MALDI-TOF MS performance compared to direct examination, culture, and 16S rDNA PCR for the rapid diagnosis of bone and joint infections

Bone and Joint Infections in Children With Sickle Cell Disease in French Guiana: A 13-year Retrospective Multicenter Review

INTRODUCTION

Sickle cell disease (SCD) is a genetic disorder with a high infectious morbidity and mortality and a heterogeneous distribution in France. One of the challenges is to differentiate a bone and joint infection (BJI) from a vaso-occlusive crisis. This challenge is particularly prevalent in French Guiana, an overseas territory with the highest incidence of SCD in France. The aim of this study was to describe the epidemiology of BJI in children with SCD in French Guiana.

METHOD

This was a retrospective multicentric descriptive study of SCD patients living in French Guiana aged under 18 and diagnosed with a BJI between 2010 and 2022. These BJI were divided into 2 groups: those with microbiological documentation (d-BJI) and those without microbiological identification (ud-BJI).

RESULTS

A total of 53 episodes of BJI in 42 patients (mean age 7.2 years) were reported. Clinical symptoms on arrival were comparable between the d-BJI and ud-BJI groups. Patients in the d-BJI group had longer average hospital stays (40.4 days vs. 16.8 days, P = 0.01) and Salmonella spp. were the most identified bacteria (n = 8/13). White blood cell count was greater in the d-BJI group (30.3 G/L vs. 18.G/L, P = 0.01) and a collection was more frequently identified on imaging (11/13 vs. 16/40, P = 0.01) in this group. Initial in-hospital antibiotic therapy was longer in the d-BJI group (17.2 days vs. 12.8, P = 0.02), as were infection-related complications (9/13 vs. 12/40 P = 0.01).

CONCLUSION

BJI in children with SCD is not sufficiently microbiologically documented. Progress must be made to improve the documentation of BJI.

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.

Decellularization of Massive Bone Allografts By Perfusion: A New Protocol for Tissue Engineering

In terms of large bone defect reconstructions, massive bone allografts may sometimes be the only solution. However, they are still burdened with a high postoperative complication rate. Our hypothesis is that the immunogenicity of residual cells in the graft is involved in this issue. Decellularization by perfusion might therefore be the answer to process and create more biologically effective massive bone allografts. Seventy-two porcine bones were used to characterize the efficiency of our sodium hydroxide-based decellularization protocol. A sequence of solvent perfusion through each nutrient artery was set up to ensure the complete decellularization of whole long bones. Qualitative (histology and immunohistochemistry [IHC]) and quantitative (fluoroscopic absorbance and enzyme-linked immunosorbent assay) evaluations were performed to assess the decellularization and the preservation of the extracellular matrix in the bone grafts. Cytotoxicity and compatibility were also tested. Comparatively to nontreated bones, our experiments showed a very high decellularization quality, demonstrating that perfusion is mandatory to achieve an entire decellularization. Moreover, results showed a good preservation of the bone composition and microarchitecture, Haversian systems and vascular network included. This protocol reduces the human leukocyte antigen antigenic load of the graft by >50%. The majority of measured growth factors is still present in the same amount in the decellularized bones compared to the nontreated bones. Histology and IHC show that the bones were cell compatible, noncytotoxic, and capable of inducing osteoblastic differentiation of mesenchymal stem cells. Our decellularization/perfusion protocol allowed to create decellularized long bone graft models, thanks to their inner vascular network, ready for in vivo implantation or to be further used as seeding matrices.

Advances in the Microbiological Diagnosis of Prosthetic Joint Infections

A significant number of prosthetic joint infections (PJI) are culture-negative and/or misinterpreted as aseptic failures in spite of the correct implementation of diagnostic culture techniques, such as tissue sample processing in a bead mill, prolonged incubation time, or sonication of removed implants. Misinterpretation may lead to unnecessary surgery and needless antimicrobial treatment. The diagnostic value of non-culture techniques has been investigated in synovial fluid, periprosthetic tissues, and sonication fluid. Different feasible improvements, such as real-time technology, automated systems and commercial kits are now available to support microbiologists. In this review, we describe non-culture techniques based on nucleic acid amplification and sequencing methods. Polymerase chain reaction (PCR) is a frequently used technique in most microbiology laboratories which allows the detection of a nucleic acid fragment by sequence amplification. Different PCR types can be used to diagnose PJI, each one requiring the selection of appropriate primers. Henceforward, thanks to the reduced cost of sequencing and the availability of next-generation sequencing (NGS), it will be possible to identify the whole pathogen genome sequence and, additionally, to detect all the pathogen sequences present in the joint. Although these new techniques have proved helpful, strict conditions need to be observed in order to detect fastidious microorganisms and rule out contaminants. Specialized microbiologists should assist clinicians in interpreting the result of the analyses at interdisciplinary meetings. New technologies will gradually be made available to improve the etiologic diagnoses of PJI, which will remain an important cornerstone of treatment. Strong collaboration among all specialists involved is essential for the correct diagnosis of PJI.

Proteomics approaches: A review regarding an importance of proteome analyses in understanding the pathogens and diseases

Proteomics is playing an increasingly important role in identifying pathogens, emerging and re-emerging infectious agents, understanding pathogenesis, and diagnosis of diseases. Recently, more advanced and sophisticated proteomics technologies have transformed disease diagnostics and vaccines development. The detection of pathogens is made possible by more accurate and time-constrained technologies, resulting in an early diagnosis. More detailed and comprehensive information regarding the proteome of any noxious agent is made possible by combining mass spectrometry with various gel-based or short-gun proteomics approaches recently. MALDI-ToF has been proved quite useful in identifying and distinguishing bacterial pathogens. Other quantitative approaches are doing their best to investigate bacterial virulent factors, diagnostic markers and vaccine candidates. Proteomics is also helping in the identification of secreted proteins and their virulence-related functions. This review aims to highlight the role of cutting-edge proteomics approaches in better understanding the functional genomics of pathogens. This also underlines the limitations of proteomics in bacterial secretome research.

Emerging Diabetic Foot Ulcer Microbiome Analysis Using Cutting Edge Technologies

One of the most prevalent complications of diabetes mellitus are diabetic foot ulcers (DFU). Diabetic foot ulcers represent a complex condition placing individuals at-risk for major lower extremity amputations and are an independent predictor of patient mortality. DFU heal poorly when standard of care therapy is applied. In fact, wound healing occurs only approximately 30% within 12 weeks and only 45% regardless of time when standard of care is utilized. Similarly, diabetic foot infections occur in half of all DFU and conventional microbiologic cultures can take several days to process before a result is known. DFU represent a significant challenge in this regard because DFU often demonstrate polymicrobial growth, become resistant to preferred antibiotic therapy, and do not inform providers about long-term prognosis. In addition, conventional culture yields may be affected by the timing of antibiotic administration and collection of tissue for analysis. This may lead to suboptimal antibiotic administration or debilitating amputations. The microbiome of DFU is a new frontier to better understand the interactions between host organisms and pathogenic ones. Newer molecular techniques are readily available to assist in analyzing the constituency of the microbiome of DFU. These emerging techniques have already been used to study the microbiome of DFU and have clinical implications that may alter standard of care practice in the near future. Here emerging molecular techniques that can provide clinicians with rapid DFU-related-information and help prognosticate outcomes in this vulnerable patient population are presented.

Novel strategies to diagnose prosthetic or native bone and joint infections

INTRODUCTION

Bone and Joint Infections (BJI) are medically important, costly and occur in native and prosthetic joints. Arthroplasties will increase significantly in absolute numbers over time as well as the incidence of Prosthetic Joint Infections (PJI). Diagnosis of BJI and PJI is sub-optimal. The available diagnostic tests have variable effectiveness, are often below standard in sensitivity and/or specificity, and carry significant contamination risks during the collection of clinical samples. Improvement of diagnostics is urgently needed.

AREAS COVERED

We provide a narrative review on current and future diagnostic microbiology technologies. Pathogen identification, antibiotic resistance detection, and assessment of the epidemiology of infections via bacterial typing are considered useful for improved patient management. We confirm the continuing importance of culture methods and successful introduction of molecular, mass spectrometry-mediated and next-generation genome sequencing technologies. The diagnostic algorithms for BJI must be better defined, especially in the context of diversity of both disease phenotypes and clinical specimens rendered available.

EXPERT OPINION

Whether interventions in BJI or PJI are surgical or chemo-therapeutic (antibiotics and bacteriophages included), prior sensitive and specific pathogen detection remains a therapy-substantiating necessity. Innovative tests for earlier and more sensitive and specific detection of bacterial pathogens in BJI are urgently needed.

Multicenter evaluation of three different MALDI-TOF MS systems for identification of clinically relevant filamentous fungi

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) holds promise as a potential tool for clinical identification of filamentous fungi. However, due to the lack of an appropriate extraction protocol and the difficulty of database building, the identification power of each system differs. In this study, we selected 126 clinical mould isolates comprising 28 species identified using internal transcribed spacer (ITS) sequencing as the reference method to evaluate three MALDI-TOF MS systems. When using cultures and sample preparation as recommended by the respective vendors, of the 126 strains tested, VITEK MS identified 121 (96.0%) to species-level and 124 (98.4%) to genus-level; Biotyper identified 53 (42.1%) to species-level and 54 (42.9%) to genus-level; Autof identified 74 (58.7%) to species-level and 76 (60.3%) to genus-level. For the Autof system, the tube extraction method recommended by the vendor performed better (59%) than the on-plate lysis (51%). Our study demonstrates that MALDI-TOF MS systems can successfully identify most clinically relevant fungi, while performance is still highly dependent on the database and sample preparation protocol.

Elaboration of a new synovial predictive score of septic origin for acute arthritis on the native joint (RESAS)

OBJECTIVE

To establish a new predictive score for the diagnosis of septic arthritis (SA) according to different synovial fluid (SF) variables.

METHODS

First, we analysed the different clinical, biological and SF variables associated with the diagnosis of SA (according to the Newman's criteria) in a monocentric cohort of acute arthritis (<30 days) (n = 233) (SYNOLACTATE cohort). A new score predictive of SA (RESAS) was created using the independent discriminant variables after multivariate analysis. A value was attributed to each variable of the score according to the weighting based on their likelihood ratio for the diagnosis of SA. RESAS performance was then tested on the first cohort (internal validation) and then checked on a second independent cohort (n = 70) (external validation).

RESULTS

After multivariate analysis, four independent variables of the SF were included for RESAS: (i) purulent SF or white blood cells count ≥70 000/mm3; (ii) absence/presence of crystals; (iii) lactate; and (iv) glucose synovial level. RESAS ranged between -4 and +13 points. The performance of RESAS to predicted SA was excellent with area under the curve (AUC)=0.928 (0.877-0.980) in internal validation and AUC=0.986 (0.962-1.00) in external validation. For a RESAS threshold ≥+4, SA was diagnosed with Se=56.0% (0.371-0.733), Sp=98.1% (0.952-0.993), LR+=29.1 (10.4-81.6) in the first cohort and with Se=91.7% (0.646-0.985), Sp=98.3% (0.909-0.997), LR+=53.2 (7.56-373) in the second cohort.

CONCLUSION

RESAS is a new composite score of four SF variables with excellent performance to predicted SA in acute arthritis population.

Rapid direct detection of pathogens for diagnosis of joint infections by MALDI-TOF MS after liquid enrichment in the BacT/Alert blood culture system

Pathogen identification is a critical step during diagnosis of infectious diseases. Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF-MS) has become the gold standard for identification of microorganisms cultured on solid media in microbiology laboratories. Direct identification of microbes from liquid specimen, circumventing the need for the additional overnight cultivation step, has been successfully established for blood culture, urine and liquor. Here, we evaluate the ability of MALDI-TOF MS for direct identification of pathogens in synovial fluid after liquid enrichment in BacT/Alert blood culture bottles. Influence of synovial specimen quality on direct species identification with the MALDI BioTyper/Sepsityper was tested with samples inoculated from pretested native synovia with concomitant inoculation of blood or pus, or highly viscous fluid. Here, we achieved >90% concordance with culture on solid medium, and only mixed-species samples posed significant problems. Performance in routine diagnostics was tested prospectively on bottles inoculated by treating physicians on ward. There, we achieved >70% concordance with culture on solid media. The major contributors to test failure were the absence of a measurable mass signal and mixed-specimen samples. The Sepsityper workflow worked well on samples derived from BacT/Alert blood culture bottles inoculated with synovial fluid, giving concordant results to identification from solid media. Host remnant material in the inoculum, such as blood or pus, had no detrimental effect on identification score values of the BioTyper system after processing with the Sepsityper workflow, and neither had the initial viscosity of the synovial sample.

Broad-range 16 s rDNA PCR in synovial fluid does not improve the diagnostic performance of septic arthritis in native joints in adults: cross-sectional single-center study in 95 patients

OBJECTIVE

To evaluate the diagnostic performance of bacterial identification by broad-range polymerase chain reaction (PCR) of ribosomal DNA (rDNA) 16 s (16S rDNA PCR) for the diagnosis of septic arthritis on native joints.

METHODS

Patients with acute mono or oligoarthritis who underwent synovial fluid puncture and prospective follow-up allowing definitive diagnosis (septic arthritis, crystal related disease, chronic inflammatory arthritis, undifferentiated arthritis) were recruited in this single-center study. Systematic analysis of synovial fluid included leukocytes count, search for urate and pyrophosphate crystals with polarized light microscopy, direct bacteriological examination (gram staining), bacteriological culture, and 16S rDNA PCR.

RESULTS

Ninety-five patients were included, 34 of which (35.8%) had septic arthritis. Nineteen (20.0%) patients had received probabilistic antibiotic therapy prior to joint puncture. Gram + cocci infection accounted for 79.4% of septic arthritis, of which nearly half (47.1%) was caused by Staphylococcus aureus. Eight (23.5%) septic arthritis patients had a 16S rDNA PCR positive in the synovial fluid with an AUC of 0.618 (95% CI, 0.493-0.742), a sensitivity of 0.24 (95% CI, 0.12-0.40), and a specificity of 1.00 (95% CI 0.94-1.00). The diagnostic performance of 16S rDNA PCR was lower than that of direct examination (AUC at 0.691, CI 95%, 0.570-0.812), blood cultures (AUC at 0.727, CI 95%, 0.610-0.844), and culture (0.925, CI 95%, 0.856-0.994) for the diagnosis of septic arthritis. There was no difference in the positivity of 16S rDNA PCR according to previous exposure to antibiotics.

CONCLUSIONS

16 s rDNA PCR in the synovial fluid does not improve the diagnostic performance of septic arthritis on native adult joints, particularly for Gram-positive cocci infections.

A Real Pain: Diagnostic Quandaries and Septic Arthritis

Rapid diagnosis and treatment of an infected joint are paramount in preserving orthopedic function. Here, we present a brief review of the many challenges associated with the diagnosis of both septic arthritis and prosthetic joint infections. We also discuss the many laboratory tests currently available to aid in the accurate diagnosis of joint infection, as well as emerging diagnostics that may have future utility in the diagnosis of these challenging clinical entities.

Direct identification of microorganisms from thioglycolate broth by MALDI-TOF MS

We developed an easy MALDI-TOF MS-based assay to identify microorganisms directly from thioglycolate broth. A total of 101 positive thioglycolate broths inoculated with 15 different kinds of samples were evaluated. In 91 samples (90.1%), direct MALDI-TOF MS identifications were the same as those obtained after conventional laboratory procedures including subcultures. In 10 samples misidentified by direct processing, yeasts or mixed cultures grew in the thioglycolate subcultures, or high cellular debris hampered a correct analysis. This rapid method can provide a fast, clinically- relevant species-level identification without disturbing the daily workflow in clinical microbiology laboratories.