Abstract
BackgroundThe performance of multiplex PCR (mPCR) for detection of antimicrobial resistance from clinical isolates is unknown. We assessed the ability of mPCR to analyse resistance genes directly from clinical samples.Patients with orthopedic infections were prospectively included. Phenotypical and genotypical resistance was evaluated in clinical samples (synovial and sonication fluid) where identical pathogens were identified by culture and mPCR.ResultA total of 94 samples were analysed, including 60 sonication fluid and 34 synovial fluid samples. For coagulase-negative staphylococcus strains, mPCR detected resistance to oxacillin in 10 of 23 isolates (44%) and to rifampin in none of 6 isolates. For S. aureus isolates, detection rate of oxacillin and rifampin-resistance was 100% (2/2 and 1/1, respectively). Fluoroquinolone-resistance was confirmed by mPCR in all 3 isolates of Enterobacteriaceae, in enterococci resistance to aminoglycoside-high level was detected in 1 of 3 isolates (33%) and in streptococci resistance to macrolides/lincosamides in none of 2 isolates. The overall sensitivity for different pathogens and antimicrobials was 46% and specificity 95%, the median concordance was 80% (range, 57–100%). Full agreement was observed for oxacillin in S. aureus, vancomycin in enterococci, carbapenems/cephalosporins in Enterobacteriaceae and rifampin in Cutibacterium species.ConclusionThe overall sensitivity for detection of antimicrobial resistance by mPCR directly from clinical samples was low. False-negative mPCR results occurred mainly in coagulase-negative staphylococci, especially for oxacillin and rifampin. However, the specificity of mPCR was high and a positive result reliably predicted antimicrobial resistance. Including universal primers in the PCR test assay may improve the detection rate but requires additional sequencing step.Trial registrationwww.clinicaltrials.gov No. NCT02530229, registered at 21 August 2015 (retrospectively registered).
Highlights
The performance of multiplex PCR for detection of antimicrobial resistance from clinical isolates is unknown
The 60 sonication fluid samples originated from 38 infected prostheses (20 knee, 15 hip, 2 shoulder, and 1 elbow prosthesis) and 22 osteosyntheses
The sensitivity and specificity of multiplex PCR (mPCR) for pathogen detection directly from clinical samples found in the published sub-cohorts ranged in sonication fluid from 51 to 71% and 92 to 94%, respectively, and in synovial fluid from 23 to 60% and 89 to 91%, respectively [6,7,8, 17]
Summary
The performance of multiplex PCR (mPCR) for detection of antimicrobial resistance from clinical isolates is unknown. We assessed the ability of mPCR to analyse resistance genes directly from clinical samples. Phenotypical and genotypical resistance was evaluated in clinical samples (synovial and sonication fluid) where identical pathogens were identified by culture and mPCR. Previous studies demonstrated limited sensitivity of periprosthetic tissue culture (45–71%) and synovial fluid culture (52–64%) for microbial detection [3,4,5,6,7,8]. Phenotypical antimicrobial testing using conventional cultures requires several days in mixed infections and if slow-growing microorganisms are involved. Inoculation of sonication fluid into blood culture bottles further improved the diagnosis of orthopaedic implant-associated infections and reduced the time to culture positivity [12]
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