Can metagenomic next-generation sequencing identify the pathogens responsible for culture-negative prosthetic joint infection?

Abstract

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.

Next generation sequencing for pathogen detection in periprosthetic joint infections

“…Interestingly, in all their samples, multiple microorganisms with multiple virulent factors were present. This and other reports 58 , 59 suggest that PJIs are polymicrobial at the microbial DNA level in a significant proportion of sequenced PJI cases, increasing the fear in the adult reconstruction orthopaedic community. This fear was confirmed by Namdari et al 58 who showed, in a series of 44 revision shoulder arthroplasties, that NGS data demonstrated that bacterial loads in revision arthroplasty are most commonly polymicrobial and a definition of infection that uses cultures is more prone to ‘probable contaminants’ than NGS.…”

Metagenomic next generation sequencing improves diagnosis of prosthetic joint infection by detecting the presence of bacteria in periprosthetic tissues

“…Through the analysis of patients who were misdiagnosed according to the microbial culture and mNGS results (Table 3), we found the following: 1).As we previously showed (Wang et al, 2020), mNGS can improve the pathogen detection rate in CN-PJI: patients 1, 2, and 3 all had prosthetic joint infections, and a large amount of purulent tissue and caseous necrosis were observed intraoperatively. The microbial culture results from the periprosthetic tissue were all negative, but mNGS found pathogenic bacteria 72 hours after sample collection (Mycobacterium abscess for patients 1 and 3 and Mycobacterium tuberculosis for patient 2).…”

“…For mNGS, periprosthetic tissues were homogenized as described above. The steps to perform mNGS included the following (Henan Li et al, 2018)(Wang et al, 2020: (1) Nucleic acid extraction: 500 ml of periprosthetic tissue homogenate was obtained, ceramic beads were utilized to break the cell walls, and total genomic DNA was extracted using a TIANamp Micro DNA Kit (DP316, Tiangen Biotech). (2) Library construction and sequencing: DNA libraries were constructed and sequenced according to the standard protocol of the BGISEQ-500 sequencing platform (BGI-Tianjin, Tianjin, China).…”

An update about molecular biology techniques to detect orthopaedic implant-related infections

“… 69 However, the detection of these pathogens cannot be considered automatically as a contaminant, and the potential existence of a ‘synovial microbiome’ opens many questions that need further research. In this sense, a recent study 73 showed that antibiotic therapy guided by the results of metagenomic next-generation sequencing was associated with a similar outcome to empirical therapy, with fewer undesired side effects.…”