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Review
. 2025 May 5;12(2):e70263.
doi: 10.1002/jeo2.70263. eCollection 2025 Apr.

Molecular diagnostics for perioperative microbial identification in periprosthetic joint infection: A scoping review and proposal of a diagnostic flow chart

Pier Francesco Indelli  1   2 , Trifon Totlis  1   3 , Bruno Lovreković  2   4 , Michael Engl  1 , Bruno Violante  1 , Pawel Skowronek  1 , Guillaume Demey  1 , Stefano Ghirardelli  5   6 , Chiara Maci  7 , Antonella Castagna  7 , Laura Schianchi  8 , Chiara Tassan Din  6 , James Harty  1 , Goksel Dikmen  1   9 , Christian Schaller  1 , Marko Ostojić  2   10   11
Affiliations
Review

Molecular diagnostics for perioperative microbial identification in periprosthetic joint infection: A scoping review and proposal of a diagnostic flow chart

Pier Francesco Indelli et al. J Exp Orthop. .

Abstract

Purpose: Periprosthetic joint infections (PJI) are among the most feared complications of joint reconstruction. Unfortunately, traditional cultures often fail to identify the aetiological agents of PJI. Molecular diagnostics can overcome the limitations of standard synovial fluid culture by utilising information from DNA/RNA samples to identify microbial species. The authors conducted a scoping review to evaluate the current state regarding the use of molecular diagnostics in the decision-making process for the surgical treatment of PJI and to create a flowchart based on molecular diagnostics.

Methods: A scoping review was conducted to provide an overview of the literature on molecular diagnostic techniques for detecting perioperative microbial infections in PJI. The population considered included patients undergoing total hip or knee arthroplasty or replacement, with a focus on molecular diagnostic methods within the perioperative period. The database search encompassed PubMed, Embase, Scopus and the Cochrane Library.

Results: Seventy-five articles were included after a preliminary review of 1315 records. Each article was assigned to one of four categories to fulfil the purpose of this review: (1) Polymerase chain reaction (PCR) related studies: n = 18; (2) Next-Generation-Sequencing (NGS) related studies: n = 40; (3) comparative studies, including systematic reviews and meta-analyses, between different molecular diagnostic methodologies: n = 7; and (4) general reviews on nucleic acid-based strategies to detect PJIs: n = 10.

Conclusions: This review confirmed that molecular diagnostics are becoming extremely valuable tools in the decision-making process for PJI treatment. Culture-based techniques still represent the gold standard in PJI microorganism identification, but our review showed that standard culture, in 2025, could be integrated with newer nucleic acid-based strategies.

Level of evidence: Level I.

Keywords: NGS; PCR; THA; TKA; molecular diagnostic; multiplex PCR; periprosthetic joint infection (PJI).

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Conflict of interest statement

Pier Francesco Indelli, MD, PhD, is a consultant for medical education for bioMérieux (France) and received research support from Biocomposites (UK). The other authors declare no conflicts of interest regarding the manuscript's content.

Figures

Figure 1
Figure 1
PRISMA flowchart.
Figure 2
Figure 2
Each article included in the current scoping review was assigned in one of four categories: (1) Polymerase chain reaction (PCR)‐related studies: n = 18; (2) Next Generation Sequencing (NGS)‐related studies: n = 40; (3) comparative studies, including systematic reviews (SR) and meta‐analyses (MA), between different molecular diagnostic methodologies: n = 7; (4) general reviews on applying nucleic acid‐based strategies to detect PJIs: n = 10.
Figure 3
Figure 3
Diagnssostic‐treatment flow chart for acute and chronic periprosthetic joint infections (PJI). The definition of a PJI as acute or chronic has been formulated according to the 2018 International Consensus Meeting on PJI as reported by Chotanaphuti et al. [6]. ACUTE*: Contraindications to DAIR include the presence of sinus tract, DTT infections, loosening of the implant, and antibiotic availability [3, 7]. There is still a lack of consensus on whether to perform DAIR without identifying micro‐organisms: a recent systematic review does not deem pathogen identification necessary before carrying out a DAIR procedure in an acute PJI setting [38]. CULTURE‐NEGATIVE***: In the presence of a sinus tract, the use of molecular diagnostics needs to be supported by future research [58]. CHRONIC INFECTIONS**: Contraindications to a 1‐stage revision also include the presence of sepsis, an infection caused by drug‐resistant bacteria or DTT, the presence of a sinus tract, severe soft‐tissue deficiency over the joint and no history of multiple revisions [35, 51, 58]. The investigation for the infecting pathogen should include a blood culture (if the patient is suspected of having a hematogenous PJI), a urinalysis (if the patient is suspected of having a urinary tract infection), evaluation for distant focus according to the pathogen and clinical signs, and evaluation for a contiguous infection. Few authors have supported chronic, suppressive antibiotic therapy as an alternative to surgical intervention in selected clinical scenarios [4]. DAIR: Debridement, Antibiotics, Implant Retention; DAPRI: Debridement, Antibiotic Pearls Retention of the Implant [5]. DTT: difficult‐to‐treat infections caused by pathogens resistant to biofilm‐active antimicrobials [7].
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