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Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing.

ABSTRACT: Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings, combined with the increasing availability of portable, random-access sequencing technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI.

SUBMITTER: Street TL

PROVIDER: S-EPMC5527411 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing.

Street Teresa L TL Sanderson Nicholas D ND Atkins Bridget L BL Brent Andrew J AJ Cole Kevin K Foster Dona D McNally Martin A MA Oakley Sarah S Peto Leon L Taylor Adrian A Peto Tim E A TEA Crook Derrick W DW Eyre David W DW

Journal of clinical microbiology 20170510 8

Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication flu ...[more]

PMID: 28490492

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Project description:BackgroundMetagenomic next-generation sequencing (mNGS) is emerging as a promising technique for pathogens detection. However, reports on the application of mNGS in mixed pulmonary infection remain scarce.MethodsFrom July 2018 to March 2019, 55 cases were enrolled in this retrospective analysis. Cases were classified into mixed pulmonary infection (36 [65.5%]) and non-mixed pulmonary infection (19 [34.5%]) according to primary diagnoses. The performances of mNGS and conventional test on mixed pulmonary infection diagnosis and pathogen identification were compared.ResultsThe sensitivity of mNGS in mixed pulmonary infection diagnosis was much higher than that of conventional test (97.2% vs 13.9%; P?< 0.01), but the specificity was the opposite (63.2% vs 94.7%; P?= 0.07). The positive predictive value of mNGS was 83.3% (95% CI, 68.0-92.5%), and the negative predictive value was 92.3% (95% CI, 62.1-99.6%). A total of 5 (9.1%) cases were identified as mixed pulmonary infection by both conventional tests and mNGS, however, the pathogens identification results were consistent between these two methods in only 1 (1.8%) case. In summary, the pathogens detected by mNGS in 3 (5.5%) cases were consistent with those by conventional test, and only 1 (1.8%) case was mixed pulmonary infection. According to our data, mNGS had a broader spectrum for pathogen detection than conventional tests. In particular, application of mNGS improved the diagnosis of pulmonary fungal infections. Within the 55 cases, mNGS detected and identified fungi in 31 (56.4%) cases, of which only 10 (18.2%) cases were positive for the same fungi by conventional test. The most common pathogen detected by mNGS was Human cytomegalovirus in our study, which was identified in 19 (34.5%) cases of mixed pulmonary infection. Human cytomegalovirus and Pneumocystis jirovecii, which were detected in 7 (12.7%) cases, were the most common co-pathogens in the group of mixed pulmonary infection.ConclusionsmNGS is a promising technique to detect co-pathogens in mixed pulmonary infection, with potential benefits in speed and sensitivity.Trial registration(retrospectively registered): ChiCTR1900023727. Registrated 9 JUNE 2019.

Project description:MINI: We compared the sensitivity and specificity of peri-implant tissue culture to the vortexing-sonication technique for the diagnosis of spinal implant infection (SII). Lower thresholds of sonicate fluid culture positivity showed increased sensitivity with maintained specificity. We recommend a threshold of 20 CFU/10 mL for sonicate culture positivity for the diagnosis of SII.Study designThis is a retrospective study comparing the diagnosis of spinal implant infection (SII) by peri-implant tissue culture to vortexing-sonication of retrieved spinal implants.ObjectiveWe hypothesized that vortexing-sonication would be more sensitive than peri-implant tissue culture.Summary of background dataWe previously showed implant vortexing-sonication followed by culture to be more sensitive than standard peri-implant tissue culture for diagnosing of SII. In this follow-up study, we analyzed the largest sample size available in the literature to compare these two culture methods and evaluated thresholds for positivity for sonicate fluid for SII diagnosis.MethodsWe compared peri-implant tissue culture to the vortexing-sonication technique which samples bacterial biofilm on the surface of retrieved spinal implants. We evaluated different thresholds for sonicate fluid positivity and assessed the sensitivity and specificity of the two culture methods for the diagnosis of SII.ResultsA total of 152 patients were studied. With more than 100 colony forming units (CFU)/10 mL as a threshold for sonicate fluid culture positivity, there were 46 patients with SII. The sensitivities of peri-implant tissue and sonicate fluid culture were 65.2% and 79.6%; the specificities were 88.7% and 93.4%, respectively. With more than 50 CFU/10 mL as a threshold, there were 50 patients with SII. The sensitivities of peri-implant tissue and sonicate fluid culture were 68.0% and 76.0%; the specificities were 92.2% for both methods. Finally, with more than or equal to 20 CFU/10 mL as a threshold, there were 52 patients with SII. The sensitivities of peri-implant tissue and sonicate fluid culture were 69.2% and 82.7%; the specificities were 94.0% and 92.0%, respectively.ConclusionImplant sonication followed by culture is a sensitive and specific method for the diagnosis of SII. Lower thresholds for defining sonicate fluid culture positivity allow for increased sensitivity with a minimal decrease in specificity, enhancing the clinical utility of implant sonication.Level of evidence4.

Project description:BACKGROUND:Sonication is a valuable tool in the diagnosis of periprosthetic joint infections (PJI). However, conditions and definition criteria for PJI vary among studies. The aim of this study was to determine the diagnostic performance (i.e., specificity, sensitivity) of sonicate fluid culture (SFC) against periprosthetic tissue culture (PTC), when using European Bone and Joint Infection Society (EBJIS) criteria. METHODS:From March 2017 to April 2018, 257 implants were submitted for sonication. PJI was defined according to the EBJIS criteria as well as according to the International Consensus Meeting criteria of 2018 (ICM 2018). Only cases with at least one corresponding tissue sample were included. Samples were cultured using traditional microbiological plating techniques. Sensitivity and specificity were determined using two-by-two contingency tables. McNemar's test was used to compare proportions among paired samples. Subgroup analysis was performed dividing the cohort according to the site of PJI, previous antibiotic treatment, and time of manifestation. Prevalence of pathogens was determined for all patients as well as for specific subgroups. RESULTS:Among the 257 cases, 145 and 112 were defined as PJI and aseptic failure, respectively. When using the EBJIS criteria, the sensitivity of SFC and PTC was 69.0 and 62.8%, respectively (p =?.04). Meanwhile, the specificity was 90.2 and 92.9%, respectively (p =?.65). When adopting ICM 2018 criteria, the sensitivity of SFC and PTC was 87.5 and 84.4% (p =?.63) respectively, while the specificity was 85.1 and 92.5% (p =?.05), respectively. The most commonly identified pathogens were coagulase-negative staphylococci (26% overall), while 31% of PJI were culture-negative and 9% polymicrobial. CONCLUSIONS:SFC exhibited significantly greater sensitivity versus PTC when using the EBJIS criteria. Nevertheless, the diagnosis of PJI remains a difficult challenge and different diagnostic tools are necessary to optimize the outcome.

Dataset Information

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing.

Publications

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing.

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