Application Of Metagenomic Sequencing Technology In The Diagnosis Of Periprosthetic Joint Infections

Part Ⅰ: Evalation of the targeted antibiotics for the treatment of culture-negative prosthetic joint infection based on metagenomic next-generation sequencing resultsPurpose: 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 was20,168.37 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).Conclusion: 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.Part Ⅱ: Preliminary assessment of nanopore-based metagenomic sequencing for the diagnosis of prosthetic joint infectionPurpose: Pathogen identification is crucial for the diagnosis and management of periprosthetic joint infection(PJI).Although culturing methods are the foundation of pathogen detection in PJI,false-negative results often occur.Oxford nanopore sequencing(ONS)is a promising alternative for detecting pathogens and providing information on their antimicrobial resistance(AMR)profiles,without culturing.Methods: To evaluate the capability of metagenomic ONS(mONS)in detecting pathogens from PJI samples,both metagenomic next-generation sequencing(mNGS)and mONS were performed in 15 osteoarticular samples from nine consecutive PJI patients according to the modified Musculoskeletal Infection Society(MSIS)criteria.The sequencing data generated from both platforms were then analyzed for pathogen identification and AMR detection using an in-house-developed bioinformatics pipeline.Results: The culture method was able to identify a single organism among all 15 PJI samples.Of the 15 culture-positive osteoarticular samples,mNGS results included the organism matched with the culture results at the species level.The mONS could not detect the organism consistent with the culture results in 3 samples.In the mNGS experiment,it took a 46–47 h turnaround time.In the mONS experiment,only a14–22 h turnaround time was required.For AMR analysis,mNGS sequencing detected three AMR reads from three samples with a mean coverage of 66.20%,and mONS detected 331304 AMR reads from five samples with a mean coverage of99.99%.background organisms from the environment and from handlers were detected with both the mNGS and mONS procedures but varied greatly between these two methods.Conclusion: We showed proof of concept that mONS can function as a rapid,accurate tool in PJI diagnostic microbiology though it mONS could not always detect the causal organisms in all samples.The mONS may be a valuable,supplemental tool for pathogen identification and AMR detection in low-income settings.