The DendrisCHIP® Technology as a New, Rapid and Reliable Molecular Method for the Diagnosis of Osteoarticular Infections

Abstract

Osteoarticular infections are major disabling diseases that can occur after orthopedic implant surgery in patients. The management of these infections is very complex and painful, requiring surgical intervention in combination with long-term antibiotic treatment. Therefore, early and accurate diagnosis of the causal pathogens is essential before formulating chemotherapeutic regimens. Although culture-based microbiology remains the most common diagnosis of osteoarticular infections, its regular failure to identify the causative pathogen as well as its long-term modus operandi motivates the development of rapid, accurate, and sufficiently comprehensive bacterial species-specific diagnostics that must be easy to use by routine clinical laboratories. Based on these criteria, we reported on the feasibility of our DendrisCHIP^® technology using DendrisCHIP^®OA as an innovative molecular diagnostic method to diagnose pathogen bacteria implicated in osteoarticular infections. This technology is based on the principle of microarrays in which the hybridization signals between oligoprobes and complementary labeled DNA fragments from isolates queries a database of hybridization signatures corresponding to a list of pre-established bacteria implicated in osteoarticular infections by a decision algorithm based on machine learning methods. In this way, this technology combines the advantages of a PCR-based method and next-generation sequencing (NGS) while reducing the limitations and constraints of the two latter technologies. On the one hand, DendrisCHIP^®OA is more comprehensive than multiplex PCR tests as it is able to detect many more germs on a single sample. On the other hand, this method is not affected by the large number of nonclinically relevant bacteria or false positives that characterize NGS, as our DendrisCHIP^®OA has been designed to date to target only a subset of 20 bacteria potentially responsible for osteoarticular infections. DendrisCHIP^®OA has been compared with microbial culture on more than 300 isolates and a 40% discrepancy between the two methods was found, which could be due in part but not solely to the absence or poor identification of germs detected by microbial culture. We also demonstrated the reliability of our technology in correctly identifying bacteria in isolates by showing a convergence (i.e., same bacteria identified) with NGS superior to 55% while this convergence was only 32% between NGS and microbial culture data. Finally, we showed that our technology can provide a diagnostic result in less than one day (technically, 5 h), which is comparatively faster and less labor intensive than microbial cultures and NGS.

Keywords: biochips; bone and joint infection; in vitro multiplex diagnostic; microbial cultures; next-generation sequencing.

Figure 1

Detection of pathogen bacteria in isolates by DendrisCHIP^®OA and microbial cultures. In (A) is represented the number of pathogens per sample as detected by DendrisCHIP^®OA. In (B) is shown the concordance and discordance in the detection of bacteria by DendrisCHIP^®OA and by the microbial cultures. In (C) is reported the distribution of the discordant results with respect to the detection by microbial culture and by DendrisCHIP^®OA. Culture Neg = negative by microbial culture/positive by DendrisCHIP^®OA; Dendris Neg = negative by DendrisCHIP^®OA/positive by microbial cultures; culture or Dendris = either one or the other as negative or positive.

Figure 2

Comparison between molecular methods and microbial cultures for identification of bacteria in isolates. A total of 101 samples were sequenced, giving rise to a total of 141 identified bacteria by NGS according to criteria defined in Materials and Methods. The identified bacteria were compared with those identified by DendrisCHIP^®OA and microbiological methods in (panel A). Comparison at the level of single bacteria species between the three methods is reported in (panel B). The abbreviation for bacteria can be found in Table 1.

Figure 3

Evaluation of the predictive positive and negative values (PPV; NPV) of diagnostic tests by DendrisCHIP^® technology and microbial cultures relative to NGS data obtained from 101 isolates.

Figure 4

Time scale for the workflow of the microbial culture, NGS, and DendrisCHIP^® technology in PJI diagnostics. The asterisk indicate the time at which a diagnostic result can be provided.