Benefits of Polymerase Chain Reaction Combined With Culture for the Diagnosis of Bone and Joint Infections: A Prospective Test Performance Study

Unmasking Bartonella henselae infection in the shadows of long COVID thanks to clinical metagenomics

The diagnosis of long COVID often relies on symptoms post-COVID-19, occasionally lacking biological evidence. This case study illustrates how investigating long COVID uncovered an underlying bartonellosis through clinical metagenomics. Following mild COVID-19, a 26-year-old woman experienced persistent symptoms during 5 months, including axillary adenopathy. Pathological examination, 16 S rRNA PCR, and clinical metagenomic analysis were done on an adenopathy biopsy. The latter revealed Bartonella henselae DNA and RNA. Treatment with clarithromycin improved symptoms. This case underscores the relevance of clinical metagenomics in diagnosing hidden infections. Post-COVID symptoms warrant thorough investigation, and bartonellosis should be considered in polyadenopathy cases, regardless of a recent history of cat or flea exposures.

A Rare Case of Streptococcus cristatus Spondylodiscitis Identified by Bacterial 16S rRNA Polymerase Chain Reaction Sequencing: A Case Report and a Review of the Literature

We report here a rare case of spondylodiscitis due to Streptococcus cristatus in a healthy 66-year-old male. Due to an abscess causing neurological deficit, which required immediate surgical intervention, a PCR targeting 16S rRNA was performed on the surgical samples as all blood and tissue cultures remained negative. This molecular assay allowed for the identification of this rare Streptococcus, a member of the mitis group and commensal of the oral cavity, whose pathogenicity remains uncertain although it has been seldom reported in cases of human infections, mostly bacteremia and endocarditis. Notably, our case is distinguished by the absence of comorbidities, although the patient's history was compatible with a dental portal of entry. This case illustrates once more that 16S rRNA PCR can be of great help for documenting the causative pathogen in osteoarticular infections when cultures remain inconclusive. We reviewed in this article the data regarding osteoarticular infections due to S. cristatus and discussed the role of molecular technique in the diagnosis of spondylodiscitis.

Optimized decision algorithm for the microbiological diagnosis of osteoarticular infections in adults using synovial fluid samples: a prospective study in two French hospitals including 423 samples of synovial fluid

No consensus exists about the techniques to use for microbiological diagnosis of bone and joint infections (BJIs). The objective herein was to define an algorithm to optimize BJI diagnosis in adults using various bacteriological methods on synovial fluid samples. This prospective multi-center study included 423 synovial fluids collected from adult patients with suspected BJIs. Culture (using five solid media, an enrichment broth, and blood culture bottles), universal 16S rRNA PCR followed by Sanger sequencing, and seven specific bacterial PCRs were systematically performed. Combinations of methods were compared to arrive at the optimized algorithm. Among 423 synovial fluids, 242 infections were diagnosed (57.2 %): 213 mono- and 29 poly-microbial for a total of 284 bacteria (staphylococci at 54.6 %, streptococci-enterococci at 16.5 %, Gram-negative bacilli at 15.5 %, anaerobic species at 8.8 %). Comparing culture techniques, blood culture bottles had the highest sensitivity (67.6 % for pediatric and 63.9 % for anaerobic bottles) but are not sufficient alone and require being combined with solid media. The 16S rDNA PCR detected only 52.3 % of the bacteria, whereas specific PCRs had a higher sensitivity (Staphylococcus spp. at 66.2 %, S. aureus at 85.2 %, Streptococcus spp. at 91.2 %). Based on these results, an algorithm was proposed associating three solid media; inoculation into blood culture bottles; and 16S, Staphylococcus spp., and Streptococcus spp. PCRs, which would have detected 90.5 % of bacteria in the present cohort versus 79.2 % using all culture techniques on synovial fluid. This prospective study shows that a combination of culture and molecular methods on synovial fluids allows the optimization of bacterial detection.

Diagnostic considerations in the clinical management of sudden swelling of the knee: a case report and review of the literature

BACKGROUND

Reactive arthritis and septic arthritis rarely present concomitantly in the same joint and patient. Reactive arthritis presenting after coronavirus disease 2019 is also exceedingly rare, with less than 30 cases reported thus far. Less common pathogens such as Clostridium difficile have been reported to cause reactive arthritis, especially in patients with a positive human leukocyte antigen B27, and therefore should be considered in diagnostic algorithms. The aim of this case report is to highlight the difficulties and precautions in discerning and diagnosing patients presenting with sudden swelling of the knee.

CASE PRESENTATION

We report the case of a 70-year-old Caucasian male with a recent history of coronavirus disease 2019 upper respiratory infection and diarrhea and negating trauma, who presented with a swollen and painful knee. Pain and swelling worsened and inflammatory parameters increased after an intraarticular corticosteroid injection. The patient was therefore treated with arthroscopic lavage and intravenous antibiotics for suspected septic arthritis. Synovial fluid and synovium samples were taken and sent for microbiological analysis. Synovial fluid cytology showed increased leukocytes at 10,980 × 106/L, while polymerase chain reaction and cultures came back sterile. Clostridium difficile toxin was later detected from a stool sample and the patient was treated with oral vancomycin. The patient was tested for the presence of human leukocyte antigen B27, which was positive. We present a review of the literature about the challenges of distinguishing septic from reactive arthritis, and about the mechanisms that predispose certain patients to this rheumatological disease.

CONCLUSIONS

It is still a challenge to differentiate between septic and reactive arthritis of the knee, and it is even more challenging to identify the exact cause of reactive arthritis. This case report of a human leukocyte antigen-B27-positive patient highlights the necessity of contemplating different, less common causes of a swollen knee joint as a differential diagnosis of an apparent septic infection, especially in the coronavirus disease 2019 era. Treating the patient for septic arthritis prevented any possible complications of such a condition, while treating the C. difficile infection contributed to the substantial relief of symptoms.

Advances in diagnosis and management of atypical spinal infections: A comprehensive review

Atypical spinal infections (ASIs) of the spine are a challenging pathology to management with potentially devastating morbidity and mortality. To identify patients with atypical spinal infections, it is important to recognize the often insidious clinical and radiographic presentations, in the setting of indolent and smoldering organism growth. Trending of inflammatory markers, and culturing of organisms, is essential. Once identified, the spinal infection should be treated with antibiotics and possibly various surgical interventions including decompression and possible fusion depending on spine structural integrity and stability. Early diagnosis of ASIs and immediate treatment of debilitating conditions, such as epidural abscess, correlate with fewer neurological deficits and a shorter duration of medical treatment. There have been great advances in surgical interventions and spinal fusion techniques for patients with spinal infection. Overall, ASIs remain a perplexing pathology that could be successfully treated with early diagnosis and immediate, appropriate medical, and surgical management.

Real-Life Experience and Diagnostic Utility of the BioFire Joint Infection PCR Panel in Bone and Joint Infections: Analysis of a Prospective Validation Study

INTRODUCTION

Microbiological diagnosis is central for adequate treatment of bone and joint infections. Culture-based methods have a limited diagnostic sensitivity and a long turnaround time (TAT). The objective of this study was to compare the diagnostic performance of BioFire Joint Infection Panel Investigational Use Only version (hereafter BioFire)-a sample-to-result multiplex PCR panel-with culture-based methods and 16S ribosomal RNA (rRNA) PCR and sequencing, when available.

METHODS

This study presents a retrospective analysis of a prospective validation study of the BioFire panel. Specimens were obtained from consecutive patients evaluated for suspected bone and joint infections and processed using culture, BioFire, and 16S rRNA PCR and sequencing. Final clinical diagnosis was used as the reference for definition of infection.

RESULTS

Samples, including synovial fluid, bone and periarticular tissue, were obtained from 57 patients, 39 of whom were finally diagnosed with a bone or joint infection. Cultures were positive in 27/39 infected patients and in 3/18 uninfected patients (sensitivity 69%, specificity 83%). BioFire was positive in 22/39 infected patients and in none of the uninfected patients (sensitivity 56%, specificity 100%). Sensitivity for PCR panel organisms was 92% (22/24) and sensitivity for organisms identified by any microbiological modality was 69% (22/32). Gram stain results were positive in 13/39 infected patients and in none of the uninfected patients (sensitivity 33%, specificity 100%). 16S rRNA was positive in 20/28 infected patients and in 0/12 uninfected patients (sensitivity 71%, specificity 100%). Net machine time for BioFire-1 h-was shorter than the mean TAT for Gram stain results, which was 4 h.

CONCLUSION

BioFire offered equivalent diagnostic performance with superior TAT for bone and joint infections, compared with conventional methods.

2022 SPILF - Clinical Practice guidelines for the diagnosis and treatment of disco-vertebral infection in adults

These guidelines are an update of those made in 2007 at the request of the French Society of Infectious Diseases (SPILF, Société de Pathologie Infectieuse de Langue Française). They are intended for use by all healthcare professionals caring for patients with disco-vertebral infection (DVI) on spine, whether native or instrumented. They include evidence and opinion-based recommendations for the diagnosis and management of patients with DVI. ESR, PCT and scintigraphy, antibiotic therapy without microorganism identification (except for emergency situations), therapy longer than 6 weeks if the DVI is not complicated, contraindication for spinal osteosynthesis in a septic context, and prolonged dorsal decubitus are no longer to be done in DVI management. MRI study must include exploration of the entire spine with at least 2 orthogonal planes for the affected level(s). Several disco-vertebral samples must be performed if blood cultures are negative. Short, adapted treatment and directly oral antibiotherapy or early switch from intravenous to oral antibiotherapy are recommended. Consultation of a spine specialist should be requested to evaluate spinal stability. Early lifting of patients is recommended.

Surveillance of osteoarticular infections caused by Staphylococcus aureus in a paediatric hospital in Mexico City

Staphylococcus aureus is the main aetiologic agent of osteoarticular infections (OAIs) in paediatric patients. The aim of this prospective unicenter study was to describe the phenotypic and genotypic characteristics of S. aureus isolates obtained from OAIs in paediatric patients admitted to tertiary care hospital. Through a surveillance program called OsteoCode, a multidisciplinary team was created and we identified 27 patients with OAIs caused by S. aureus from 2019 to 2021. The susceptibility profile, virulence factors, biofilm formation, pulsed-field gel electrophoresis (PFGE), clonal complex (CC) and sequence type (ST) were determined. In addition, the clinical characteristics and evolution of the patients presented six months after the diagnosis of OAIs were described. Ninety-two percent of the isolates were methicillin-sensitive S. aureus (MSSA). In methicillin-resistant S. aureus (MRSA), SCCmec-II and SCCmec-V were detected. The pvl gene was only observed in MSSA (18.5%) and was associated with highest fever (p=0.015), multiple localization (p=0.017), and soft tissue sites of infection beyond the bone (pyomyositis, pulmonary abscess) (p=0.017). Biofilm formation was detected in 55.6% of isolates. The most common CC were CC5 and CC30 which represent the most common linages for bone and joint infections worldwide. The isolates were distributed in different STs, and ST672 was predominant. MRSA were associated with a longer duration of intravenous treatment and a prolonged hospital stay (p=0.023). Recurrent infection occurred in five children and orthopaedic complications in 33.3% of patients. This is the first study that reflects the epidemiology of S. aureus in OAIs in paediatric patients in Mexico; a clear predominance of MSSA distributed in different STs was observed. Our findings highlight that a multidisciplinary team is required for the diagnosis and treatment of OAIs.

Sonication versus the conventional method for evaluation of the dental microbiome: a prospective pilot study

Objectives

To investigate sonication as a new tool in microbiological probing of dental infections.

Methods

Comparison of a standard probing method: intraoperative swab, with sonication, and vortex of the removed tooth, was performed on 20 carious destructed teeth. Illumina high throughput sequencing of the 16S-rRNA-gene was used for assessing the microbial composition. Antibiotic susceptibility has been assigned based on known resistances of each detected species. Probing procedures were compared using Bland–Altmann-Test, and antibiotic susceptibility using the Friedmann-Test and alpha-adjusted post-hoc-analysis.

Results

In total, 60 samples were analysed: 20 intraoperative swabs, 20 vortex fluids, and 20 sonication fluids. Sonication fluid yielded the highest number of bacterial sequencing reads in all three procedures. Comparing the operational taxonomic units (OTUs) of the identified bacteria, significantly more OTUs were found in sonication fluid samples. Phylum and order abundances varied between the three procedures. Significantly more Actinomycetales have been found in sonication fluid samples compared to swab samples. The assigned resistance rates for the identified bacteria (1.79–31.23%) showed no differences between the tested probing procedures. The lowest resistance rates were found for amoxicillin + clavulanate (3.95%) and levofloxacin (3.40%), with the highest in amoxicillin (30.21%) and clindamycin (21.88%).

Conclusions

By using sonication on extracted teeth, it is possible to get a more comprehensive image of the residing microbial flora compared to the standard procedure. If sonication is not available, vortexing is a potential alternative. In immunocompromised patients, especially when actinomycosis is suspected, sonication should be considered for a more detailed microbiological evaluation of the potential disease-causing microbiome. Due to the high rates of antibiotic resistance, a more targeted antibiotic therapy is favourable. Levofloxacin should be considered as a first-line alternative to amoxicillin + clavulanate in patients with an allergy to penicillin.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-022-02374-0.

Evaluation of a syndromic panel polymerase chain reaction (spPCR) assay for the diagnosis of device-associated bone and joint infections (BJI)

OBJECTIVE

Pathogen detection is crucial for diagnosis and targeted therapy in implant-associated bone and joint infections (BJI). Culture-based microbiology regularly fails to identify causative pathogens. This study evaluated the diagnostic accuracy and clinical usefulness of a syndromic panel polymerase chain reaction (spPCR) assay targeting common BJI pathogens in tissue specimens from patients with implant-associated BJI.

METHODS

Results obtained by spPCR assay and a 16S rDNA PCR were compared with results obtained from a standard of care (SOC) culture-based diagnostics, serving as a gold standard. In total, 126 specimens obtained from 73 patients were analyzed.

RESULTS

The spPCR assay correctly identified 33/40 culture-positive samples (82.5 %) and was positive in 9/86 (10.5 %) culture-negative samples, resulting in an overall sensitivity of 84.6 % (95% confidence interval [CI] 68.79-93.59%) and specificity of 89.35% (95% CI 80.6-94.81%). The spPCR was more sensitive compared with the 16S rDNA PCR (37.5%). The spPCR identified pathogens in 7/51 (13.7%) SOC-negative patients. Re-evaluation of spPCR results in clinical context suggested their clinical significance.

CONCLUSION

An spPCR assay targeting common pathogens causing implant-associated BJI may help to identify causative agents in culture-negative cases. As false-negative results are possible, spPCR assays appear as an add-on approach for pathogen detection in implant-associated BJI.

Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections

INTRODUCTION

Prosthetic joint infections (PJIs) can be challenging to eradicate and have high morbidity and mortality. Current microbiology culture methods can be associated with a high false-negative rate of up to 50%. Early and accurate diagnosis is crucial for effective treatment, and negative results have been linked to a greater rate of reoperation.

AREAS COVERED

There has been increasing investigation of the use of next-generation sequencing (NGS) technology such as metagenomic shotgun sequencing to help identify causative organisms and decrease the uncertainty around culture-negative infections. The clinical importance of the organisms detected and their management, however, requires further study. The polymerase chain reaction (PCR) has shown promise, but in recent years multiple studies have reported similar or lower sensitivity for bacteria detection in PJIs when compared to traditional culture. Furthermore, issues such as high cost and complexity of sample preparation and data analysis are to be addressed before it can move further toward routine clinical practice.

EXPERT OPINION

Metagenomic NGS has shown results that inspire cautious optimism - both in culture-positive and culture-negative cases of joint infection. Refinement of technique could revolutionize the way PJIs are diagnosed, managed, and drastically improve outcomes from this currently devastating complication.

Challenging Methicillin Resistance Detection in Bone and Joint Infections: Focus on the MRSA/SA SSTI® Strategy

The genus Staphylococcus is the main causative agent of bone and joint infections (BJI) in which outcomes are impacted by both effective surgical and appropriate antimicrobial management. In this context, methicillin resistance (MR) detection is a microbiological challenge to optimize the anti-staphylococcal drug coverage and to secure the surgical procedure. During the last decade, molecular tools have been developed to rapidly detect bacterial-resistant strains in clinical samples. The GeneXpert MRSA/SA SSTI^® assay (Cepheid, Sunnyvale, CA, USA) is a real-time PCR method aimed at detecting methicillin-resistant Staphylococcus aureus (MRSA) in skin and soft tissues infections. In the literature, this test has been reported to be diverted from its original purpose to be evaluated in surgical samples. Within the current review, we update the GeneXpert MRSA/SA SSTI^® assay performance in staphylococcal species determination (i.e., S. aureus vs. coagulase-negative species) together with MR genotype detection, when performed in osteoarticular infections.

Sampling challenges in diagnosis of chronic bacterial infections

In recent decades there has been an increase in knowledge of the distribution, species diversity and growth patterns of bacteria in human chronic infections. This has challenged standard diagnostic methods, which have undergone a development to both increase the accuracy of testing as well as to decrease the occurrence of contamination. In particular, the introduction of new technologies based on molecular techniques into the clinical diagnostic process has increased detection and identification of infectious pathogens. Sampling is the first step in the diagnostic process, making it crucial for obtaining a successful outcome. However, sampling methods have not developed at the same speed as molecular identification. The heterogeneous distribution and potentially small number of pathogenic bacterial cells in chronic infected tissue makes sampling a complicated task, and samples must be collected judiciously and handled with care. Clinical sampling is a step in the diagnostic process that may benefit from innovative methods based on current knowledge of bacteria present in chronic infections. In the present review, we describe and discuss different aspects that complicate sampling of chronic infections. The purpose is to survey representative scientific work investigating the presence and distribution of bacteria in chronic infections in relation to various clinical sampling methods.

Patients with surgically treated culture-negative native joint septic arthritis have less severe disease and better outcomes

Background: Patients with culture-negative septic arthritis patients are often treated surgically but might be successfully managed medically. We compared clinical characteristics and outcomes in patients with culture negative and culture positive native joint monoarticular septic arthritis.Methods: This retrospective study included all patients age ≥18 years admitted to a single, tertiary-care hospital between 1998 and 2015 with native joint monoarticular SA and treated with antibiotics and surgery.Results: Of 306 patients, 85 had negative and 221 had positive cultures. Mean C-reactive protein (p < .01) and mean percentage of peripheral polymorphonuclear cells (p = .01) were higher in culture-positive patients who had higher intensive care unit admission rates (16.7% vs. 4.7%, respectively, [p < .01]), longer length of hospital stay (11.4 vs. 7.1 days, respectively, [p < .01]) and higher mortality rates within 30 days (0% vs. 5.5%, respectively,[p = .02]). Of culture-negative patients, 28.6% received an alternative diagnosis within one year. Logistic regression models showed that culture positive patients had an adjusted odds ratio for length of stay of 4.5 (2.69, 7.51), intensive care unit admission of 5.76 (1.31, 25.22), discharge to rehabilitation of 4.7 (2.28, 9.71) and an alternative diagnosis within one year of 0.05 (0.02, 0.15) compared to culture negative patients.Conclusion: Patients with culture-negative native joint septic arthritis had less severe disease, better outcomes and higher rates of alternative diagnosis within one year than patients with positive cultures.