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Bacteriology

Differential Contributions of Specimen Types, Culturing, and 16S rRNA Sequencing in Diagnosis of Prosthetic Joint Infections

Lone Heimann Larsen, Vesal Khalid, Yijuan Xu, Trine Rolighed Thomsen, Henrik C. Schønheyder
Robin Patel, Editor
Lone Heimann Larsen
aDepartment of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
bCenter for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Vesal Khalid
cDepartment of Orthopaedic Surgery, Aalborg University Hospital, Aalborg, Denmark
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Yijuan Xu
bCenter for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
dBiotech, Danish Technological Institute, Aarhus, Denmark
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Trine Rolighed Thomsen
bCenter for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
dBiotech, Danish Technological Institute, Aarhus, Denmark
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Henrik C. Schønheyder
aDepartment of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
eDepartment of Clinical Medicine, Aalborg University, Aalborg, Denmark
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Robin Patel
Mayo Clinic
Roles: Editor
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DOI: 10.1128/JCM.01351-17
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  • FIG 1
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    FIG 1

    Flow diagram shows the patient selection and allocations. Numbers in brackets refer to patients, but numbers of cases are also indicated due to some patients being admitted more than once.

  • FIG 2
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    FIG 2

    Days of incubation until growth by type of specimen (5-STB, five soft-tissue biopsy specimens; JF, joint fluid; PC, prosthetic components; SW, swabs from the prosthesis, collected in situ; BB, bone biopsy specimen). Incubation was planned for 14 days but occasionally was extended due to weekends and holidays.

  • FIG 3
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    FIG 3

    Days to positive culture for the first specimen type (black columns) and subsequent specimen types (hatched).

  • FIG 4
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    FIG 4

    Contribution of specimen types to the diagnosis of prosthetic joint infection. (A) Thirty-five cases were diagnosed based on positive cultures of the minimum set comprising tissue biopsy specimens (5-STB), prosthetic components (PC), and joint fluid (JF). (B) A subgroup of 28 cases was evaluated based on all specimen types. It is apparent that neither the bone biopsy specimen (BB) nor the prosthetic swab (in situ) (SW) culture contributed independently to the diagnosis. *, one case diagnosis was supported by next-generation sequencing; **, one case showed a negative result in the culture of joint fluid; ***, one case showed negative results in the culture of prosthetic components; ****, in four cases, only one or two specimen types contributed to the culture-positive findings.

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  • TABLE 1

    Diagnostic accuracy measured by likelihood ratios

    Specimen,c culture duration (days) or 16S rRNA sequencingNo. of cases with a positive test/no. of cases testedLRa
    PJI (n = 42)AF (n = 66)Positive (95% CI)Negative (95% CI)
    5-STB, 631/420/66Infinityb0.3 (0.2–0.4)
    5-STB, 1437/420/66Infinity0.1 (0.05–0.3)
    JF, 626/391/5738 (5–269)0.3 (0.2–0.5)
    JF, 1434/392/5624 (6–96)0.1 (0.06–0.3)
    PC, 624/371/6039 (5–276)0.4 (0.2–0.6)
    PC, 1433/375/6011 (5–25)0.1 (0.05–0.3)
    SW (in situ), 69/320/59Infinity0.7 (0.6–0.9)
    SW (in situ), 1416/322/5915 (4–60)0.5 (0.4–0.7)
    BB, 69/320/54Infinity0.8 (0.7–0.9)
    BB, 1413/321/5422 (3–160)0.6 (0.5–0.8)
    Periprosthetic tissue, 16S rRNA sequencing8/320/53Infinity0.8 (0.6–0.9)
    Synovial fluid, 16S rRNA sequencing25/351/6546 (7–328)0.3 (0.2–0.5)
    PC, 16S rRNA sequencing32/371/6455 (8–389)0.1 (0.06–0.3)
    SW (in situ), 16S rRNA sequencing15/344/526 (2–16)0.6 (0.4–0.8)
    BB, 16S rRNA sequencing4/292/473 (0.6–17)0.9 (0.8–1.0)
    • ↵a Positive describes how probability of infection shifts with positive results, and negative describes how probability of infection wanes with negative results. CI, confidence interval.

    • ↵b An incalculably large number.

    • ↵c For abbreviations of specimen types, see the text.

  • TABLE 2

    Infecting microorganisms in prosthetic joint infections in hips and knees

    MicroorganismNo. of organisms found in culturea (n = 39)No. of organisms determined by 16S rRNA sequencing (n = 33)
    TotalSubgroup
    Polymicrobial115
    Staphylococcus spp.1416
        S. aureus7
        S. epidermidis2
        S. lugdunensis3
        S. capitis1
    CoNS, others1
    Streptococcus spp.46
        Hemolytic streptococcus group Cb2
        Hemolytic streptococcus group Gb2
    Enterococcus faecalis32
    Escherichia coli2
    Pseudomonas aeruginosa1
    Salmonella serovar Dublin11
    Propionibacterium spp.22
        P. acnes2
    Finegoldia magna11
    • ↵a Culturing showed positive results in 39 cases, and sequencing showed positive results in 33 cases. Due to the limited resolution in the 16S rRNA sequencing results, it was not possible to differentiate between species within the genera Staphylococcus, Streptococcus, and Propionibacterium.

    • ↵b The hemolytic streptococci all were identified in culture as Streptococcus dysgalactiae.

Additional Files

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  • Supplemental material

    • Supplemental file 1 -

      Text S1 (Detailed culture methods)

      PDF, 193K

    • Supplemental file 2 -

      Table S2 (Overview of culturing and molecular data)

      XLSX, 23K

    • Supplemental file 3 -

      Text S3 (Background subtraction in 16S amplicon data analysis)

      PDF, 85K

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Differential Contributions of Specimen Types, Culturing, and 16S rRNA Sequencing in Diagnosis of Prosthetic Joint Infections
Lone Heimann Larsen, Vesal Khalid, Yijuan Xu, Trine Rolighed Thomsen, Henrik C. Schønheyder the PRIS Study Group
Journal of Clinical Microbiology Apr 2018, 56 (5) e01351-17; DOI: 10.1128/JCM.01351-17

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Differential Contributions of Specimen Types, Culturing, and 16S rRNA Sequencing in Diagnosis of Prosthetic Joint Infections
Lone Heimann Larsen, Vesal Khalid, Yijuan Xu, Trine Rolighed Thomsen, Henrik C. Schønheyder the PRIS Study Group
Journal of Clinical Microbiology Apr 2018, 56 (5) e01351-17; DOI: 10.1128/JCM.01351-17
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    • ABSTRACT
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KEYWORDS

joint prosthesis
infection
biofilm
diagnosis (microbiology)
RNA
ribosomal
16S
16S RNA
biofilms
diagnostics
joint infections
prospective clinical study
prosthesis infections

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