Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach

Diagnostic value of metagenomic next-generation sequencing in patients with osteoarticular infections: a prospective study

Due to the limits of traditional microbiological methods and the complexity of osteoarthritis pathogens, only a few pathogens can be detected. We evaluated metagenomic next-generation sequencing (mNGS) for detecting pathogens in osteoarthritis infection samples. We prospectively included 150 patients with osteoarthritis infection who visited the Orthopedics Department of Shandong Provincial Public Health Center from 2023 to 2024, including 124 cases of primary osteoarthritis (POI) and 26 cases of invasive osteoarthritis (IOI). The most common pathogenic bacteria were Mycobacterium tuberculosis complex, Staphylococcus aureus, and Brucella melitensis. mNGS (75.33%) significantly improved the detection of pathogens in osteoarticular infections compared to conventional tests (CT) methods (36.67%). mNGS could detect a wider spectrum of pathogens compared to CT methods, especially for mixed and rare pathogens. The treatment strategies for patients with osteoarthritis infection could be adjusted based on the results obtained from mNGS testing. Furthermore, the abundance of M. tuberculosis complex, B. melitensis, and Staphylococcus epidermidis was significantly correlated with clinical indicators.IMPORTANCEIdentifying the microorganisms responsible for osteoarthritis infection could help with early diagnosis and treatment. In this study, we compared the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and CT methods in patients with osteoarthritis infection and found that mNGS had a higher microbial detection rate and a broader spectrum of pathogens (especially for mixed pathogens). This study demonstrates that mNGS is an ideal tool for detecting pathogens in patients with osteoarticular infections.

The contribution of metagenomic next-generation sequencing to a diagnosis of gas-producing Fusobacterium-induced septic hip arthritis: A case report

Pyogenic arthritis with gas gangrene triggered by intra-articular steroid injections can occasionally result in fatal complications. Clostridium perfringens is typically the causative pathogen, with infections caused by Fusobacterium species being relatively rare. Fusobacterium species are known to cause pyogenic infections, but due to their extreme sensitivity to oxygen, they can be difficult to detect with traditional culture methods. Recently, metagenomic next-generation sequencing (mNGS) has gained attention as an alternative diagnostic tool to traditional culture, enabling rapid identification of causative pathogens in infectious diseases, including pyogenic arthritis. Its use is illustrated in the following case report, which demonstrates the diagnostic utility of mNGS in pyogenic arthritis with gas gangrene triggered by an intra-articular steroid injection. Using mNGS as a complement to conventional culture testing allows for a more precise narrowing-down of causative pathogens, enabling targeted therapy and improving patient outcomes. This approach may also help reduce the use of broad-spectrum antibiotics and prevent the emergence of antibiotic-resistant bacteria.

Academic and clinical perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study

BACKGROUND

Effective infectious disease diagnostics (IDD) are vital for informing clinical decision-making regarding the treatment and patient management of disease and infections. In England, conventional clinical methods rely upon culture-dependent techniques, and there has been little shift in the acceptance and integration of culture-independent sequencing methods into routine clinical IDD. This study explored stakeholders' experiences within IDD, including those working in clinical settings and those conducting research at the forefront of microbial genomics. From the participants' experiences, the study aimed to identify barriers and facilitators driving the development and implementation of metagenome sequencing as a routine diagnostic.

METHODS

Virtual semi-structured interviews were conducted with purposively selected individuals involved in IDD. The interviews explored the experiences of implementing metagenome sequencing as a diagnostic tool and decisions about which diagnostics are used for identifying bacteria-causing infections. Thematic analysis was used to analyse the data, and an Interpretive Phenomenological approach was used throughout.

RESULTS

Ten individuals were interviewed between July 2021 and October 2021, including clinical scientists, consultants, and professors in academia. Their experience ranged from limited knowledge of metagenome sequencing to an expert understanding of the phenomenon. The thoughts and perspectives of participants of the study could be grouped into five themes: Availability of diagnostics for infectious diseases; Clinical laboratory infrastructure; Ethical Data Sharing: Enhancing metagenomics through Open Access; Case study in action: COVID-19; and The importance of communication to improve developments of new diagnostics. Participants recognised the need for new diagnostics to be implemented to overcome the limitations of current diagnostic approaches but highlighted the barriers to integrating new diagnostics into clinical settings, such as the impact on clinical decision-making, accreditation, and cost. Further, participants felt that lessons could be learnt from using metagenomics in COVID-19 and how other diagnostic platforms have been integrated into clinical settings over the last 20 years.

CONCLUSIONS

The study provided insights into stakeholders' perspectives and opinions to address the knowledge gap in current literature and identified barriers and facilitators which drive the implementation of metagenome sequencing as a routine IDD in clinical settings. Knowledge of new and upcoming genomic diagnostic testing is not equally distributed throughout the UK, impacting the understanding and drive to integrate metagenome sequencing into routine clinical diagnostics. Improvements in access to new diagnostics could improve patient treatment and management and positively impact population health.

Leveraging innovative diagnostics as a tool to contain superbugs

The evolutionary adaptation of pathogens to biological materials has led to an upsurge in drug-resistant superbugs that significantly threaten public health. Treating most infections is an uphill task, especially those associated with multi-drug-resistant pathogens, biofilm formation, persister cells, and pathogens that have acquired robust colonization and immune evasion mechanisms. Innovative diagnostic solutions are crucial for identifying and understanding these pathogens, initiating efficient treatment regimens, and curtailing their spread. While next-generation sequencing has proven invaluable in diagnosis over the years, the most glaring drawbacks must be addressed quickly. Many promising pathogen-associated and host biomarkers hold promise, but their sensitivity and specificity remain questionable. The integration of CRISPR-Cas9 enrichment with nanopore sequencing shows promise in rapid bacterial diagnosis from blood samples. Moreover, machine learning and artificial intelligence are proving indispensable in diagnosing pathogens. However, despite renewed efforts from all quarters to improve diagnosis, accelerated bacterial diagnosis, especially in Africa, remains a mystery to this day. In this review, we discuss current and emerging diagnostic approaches, pinpointing the limitations and challenges associated with each technique and their potential to help address drug-resistant bacterial threats. We further critically delve into the need for accelerated diagnosis in low- and middle-income countries, which harbor more infectious disease threats. Overall, this review provides an up-to-date overview of the diagnostic approaches needed for a prompt response to imminent or possible bacterial infectious disease outbreaks.

Pathogenic Detection by Metagenomic Next-generation Sequencing in Spinal Infections

STUDY DESIGN

A retrospective, observational study.

OBJECTIVE

To evaluate the ability and value of metagenomic next-generation sequencing (mNGS) in detecting pathogens from spinal infections.

BACKGROUND

The pathogenic diagnosis of primary spinal infection is challenging. The widespread application of mNGs in clinical practice makes it particularly useful in detecting rare, emerging, and atypical complex infectious diseases.

METHODS

From January 2019 to December 2023, 120 samples were retrospectively collected from patients suspected of spinal infections and undergoing treatment. Pairwise comparisons between traditional laboratory tests and mNGS were conducted for all cases.

RESULTS

Among the 120 cases, 95 were diagnosed as spinal infections, while 25 were classified as noninfectious. Microbiological evidence was found in 59 cases, while 36 cases were clinically diagnosed as spinal infections without definitive microbiological evidence. Rare microorganisms such as Aspergillus fumigatus , Taifanglania major , and Coxiella burnetii were detected by mNGS. The positive rate of mNGS was significantly higher at 88.42% compared with microbiological culture (43.16%), P <0.001. At the genus level, mNGS exhibited a consistency rate of 86.44% (51/59) with confirmed microorganisms. MNGS demonstrated very good agreement with clinically confirmed microorganisms at the genus level (κ=0.833). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were 86.44%, 92.00%, 96.23%, and 74.19%, respectively.

CONCLUSIONS

The mNGS test exhibits rapidity, efficiency, and accuracy, rendering it of immense diagnostic and therapeutic value in the realm of spinal infection diseases.

Pseudomonas aeruginosa alkyl quinolone response is dampened by Enterococcus faecalis

The bacterium Pseudomonas aeruginosa is an opportunistic pathogen that can cause lung, skin, wound, joint, urinary tract, and eye infections. While P. aeruginosa is known to exhibit a robust competitive response toward other bacterial species, this bacterium is frequently identified in polymicrobial infections where multiple species survive. For example, in prosthetic joint infections, P. aeruginosa can be identified along with other pathogenic bacteria including Staphylococcus aureus, Enterococcus faecalis, and Corynebacterium striatum. Here, we have explored the survival and behavior of such microbes and find that E. faecalis readily survives culturing with P. aeruginosa while other tested species do not. In each of the tested conditions, E. faecalis growth remained unchanged by the presence of P. aeruginosa, indicating a unique mutualistic interaction between the two species. We find that E. faecalis proximity leads P. aeruginosa to attenuate competitive behaviors as exemplified by reduced production of Pseudomonas quinolone signal and pyocyanin. Reduced alkyl quinolones are important to E. faecalis as these will grow in supernatant from a quinolone mutant but not P. aeruginosa wild-type in planktonic culture. The reduced pyocyanin production of P. aeruginosa is attributable to production of ornithine by E. faecalis, which we recapitulate by adding exogenous ornithine to P. aeruginosa monocultures. Similarly, co-culture with an ornithine-deficient strain of E. faecalis leads P. aeruginosa to yield near monoculture amounts of pyocyanin. Here, we directly demonstrate how notorious pathogens such as P. aeruginosa might persist in polymicrobial infections under the influence of metabolites produced by other bacterial species.

IMPORTANCE

While we now appreciate that many infections are polymicrobial, we understand little of the specific actions between a given set of microbes to enable combinatorial survival and pathogenesis. The bacteria Pseudomonas aeruginosa and Enterococcus faecalis are both prevalent pathogens in wound, urinary tract, and bacteremic infections. While P. aeruginosa often kills other species in standard laboratory culture conditions, we present here that E. faecalis can be reliably co-cultured with P. aeruginosa. We specifically detail that ornithine produced by E. faecalis reduces the Pseudomonas quinolone signal response of P. aeruginosa. This reduction of the Pseudomonas quinolone signal response aids E. faecalis growth.

Periprosthetic joint infections: state-of-the-art

In general, periprosthetic joint infection (PJI) is regarded as one of the most common complications of total joint arthroplasty (TJA) and may lead to surgical failure, revision surgery, amputation or death. Nowadays, PJI has become a global health concern, which brings a great burden to public healthcare. In addition, there are still obstacles to achieve high success rates in the prevention, diagnosis and treatment of PJI. However, promising studies are also available with the advancements in biotechnology. This article will present an overview of the current methods used in the prevention, diagnosis and management of PJI while underlining the new technologies utilized.

State-of-the-Art Metagenomic Sequencing and Its Role in the Diagnosis of Periprosthetic Joint Infections

Metagenomic next-generation sequencing (mNGS) is increasingly being recognized as a valuable diagnostic tool for periprosthetic joint infections (PJIs). This study reviews the diagnostic utility of mNGS, highlighting its improved sensitivity in detecting pathogens, particularly in culture-negative and polymicrobial infections. However, the clinical application of this method is hindered by challenges such as the prevalence of host DNA, the necessity for extensive bioinformatic analysis, and the potential for contamination, which can lead to misinterpretation of results. As mNGS continues to evolve, it holds significant potential to improve the management of PJI and enhance the application of precision medicine in orthopedic infections.

Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases

Metagenomic next-generation sequencing (mNGS) is a transformative approach in the diagnosis of infectious diseases, utilizing unbiased high-throughput sequencing to directly detect and characterize microbial genomes from clinical samples. This review comprehensively outlines the fundamental principles, sequencing workflow, and platforms utilized in mNGS technology. The methodological backbone involves shotgun sequencing of total nucleic acids extracted from diverse sample types, enabling simultaneous detection of bacteria, viruses, fungi, and parasites without prior knowledge of the infectious agent. Key advantages of mNGS include its capability to identify rare, novel, or unculturable pathogens, providing a more comprehensive view of microbial communities compared to traditional culture-based methods. Despite these strengths, challenges such as data analysis complexity, high cost, and the need for optimized sample preparation protocols remain significant hurdles. The application of mNGS across various systemic infections highlights its clinical utility. Case studies discussed in this review illustrate its efficacy in diagnosing respiratory tract infections, bloodstream infections, central nervous system infections, gastrointestinal infections, and others. By rapidly identifying pathogens and their genomic characteristics, mNGS facilitates timely and targeted therapeutic interventions, thereby improving patient outcomes and infection control measures. Looking ahead, the future of mNGS in infectious disease diagnostics appears promising. Advances in bioinformatics tools and sequencing technologies are anticipated to streamline data analysis, enhance sensitivity and specificity, and reduce turnaround times. Integration with clinical decision support systems promises to further optimize mNGS utilization in routine clinical practice. In conclusion, mNGS represents a paradigm shift in the field of infectious disease diagnostics, offering unparalleled insights into microbial diversity and pathogenesis. While challenges persist, ongoing technological advancements hold immense potential to consolidate mNGS as a pivotal tool in the armamentarium of modern medicine, empowering clinicians with precise, rapid, and comprehensive pathogen detection capabilities.

Application of a metatranscriptomics technology, CSI-Dx, for the detection of pathogens associated with prosthetic joint infections

Preoperative identification of causal organism(s) is crucial for effective prosthetic joint infection treatment. Herein, we explore the clinical application of a novel metatranscriptomic (MT) workflow, CSI-Dx, to detect pathogens associated with prosthetic joint infection. MT provides insight into transcriptionally active microbes, overcoming limitations of culture-based and available molecular methods. This study included 340 human synovial fluid specimens subjected to CSI-Dx and traditional culture-based methods. Exploratory analyses were conducted to determine sensitivity and specificity of CSI-Dx for detecting clinically-relevant taxa. Our findings provide insights into the active microbial community composition of synovial fluid from arthroplasty patients and demonstrate the potential clinical utility of CSI-Dx for aiding prosthetic joint infection diagnosis. This approach offers potential for improved sensitivity and acceptable specificity compared to synovial fluid culture, enabling detection of culturable and non-culturable microorganisms. Furthermore, CSI-Dx provides valuable information on antimicrobial resistance gene expression. While further optimization is needed, integrating metatranscriptomic technologies like CSI-Dx into routine clinical practice can revolutionize prosthetic joint infection diagnosis by offering a comprehensive and active snapshot of associated pathogens.

Pseudomonas aeruginosa Alkyl Quinolone Response is dampened by Enterococcus faecalis

The bacterium Pseudomonas aeruginosa is an opportunistic pathogen that can cause lung, skin, wound, joint, urinary tract, and eye infections. While P. aeruginosa is known to exhibit a robust competitive response towards other bacterial species, this bacterium is frequently identified in polymicrobial infections where multiple species survive. For example, in prosthetic joint infections (PJIs), P. aeruginosa can be identified along with other pathogenic bacteria including Staphylococcus aureus, Enterococcus faecalis, and Corynebacterium striatum. Here we have explored the survival and behavior of such microbes and find that E. faecalis readily survives culturing with P. aeruginosa while other tested species do not. In each of the tested conditions, E. faecalis growth remained unchanged by the presence of P. aeruginosa, indicating a unique mutualistic interaction between the two species. We find that E. faecalis proximity leads P. aeruginosa to attenuate competitive behaviors as exemplified by reduced production of Pseudomonas quinolone signal (PQS) and pyocyanin. Reduced alkyl quinolones is important to E. faecalis as it will grow in supernatant from a quinolone mutant but not P. aeruginosa wildtype in planktonic culture. The reduced pyocyanin production of P. aeruginosa is attributable to production of ornithine by E. faecalis, which we recapitulate by adding exogenous ornithine to P. aeruginosa monocultures. Similarly, co-culture with an ornithine-deficient strain of E. faecalis leads P. aeruginosa to yield near mono-culture amounts of pyocyanin. Here, we directly demonstrate how notorious pathogens such as P. aeruginosa might persist in polymicrobial infections under the influence of metabolites produced by other bacterial species.

The diagnostic value of metagenomic next-generation sequencing in critically ill patients with sepsis: A retrospective cohort study

Metagenomic next-generation sequencing (mNGS) is a new high-throughput sequencing method that may have great importance in early diagnosis and clinical management of sepsis. This study aimed to detect the difference between mNGS and comprehensive routine microbiological test (CMT), and to explore the diagnostic efficacy of mNGS in septic patients. This study retrospectively analyzed 150 sepsis patients who were admitted to the intensive care units of 4 hospitals in Southwest China from October 1, 2018, to October 1, 2021, and underwent both blood mNGS and CMT. The demographic and clinical characteristics of the patients were recorded, and the distribution of pathogens was analyzed. Additionally, the diagnostic performance and concordance between mNGS and CMT were compared to evaluate the etiological diagnostic value of mNGS in sepsis patients. In this study of 150 sepsis patients, bacterial infections were identified in 126 (84.0%), viral in 15 (10.0%), and fungal in 9 (6.0%). Among the sample types, sputum was most common, representing 62% of the total cases. Bronchoalveolar lavage fluid constituted 58.7%, blood 56.0%, with other specimens including pleural fluid at 29.3%, pus at 19.3%, swabs at 9.3%, cerebrospinal fluid at 8.7%, tissue at 6.0%, and bone marrow at 5.3%. mNGS demonstrated a diagnostic accuracy of 56.0% for sepsis, with a sensitivity of 84.4%, specificity of 26.0%, a positive predictive value of 54.6%, a negative predictive value of 61.3%. Metagenomic testing enables the rapid and early identification of infectious pathogens in sepsis patients, especially fungi and viruses. The study found that mNGS has high sensitivity in diagnosing sepsis patients, particularly for fungal and viral infections. mNGS technology is beneficial for critically ill sepsis patients.

Higher diagnostic value of next-generation sequencing versus culture in periprosthetic joint infection: A systematic review and meta-analysis

BACKGROUND

The next-generation sequencing (NGS) has developed rapidly in the past decade and is becoming a promising diagnostic tool for periprosthetic infection (PJI). However, its diagnostic value for PJI is still uncertain. The purpose of this systematic review and meta-analysis was to evaluate the diagnostic value of NGS compared to culture.

METHODS

In this systematic review and meta-analysis, electronic databases including PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science and clinicaltrials.gov were searched for studies from inception to 12 November 2023. Diagnostic parameters, such as sensitivity, specificity, diagnostic odds ratio and area under the summary receiver-operating characteristic (SROC) curve (AUC), were calculated for the included studies. A systematic review and meta-analysis was performed.

RESULTS

A total of 22 studies with 2461 patients were included in our study. The pooled sensitivity, specificity and diagnostic odds ratio of NGS were 87% (95% confidence interval [CI]: 83-90), 94% (95% CI: 91-96) and 111 (95% CI: 70-177), respectively. On the other hand, the pooled sensitivity, specificity and diagnostic odds ratio of culture were 63% (95% CI: 58-67), 98% (95% CI: 96-99) and 93 (95% CI: 40-212), respectively. The SROC curve for NGS and culture showed that the AUCs are 0.96 (95% CI: 0.94-0.98) and 0.82 (95% CI: 0.79-0.86), respectively.

CONCLUSION

This systematic review and meta-analysis found NGS had higher sensitivity and diagnostic accuracy but slightly lower specificity than culture. Based on the pooled results, we suggested NGS may have the potential to be a new tool for the diagnosis of PJI.

LEVEL OF EVIDENCE

Level IV.

Respiratory microbiome and clinical course of carbapenem-resistant Acinetobacter baumannii pneumonia in critically Ill patients

Carbapenem-resistant Acinetobacter baumannii (CRAB) pneumonia has been a serious problem in the intensive care unit (ICU). However, defined characteristics of respiratory microbiome in CRAB pneumonia are lacking nowadays. This study aimed to analyze respiratory microbiome of CRAB pneumonia compared to non-CRAB pneumonia and reveal the clinical significance of respiratory microbiome data in these patients. Patients diagnosed with severe pneumonia with mechanical ventilation were enrolled in the ICU of a tertiary care hospital. Respiratory specimens were collected on days 1, 4, 7, and 14 in each participant via tracheal aspiration. Clinical data and outcomes of each enrolled patient were collected via electronic medical records. Microbiome analysis was conducted with collected respiratory specimens undergone by next-generation sequencing of microbial 16S ribosomal DNA. Six CRAB pneumonia, 4 non-CRAB pneumonia and 5 healthy controls were enrolled. In CRAB pneumonia, CRAB was detected in 3 patients by sputum culture at day 1, while it was negative at day 1 and detected later in the others by follow-up sputum culture. Beta diversity plot analysis showed differences between each group. Shannon index was decreased markedly at day 4 in CRAB pneumonia compared to the others. Among CRAB pneumonia cases, 3 respiratory specimens were culture-negative, but positive by microbiome analysis. Lower respiratory microbiome in CRAB pneumonia had distinct characteristics and early loss of diversity compared to non-CRAB pneumonia, which might be related to poor clinical course. Moreover, CRAB acquisition and colonization would be predicted by preemptive microbiome analysis, which will contribute to effective infection control in the ICU.

Pathogen-Agnostic Advanced Molecular Diagnostic Testing for Difficult-to-Diagnose Clinical Syndromes-Results of an Emerging Infections Network Survey of Frontline US Infectious Disease Clinicians, May 2023

During routine clinical practice, infectious disease physicians encounter patients with difficult-to-diagnose clinical syndromes and may order advanced molecular testing to detect pathogens. These tests may identify potential infectious causes for illness and allow clinicians to adapt treatments or stop unnecessary antimicrobials. Cases of pathogen-agnostic disease testing also provide an important window into known, emerging, and reemerging pathogens and may be leveraged as part of national sentinel surveillance. A survey of Emerging Infections Network members, a group of infectious disease providers in North America, was conducted in May 2023. The objective of the survey was to gain insight into how and when infectious disease physicians use advanced molecular testing for patients with difficult-to-diagnose infectious diseases, as well as to explore the usefulness of advanced molecular testing and barriers to use. Overall, 643 providers answered at least some of the survey questions; 478 (74%) of those who completed the survey had ordered advanced molecular testing in the last two years, and formed the basis for this study. Respondents indicated that they most often ordered broad-range 16S rRNA gene sequencing, followed by metagenomic next-generation sequencing and whole genome sequencing; and commented that in clinical practice, some, but not all tests were useful. Many physicians also noted several barriers to use, including a lack of national guidelines and cost, while others commented that whole genome sequencing had potential for use in outbreak surveillance. Improving frontline physician access, availability, affordability, and developing clear national guidelines for interpretation and use of advanced molecular testing could potentially support clinical practice and public health surveillance.

Commercial Synovial Antigen Testing is Inferior to Traditional Culture for the Diagnosis of Periprosthetic Joint Infection in Patients Undergoing Revision Total Knee Arthroplasty

BACKGROUND

Despite its limitations, a culture remains the "gold standard" for pathogen identification in patients who have periprosthetic joint infection (PJI). Recently, a synovial fluid antigen test has been introduced by a commercial entity. The purpose of this multicenter study was to determine the accuracy of the antigen test in the diagnosis of PJI.

METHODS

This retrospective study identified 613 patients undergoing revision total knee arthroplasty who had undergone preoperative synovial fluid analysis. A PJI was defined using the 2018 International Consensus Meeting (ICM) criteria. Patients who had an extended period (> 180 days) from aspiration to revision procedure (n = 62), those presenting within 90 days of their index arthroplasty procedure (n = 17), and patients who had an inconclusive ICM score (n = 8) were excluded. Using receiver operator characteristic curve analyses, we examined the utility of the microbial identification (MID) antigen test and any positive culture (either preoperative or intraoperative) in the diagnosis of PJI.

RESULTS

A total of 526 patients were included. Of these, 125 (23.8%) were ICM positive and 401 (76.2%) were ICM negative. Culture demonstrated an area under the curve (AUC) of 0.864, sensitivity of 75.2%, and specificity of 97.5%. On the other hand, the MID test exhibited an AUC of 0.802, sensitivity of 61.6%, and specificity of 98.8%. The AUC of culture was significantly higher than that of the MID test (P = .037). The MID test was positive in 41.9% of culture-negative PJI cases. We also observed a high rate of discordance (29.7%) when both culture and the MID test were positive in the ICM-positive group.

CONCLUSIONS

Synovial fluid antigen testing does not provide additional clinical benefit when compared to traditional cultures for the diagnosis of PJI. The antigen test had low sensitivity in the diagnosis of PJI and a relatively high rate of discordance with culture.

LEVEL OF EVIDENCE

Level III.

Enhancing Pathogen Detection in Implant-Related Infections through Chemical Antibiofilm Strategies: A Comprehensive Review

Implant-related infections (IRIs) represent a significant challenge to modern surgery. The occurrence of these infections is due to the ability of pathogens to aggregate and form biofilms, which presents a challenge to both the diagnosis and subsequent treatment of the infection. Biofilms provide pathogens with protection from the host immune response and antibiotics, making detection difficult and complicating both single-stage and two-stage revision procedures. This narrative review examines advanced chemical antibiofilm techniques with the aim of improving the detection and identification of pathogens in IRIs. The articles included in this review were selected from databases such as PubMed, Scopus, MDPI and SpringerLink, which focus on recent studies evaluating the efficacy and enhanced accuracy of microbiological sampling and culture following the use of chemical antibiofilm. Although promising results have been achieved with the successful application of some antibiofilm chemical pre-treatment methods, mainly in orthopedics and in cardiovascular surgery, further research is required to optimize and expand their routine use in the clinical setting. This is necessary to ensure their safety, efficacy and integration into diagnostic protocols. Future studies should focus on standardizing these techniques and evaluating their effectiveness in large-scale clinical trials. This review emphasizes the importance of interdisciplinary collaboration in developing reliable diagnostic tools and highlights the need for innovative approaches to improve outcomes for patients undergoing both single-stage and two-stage revision surgery for implant-related infections.

Pathogens in FRI - Do bugs matter? - An analysis of FRI studies to assess your enemy

Fracture-related infection (FRI) is a devasting complication for both patients and their treating Orthopaedic surgeon that can lead to loss of limb function or even amputation. The unique and unpredictable features of FRI make its diagnosis and treatment a significant challenge. It has substantial morbidity and financial implications for patients, their families and healthcare providers. In this article, we perform an in-depth and comprehensive review of FRI through recent and seminal literature to highlight evolving definitions, diagnostic and treatment approaches, focusing on common pathogens such as Staphylococcus aureus, polymicrobial infections and multi-drug-resistant organisms (MDRO). Furthermore, multiple resistance mechanisms and adaptations for microbial survival are discussed, as well as modern evidence-based medical and surgical advancements in treatment strategies in combating FRI.

Practical Guidance for Clinical Microbiology Laboratories: Microbiologic diagnosis of implant-associated infections

SUMMARYImplant-associated infections (IAIs) pose serious threats to patients and can be associated with significant morbidity and mortality. These infections may be difficult to diagnose due, in part, to biofilm formation on device surfaces, and because even when microbes are found, their clinical significance may be unclear. Despite recent advances in laboratory testing, IAIs remain a diagnostic challenge. From a therapeutic standpoint, many IAIs currently require device removal and prolonged courses of antimicrobial therapy to effect a cure. Therefore, making an accurate diagnosis, defining both the presence of infection and the involved microorganisms, is paramount. The sensitivity of standard microbial culture for IAI diagnosis varies depending on the type of IAI, the specimen analyzed, and the culture technique(s) used. Although IAI-specific culture-based diagnostics have been described, the challenge of culture-negative IAIs remains. Given this, molecular assays, including both nucleic acid amplification tests and next-generation sequencing-based assays, have been used. In this review, an overview of these challenging infections is presented, as well as an approach to their diagnosis from a microbiologic perspective.

Culture-negative periprosthetic joint infections: Do we have an issue?

Culture-negative periprosthetic joint infection (PJI) poses a significant challenge in clinical settings. The lack of information on causative organism(s) leads to uncertainties regarding the choice of antimicrobial treatment, which can potentially adversely influence the outcome. Recent advances in molecular-based diagnostic methods have the potential to address the difficulties associated with culture-negative PJIs. These technologies offer a solution to the existing clinical dilemma by providing identification of pathogens and guiding appropriate antimicrobial treatment. In this narrative review, we provide information regarding: 1) incidence and risk factors for culture-negative PJI; 2) the optimal antimicrobial therapy and duration of treatment for culture-negative PJI; 3) outcome comparison between culture-positive and culture-negative PJI; and 4) utilization of novel molecular diagnostic methods in culture-negative PJI, including pathogen identification, and the implementation of an antibiotic stewardship program.

Identification of prosthetic joint infections with 16S amplicon metagenomic sequencing - comparison with standard cultivation approach

Prosthetic joint infections (PJIs) are commonly diagnosed via culture-based methods, which may miss hard-to-grow pathogens. This study contrasts amplicon metagenomic sequencing (16S AS) with traditional culture techniques for enhanced clinical decision-making. We analyzed sonicate fluid from 27 patients undergoing revision arthroplasty using both methods, emphasizing the distinction between contaminants and true positives. Our findings show moderate agreement between the two methods, with a Cohen's kappa of 0.490, varying across bacterial genera (Cohen's kappa -0.059 to 1). The sensitivity of 16S AS compared to culture was 81% (95% CI, 68% to 94%). Sequencing revealed greater microbial diversity, including anaerobic genera like Anaerococcus and Citrobacter. Interestingly, several culture-negative PJI samples showed diverse bacteria via 16S AS. Despite rigorous controls and algorithms to eliminate contaminants, confirming bacteria presence with 16S AS remains a challenge. This highlights the need for improved PJI diagnostic methods, while also pointing out the limitations of next-generation sequencing (NGS) as a clinical diagnostic tool.

Application of Metagenomic Next-Generation Sequencing in Suspected Spinal Infectious Diseases

OBJECTIVE

This study aimed to explore the clinical efficacy of metagenomic next-generation sequencing (mNGS) in diagnosing and treating suspected spinal infectious diseases.

METHODS

Between October 2022 to December 2023, a retrospective analysis was performed on patient records within the Department of Spinal Surgery at Guilin People's Hospital. The analysis included comprehensive data on patients with presumed spinal infectious diseases, incorporating results from mNGS tests conducted externally, conventional pathogen detection results, laboratory examination results, and imaging findings. The study aimed to assess the applicability of mNGS in the context of suspected spinal infectious lesions.

RESULTS

Twenty-seven patients were included in the final analysis. Pathogenic microorganisms were identified in 23 cases. The included cases encompassed 1 case of tuberculous spondylitis, 1 case of fungal infection, 3 cases of Brucella spondylitis, 3 cases of viral infection, 9 cases of bacterial infection, and 6 cases of mixed infections. Pathogenic microorganisms remained elusive in 4 cases. The application of the mNGS method demonstrated a significantly elevated positive detection rate compared to conventional methods (85.19% vs. 48.15%, P < 0.05). Moreover, the mNGS method detected a greater variety of pathogen species than traditional methods (Z = 10.69, P < 0.05). Additionally, the mNGS method exhibited a shorter detection time.

CONCLUSIONS

mNGS demonstrated significantly higher detection rates for bacterial, fungal, viral, and mixed infections in cases of suspected spinal infectious diseases. The clinical implementation of mNGS could further enhance the efficiency of diagnosing and treating suspected spinal infectious diseases.

Accurate etiological diagnosis of Mycoplasma hominis mediastinitis in immunocompetent patients using metagenomic next-generation sequencing: a case series and literature review

Background

As a culture-independent method, metagenomic next-generation sequencing (mNGS) is widely used in microbiological diagnosis with advantages in identifying potential pathogens, guiding antibiotic therapy, and improving clinical prognosis, especially in culture-negative cases. Mycoplasma hominis (M. hominis) mediastinitis is a rare and severe disease for which etiological diagnosis is important but challenging. The application of mNGS in the etiological diagnosis of mediastinitis has seldom been studied.

Methods

By searching the electronic medical history retrieval system with "Mycoplasma hominis" and "mediastinitis", seven patients diagnosed with M. hominis mediastinitis were reviewed in Zhongshan Hospital, Fudan University, Shanghai from 9 December 2020 to 14 February 2023. Microbiological cultures and mNGS were conducted for blood, abscess, and/or mediastinal fluid. Adjustment of the antibiotic therapy due to mNGS was assessed. A literature review was conducted in the PubMed database beginning in 1970 for M. hominis infection and mediastinitis.

Results

For the seven patients, cultures of blood, abscess, and mediastinal fluid were negative whereas mNGS identified M. hominis in serum, abscess, and/or mediastinal fluid and was used to guide specific antibiotic therapy. The stringent mapped reads number of genera (SMRNG), stringent mapped reads number of species (SMRN), and coverage rate of M. hominis detection by mNGS were significantly higher in body fluid (abscess or mediastinal fluid) than in serum. All seven patients had underlying heart diseases and underwent previous cardiac surgery. The most common symptoms were fever and sternal pain. After detection of M. hominis, antibiotics were adjusted to quinolones or doxycycline except for one patient, whose diagnosis was clarified after death. Two patients died. Literature review since 1970 identified 30 cases of extra-genital infection caused by M. hominis. Including our seven new cases, 2 (5.4%) were neonates and 35 (94.6%) were adults. Thirty (81.1%) cases were postoperative infection and 15 (40.5%) had implanted devices. Five patients (13.5%) died.

Conclusions

mNGS might be a promising technology in the detection of fastidious pathogens such as M. hominis. Accurate etiological diagnosis by mNGS could guide antibiotic therapy and facilitate clinical management.

Exploring viral aetiology in upper respiratory tract infections: insights from metagenomic next-generation sequencing in Swiss outpatients before and during the SARS-CoV-2 pandemic

AIMS OF THE STUDY

Upper respiratory tract infections are among the most common reasons for primary care consultations. They are diagnosed predominantly based on clinical assessment. Here, we investigated the benefit of viral metagenomic next-generation sequencing (mNGS) in an outpatient setting.

METHODS

This prospective cross-sectional study included immunocompetent patients with acute upper respiratory tract infections. General practitioners collected pharyngeal swabs and demographic and clinical data. Specimens were analysed using viral mNGS and conventional tests.

RESULTS

Two hundred seventy-seven patients were recruited by 21 general practitioners between 10/2019 and 12/2020, of which 91% had a suspected viral aetiology. For 138 patients (49.8%), mNGS identified one or more respiratory viruses. The mNGS showed a high overall agreement with conventional routine diagnostic tests. Rhinoviruses were the most frequently detected respiratory viruses (20.2% of patients). Viral mNGS reflected the influenza wave in early 2020 and the SARS-CoV-2 pandemic outbreak in Switzerland in March 2020. Notably, rhinoviruses continued to circulate despite non-pharmaceutical hygiene measures.

CONCLUSIONS

Viral mNGS allowed the initial diagnosis to be retrospectively re-evaluated. Assuming reduced turnaround times, mNGS has the potential to directly guide the treatment of upper respiratory tract infections. On an epidemiological level, our study highlights the utility of mNGS in respiratory infection surveillance, allowing early detection of epidemics and providing information crucial for prevention.

Recurrent Periprosthetic Joint Infections: Diagnosis, Management, and Outcomes

Periprosthetic joint infection (PJI) remains one of the most common complications after total joint arthroplasty. It is challenging to manage, associated with significant morbidity and mortality, and is a financial burden on the health care system. Failure of 2-stage management for chronic PJI is not uncommon. Repeat infections are oftentimes polymicrobial, multiple drug-resistant microorganisms, or new organisms. Optimizing the success of index 2-stage revision is the greatest prevention against failure of any subsequent management options and requires a robust team-based approach.

Innovations in the Isolation and Treatment of Biofilms in Periprosthetic Joint Infection: A Comprehensive Review of Current and Emerging Therapies in Bone and Joint Infection Management

Periprosthetic joint infections (PJIs) are a devastating complication of joint arthroplasty surgeries that are often complicated by biofilm formation. The development of biofilms makes PJI treatment challenging as they create a barrier against antibiotics and host immune responses. This review article provides an overview of the current understanding of biofilm formation, factors that contribute to their production, and the most common organisms involved in this process. This article focuses on the identification of biofilms, as well as current methodologies and emerging therapies in the management of biofilms in PJI.

Combination of metagenomic next-generation sequencing and conventional tests unraveled pathogen profiles in infected patients undergoing allogeneic hematopoietic stem cell transplantation in Jilin Province of China

Background

Infection is the main cause of death for patients after allogeneic hematopoietic stem cell transplantation (HSCT). However, pathogen profiles still have not been reported in detail due to their heterogeneity caused by geographic region.

Objective

To evaluate the performance of metagenomic next-generation sequencing (mNGS) and summarize regional pathogen profiles of infected patients after HSCT.

Methods

From February 2021 to August 2022, 64 patients, admitted to the Department of Hematology of The First Hospital of Jilin University for HSCT and diagnosed as suspected infections, were retrospectively enrolled.

Results

A total of 38 patients were diagnosed as having infections, including bloodstream (n =17), pulmonary (n =16), central nervous system (CNS) (n =4), and chest (n =1) infections. Human betaherpesvirus 5 (CMV) was the most common pathogen in both bloodstream (n =10) and pulmonary (n =8) infections, while CNS (n =2) and chest (n =1) infections were mainly caused by Human gammaherpesvirus 4 (EBV). For bloodstream infection, Mycobacterium tuberculosis complex (n =3), Staphylococcus epidermidis (n =1), and Candida tropicalis (n =1) were also diagnosed as causative pathogens. Furthermore, mNGS combined with conventional tests can identify more causative pathogens with high sensitivity of 82.9% (95% CI 70.4-95.3%), and the total coincidence rate can reach up to 76.7% (95% CI 64.1-89.4%).

Conclusions

Our findings emphasized the importance of mNGS in diagnosing, managing, and ruling out infections, and an era of more rapid, independent, and impartial diagnosis of infections after HSCT can be expected.

Optimal selection of specimens for metagenomic next-generation sequencing in diagnosing periprosthetic joint infections

Objective

This study aimed to assess the diagnostic value of metagenomic next-generation sequencing (mNGS) across synovial fluid, prosthetic sonicate fluid, and periprosthetic tissues among patients with periprosthetic joint infection (PJI), intending to optimize specimen selection for mNGS in these patients.

Methods

This prospective study involved 61 patients undergoing revision arthroplasty between September 2021 and September 2022 at the First Affiliated Hospital of Zhengzhou University. Among them, 43 cases were diagnosed as PJI, and 18 as aseptic loosening (AL) based on the American Musculoskeletal Infection Society (MSIS) criteria. Preoperative or intraoperative synovial fluid, periprosthetic tissues, and prosthetic sonicate fluid were collected, each divided into two portions for mNGS and culture. Comparative analyses were conducted between the microbiological results and diagnostic efficacy derived from mNGS and culture tests. Furthermore, the variability in mNGS diagnostic efficacy for PJI across different specimen types was assessed.

Results

The sensitivity and specificity of mNGS diagnosis was 93% and 94.4% for all types of PJI specimens; the sensitivity and specificity of culture diagnosis was 72.1% and 100%, respectively. The diagnostic sensitivity of mNGS was significantly higher than that of culture (X2 = 6.541, P=0.011), with no statistically significant difference in specificity (X2 = 1.029, P=0.310). The sensitivity of the synovial fluid was 83.7% and the specificity was 94.4%; the sensitivity of the prosthetic sonicate fluid was 90.7% and the specificity was 94.4%; and the sensitivity of the periprosthetic tissue was 81.4% and the specificity was 100%. Notably, the mNGS of prosthetic sonicate fluid displayed a superior pathogen detection rate compared to other specimen types.

Conclusion

mNGS can function as a precise diagnostic tool for identifying pathogens in PJI patients using three types of specimens. Due to its superior ability in pathogen identification, prosthetic sonicate fluid can replace synovial fluid and periprosthetic tissue as the optimal sample choice for mNGS.

Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health

To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.

Surveillance for Emerging and Reemerging Pathogens Using Pathogen Agnostic Metagenomic Sequencing in the United States: A Critical Role for Federal Government Agencies

The surveillance and identification of emerging, reemerging, and unknown infectious disease pathogens is essential to national public health preparedness and relies on fluidity, coordination, and interconnectivity between public and private pathogen surveillance systems and networks. Developing a national sentinel surveillance network with existing resources and infrastructure could increase efficiency, accelerate the identification of emerging public health threats, and support coordinated intervention strategies that reduce morbidity and mortality. However, implementing and sustaining programs to detect emerging and reemerging pathogens in humans using advanced molecular methods, such as metagenomic sequencing, requires making large investments in testing equipment and developing networks of clinicians, laboratory scientists, and bioinformaticians. In this study, we sought to gain an understanding of how federal government agencies currently support such pathogen agnostic testing of human specimens in the United States. We conducted a landscape analysis of federal agency websites for publicly accessible information on the availability and type of pathogen agnostic testing and details on flow of clinical specimens and data. The website analysis was supplemented by an expert review of results with representatives from the federal agencies. Operating divisions within the US Department of Health and Human Services and the US Department of Veterans Affairs have developed and sustained extensive clinical and research networks to obtain patient specimens and perform metagenomic sequencing. Metagenomic facilities supported by US agencies were not equally geographically distributed across the United States. Although many entities have work dedicated to metagenomics and/or support emerging infectious disease surveillance specimen collection, there was minimal formal collaboration across agencies.

Performance of Metagenomic Next-Generation Sequencing of Cell-Free DNA From Vitreous and Aqueous Humor for Diagnoses of Intraocular Infections

BACKGROUND

Delayed diagnosis and improper therapy for intraocular infections usually result in poor prognosis. Due to limitations of conventional culture and polymerase chain reaction methods, most causative pathogens cannot be identified from vitreous humor (VH) or aqueous humor (AH) samples with limited volume.

METHODS

Patients with suspected intraocular infections were enrolled from January 2019 to August 2021. Metagenomic next-generation sequencing (mNGS) was used to detected causative pathogens.

RESULTS

This multicenter prospective study enrolled 488 patients, from whom VH (152) and AH (336) samples were respectively collected and analyzed using mNGS of cell-free DNA (cfDNA). Taking final comprehensive clinical diagnosis as the gold standard, there were 39 patients with indefinite final diagnoses, whereas 288 and 161 patients were diagnosed as definite infectious and noninfectious diseases, respectively. Based on clinical adjudication, the sensitivity (92.2%) and total coincidence rate (81.3%) of mNGS using VH samples were slightly higher than those of mNGS using AH samples (85.4% and 75.4%, respectively).

CONCLUSIONS

Using mNGS of cfDNA, an era with clinical experience for more rapid, independent, and impartial diagnosis of bacterial and other intraocular infections can be expected.

Will previous antimicrobial therapy reduce the positivity rate of metagenomic next-generation sequencing in periprosthetic joint infections? A clinical study

Background

Metagenomic next-generation sequencing (mNGS) is a culture-independent massively parallel DNA sequencing technology and it has been widely used for rapid etiological diagnosis with significantly high positivity rate. Currently, clinical studies on evaluating the influence of previous antimicrobial therapy on positivity rate of mNGS in PJIs are rarely reported. The present study aimed to investigate whether the positivity rate of mNGS is susceptible to previous antimicrobial therapy.

Methods

We performed a prospective trial among patients who undergone hip or knee surgery due to periprosthetic joint infection (PJI) to compare the positivity rate of culture and mNGS between cases with and without previous antimicrobial therapy, and the positivity rates between cases with different antimicrobial-free intervals were also analysed.

Results

Among 131 included PJIs, 91 (69.5%) had positive cultures and 115 (87.8%) had positive mNGS results. There was no significant difference in the positivity rate of deep-tissue culture and synovial fluid mNGS between cases with and without previous antimicrobial therapy. The positivity rate of synovial fluid culture was higher in cases with previous antimicrobial therapy. The positivity rates of mNGS in synovial fluid decreased as the antimicrobial-free interval ranged from 4 to 14 days to 0 to 3 days.

Conclusion

mNGS is more advantageous than culture with a higher pathogen detection rate. However, our data suggested that antimicrobial agents may need to be discontinued more than 3 days before sampling to further increase the positivity rate of mNGS for PJIs.

Diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture for spinal infection: a retrospective comparative study

PURPOSE

The study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) as a diagnostic test for biopsy samples from patients with suspected spinal infection (SI) and compared the diagnostic performance of mNGS with that of microbial culture.

METHODS

All patients diagnosed with clinical suspicion of SI were enrolled, and data were collected through a retrospective chart review of patient records. Biopsy specimens obtained from each patient were tested via mNGS and microbial culture. Samples were enriched for microbial DNA using the universal DNA extraction kit, whole-genome amplified, and sequenced using MGISEQ-200 instrument. After Low-quality reads removed, the remaining sequences for microbial content were analyzed and aligned using SNAP and kraken2 tools.

RESULTS

A total of 39 patients (19 men and 20 women) were deemed suitable for enrollment. The detection rate for pathogens of mNGS was 71.8% (28/39), which was significantly higher than that of microbial culture (23.1%, p = 0.016). Mycobacterium tuberculosis complex was the most frequently isolated. Using pathologic test as the standard reference for SI, thirty-one cases were classified as infected, and eight cases were considered aseptic. The sensitivity and specificity values for detecting pathogens with mNGS were 87.1% and 87.5%, while these rates were 25.8% and 87.5% with conventional culture. mNGS was able to detect 88.9% (8/9) of pathogens identified by conventional culture, with a genus-level sensitivity of 100% (8/8) and a species-level sensitivity of 87.5% (7/8).

CONCLUSION

The present work suggests that mNGS might be superior to microbial culture for detecting SI pathogens.

Evaluation of the contribution of shotgun metagenomics in the microbiological diagnosis of liver abscesses

BACKGROUND

Shotgun metagenomics (SMg) sequencing has gained a considerable interest, as it enables the detection of any microorganisms through a single analysis. Due to the limitations of standard microbiological approaches, the microbial documentation of liver abscesses (LA), which is crucial for their medical management, can be difficult. Here we aimed to compare the performance of SMg with standard approaches for the microbiological documentation of LA.

METHODS

In this retrospective study conducted at two centers, we compared the results of standard microbiology with metagenomics analysis of consecutive LA samples. For samples tested positive for Klebsiella pneumoniae, we compared the analysis of virulence and resistance genes using metagenomics data to whole-genome sequencing of corresponding isolates obtained in culture.

RESULTS

Out of the 62 samples included, standard approaches and SMg yielded documentation in 80.6% and 96.8%, respectively. In 37.1% (23/62) of cases, both methods showed identical results, whereas in 43.5% (27/62) of cases, the samples were positive by both methods, but SMg found additional species in 88.9% (24/27), mostly anaerobes. When the standard approaches were negative, the SMg was able to detect microorganisms in 80.0% of cases (8/10). Overall, SMg identified significantly more microorganisms than culture (414 vs.105; p<0.05). K. pneumoniae genome analysis was able to detect resistance and virulence genes with a level of sensitivity depending on the depth of sequencing.

DISCUSSION

Overall, we showed that SMg had better performance in detecting and identifying microorganisms from LA samples and could help characterizing strain's resistome and virulome. Although still costly and requiring specific skills and expensive equipment, MGs methods are set to expand in the future.

Is Metagenomics the Future Routine Diagnosis Tool for Brain Abscesses? About a Case

Shotgun metagenomics (SMg) usefulness for brain abscess diagnosis is not known. We describe a case of brain abscess diagnosed with SMg and provide a review of the literature. A 70-year-old woman was diagnosed with multiple brain abscesses. Standard culture techniques and 16S rRNA gene sequencing of abscess samples remained negative. SMg finally revealed the presence of sequences from Streptococcus anginosus and Fusobacterium nucleatum, leading to antimicrobial treatment adaptation and corticosteroids initiation. The patient finally recovered. A literature review retrieved fifteen other cases of brain abscesses diagnosed with SMg. SMg results led to changes in patient management in most cases. The existing literature about the performances of SMg, its advantages, future evolutions, and limitations is then discussed. SMg place in routine should be evaluated and defined through prospective studies.

A case report on Mycobacterium houstonense infection after total hip arthroplasty

BACKGROUND

Mycobacterium houstonense is a category of rapidly growing mycobacteria that is gram-positive, acid-fast, polycrystalline, and non-spore-forming. There have been few reports of human infection caused by Mycobacterium houstonense worldwide.

CASE PRESENTATION

We present a case of chronic periprosthetic joint infection caused by Mycobacterium houstonense in an elderly female patient. The patient developed signs of infection after undergoing total hip arthroplasty. Despite receiving antibiotic treatment and revision surgery, the signs of infection recurred repeatedly. Multiple bacterial cultures during the treatment period were negative. Later, we identified the pathogenic bacteria Mycobacterium houstonense through mNGS testing, isolated the bacteria from the ultrasonically centrifuged fluid of the prosthesis and obtained drug sensitivity results. Finally, we performed a revision surgery and treated the patient with moxifloxacin and clindamycin. After treatment, the patient did not show signs of infection recurrence during 24 months of follow-up.

CONCLUSION

Through a relevant literature search, we believe that Mycobacterium houstonense may show higher sensitivity to amikacin and quinolone antibiotics. Additionally, clarifying occult infection sources through methods such as gene testing will improve the diagnosis and treatment of periprosthetic joint infection.

Role of α-Defensin and the Microbiome in Prosthetic Joint Infection: A Prospective Cohort Study in Korea

The utility of α-defensin (AD), leukocyte esterase (LE) levels, and metagenomics sequencing as diagnostic tools for prosthetic joint infection (PJI) has been suggested, but there are few studies among the Asian population. This study aimed to evaluate the diagnostic performance of various biomarkers for PJI and the role of the microbiome in the synovial fluid of patients with prostheses. Patients with suspected knee PJI were enrolled, and their blood and synovial fluid were collected. The cases were classified into the PJI and non-PJI groups. Significant differences between the two groups were observed in the levels of AD (4698 µg/L vs. 296 µg/L, p < 0.001) and positivity for LE (62.5% vs. 21.1%, p = 0.01). AD had 94.4% sensitivity and 89.5% specificity for diagnosing PJI, whereas LE had 37.5% sensitivity and 100% specificity. Microbiome taxonomic profiling showed high sensitivity. The number of operational taxonomic units and the richness of the microbiome in the synovial fluid were higher in the non-PJI than in the PJI group. AD has shown encouraging results in the Asian population as a diagnostic biomarker for PJI, and LE can be used as a diagnostic adjunct. The bacterial richness of the synovial fluid is likely associated with infections.

Mass spectrometry-based proteomic profiling of sonicate fluid differentiates Staphylococcus aureus periprosthetic joint infection from non-infectious failure: A pilot study

PURPOSE

This pilot study aimed to use proteomic profiling of sonicate fluid samples to compare host response during Staphylococcus aureus-associated periprosthetic joint infection (PJI) and non-infected arthroplasty failure (NIAF) and identify potential novel biomarkers differentiating the two.

EXPERIMENTAL DESIGN

In this pilot study, eight sonicate fluid samples (four from NIAF and four from S. aureus PJI) were studied. Samples were reduced, alkylated, and trypsinized overnight, followed by analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a high-resolution Orbitrap Eclipse mass spectrometer. MaxQuant software suite was used for protein identification, filtering, and label-free quantitation.

RESULTS

Principal component analysis of the identified proteins clearly separated S. aureus PJI and NIAF samples. Overall, 810 proteins were identified based on their detection in at least three out of four samples from each group; 35 statistically significant differentially abundant proteins (DAPs) were found (two-sample t-test p-values ≤0.05 and log2 fold-change values ≥2 or ≤-2). Gene ontology pathway analysis found that microbial defense responses, specifically those related to neutrophil activation, to be increased in S. aureus PJI compared to NIAF samples.

CONCLUSION AND CLINICAL RELEVANCE

Proteomic profiling of sonicate fluid using LC-MS/MS differentiated S. aureus PJI and NIAF in this pilot study. Further work is needed using a larger sample size and including non-S. aureus PJI and a diversty of NIAF-types.

Comparison of microbial detection rates in microbial culture methods versus next-generation sequencing in patients with prosthetic joint infection: a systematic review and meta-analysis

BACKGROUND

Accurate diagnosis of prosthetic joint infection (PJI) enables early and effective treatment. However, there is currently no gold standard test for microbial detection of PJI and traditional synovial fluid culture is relatively insensitive. Recently, it has been reported that sonicating fluid culture and next-generation sequencing (NGS) improve microbial detection rates. Hence, we performed a systematic review and meta-analysis to compare microbial detection rates in microbial culture methods with and without sonication versus NGS.

METHODS

We systematically searched EMBASE, PubMed, Scopus, CINAHL, and Ichushi databases and other sources (previous reviews) until August 2022. We evaluated the detection rates of pathogens in NGS and microbial cultures using samples of synovial or sonicated fluid.

RESULTS

Of the 170 citations identified for screening, nine studies were included. Pooled analysis indicated that NGS had the highest detection rate among the microbial detection methods (NGS vs. sonicated, odds ratios [OR] 5.09, 95% confidential interval [CI] 1.67-15.50; NGS vs. synovial, OR 4.52, 95% CI 2.86-7.16). Sonicated fluid culture showed a higher detection rate than synovial fluid culture (OR 2.11, 95% CI 1.23-3.62).

CONCLUSION

NGS might be useful as a screening tool for culture-negative patients. In clinical settings, sonicated fluid culture is a practical method for diagnosing PJI.

Characterization of periprosthetic environment microbiome in patients after total joint arthroplasty and its potential correlation with inflammation

AIMS

Periprosthetic joint infection (PJI) is one of the most serious complications after total joint arthroplasty (TJA) but the characterization of the periprosthetic environment microbiome after TJA remains unknown. Here, we performed a prospective study based on metagenomic next-generation sequencing to explore the periprosthetic microbiota in patients with suspected PJI.

METHODS

We recruited 28 patients with culture-positive PJI, 14 patients with culture-negative PJI, and 35 patients without PJI, which was followed by joint aspiration, untargeted metagenomic next-generation sequencing (mNGS), and bioinformatics analysis. Our results showed that the periprosthetic environment microbiome was significantly different between the PJI group and the non-PJI group. Then, we built a "typing system" for the periprosthetic microbiota based on the RandomForest Model. After that, the 'typing system' was verified externally.

RESULTS

We found the periprosthetic microbiota can be classified into four types generally: "Staphylococcus type," "Pseudomonas type," "Escherichia type," and "Cutibacterium type." Importantly, these four types of microbiotas had different clinical signatures, and the patients with the former two microbiota types showed obvious inflammatory responses compared to the latter ones. Based on the 2014 Musculoskeletal Infection Society (MSIS) criteria, clinical PJI was more likely to be confirmed when the former two types were encountered. In addition, the Staphylococcus spp. with compositional changes were correlated with C-reactive protein levels, the erythrocyte sedimentation rate, and the synovial fluid white blood cell count and granulocyte percentage.

CONCLUSIONS

Our study shed light on the characterization of the periprosthetic environment microbiome in patients after TJA. Based on the RandomForest model, we established a basic "typing system" for the microbiota in the periprosthetic environment. This work can provide a reference for future studies about the characterization of periprosthetic microbiota in periprosthetic joint infection patients.

Rapid Diagnostics of Joint Infections Using IS-Pro

Diagnosis of bone and joint infections (BJI) relies on microbiological culture which has a long turnaround time and is challenging for certain bacterial species. Rapid molecular methods may alleviate these obstacles. Here, we investigate the diagnostic performance of IS-pro, a broad-scope molecular technique that can detect and identify most bacteria to the species level. IS-pro additionally informs on the amount of human DNA present in a sample, as a measure of leukocyte levels. This test can be performed in 4 h with standard laboratory equipment. Residual material of 591 synovial fluid samples derived from native and prosthetic joints from patients suspected of joint infections that were sent for routine diagnostics was collected and subjected to the IS-pro test. Bacterial species identification as well as bacterial load and human DNA load outcomes of IS-pro were compared to those of culture. At sample level, percent positive agreement (PPA) between IS-pro and culture was 90.6% (95% CI 85.7- to 94%) and negative percent agreement (NPA) was 87.7% (95% CI 84.1 to 90.6%). At species level PPA was 80% (95% CI 74.3 to 84.7%). IS-pro yielded 83 extra bacterial detections over culture for which we found supporting evidence for true positivity in 40% of the extra detections. Missed detections by IS-pro were mostly related to common skin species in low abundance. Bacterial and human DNA signals measured by IS-pro were comparable to bacterial loads and leukocyte counts reported by routine diagnostics. We conclude that IS-pro showed an excellent performance for fast diagnostics of bacterial BJI.

Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis

Objectives

Periprosthetic joint infection (PJI) diagnosis remains challenging, and the identification of the causative microorganism is, by far, the most important aspect. Here, we use multiple PCR-based targeted next-generation sequencing (tNGS) to detect pathogens in PJI. To explore 1. the ability of targeted next-generation sequencing (tNGS) to detect pathogens in PJI; 2. the consistency of tNGS, metagenomic NGS (mNGS), and culture results; and 3. the ability of tNGS to detect drug resistance genes in PJI.

Methods

PJI was diagnosed according to the Musculoskeletal Infection Society (MSIS) criteria. The microorganisms were detected by culture, mNGS and tNGS to compare the diagnostic effectiveness of the three methods for PJI and to compare their consistency in detecting microorganisms. Drug resistance genes were detected using tNGS. The costs and turnaround times of mNGS and tNGS were compared.

Results

Forty-three patients with PJI, 21 patients without PJI and 10 negative control cases were included. The culture, tNGS, and mNGS sensitivities for PJI diagnosis were 74.41%, 88.37%, and 93.02%, respectively, with no significant differences. The specificities were 90.48%, 95.24%, and 95.24%, respectively, with no significant differences. tNGS detected drug resistance genes in 37.5% of culture-positive PJIs. tNGS was superior to mNGS for turnaround time (14.5 h vs. 28 h) and cost ($150 vs. $260).

Conclusions

tNGS can effectively identify PJI pathogens and may provide drug resistance information, while tNGS is superior to mNGS regarding cost and turnaround time. A multidisciplinary, multi-technology based algorithm to diagnose PJI is appropriate.

Highlights

298 microorganisms and 86 drug resistance genes were included in the tNGS panel.Diagnostic efficacy of tNGS is not inferior to that of commonly used indicators.tNGS is superior to mNGS in cost and turnaround time.

Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent

Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria.

Direct detection and identification of periprosthetic joint infection pathogens by metagenomic next-generation sequencing

This study assessed the application of metagenomic next-generation sequencing in pathogen detection of periprosthetic joint infections. A total of 95 cases who previously had undergone hip and knee replacement undergoing revision from January 2018 to January 2021 were included in this study. Specimens of synovial fluid and deep-tissue were collected for culture and metagenomic next-generation sequencing, and patients were retrospectively categorized as infected or aseptic using the Musculoskeletal Infection Society criteria after revision surgery. The sensitivity, specificity, positive and negative predictive values were compared. A total of 36 cases had positive culture results and 59 cases had positive metagenomic next-generation sequencing results. Culture was positive in 34 infected cases (58.6%) and 2 aseptic cases (5.4%). Metagenomic next-generation sequencing was positive in 55 infected cases (94.8%) and 4 aseptic cases (10.8%). Five cases diagnosed with infection had other potential pathogens detected by metagenomic next-generation sequencing. Among the 24 culture-negative periprosthetic joint infections, metagenomic next-generation sequencing was able to identify potential pathogens in 21 cases (87.5%). From sampling to reporting, the average time needed for culture was 5.2 (95% CI 3.1-7.3) days, while that for metagenomic next-generation sequencing was 1.3 (95% CI 0.9-1.7) days. Metagenomic next-generation sequencing is more advantageous in pathogen detection of periprosthetic joint infection after total joint replacement, especially in patients with multiple infections or negative culture results.

Metagenomic Next-Generation Sequencing for Periprosthetic Joint Infections

Periprosthetic joint infection (PJI) after arthroplasty is a major complication, which requires significant resources, resulting in high costs for the medical system. In recent years, significant progress has been made in the diagnosis and treatment of periprosthetic infections, the identification of the pathogen being the central element in the establishment of targeted antibiotic therapy. Next-generation sequencing (NGS) or metagenomic NGS (mNGS) represents a promising, fast alternative, with increased specificity and sensitivity compared to identification methods using conventional culture media, thus enabling an increased rate of identification of pathogenic microorganisms and antibiotic resistance genes (ARG). The purpose of this article was to highlight new molecular diagnostic methods for periprosthetic joint infections and their involvement in treatment efficiency. NGS technologies are cutting-edge techniques that may challenge the PJI diagnostic model.

Role of Resident Microbial Communities in Biofilm-Related Implant Infections: Recent Insights and Implications

The use of medical implants continues to grow as the population ages. Biofilm-related implant infection is the leading cause of medical implant failure and remains difficult to diagnose and treat. Recent technologies have enhanced our understanding of the composition and complex functions of microbiota occupying various body site niches. In this review, we leverage data from molecular sequencing technologies to explore how silent changes in microbial communities from various sites can influence the development of biofilm-related infections. Specifically, we address biofilm formation and recent insights of the organisms involved in biofilm-related implant infections; how composition of microbiomes from skin, nasopharyngeal, and nearby tissue can impact biofilm-formation, and infection; the role of the gut microbiome in implant-related biofilm formation; and therapeutic strategies to mitigate implant colonization.

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.