Value of multiplex PCR for detection of antimicrobial resistance in samples retrieved from patients with orthopaedic infections.
Adult
Aged
Aged, 80 and over
Anti-Bacterial Agents
/ pharmacology
Bone Diseases
/ microbiology
Drug Resistance, Bacterial
Enterobacteriaceae
/ drug effects
Female
Fracture Fixation, Internal
/ adverse effects
Genotyping Techniques
/ methods
Humans
Male
Microbial Sensitivity Tests
Middle Aged
Multiplex Polymerase Chain Reaction
Prospective Studies
Prosthesis-Related Infections
/ diagnosis
Sensitivity and Specificity
Sonication
Staphylococcus
/ drug effects
Synovial Fluid
/ microbiology
Antimicrobial resistance
Diagnosis
Molecular methods
Multiplex PCR
Periprosthetic joint infection
Sonication
Journal
BMC microbiology
ISSN: 1471-2180
Titre abrégé: BMC Microbiol
Pays: England
ID NLM: 100966981
Informations de publication
Date de publication:
14 04 2020
14 04 2020
Historique:
received:
11
04
2019
accepted:
03
03
2020
entrez:
16
4
2020
pubmed:
16
4
2020
medline:
27
5
2021
Statut:
epublish
Résumé
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. 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. A 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. The 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. www.clinicaltrials.gov No. NCT02530229, registered at 21 August 2015 (retrospectively registered).
Sections du résumé
BACKGROUND
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. 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.
RESULT
A 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.
CONCLUSION
The 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 REGISTRATION
www.clinicaltrials.gov No. NCT02530229, registered at 21 August 2015 (retrospectively registered).
Identifiants
pubmed: 32290833
doi: 10.1186/s12866-020-01741-7
pii: 10.1186/s12866-020-01741-7
pmc: PMC7155317
doi:
Substances chimiques
Anti-Bacterial Agents
0
Banques de données
ClinicalTrials.gov
['NCT02530229']
Types de publication
Clinical Trial
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
88Subventions
Organisme : Deutsche Forschungsgemeinschaft
ID : Open Access Publication Fund of Charité
Pays : International
Organisme : PRO-IMPLANT Foundation, Berlin
ID : N/A
Pays : International
Références
N Engl J Med. 2004 Oct 14;351(16):1645-54
pubmed: 15483283
Infection. 2017 Dec;45(6):877-884
pubmed: 28983865
J Orthop Res. 2013 Dec;31(12):2021-4
pubmed: 23893822
Clin Infect Dis. 2007 Nov 1;45(9):1113-9
pubmed: 17918072
J Clin Microbiol. 2010 Apr;48(4):1208-14
pubmed: 20164283
Acta Orthop. 2012 Jun;83(3):299-304
pubmed: 22616742
Antimicrob Agents Chemother. 2012 Apr;56(4):1885-91
pubmed: 22252806
J Clin Microbiol. 2015 May;53(5):1622-7
pubmed: 25740775
J Orthop Res. 2011 Apr;29(4):617-22
pubmed: 21337398
Injury. 2018 Apr;49(4):806-811
pubmed: 29486892
PLoS One. 2011;6(5):e20191
pubmed: 21637845
J Clin Microbiol. 1998 Oct;36(10):2932-9
pubmed: 9738046
J Clin Microbiol. 2012 Nov;50(11):3501-8
pubmed: 22895042
N Engl J Med. 2007 Aug 16;357(7):654-63
pubmed: 17699815
J Rheumatol. 2018 Nov;45(11):1588-1593
pubmed: 30219763
Antimicrob Agents Chemother. 2014 May;58(5):2547-53
pubmed: 24550327
J Infect. 2012 Dec;65(6):541-8
pubmed: 22960370
N Engl J Med. 2009 Aug 20;361(8):787-94
pubmed: 19692690
Clin Microbiol Infect. 2018 Jan;24(1):83.e1-83.e6
pubmed: 28559002
Nat Microbiol. 2016 Jul 26;1(8):16120
pubmed: 27573119
J Clin Microbiol. 2016 Jan;54(1):120-6
pubmed: 26537446
Diagn Microbiol Infect Dis. 2018 Feb;90(2):115-119
pubmed: 29191466
Antimicrob Agents Chemother. 1991 Apr;35(4):741-6
pubmed: 2069381
Int Orthop. 2019 Aug;43(8):1891-1898
pubmed: 30191275
Infection. 2015 Oct;43(5):551-60
pubmed: 26021312
J Microbiol Methods. 2016 Feb;121:27-32
pubmed: 26689142