureus
 14 FRI lower limb Cefotaxime 3 1/1 Not detected Culture negative
 15 FRI hip Cefotaxime + Clindamycin 2 5/5 S. aureus S. aureus
 16 PJI hip Cloxacillin + Rifampicin 18 3/3 Pseudomonas aeruginosa P. aeruginosa
 17 Postop arthritis Ciprofloxacin 9 1/6 Not detected Culture negative
 19 = 22 FRI upper limb Cloxacillin + Penicillin G 3 2/2 Bacillus cereus B. cereus
 23 FRI lower limb Cloxacillin + Clindamycin 1 2/3 Not detected Culture negative
 28 FRI upper limb Prophylaxis only—Clindamycin 0 3/3 S. aureus S. aureus
 27 PJI hip Ceftriaxone 3 6/6 Streptococcus dysgalactiae S. dysgalactiae
Different results when comparing conventional culture and 16S rDNA sequencing
 18 FRI upper limb Isoxazolylpenicillin 28 1/1 Not detected S. aureus
 20 = 24 FRI lower limb Isoxazolylpenicillin + Ciprofloxacin 13 1/5 Enterobacterales + Enterococcus spp. + Anaerococcus spp. Citrobacter freundii + Enterococcus faecalis + Enterococcus faecium
 24 = 20 FRI lower limb Imipenem 60 4/4 Enterococcus spp.h E. faecium
 26 FRI pelvis Imipenem + Linezolid 13 6/6 Not detected CoNSi
 8 PJI hip Cefuroxime 3 7/7 Proteus mirabilis P. mirabilis + Corynebacterium spp.
 3 FRI spine Cloxacillin 5 2/2 S. aureus S. aureus + Cutibacterium acnes
 10 PJI knee Clindamycin 5   Acinetobacter spp. + E. faecalis Acinetobacter spp. + E. faecalis + CoNS
 11 FRI lower limb Cloxacillin + Penicillin G 9 2/2 Not detected CoNS
  1. PJI prosthetic joint infection; FRI fracture related infection; CoNS coagulase negative staphylococci; rDNA ribosomal DNA; S. aureus Staphylococcus aureus, B. cereus Bacillus cereus; S. dysgalactiae Streptococcus dysgalactiae; E. coli Escherichia coli; Spp. species; P. aeruginosa Pseudomonas aeruginosa; faecalis Enterococcus faecalis, Enterococcus faecium
  2. aRelevant finding defined as presence in at least 50% of the samples in the case of multiple samples
  3. bEnvironmental bacteria excluded from the analysis
  4. cLater biopsies showed S. aureus in all biopsies and B. cereus in only one biopsy
  5. dB. cereus in 3/3 biopsies
  6. eB. cereus in 1/4 biopsies
  7. fS. aureus in 1/3 biopsies. A clinician would likely regard this finding as significant despite diagnostic criteria. Bacillus spp. in 1/3 biopsies
  8. gEnvironmental contaminants excluded through analysing several biopsies
  9. hListed as discrepant since sequencing failed to identify enterococcal species, a disadvantage concerning choice of antibiotic
  10. iMultiple strains of CoNS, suspected contamination