Aims: The aim of this study was to evaluate the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens from synovial fluid of prosthetic joint infection (PJI) patients. Methods: A group of 75 patients who underwent revision knee or hip arthroplasties were enrolled prospectively. Ten patients with primary arthroplasties were included as negative controls. Synovial fluid was collected for mNGS analysis. Optimal thresholds were determined to distinguish pathogens from background microbes. Synovial fluid, tissue, and sonicate fluid were obtained for culture. Results: A total of 49 PJI and 21 noninfection patients were finally included. Of the 39 culture-positive PJI cases, mNGS results were positive in 37 patients (94.9%), and were consistent with culture results at the genus level in 32 patients (86.5%) and at the species level in 27 patients (73.0%). Metagenomic next-generation sequencing additionally identified 15 pathogens from five culture-positive and all ten culture-negative PJI cases, and even one pathogen from one noninfection patient, while yielding no positive findings in any primary arthroplasty. However, seven pathogens identified by culture were missed by mNGS. The sensitivity of mNGS for diagnosing PJI was 95.9%, which was significantly higher than that of comprehensive culture (79.6%; p = 0.014). The specificity is similar between mNGS and comprehensive culture (95.2% and 95.2%, respectively; p = 1.0). Conclusion: Metagenomic next-generation sequencing can effectively identify pathogens from synovial fluid of PJI patients, and demonstrates high accuracy in diagnosing PJI. Cite this article: Bone Joint Res 2020;9(7):440–449.

The purpose of this study was to explore the role of mNGS in the diagnosis of PJI by detecting the presence of bacteria in periprosthetic tissues. Patients who were suspected of PJI and underwent surgery in our center were enrolled. Microbial culture and mNGS were performed on periprosthetic tissues collected intraoperatively. Patient age, body mass index (BMI), laboratory tests, microbial culture and mNGS results were recorded. The diagnostic performance of microbial culture and mNGS in the diagnosis of PJI was compared. A total of 44 patients were included. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of periprosthetic tissue microbial culture in the diagnosis of PJI were 72.72%, 77.27%, 76.19%, 73.91% and 75%, respectively. The sensitivity, specificity, PPV, NPV and accuracy of periprosthetic tissue mNGS in the diagnosis of PJI were 95.45%, 90.91%, 91.3%, 95.24% and 93.18%, respectively. The sensitivity and specificity of mNGS in the diagnosis of PJI were superior to those of microbial culture. Periprosthetic tissue can be used as an alternative to synovial fluid and sonication fluid, as mNGS can improve the diagnosis of PJI. mNGS of the periprosthetic tissues showed higher sensitivity than microbial culture.

Objectives: To evaluate metagenomic next-generation sequencing (mNGS) as a diagnostic tool in detecting pathogens from osteoarticular infection (OAI) samples. Methods: 130 samples of joint fluid, sonicate fluid, and tissue were prospectively collected from 92 patients with OAI. The performance of mNGS and microbiology culture was compared pairwise. Results: The overall sensitivity of mNGS was 88.5% (115/130), significantly higher than that of microbiological culture, which had a sensitivity of 69.2% (90/130, p < 0.01). Sensitivity was significantly higher for joint fluid (mNGS: 86.7% vs. microbiology culture: 68.7%, p < 0.01) and sonicate fluid (mNGS: 100% vs. microbiology culture: 66.7%, p < 0.05) samples. mNGS detected 12 pathogenic strains undetected by microbiological culture. Additional pathogens detected by mNGS were Coagulase-negative Staphylococci, Gram-negative Bacillus, Streptococci, Anaerobe, non-tuberculosis mycobacterium, MTCP (p > 0.05), and Mycoplasma (OR = ∞, 95% confidence interval, 5.12–∞, p < 0.001). Additionally, sensitivity by mNGS was higher in antibiotic-treated samples compared to microbiological culture (89.7 vs. 61.5%, p < 0.01). Conclusions: mNGS is a robust diagnostic tool for pathogenic detection in samples from OAI patients, compared to routine cultures. The mNGS technique is particularly valuable to diagnose pathogens that are difficult to be cultured, or to test samples from patients previously treated with antibiotics.

Background: The aims of this study were to (1) evaluate the efficacy and safety of targeted antibiotics for the treatment of culture-negative prosthetic joint infection based on metagenomic next-generation sequencing results and (2) verify the accuracy and reliability of metagenomic next-generation sequencing for identifying pathogens related to culture-negative prosthetic joint infection.Methods: Ninety-seven consecutive PJI patients, including 27 patients with culture-negative prosthetic joint infection, were treated surgically at our center. Thirteen of the 27 culture-negative prosthetic joint infection patients, who were admitted before June 2017 and treated with empirical antibiotics, comprised the empirical antibiotic group (EA group), and the other 14 patients, who were admitted after June 2017 and treated with targeted antibiotics according to their metagenomic next-generation sequencing results, were classified as the targeted antibiotic group (TA group). The short-term infection control rate, incidence of antibiotic-related complications and costs were compared between the two groups.Results: Two of the patients in the EA group experienced debridement and prolonged antimicrobial therapy due to wound infection after the initial revision surgery. No recurrent infections were observed in the TA group; however, no significant difference in the infection control rate was found between the two groups (83.33% vs 100%,P = 0.217). More cases of antibiotic-related complications were recorded in the EA group (6 cases) than in the TA group (1 case), but the difference was not statistically significant (P = 0.0697). The cost of antibiotics obtained for the EA group was 20,168.37 Yuan (3236.38–45,297.16), which was higher than that found for the TA group (10,164.16 Yuan, 2959.54–16,661.04,P = 0.04).Conclusions: Targeted antibiotic treatment for culture-negative prosthetic joint infection based on metagenomic next-generation sequencing results is associated with a favorable outcome, and metagenomic next-generation sequencing is a reliable tool for identifying pathogens related to culture-negative prosthetic joint infection.

Objectives: The purpose of this study was to explore the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of polymicrobial periprosthetic joint infection (PJI). Methods: Patients with complete data who underwent surgery at our hospital between July 2017 and January 2021 for suspected periprosthetic joint infection (PJI), according to the 2018 ICE diagnostic criteria, were enrolled, and all patients underwent microbial culture and mNGS detection, which were performed on the BGISEQ-500 platform. Microbial cultures were performed on two samples of synovial fluid, six samples of tissue, and two samples of prosthetic sonicate fluid for each patient. The mNGS was performed on 10 tissues, 64 synovial fluid samples, and 17 prosthetic sonicate fluid samples. The results of mNGS testing were based on the interpretation of mNGS results in the previous literature and the assertions of microbiologists and orthopedic surgeons. The diagnostic efficacy of mNGS in polymicrobial PJI was assessed by comparing the results of conventional microbial cultures and mNGS. Results: A total of 91 patients were finally enrolled in this study. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of PJI were 71.0%, 95.4%, and 76.9%, respectively. The sensitivity, specificity, and accuracy of mNGS for the diagnosis of PJI were 91.3%, 86.3%, and 90.1%, respectively. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of polymicrobial PJI were 57.1%, 100%, and 91.3%, respectively. mNGS had a sensitivity, specificity, and accuracy of 85.7%, 60.0%, and 65.2%, respectively, for the diagnosis of polymicrobial PJI. Conclusions: mNGS can improve the diagnosis efficiency of polymicrobial PJI, and the combination of culture and mNGS is a promising method to diagnose polymicrobial PJI.

The aims of our study were to (1) evaluate the concordance of both methods for detecting prosthetic joint infection (PJI) pathogens in joint fluid and to (2) clarify whether broad-range polymerase chain reaction (BR-PCR) can be used as a verification method for metagenomic next-generation sequencing (mNGS) for PJI diagnosis. In total, 63 patients underwent total joint arthroplasty, with 45 PJI and 18 aseptic failure patients included. Joint fluids were sampled after antibiotics were withheld for more than 2 weeks, and then, culture, BR-PCR and mNGS were performed for all samples. The joint fluid BR-PCR sensitivity was 82.2%, which was not significantly different from that of mNGS (95.6%) or culture (77.8%). The specificities of the 3 methods were all 94.4%. BR-PCR failed to identify the pathogens in 1 polymicrobial infection patient and 4 fungal infection patients. mNGS was more sensitive than BR-PCR for detecting PJI pathogens in joint fluid. BR-PCR is insufficient for use as an mNGS verification method.