Detecting the Presence of Bacterial DNA and RNA by Polymerase Chain Reaction to Diagnose Suspected Periprosthetic Joint Infection after Antibiotic Therapy

Diagnostic Performance of a Molecular Assay in Synovial Fluid Targeting Dominant Prosthetic Joint Infection Pathogens

Prosthetic joint infection (PJI) is one of the most serious complications of joint replacement surgery among orthopedic surgeries and occurs in 1 to 2% of primary surgeries. Additionally, the cause of PJIs is mostly bacteria from the Staphylococcus species, accounting for more than 98%, while fungi cause PJIs in only 1 to 2% of cases and can be difficult to manage. The current gold-standard microbiological method of culturing synovial fluid is time-consuming and produces false-negative and -positive results. This study aimed to identify a novel, accurate, and convenient molecular diagnostic method. The DreamDX primer-hydrolysis probe set was designed for the pan-bacterial and pan-fungal detection of DNA from pathogens that cause PJIs. The sensitivity and specificity of DreamDX primer-hydrolysis probes were 88.89% (95% CI, 56.50-99.43%) and 97.62% (95% CI, 87.68-99.88%), respectively, compared with the microbiological method of culturing synovial fluid, and receiver operating characteristic (ROC) area under the curve (AUC) was 0.9974 (*** p < 0.0001). It could be concluded that the DreamDX primer-hydrolysis probes have outstanding potential as a molecular diagnostic method for identifying the causative agents of PJIs, and that host inflammatory markers are useful as adjuvants in the diagnosis of PJIs.

Development of advanced control material for reverse transcription-mediated bacterial nucleic acid amplification tests

Detection of bacterial RNA by nucleic acid amplification tests (NAATs), such as reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP), offers distinct advantages over DNA-based methods. However, such assays also present challenges in ascertaining positive and internal control material that can reliably monitor success over all phases of testing (bacterial lysis, nucleic acid recovery, reverse transcription, amplification, and signal detection): since they are unable to distinguish between amplification of bacterial RNA transcripts and the DNA templates that encode them, using intact organisms as controls can inform cell lysis but not successful detection of RNA. We developed a control strategy for RNA-based bacterial NAATs that allows ready discrimination of RNA from DNA templates using self-splicing bacterial introns, such that those nucleic acids ultimately encode different sequences. We engineered two vectors encoding synthetic transgenes based on this principle, one that is active in the Gram-negative bacterium Escherichia coli and one that functions in both E. coli and the Gram-positive organism Staphylococcus aureus. We subsequently designed RT-LAMP assays that either target RNA and DNA from transgenic organisms or target RNA exclusively and demonstrated the specificity of amplification using purified nucleic acids. Using multiplex fluorescent RT-LAMP of heat-lysed specimens, we showed the practicality of deploying such transgenic organisms as an internal control to ascertain sample integrity and assay performance during clinical diagnostic testing. Our approach has broad utility for RNA-based bacterial NAATs, especially point-of-care assays and other applications where nucleic acids are nonspecifically liberated for testing.

Application of Nucleic Acid-Based Strategies to Detect Infectious Pathogens in Orthopaedic Implant-Related Infection

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Implant-associated infection in orthopaedic surgery remains an enormous and largely unsolved clinical problem with a high rate of persistent or recurrent infection. This may be due, at least in part, to the potential for underdiagnosis by traditional microbial culture or the potential for culture to incompletely identify the microbial species present.

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Nucleic acid-based diagnostic techniques, focused on using the diagnostic information contained in DNA or RNA to identify microbial species, have been developing rapidly and have garnered escalating interest for both clinical and research applications.

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Commonly applied techniques include end-point polymerase chain reaction (PCR), quantitative PCR, Sanger sequencing, and next-generation sequencing. Understanding the specific strengths and weaknesses of each technique is critical to understanding their utility, applying the correct assessment strategy, and critically understanding and interpreting research.

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The best practices for interpreting nucleic acid-based diagnostic techniques include considering positive and negative controls, reads per sample, detection thresholds (for differentiating contaminants from positive results), and the primer set or targeted regions.

Reliable Diagnostic Tests and Thresholds for Preoperative Diagnosis of Non-Inflammatory Arthritis Periprosthetic Joint Infection: A Meta-analysis and Systematic Review

Objective

The current diagnostic criteria for periprosthetic joint infection (PJI) are diverse and controversial, leading to delayed diagnosis. This study aimed to evaluate and unify their diagnostic accuracy and the threshold selection of serum and synovial routine tests for PJI at an early stage.

Methods

We searched the MEDLINE and Embase databases for retrospective or prospective studies which reported preoperative‐available assays (serum, synovial, or culture tests) for the diagnosis of chronic PJI among inflammatory arthritis (IA) or non‐IA populations from January 1, 2000 to June 30, 2022. Threshold effective analysis was performed on synovial polymorphonuclear neutrophils (PMN%), synovial white blood cell (WBC), serum C‐reactive protein (CRP), and erythrocyte sedimentation rate (ESR) to find the relevant cut‐offs.

Results

Two hundred and sixteen studies and information from 45,316 individuals were included in the final analysis. Synovial laboratory‐based α‐defensin and calprotectin had the best comprehensive sensitivity (0.91 [0.86–0.94], 0.95 [0.88–0.98]) and specificity (0.96 [0.94‐0.97], 0.95 [0.89–0.98]) values. According to the threshold effect analysis, the recommended cut‐offs are 70% (sensitivity 0.89 [0.85–0.92], specificity 0.90 [0.87–0.93]), 4100/μL (sensitivity 0.90 [0.87–0.93], specificity 0.97 [0.93–0.98]), 13.5 mg/L (sensitivity 0.84 [0.78–0.89], specificity 0.83 [0.73–0.89]), and 30 mm/h (sensitivity 0.79 [0.74–0.83], specificity 0.78 [0.72–0.83]) for synovial PMN%, synovial WBC, serum CRP, and ESR, respectively, and tests seem to be more reliable among non‐IA patients.

Conclusions

The laboratory‐based synovial α‐defensin and synovial calprotectin are the two best independent preoperative diagnostic tests for PJI. A cut off of 70% for synovial PMN% and tighter cut‐offs for synovial WBC and serum CRP could have a better diagnostic accuracy for non‐IA patients with chronic PJI.

Diagnosis and Treatment of Culture-Negative Periprosthetic Joint Infection

Identification of the causative organism(s) in periprosthetic joint infection (PJI) is a challenging task. The shortcomings of traditional cultures have been emphasized in recent literature, culminating in a clinical entity known as "culture-negative PJI." Amidst the growing burden of biofilm infections that are inherently difficult to culture, the field of clinical microbiology has seen a paradigm shift from culture-based to molecular-based methods. These novel techniques hold much promise in the demystification of culture-negative PJI and revolutionization of the microbiology laboratory. This article outlines the clinical implications of culture-negative PJI, common causes of this diagnostic conundrum, established strategies to improve culture yield, and newer molecular techniques to detect infectious organisms.

Development and Evaluation of Rapid and Accurate CRISPR/Cas13-Based RNA Diagnostics for Pneumocystis jirovecii Pneumonia

Background

Pneumocystis jirovecii can result in a serious pulmonary infection, Pneumocystis jirovecii pneumonia, in immunocompetent hosts. The diagnosis of Pneumocystis jirovecii pneumonia has long been a major clinical concern, and there are limitations with the currently utilized immunostaining and polymerase chain reaction diagnosis/detection technologies (e.g., insufficient sensitivity and accuracy). Hence, we sought to establish a rapid and RNA-specific transcription mediated amplification and CRISPR/Cas13a-based diagnostics targeted P. jirovecii-mitochondrial large subunit ribosomal RNA.

Methods

The procedure of the diagnostics included amplification of the extracted RNA samples by transcription mediated amplification, followed by CRISPR/Cas13 detection, and ultimately, the judgment of the results after 30 minutes of fluorescence signal. Later, the diagnostic performance of the CRISPR/Cas13-based diagnostics were tested on the 62 surplus clinical samples.

Results

This CRISPR/Cas13-based diagnostics achieved limits of detection of approximately 2 copies/µL transcribed RNA templates, with no cross reaction to other respiratory pathogens, including bacteria and fungi. Similar to in-house quantitative real-time polymerase chain reaction, CRISPR/Cas13-based diagnostics was still positive in 243-fold diluted bronchial alveolar lavage fluid. A preliminary evaluation of 62 surplus bronchial alveolar lavage fluid samples from patients suspected of Pneumocystis jirovecii pneumonia showed that CRISPR/Cas13-based diagnostics achieved a 78.9% sensitivity and a 97.7% specificity in the diagnosis of Pneumocystis jirovecii pneumonia.

Conclusion

Our study demonstrates that the CRISPR/Cas13-based diagnostics technique has good performance for the accurate and specific diagnosis of Pneumocystis jirovecii pneumonia.

Debridement, antibiotics, and implant retention in non-oncological femoral megaprosthesis infections: minimum 5 year follow-up

Purpose

Megaprostheses are increasingly utilised outside of the oncological setting, and remain at significant risk of periprosthetic joint infection (PJI). Debridement, antibiotic, and implant retention (DAIR) is an established treatment for PJI, however its use in non-oncological patients with femoral megaprostheses has not been widely reported. There are significant differences in patient physiology, treatment goals, and associated risks between these patient cohorts.

Methods

We identified 14 patients who underwent DAIR for a PJI of their femoral megaprostheses, between 2000 and 2014, whom had their index procedure secondary to non-oncological indications. Patients were managed as part of a multidisciplinary team, with our standardised surgical technique including exchange of all mobile parts, and subsequent antibiotic therapy for a minimum of 3 months. Patients were followed up for a minimum of 5 years.

Results

Patients included six proximal femoral replacements, five distal femoral replacements, and three total femoral replacements. No patients were lost to follow-up. There were six males and eight females, with a mean age of 67.2 years, and mean ASA of 2.3.

Nine patients (64.3%) successfully cleared their infection following DAIR at a minimum of 5 year follow-up. Five patients (35.7%) required further revision surgery, with four patients cleared of infection. No patients who underwent DAIR alone suffered complications as a result of the procedure.

Conclusions

The use of DAIR in these complex patients can lead to successful outcomes, but the risk of further revision remains high. The success rate (64.3%) remains on par with other studies evaluating DAIR in megaprostheses and in primary arthroplasty. This study indicates judicious use of DAIR can be an appropriate part of the treatment algorithm.

Level of evidence

II

Synovial fluid calprotectin performs better than synovial fluid polymerase chain reaction and interleukin-6 in the diagnosis of periprosthetic joint infection : a systematic review and meta-analysis

AIMS

The preoperative diagnosis of periprosthetic joint infection (PJI) remains a challenge due to a lack of biomarkers that are both sensitive and specific. We investigated the performance characteristics of polymerase chain reaction (PCR), interleukin-6 (IL6), and calprotectin of synovial fluid in the diagnosis of PJI.

METHODS

We performed systematic search of PubMed, Embase, The Cochrane Library, Web of Science, and Science Direct from the date of inception of each database through to 31 May 2021. Studies which described the diagnostic accuracy of synovial fluid PCR, IL6, and calprotectin using the Musculoskeletal Infection Society criteria as the reference standard were identified.

RESULTS

Overall, 31 studies were identified: 20 described PCR, six described IL6, and five calprotectin. The sensitivity and specificity were 0.78 (95% confidence interval (CI) 0.67 to 0.86) and 0.97 (95% CI 0.94 to 0.99), respectively, for synovial PCR;, 0.86 (95% CI 0.74 to 0.92), and 0.94 (95% CI 0.90 to 0.96), respectively, for synovial IL6; and 0.94 (95% CI 0.82 to 0.98) and 0.93 (95% CI 0.85 to 0.97), respectively, for synovial calprotectin. Likelihood ratio scattergram analyses recommended clinical utility of synovial fluid PCR and IL6 as a confirmatory test only. Synovial calprotectin had utility in the exclusion and confirmation of PJI.

CONCLUSION

Synovial fluid PCR and IL6 had low sensitivity and high specificity in the diagnosis of PJI, and is recommended to be used as confirmatory test. In contrast, synovial fluid calprotectin had both high sensitivity and specificity with utility in both the exclusion and confirmation of PJI. We recommend use of synovial fluid calprotectin studies in the preoperative workup of PJI. Cite this article: Bone Joint J 2022;104-B(3):311-320.

Think Twice before Prescribing Antibiotics for That Swollen Knee: The Influence of Antibiotics on the Diagnosis of Periprosthetic Joint Infection

Periprosthetic joint infection (PJI) is a rare but devastating complication after total joint arthroplasty. An estimated 7-12% of patients have negative cultures despite clear clinical evidence of infection. One oft-cited reason for this occurrence is the administration of antibiotics in the weeks prior to obtaining cultures. This article reviews the influence of antibiotics on the diagnosis of PJI. Specifically, we examine the effect of prophylactic and therapeutic antibiotic administration on the diagnostic accuracy of microbiological cultures as well as serum and synovial biomarkers. We also explore the potential of molecular techniques in overcoming these limitations in patients who have received antibiotics before specimen collection and propose areas for future research.

Current Clinical Methods for Detection of Peri-Prosthetic Joint Infection

Background: Currently, one of the most pressing problems in the field of orthopedic surgery is peri-prosthetic joint infection [PJI]. While there are numerous ways to detect PJI, current clinical detection methods differ across institutions and have varying criteria and protocols. Some of these methods include the Modified Musculoskeletal Infection Society system, culturing, polymerase chain reaction, the determination of the presence of certain biomarkers, testing for the presence of alpha defensin peptides, and leukocyte level testing. Methods: This review summarizes the most recent publications in the field of PJI detection to highlight current strengths as well as provide future directions to find the system for the quickest, cost-effective, and most accurate way to diagnose these types of infections. Results: The results of this literature review suggest that, while each method of diagnosis has its advantages, each has various drawbacks as well. Current methods can be expensive, take days to weeks to complete, be prone to contamination, and can produce ambiguous results. Conclusions: The findings in this review emphasize the need for a more comprehensive and accurate system for diagnosing PJI. In addition, the specific comparison of advantages and drawbacks can be useful for researchers and clinicians with goals of creating new diagnostic tests for PJIs, as well as in clinical scenarios to determine the correct treatment for patients.

Advantages of 16S rRNA PCR for the diagnosis of prosthetic joint infection

16S ribosomal RNA (rRNA) PCR has been reported to be an effective diagnostic means in patients with prosthetic joint infection (PJI). The aim of the present meta-analysis is to establish the overall diagnostic accuracy of the measurement of 16S rRNA PCR for diagnosing PJI. PubMed, Web of Science, Cochrane Library, EMBASE and Wiley Online Library were searched for studies on 16S rRNA PCR in the diagnosis of PJI. The search incorporated all literature published up until December 2018 and the QUADAS-2 checklist were used for quality assessment. The sensitivity, specificity and other measures of accuracy of 16S rRNA PCR in the diagnosis of PJI were pooled. Statistical analysis was performed by employing Meta-Disc 1.4 and Stata 12.0 software. A total of 15 studies met the inclusion criteria. The summary estimates for 16S rRNA PCR in the diagnosis of PJI in these studies were pooled: Sensitivity, 0.70 (95% CI, 0.67-0.73); specificity, 0.93 (95% CI, 0.91-0.94); positive likelihood ratio, 10.93 (95% CI, 5.55-21.51); negative likelihood ratio, 0.33 (95% CI, 0.28-0.40); diagnostic odds ratio, 41.77 (95% CI, 19.90-87.68); and the area under the curve, 0.89. Subgroup analysis showed that the use of sonicate fluid and periprosthetic tissue has higher sensitivity (0.76; 95% CI, 0.69-0.82; and 0.73; 95% CI, 0.68-0.78, respectively), specificity (0.93, 95% CI, 0.90-0.96; and 0.95; 95% CI, 0.90-0.98, respectively) and area under the curve (0.93 and 0.98, respectively). 16S rRNA PCR assay plays an important role in the diagnosis of PJI. The results of 16S rRNA PCR assays should be interpreted in parallel with clinical findings, the results of microbiological, and other laboratory tests.

Detecting the presence of bacterial RNA by polymerase chain reaction in low volumes of preoperatively aspirated synovial fluid from prosthetic joint infections

Aims

Preoperative diagnosis is important for revision surgery after prosthetic joint infection (PJI). The purpose of our study was to determine whether reverse transcription-quantitative polymerase chain reaction (RT-qPCR), which is used to detect bacterial ribosomal RNA (rRNA) preoperatively, can reveal PJI in low volumes of aspirated fluid.

Methods

We acquired joint fluid samples (JFSs) by preoperative aspiration from patients who were suspected of having a PJI and failed arthroplasty; patients with preoperative JFS volumes less than 5 ml were enrolled. RNA-based polymerase chain reaction (PCR) and bacterial culture were performed, and diagnostic efficiency was compared between the two methods.According to established Musculoskeletal Infection Society (MSIS) criteria, 21 of the 33 included patients were diagnosed with PJI.

Results

RNA-based PCR exhibited 57.1% sensitivity, 91.7% specificity, 69.7% accuracy, 92.3% positive predictive value, and 55.0% negative predictive value. The corresponding values for culture were 28.6%, 83.3%, 48.5%, 75.0%, and 40.0%, respectively. A significantly higher sensitivity was thus obtained with the PCR method versus the culture method.

Conclusion

In situations in which only a small JFS volume can be acquired, RNA-based PCR analysis increases the utility of preoperative puncture for patients who require revision surgery due to suspected PJI.

Cite this article:Bone Joint Res. 2020;9(5):219–224.

Value of mNGS in sonication fluid for the diagnosis of periprosthetic joint infection

Objective

To evaluate the effectiveness of metagenomics next-generation sequencing (mNGS) for the detection of pathogenic microorganisms in periprosthetic joint infection (PJI) using the sonication fluid from removed prosthesis.

Methods

In this prospective diagnostic cohort study, 44 patients who underwent revision arthroplasty in our hospital from December 2016 to December 2018 were screened. Seven cases were excluded due to incomplete clinical data, insufficient synovial fluid or failure of sequencing. According to the PJI diagnostic criteria recommended by the Musculoskeletal Infection Society (MSIS), the patients were defined as PJI or aseptic failure (AF). Conventional culture, sonication fluid culture and mNGS were performed, in order to assess the value of mNGS using sonication fluid for the diagnosis of PJI, and the mNGS results were analyzed and compared with the conventional and sonication fluid culture.

Results

Among the 37 patients, 24 were diagnosed with PJI (64.86%), while 13 were diagnosed with aseptic failure. Among the 24 patients diagnosed with PJI, 15 cases (62.5%), 17 cases (70.8%) and 24 cases (100%) yielded positive results in conventional culture, sonication fluid culture and mNGS, respectively. In addition, mNGS detected the same pathogenic microorganisms in 16 out of the 17 (94.12%) culture-positive (conventional + sonication fluid) PJI cases. In the only one discrepancy case, Enterococcus faecalis was identified in the cultures, while Enterobacter cloacae was detected by mNGS. In the AF group, the results of the conventional culture were all negative. Nevertheless, Staphylococcus epidermidis was detected in the sonication fluid culture and mNGS in one case. The diagnostic sensitivity of mNGS for PJI was 100%, which was significantly higher than 70.83% (P = 0.039) of the sonication fluid culture and 62.5% (P = 0.021) of the conventional culture. The diagnostic specificity of mNGS for PJI was 92.31%, which was not significantly different (P > 0.05) from those of the conventional culture (100%) and sonication fluid culture (92.31%).

Conclusion

We demonstrated that mNGS using sonication fluid can improve the detection rate of pathogenic microorganisms and provide valuable information for the diagnosis of PJI. In addition, mNGS can effectively identify pathogenic microorganisms in culture-negative PJIs cases, especially for the cases who have been treated with antibiotics before sample acquisition or have fastidious microorganisms. Therefore, this method can potentially help to guide the clinical use of antibiotics.

Diagnostic Accuracy of Serum, Synovial, and Tissue Testing for Chronic Periprosthetic Joint Infection After Hip and Knee Replacements: A Systematic Review

BACKGROUND

Chronic periprosthetic joint infection (PJI) is a devastating complication that can occur following total joint replacement. Patients with chronic PJI report a substantially lower quality of life and face a higher risk of short-term mortality. Establishing a diagnosis of chronic PJI is challenging because of conflicting guidelines, numerous tests, and limited evidence. Delays in diagnosing PJI are associated with poorer outcomes and morbid revision surgery. The purpose of this systematic review was to compare the diagnostic accuracy of serum, synovial, and tissue-based tests for chronic PJI.

METHODS

This review adheres to the Cochrane Collaboration's diagnostic test accuracy methods for evidence searching and syntheses. A detailed search of MEDLINE, Embase, the Cochrane Library, and the grey literature was performed to identify studies involving the diagnosis of chronic PJI in patients with hip or knee replacement. Eligible studies were assessed for quality and bias using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. Meta-analyses were performed on tests with sufficient data points. Summary estimates and hierarchical summary receiver operating characteristic (HSROC) curves were obtained using a bivariate model.

RESULTS

A total of 12,616 citations were identified, and 203 studies met the inclusion criteria. Of these 203 studies, 170 had a high risk of bias. Eighty-three unique PJI diagnostic tests were identified, and 17 underwent meta-analyses. Laboratory-based synovial alpha-defensin tests and leukocyte esterase reagent (LER) strips (2+) had the best performance, followed by white blood-cell (WBC) count, measurement of synovial C-reactive protein (CRP) level, measurement of the polymorphonuclear neutrophil percentage (PMN%), and the alpha-defensin lateral flow test kit (Youden index ranging from 0.78 to 0.94). Tissue-based tests and 3 serum tests (measurement of interleukin-6 [IL-6] level, CRP level, and erythrocyte sedimentation rate [ESR]) had a Youden index between 0.61 to 0.75 but exhibited poorer performance compared with the synovial tests mentioned above.

CONCLUSIONS

The quality of the literature pertaining to chronic PJI diagnostic tests is heterogeneous, and the studies are at a high risk for bias. We believe that greater transparency and more complete reporting in studies of diagnostic test results should be mandated by peer-reviewed journals. The available literature suggests that several synovial fluid-based tests perform well for diagnosing chronic PJI and their use is recommended in the work-up of any suspected case of chronic PJI.

LEVEL OF EVIDENCE

Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.