Next-Generation Sequencing Supports Targeted Antibiotic Treatment for Culture Negative Orthopedic Infections

A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of urogenital samples

BACKGROUND

The application of molecular sequencing methods for microbiome profiling of biological samples are largely restricted to research use. However, they require significant resources such as time and cost and can suffer from amplification biases that may hamper interpretation of complex systems. These issues are also a barrier to adoption as standard clinical tools in, for example, diagnosis of urogenital infections. We report a new method that utilises third generation long-read nanopore sequencing to produce fast, accurate and fully quantitated metagenomic microbiome profiles. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.

RESULTS

We show that our method is capable of accurately and reproducibly detecting both levels and composition of a synthetic mixture of ten species comprising known amounts of hard to lyse gram-positive bacteria, gram-negative bacteria and yeast. When applied to urogenital samples, we confirm previous observations that the female asymptomatic vaginal and urinary microbiomes are predominated by Gardnerella spp. or one of several Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii) that conform to previously defined community state types. We show the tight relationship between vaginal and urinary populations of the same individual at both species and strain level, provide evidence for the previously observed dynamic nature of these microbiomes over a menstrual cycle and compare biomass and complexity of male and female urobiomes.

CONCLUSIONS

We set out to develop an unbiased, amplification and culture-free, fully quantitative metagenomic microbiome profiling tool. Our initial observations suggest our method represents a viable alternative to existing molecular research tools employed in the analysis of complex microbiomes.

The Utility of Synovial Fluid Interleukin-10 in Diagnosing Chronic Periprosthetic Joint Infection: A Prospective Cohort Study

Background

Diagnosing chronic periprosthetic joint infection (PJI) is challenging. Synovial fluid interleukin-10 (SF IL-10), an anti-inflammatory cytokine produced by leukocytes, plays a pivotal role in inflammation and infection regulation. However, limited research has explored the diagnostic potential of SF IL-10 in chronic PJI patients.

Objective

The study aimed to investigate the relationship between SF IL-10 and incidence of chronic PIJ, and to evaluate its diagnostic reliability.

Design and Methods

We analyzed data from 137 patients who underwent revision surgery for aseptic loosening or chronic PJI between 2017 and 2019 in our hospital. PJI diagnoses followed the 2013 International Consensus Meeting criteria. We measured serum ESR, serum CRP, SF PMN%, SF WBC and SF IL-10 levels, using logistic regression and receiver operating characteristic (ROC) curves to evaluate associations and diagnostic accuracy.

Results

Demographic data showed no significant differences. However, SF IL-10 levels differed significantly between groups. Logistic regression indicated a strong association between SF IL-10 and chronic PJI (OR = 1.11, 95% CI 1.05~1.17, p < 0.001). At a cut-off of 10.305 pg/mL, SF IL-10 had an area under the ROC curve (AUC) of 0.891, with 92.16% sensitivity and 77.91% specificity. Adding SF IL-10 to traditional models improved risk prediction for chronic PJI (net reclassification improvement [NRI]: 0.167 [0.023 ~ 0.312]; integrated discrimination improvement [IDI]: 0.160 [0.096 ~ 0.224]).

Conclusion

Higher SF IL-10 levels were significantly associated with chronic PJI in revision surgery patients, and incorporating SF IL-10 into the traditional risk model enhanced its predictive value for chronic PJI in these patients.

Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks

For the past 3-4 decades, the discovery of Sanger's method of pyrosequencing was the only method unparalleled till 2005 being employed as a method of whole genome sequencing (WGS). Following this, a revolutionary extensive parallel sequencing method, Next Generation Sequencing (NGS), was engineered. NGS supported a substantial number of bases under a high throughput metagenomic interrogation. Bioinformatics contributed notably to this advancement. It provided alignment tools, assembly algorithms, and protocols such as Illumina and hybridization capture which have metamorphosed clinical and translational diagnostics. With the extension in precision medicine and targeted therapy under NGS sectors such as epigenetics, transcriptomics, mutation detection, prognosis, therapeutics, and patient management have been gaining progress. Using NGS in real-time clinical settings has been proven to produce positive outcomes. The most recent instrumental benefaction of NGS has been decoding the SARS-CoV-2 virus epidemiology with the assistance of multiplex PCR. So far, it had been employed to inspect different levels of viral loads from low to mid. This has been executed by amplification and phylogenetic examination of the load to raise a connective link with the evolutionary history leading up to the period of origin. The depletion in the consumed time and extensive genome size under analysis was further coupled by a cutback in the cost of sequencing while executing NGS. With the aid of this review paper, we aspire to manifest how the above-mentioned elements have boosted, tissue, microbial, and molecular data interrogation. Along with this, promoting, and stimulating an extensive evaluation and expansion in the paradigm of morphological and phenotypic study, via bioinformatics can facilitate further advancement in personalized and concise clinical research.

Arthroscopic Debridement Enhanced by Intra-Articular Antibiotic-Loaded Calcium Sulphate Beads for Septic Arthritis of a Native Knee Following Iatrogenic Joint Injection: A Case Report

Septic arthritis (SA) represents an orthopedics urgency and mainly affects the knee joint. Due to its devastating effects on cartilage, immediate management is crucial. SA is characterized by an annual incidence of 2 to 10 cases per 100,000 individuals, with mortality rates fluctuating between 0.5% and 15%, with a substantially higher mortality rate observed in older people (15%) in contrast to younger cohorts (4%). The etiology of septic arthritis is multifactorial: a spectrum of Gram-positive and Gram-negative bacteria can contribute to the development of this condition, especially Staphylococcus aureus. The treatment involves urgent (arthroscopic or arthrotomic) debridement associated with adequate antibiotic therapy. Intra-articular antibiotic carriers can also be used to increase their local concentration and effectiveness. The case of a 67-year-old woman affected by knee SA from methicillin-susceptible S. aureus is presented. She was treated with an arthroscopic debridement enhanced by intra-articular antibiotic-loaded calcium sulphate beads, together with antibiotic therapy. At 2-year follow up, the infection had been eradicated and the patient fully recovered. This is the first description, to our knowledge, in the English literature, of the use of antibiotic-loaded calcium sulphate beads as an adjuvant in the surgical treatment of SA of a native knee joint.

Augmented pathogen detection in brain abscess using metagenomic next-generation sequencing: a retrospective cohort study

Brain abscess is a severe infection characterized by the accumulation of pus within the brain parenchyma. Accurate identification of the causative pathogens is crucial for effective treatment and improved patient outcomes. This 10-year retrospective, single-center study aimed to compare the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) in brain abscess. We reviewed 612 patients diagnosed with brain abscess and identified 174 cases with confirmed etiology. The median age was 52 years, with 69.5% males. Culture tests predominately identified gram-positive bacteria, particularly Streptococcus spp. Gram-negative bacteria, including Klebsiella spp., were also detected. However, mNGS revealed a more diverse pathogen spectrum, focusing on anaerobes (e.g., Fusobacterium spp., Parvimonas spp., Porphyromonas spp., Prevotella spp., and Tannerella spp.). mNGS exhibited significantly higher overall pathogen-positive rates in pus samples (85.0% vs 50.0%, P = 0.0181) and CSF samples (84.2% vs 7.9%, P < 0.0001) compared to culture. Furthermore, the detection rates for anaerobes displayed a notable disparity, with mNGS yielding significantly higher positive detections in both pus samples (50.0% vs 10%, P = 0.0058) and CSF samples (18.4% vs 0%, P = 0.0115) when compared to culture methods. The assistance of mNGS in pathogen detection, particularly anaerobes in brain abscess, was evident in our findings. mNGS demonstrated the ability to identify rare and fastidious pathogens, even in culture-negative cases. These results emphasize the clinical value of mNGS as a supplement for brain abscess, enabling more comprehensive and accurate pathogen identification.IMPORTANCEThe accurate identification of pathogens causing brain abscess is crucial for effective treatment and improved patient outcomes. In this 10-year retrospective study, the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) was compared. The study analyzed 612 patients with brain abscess and confirmed etiology in 174 cases. The results showed that culture tests predominantly identified gram-positive bacteria, while mNGS unveiled a broader diverse pathogen spectrum, particularly anaerobes. The mNGS method exhibited significantly higher overall rates of pathogen positivity both in pus and cerebrospinal fluid (CSF) samples, surpassing the culture methods. Notably, mNGS detected a significantly higher number of anaerobes in both pus and CSF samples compared to culture methods. These findings underscore the clinical value of mNGS as a supplement for brain abscess diagnosis, enabling more comprehensive and accurate pathogen identification, particularly for rare and fastidious pathogens that evade detection by conventional culture methods.

Field-Deployable Colorimetric Array for On-Site Diagnosis of Urinary Tract Infection and Identification of Causative Pathogens

Urinary tract infection (UTI) is a common and prevalent disease caused by a spectrum of pathogens. Lack of access to rapid, portable, and high-quality diagnostics in resource-limited settings aggravates the improper treatment of UTIs, which is also a major driver of antibiotic misuse worldwide. Here, we describe a custom-made portable colorimetric array (PoCA) for reading out polymerase chain reaction (PCR) amplicons, the rationale of which is to transfer the previously developed dsDNA-based photosensitization colorimetric assay (solution) onto paper discs for detection. By integrating mini-LED irradiation and paper discs, the PoCA can read out 96 PCR tests in one pot, thus allowing diagnosis and identification of 12 prevailing UTI pathogens in less than 2 h, coupled with a portable thermal cycler for PCR. After analyzing 200 clinical urine samples, the pathogen profiling accuracy of the PoCA was demonstrated to be higher than the standard urine culture (confirmed with metagenomic next-generation sequencing). The PoCA platform could be used in primary care for rapid UTI diagnosis and pathogen identification.

Clinical characteristics of and risk factors for poor outcomes in children with bacterial culture-negative septic arthritis of the hip

BACKGROUND

Septic arthritis of the hip is a serious infection in children. However, blood and joint fluid cultures are often negative, which makes the diagnosis and treatment challenging. We analyzed the clinical features of children with septic arthritis of the hip with negative bacterial cultures and identified the risk factors for poor outcomes.

METHODS

The clinical data of children with septic arthritis of the hip with negative bacterial cultures who were treated at our hospital from January 2010 to December 2020 were retrospectively analyzed. The clinical characteristics and outcomes of the culture-negative cohort were compared with those of children with positive bacterial cultures treated during the same period. Culture-negative patients were divided into a group with good outcomes and a group with poor outcomes. The differences between the two groups were compared.

RESULTS

Thirty-nine children with culture-negative septic arthritis of the hip were compared with 37 children with culture-positive sepsis. Compared with the culture-positive group, the culture-negative group had a significantly younger mean age and a significantly lower mean serum C-reactive protein concentration. Logistic regression analysis of culture-negative patients with good versus poor outcomes revealed that the independent risk factors for poor outcomes were an increased serum C-reactive protein concentration and prolonged time from onset to surgery. The cut-off values for predicting a poor outcome in the culture-negative group were a time from onset to surgery of greater than 21 days and a C-reactive protein concentration of greater than 23 mg/L.

CONCLUSIONS

Culture-negative septic arthritis of the hip has similar clinical features to culture-positive septic arthritis of the hip and can result in sequelae of varying severity. Therefore, active anti-infective and hip drainage therapy should be performed when children present with clinical symptoms, inflammatory marker concentrations, and imaging findings that are clinically diagnostic for septic arthritis of the hip.

LEVEL OF EVIDENCE

Level II, retrospective study.

Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections

Bacterial infections pose significant global health challenges, often underestimated due to difficulties in accurate diagnosis, especially when culture-based diagnostics fail. This study assesses the effectiveness of 16S-based metagenomic next generation sequencing (NGS) for identifying pathogens in culture-negative clinical samples across various medical settings. Overall, 48% of samples were collected from orthopedics, 15% from neurosurgery, and 12% in cardiac surgery, among others. The detection rate of monomicrobial infections was 68.6%, and 5.7% for polymicrobial infections. In addition, NGS detected bacteria in all samples from the lungs, head and neck, and eye specimens. Cutibacterium acnes (11%, 12/105) was the most frequent microorganism, followed by Staphylococcus epidermidis (10.4%, 11/105), and Staphylococcus aureus (9.5%, 10/105). In conclusion, 16S-targeted metagenomic sequencing enhances pathogen detection capabilities, particularly in instances where traditional cultures fail. By the combination of NGS and bacterial cultures, microbiologists might provide a more accurate diagnosis, guiding more effective treatments and potentially reducing healthcare costs associated with empirical treatments.

Evaluation of targeted sequencing for pathogen identification in bone and joint infections: a cohort study from China

PURPOSE

Bone and joint tuberculosis (BJTB) is a distinct variant of tuberculosis in which clinical diagnosis often leads to relative misdiagnosis and missed diagnoses. This study aimed to evaluate the diagnostic accuracy of the targeted nanopore sequencing (TNPseq) assay for BJTB patients in China.

METHOD

The study enrolled a cohort of 163 patients with suspected BJTB. Diagnostic testing was performed using the TNPseq assay on samples including punctured tissue, pus, and blood. The diagnostic accuracy of the TNPseq assay was then compared with that of the T-SPOT and Xpert MTB/RIF assays.

RESULT

TNPseq exhibited superior performance in terms of accuracy, demonstrating a sensitivity of 76.3% (95% CI: 71.0-81.6%) and a specificity of 98.8% (95% CI: 93.5-100%) in clinical diagnosis. When evaluated against a composite reference standard, TNPseq demonstrated a sensitivity of 74.4% (95% CI: 69.3-79.5%) and a specificity of 98.8% (95% CI: 93.7-100%). These results exceed the performance of both the T-SPOT and Xpert MTB/RIF tests. Notably, TNPseq demonstrated high specificity and accuracy in puncture specimens, with a sensitivity of 75.0% (95% CI: 70.2-79.8%) and a specificity of 98.3% (95% CI: 92.7-100%), as well as in pus samples, with a sensitivity of 83.3% (95% CI: 78.6-88.1%) and a specificity of 100% (95% CI: 100-100%). Additionally, TNPseq facilitated the detection of mixed infection scenarios, identifying 20 cases of bacterial-fungal co-infection, 17 cases of bacterial-viral co-infection, and two cases of simultaneous bacterial-fungal-viral co-infection.

CONCLUSION

TNPseq demonstrated great potential in the diagnosis of BJTB due to its high sensitivity and specificity. The ability of TNPseq to diagnose pathogens and detect drug resistance genes can also guide subsequent treatment. Expanding the application scenarios and scope of TNPseq will enable it to benefit more clinical treatments.

Metagenomic next-generation sequencing targeted and metagenomic next-generation sequencing for pulmonary infection in HIV-infected and non-HIV-infected individuals

Background

When individuals infected with human immunodeficiency virus (HIV) experience pulmonary infections, they often exhibit severe symptoms and face a grim prognosis. Consequently, early, rapid, and accurate pathogen diagnosis is vital for informing effective treatment strategies. This study aimed to use metagenomic next-generation sequencing (mNGS) and targeted mNGS (tNGS) to elucidate the characteristics of pulmonary infections in HIV and non-HIV individuals.

Methods

This study enrolled 90 patients with pulmonary infection at the Department of Infectious Diseases of The First Hospital of Jilin University from June 2022 to May 2023, and they were divided into HIV (n=46) and non-HIV (n=44) infection groups. Their bronchoalveolar lavage fluid (BALF) was collected for mNGS analysis to evaluate the differences in pulmonary infection pathogens, and tNGS detection was performed on BALF samples from 15 HIV-infected patients.

Results

A total of 37 pathogens were identified in this study, including 21 bacteria, 5 fungi, 5 viruses, 5 mycobacteria, and 1 mycoplasma. The sensitivity of mNGS was 78.9% (71/90), which is significantly higher than that of conventional methods (CTM) (39/90, P=1.5E-8). The combination of mNGS with CTM can greatly enhance the sensitivity of pathogen detection. The prevalence of Pneumocystis jirovecii (82.6% vs. 9.1%), cytomegalovirus (CMV) (58.7% vs. 0%), and Epstein-Barr virus (EBV) (17.4% vs. 2.3%) was significantly higher in the HIV infection group than in the non-HIV infection group (P<0.05). Although no statistically significant difference was observed, the detection rate of Mycobacteria was higher in HIV-infected patients (17.4%) than in the non-HIV group (6.8%). Furthermore, the tNGS results of BALF from 15 HIV-infected patients were not entirely consistent with the mNGS results., and the concordance rate of tNGS for the detection of main pathogens reached 86.7% (13/15).

Conclusion

Next-generation sequencing (NGS) can accurately detect pathogens in the BALF of patients with pulmonary infection. The sensitivity of tNGS is comparable to that of mNGS. Therefore, this technique should be promoted in the clinic for better patient outcomes.

Do Organism Profile and Resistance Patterns Change between First and Subsequent Two-Stage Revision for Periprosthetic Joint Infection?

Increasing antibiotic resistance has been reported as an issue in the treatment of periprosthetic joint infection (PJI). A repeat two-stage revision for recurrent PJI is at high risk of reinfection. However, it is unclear if the microorganism profile plays a role with potentially more resistant or polymicrobial infections. This is a retrospective, single-center analysis of two-stage revisions performed between 2011 and 2017. We identified 46 patients who underwent a repeat resection arthroplasty for recurrent PJI of the same joint after a previous two-stage revision of the same joint at the same department. All microbiological findings were analyzed focusing on microbiological spectrum and resistance testing as well as the potential impact on reinfection-free survival. The most common organism found at the time of recurrent PJI were coagulase-negative Staphylococci (39%) followed by Gram-negative organisms (28%). The risk of polymicrobial infections, difficult-to-treat resistant organisms, and Gram-negative infections increased significantly. Among staphylococcal infections, there was a high percentage of methicillin-resistant species and resistance to oral antibiotics. Patients with Gram-negative organisms had a reduced infection-free survivorship, while resistant organisms were not associated with decreased survival. Patients who undergo a repeat two-stage revision for recurrent PJI have more polymicrobial and resistant organisms, although the impact on survivorship is unclear.

Application of metagenomic next-generation sequencing for rapid molecular identification in spinal infection diagnosis

Objective

This study aimed to determine the sensitivity and specificity of metagenomic next-generation sequencing (mNGS) for detecting pathogens in spinal infections and to identify the differences in the diagnostic performance between mNGS and targeted next-generation sequencing (tNGS).

Methods

A total of 76 consecutive patients with suspected spinal infections who underwent mNGS, culture, and histopathological examinations were retrospectively studied. The final diagnosis of the patient was determined by combining the clinical treatment results, pathological examinations, imaging changes and laboratory indicators. The sensitivity and specificity of mNGS and culture were determined.

Results

The difference between the two detection rates was statistically significant (p < 0.001), with mNGS exhibiting a significantly higher detection rate (77.6% versus 18.4%). The average diagnosis time of mNGS was significantly shorter than that of bacterial culture (p < 0.001, 1.65 versus 3.07 days). The sensitivity and accuracy of mNGS were significantly higher than that of the culture group (p < 0.001, 82.3% versus 17.5%; 75% versus 27.6%), whereas the specificity of mNGS (42.9%) was lower than that of the culture group (p > 0.05, 42.9% versus 76.9%). The sensitivity, specificity, accuracy, and positive predictive value (PPV) of pus were higher than those of tissue samples for mNGS, whereas for culture, the sensitivity, specificity, accuracy, and PPV of tissue samples were higher than those of pus. tNGS demonstrated higher sensitivity and accuracy in diagnosing tuberculosis (TB) than mNGS (80% versus 50%; 87.5% versus 68.8%).

Conclusion

mNGS for spinal infection demonstrated better diagnostic value in developing an antibiotic regimen earlier, and it is recommended to prioritize pus samples for testing through mNGS. Moreover, tNGS outperformed other methods for diagnosing spinal TB and identifying antibiotic-resistance genes in drug-resistant TB.

Improved cure rate of periprosthetic joint infection through targeted antibiotic therapy based on integrated pathogen diagnosis strategy

Objectives

This study aimed to determine whether combined of pathogen detection strategies, including specimen acquisition, culture conditions, and molecular diagnostics, can improve treatment outcomes in patients with periprosthetic joint infections (PJI).

Methods

This retrospective study included suspected PJI cases from three sequential stages at our institution: Stage A (July 2012 to June 2015), Stage B (July 2015 to June 2018), and Stage C (July 2018 to June 2021). Cases were categorized into PJI and aseptic failure (AF) groups based on European Bone and Joint Infection Society (EBJIS) criteria. Utilization of pathogen diagnostic strategies, pathogen detection rates, targeted antibiotic prescription rates, and treatment outcomes were analyzed and compared across the three stages.

Results

A total of 165 PJI cases and 38 AF cases were included in this study. With the progressive implementation of the three optimization approaches across stages A, B and C, pathogen detection rates exhibited a gradual increase (χ2 = 8.282, P=0.016). Similarly, utilization of targeted antibiotic therapy increased stepwise from 57.1% in Stage A, to 82.3% in Stage B, and to 84% in Stage C (χ2 = 9.515, P=0.009). The 2-year infection control rate exceeded 90% in both stages B and C, surpassing stage A (71.4%) (χ2 = 8.317, P=0.011). Combined application of all three optimized protocols yielded the highest sensitivity of 91.21% for pathogen detection, while retaining higher specificity of 92.11%.

Conclusion

The utilization of combined pathogen diagnostic strategies in PJI can increase pathogen detection rates, improve targeted antibiotic prescription, reduce the occurrence of antibiotic complications, and achieve better treatment outcomes.

Triggered Release of Ampicillin from Metallic Implant Coatings for Combating Periprosthetic Infections

Periprosthetic infections caused by Staphylococcus aureus (S. aureus) pose unique challenges in orthopedic surgeries, in part due to the bacterium's capacity to invade surrounding bone tissues besides forming recalcitrant biofilms on implant surfaces. We previously developed prophylactic implant coatings for the on-demand release of vancomycin, triggered by the cleavage of an oligonucleotide (Oligo) linker by micrococcal nuclease (MN) secreted by the Gram-positive bacterium, to eradicate S. aureus surrounding the implant in vitro and in vivo. Building upon this coating platform, here we explore the feasibility of extending the on-demand release to ampicillin, a broad-spectrum aminopenicillin β-lactam antibiotic that is more effective than vancomycin in killing Gram-negative bacteria that may accompany S. aureus infections. The amino group of ampicillin was successfully conjugated to the carboxyl end of an MN-sensitive Oligo covalently integrated in a polymethacrylate hydrogel coating applied to titanium alloy pins. The resultant Oligo-Ampicillin hydrogel coating released the β-lactam in the presence of S. aureus and successfully cleared nearby S. aureus in vitro. When the Oligo-Ampicillin-coated pin was delivered to a rat femoral canal inoculated with 1000 cfu S. aureus, it prevented periprosthetic infection with timely on-demand drug release. The clearance of the bacteria from the pin surface as well as surrounding tissue persisted over 3 months, with no local or systemic toxicity observed with the coating. The negatively charged Oligo fragment attached to ampicillin upon cleavage from the coating did diminish the antibiotic's potency against S. aureus and Escherichia coli (E. coli) to varying degrees, likely due to electrostatic repulsion by the anionic surfaces of the bacteria. Although the on-demand release of the β-lactam led to adequate killing of S. aureus but not E. coli in the presence of a mixture of the bacteria, strong inhibition of the colonization of the remaining E. coli on hydrogel coating was observed. These findings will inspire considerations of alternative broad-spectrum antibiotics, optimized drug conjugation, and Oligo linker engineering for more effective protection against polymicrobial periprosthetic infections.

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.

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.

Next Generation Sequencing in orthopaedic infections - Where is the road headed?

Next-generation sequencing (NGS) has emerged as a game changer in the field of orthopaedic diagnostics, notably in the detection and management of infections associated with prosthetic joints and implants. This paper conducts an exhaustive examination of the pivotal role, outcomes, and prospective future uses of NGS in diagnosing orthopaedic infections. In comparison to conventional culture-based methods, NGS offers a marked improvement in sensitivity thereby facilitating prompt and comprehensive identification of pathogens. This encompasses the ability to detect polymicrobial infections, antibiotic-resistant strains, and previously imperceptible microorganisms. Furthermore, this article delves into the technology's contribution to advancing personalized medicine and promoting judicious antibiotic use. Nonetheless, the seamless integration of NGS into routine clinical practice is impeded by challenges such as substantial financial outlays, the requisite for specialized equipment and expertise, and the intricacy associated with data analysis. Notwithstanding these impediments, the potential for NGS to revolutionize orthopaedic diagnostics remains substantial, with ongoing advancements poised to address current limitations and broaden its scope within clinical applications.

Comparison of metagenomic next-generation sequencing and conventional culture for the diagnostic performance in febrile patients with suspected infections

BACKGROUND

Timely and accurate identification of pathogens is crucial for appropriate treatment and prognosis of infectious diseases. As an increasingly popular pathogen detection method, the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens in febrile patients with suspected infection requires further exploration.

METHODS

This study included 368 febrile patients with suspected infections who were admitted to the Infectious Disease Department of Qilu Hospital, Shandong University between January 5, 2021 and April 14, 2023. Both mNGS testing and conventional culture were performed in all patients. Clinical data of enrolled patients were collected, and the diagnostic performances of mNGS and culture were compared.

RESULTS

Of the 368 enrolled patients, 231 were finally diagnosed with infection and 137 were with diseases other than infection. The sensitivity (58.01% vs. 21.65%, p < 0.001) and negative predictive value (54.67% vs. 42.9%) of mNGS were superior to those of culture. In contrast, the culture exhibited higher specificity (99.27% vs. 85.40%, p < 0.001) and positive predictive value (98.84% vs. 87.01%) than mNGS. Among infected patients with positive mNGS results, 64 received adjusted antibiotic therapy including treatment transitions, antibiotic downgrading, and combination therapy. Among them, 9 had additional antifungal drugs and 21 patients had a treatment turning point based on the mNGS results and these patients recovered and discharged due to timely antibiotic adjustment. Both positive rates of puncture fluid mNGS and tissue mNGS were higher than those of culture in the patients who had prior antibiotic use, and this difference was statistically significant (p = 0.000).

CONCLUSION

mNGS is more sensitive and accurate than traditional culture, making it ideal for identifying pathogens and screening infectious diseases, especially for those with uncultivated or difficult-to-cultivate species. Early diagnosis allows for prompt treatment with targeted antibiotics, and mNGS is recommended when samples are limited.

Culture Negative Pasteurella multocida Confirmed Prosthetic Hip Infection using Next-generation Sequencing

Introduction

Prosthetic joint infections (PJIs) are a dreaded complication of joint arthroplasty. Zoonotic organisms such as Pasteurella multocida (PM) rarely cause PJIs. Still, these organisms can be challenging to treat due to a low suspicion index and inadequate growth on culture. Next-generation sequencing (NGS) can be used to identify organisms in culture-negative PJIs. This is the first reported case of a PM positive total hip arthroplasty PJI using NGS.

Case Report

We report the case of a 70-year-old male presenting with a periprosthetic hip infection. PM was identified in high relative abundance on NGS and grew in culture. Subsequent intraoperative samples were culture negative for Pasteurella, but NGS demonstrated continued presence of Pasteurella.

Conclusion

PM is a rare case of PJI, but a high index of suspicion must be maintained in the appropriate clinical context. NGS is a vital tool for the identification of culture-negative organisms like PM.

Potential value of a rapid syndromic multiplex PCR for the diagnosis of native and prosthetic joint infections: a real-world evidence study

Introduction: The BIOFIRE Joint Infection (JI) Panel is a diagnostic tool that uses multiplex-PCR testing to detect microorganisms in synovial fluid specimens from patients suspected of having septic arthritis (SA) on native joints or prosthetic joint infections (PJIs). Methods: A study was conducted across 34 clinical sites in 19 European and Middle Eastern countries from March 2021 to June 2022 to assess the effectiveness of the BIOFIRE JI Panel. Results: A total of 1527 samples were collected from patients suspected of SA or PJI, with an overall agreement of 88.4 % and 85 % respectively between the JI Panel and synovial fluid cultures (SFCs). The JI Panel detected more positive samples and microorganisms than SFC, with a notable difference on Staphylococcus aureus, Streptococcus species, Enterococcus faecalis, Kingella kingae, Neisseria gonorrhoeae, and anaerobic bacteria. The study found that the BIOFIRE JI Panel has a high utility in the real-world clinical setting for suspected SA and PJI, providing diagnostic results in approximately 1 h. The user experience was positive, implying a potential benefit of rapidity of results' turnover in optimising patient management strategies. Conclusion: The study suggests that the BIOFIRE JI Panel could potentially optimise patient management and antimicrobial therapy, thus highlighting its importance in the clinical setting.

Traditional Cultures versus Next Generation Sequencing for Suspected Orthopedic Infection: Experience Gained from a Reference Centre

(Background) The diagnosis and the antimicrobial treatment of orthopedic infection are challenging, especially in cases with culture-negative results. New molecular methods, such as next-generation sequencing (NGS), promise to overcome some limitations of the standard culture, such as the detection of difficult-to-grow bacteria. However, data are scarce regarding the impact of molecular techniques in real-life scenarios. (Methods) We included cases of suspected orthopedic infection treated with surgery from May 2021 to September 2023. We combined traditional cultures with NGS. For NGS, we performed a metagenomic analysis of ribosomal 16s, and we queried dedicated taxonomic libraries to identify the species. To avoid false positive results, we set a cut-off of 1000 counts of the percentage of frequency of reads. (Results) We included 49 patients in our study. Our results show the presence of bacteria in 36/49 (73%) and 29/49 (59%) cases studied with NGS and traditional cultures, respectively. The concordance rate was 61%. Among the 19/49 discordant cases, in 11/19 cases, cultures were negative and NGS positive; in 4/19, cultures were positive and NGS negative; and in the remaining 4/19, different species were detected by traditional cultures and NGS. (Conclusions) Difficult-to-grow microorganisms, such as slow-growing anaerobic bacteria, were better detected by NGS compared to traditional culture in our study. However, more data to distinguish between true pathogens and contaminants are needed. NGS can be an additional tool to be used for the diagnosis of orthopedic infections and the choice of appropriate antimicrobial therapy.

Comparative Effectiveness Randomized Clinical Trial Using Next-generation Microbial Sequencing to Direct Prophylactic Antibiotic Choice Before Urologic Stone Lithotripsy Using an Interprofessional Model

Background

Next-generation sequencing (NGS) methods for microbial profiling have increased sensitivity to detect urinary pathogens.

Objective

To determine whether NGS microbial profiling can be used to guide antibiotic prophylaxis and reduce infection compared with the standard of care.

Design setting and participants

A prospective randomized controlled clinical trial of patients undergoing urologic stone interventions at an academic health center from December 2019 to January 2022 was conducted. Urine was collected at the preoperative visit for standard culture and intervention NGS diagnostics. Evaluable patients were culture negative, met 2-wk follow-up, and did not cancel surgery. Of 240 individuals (control = 121, intervention = 119), 83 control and 74 intervention patients were evaluable.

Intervention

Microbial findings (paired quantitative polymerase chain reaction and NGS) were sent to an infectious disease pharmacist to recommend prophylactic antimicrobial regimen.

Outcome measurements and statistical analysis

The primary outcome was postoperative urinary infection within the follow-up period (Fisher's exact test). The primary outcome was analyzed by modified intent-to-treat (mITT) and per-protocol analyses. Secondary endpoints considered included positive culture concordance, antibiotic use, and adverse events. Additional post hoc analyses investigated factors contributing to infection (univariate logistic regression).

Results and limitations

The intervention significantly reduced postsurgical urinary infection risk by 7.1% (-0.73%, 15%) compared with the standard of care in the mITT analysis (1.4% vs 8.4%, p = 0.045) or by 8.5% (0.88%, 16%) compared with the per-protocol analysis (0% vs 8.5%, p = 0.032). NGS-guided treatment altered the distribution of antibiotics used (p = 0.025), and antibiotics poorly matched with NGS findings were associated with increased infection odds (odds ratio [OR] = 5.9, p = 0.046). Women were at greater odds to develop infection (OR = 10, p = 0.03) and possessed differentiated microbial profiles (p < 0.001).

Conclusions

Urinary microbial NGS-guided antibiotic prophylaxis before endoscopic urologic stone lithotripsy improves antibiotic selection to reduce healthcare-associated urinary infections; however, treatment efficacy may be limited by the ability to adhere to the recommended protocol.

Patient summary

We investigated whether microbial DNA sequencing could improve the selection of antibiotics before kidney stone surgery in patients not known to have any bacteria in the urine on standard culture. We found that using microbe DNA to guide antibiotic choices decreased postoperative infection rate and may encourage individualized use of available antibiotics.

Executive Summary: Periprosthetic Joint Infection-Current Clinical Challenges

Over the last several decades, periprosthetic joint infection (PJI) has been increasing in incidence and is occurring in more complex patients. While there have been advances in both surgical and medical treatment strategies, there remain important gaps in our understanding. Here, we share our current approaches to the diagnosis and management of PJI, focusing on frequent clinical challenges and collaborative interdisciplinary care. The more detailed review including diagnosis, surgical considerations, and a detailed antimicrobial discussion is presented in the online version.

Periprosthetic Joint Infection: Current Clinical Challenges

Over the last several decades, periprosthetic joint infection has been increasing in incidence and is occurring in more complex patients. While there have been advances in both surgical and medical treatment strategies, there remain important gaps in our understanding. Here, we share our current approaches to the diagnosis and management of periprosthetic joint infection, focusing on frequent clinical challenges and collaborative interdisciplinary care.

Enhancing Surgical Outcomes: A Critical Review of Antibiotic Prophylaxis in Orthopedic Surgery

The postoperative burden remains significant due to the possibility of prolonged hospitalization, escalated healthcare costs, and patient distress caused by postorthopedic surgical site infections (SSIs). Orthopedic surgery is likewise faced with a significant challenge posed by these conditions. A positive association has been observed between the presence of postorthopedic SSIs and heightened susceptibility to adverse health outcomes, along with elevated rates of morbidity and mortality. Systemic antibiotic prophylaxis (SAP) reduces the risk of acquiring an SSI. Closed fractures, open fractures, arthroplasty, and percutaneous fixation each possess distinct attributes that impact the data and antimicrobial therapy. When implementing SAP, it is crucial to strike a delicate equilibrium between maintaining effective antibiotic stewardship protocols and preventing the occurrence of SSIs. This practice effectively prevents both the incidence of negative consequences and the emergence of antibiotic resistance. The objective of this study was to examine the existing literature on the use of surgical antibiotic prophylaxis in orthopedic surgery and explore the potential consequences associated with the inappropriate administration of antibiotics.

Prosthetic joint infection caused by an atypical gram-negative bacilli: Odoribactersplanchnicus

Prosthetic joint infection (PJI) is a devastating complication after total hip arthroplasty. Its management consists of both: a radical debridement and implant retention or exchange (depending on the timing of symptoms) and directed antibiotic therapy. Thus, the isolation of atypical microorganisms implies a challenge, where anaerobes are responsible for only 4% of cases. However, Odoribacter splanchnicus has not been reported as a cause of PJI yet. We present an 82 year-old woman who was diagnosed with hip PJI. A radical debridement, prosthetic withdrawal, and spacer introduction was performed. Despite the directed antibiotic therapy against E. coli which was first isolated, the patient persisted clinically febrile. An anaerobic Gram-negative rod was isolated and finally, Odoribacter splanchnicus was identified and confirmed by 16S rRNA gene sequencing. Then, antibiotic bitherapy with ciprofloxacin and metronidazole was started until 6 weeks after surgery. The patient had no signs of infection recurrence after then. This case report also shows the importance of genomic identification of rare microorganisms causing PJI, and also allows setting a directed antibiotic therapy which is crucial for infection eradication.

Microbe-metabolite interaction networks, antibiotic resistance, and in vitro reconstitution of the penile prosthesis biofilm support a paradigm shift from infection to colonization

To understand differences between asymptomatic colonized and infected states of indwelling medical devices, we sought to determine penile prosthesis biofilm composition, microbe-metabolite interaction networks, and association with clinical factors. Patients scheduled for penile prosthesis removal/revision were included. Samples from swabbed devices and controls underwent next-generation sequencing, metabolomics, and culture-based assessments. Biofilm formation from device isolates was reconstituted in a continuous-flow stir tank bioreactor. 93% of 27 analyzed devices harbored demonstrable biofilm. Seven genera including Faecalibaculum and Jeotgalicoccus were more abundant in infected than uninfected device biofilms (p < 0.001). Smokers and those with diabetes mellitus or cardiac disease had lower total normalized microbial counts than those without the conditions (p < 0.001). We identified microbe-metabolite interaction networks enriched in devices explanted for infection and pain. Biofilm formation was recapitulated on medical device materials including silicone, PTFE, polyurethane, and titanium in vitro to facilitate further mechanistic studies. Nearly all penile prosthesis devices harbor biofilms. Staphylococcus and Escherichia, the most common causative organisms of prosthesis infection, had similar abundance irrespective of infection status. A series of other uncommon genera and metabolites were differentially abundant, suggesting a complex microbe-metabolite pattern-rather than a single organism-is responsible for the transition from asymptomatic to infected or painful states.

Rates of Septic Arthritis After ACL Reconstruction: A Single-Center Analysis Highlighting Quadriceps Tendon Grafts

BACKGROUND

Although the infection rates for bone-patellar tendon-bone autograft (BTB), hamstring tendon autograft (HT), and allograft have been reported previously, there are limited data available for a large cohort of individuals undergoing anterior cruciate ligament (ACL) reconstruction (ACLR) using quadriceps tendon autograft (QT).

PURPOSE

The aims of this study are (1) to compare rates of septic arthritis after primary and revision ACLR with QT, BTB, HT, and allograft and (2) to evaluate the association between an infection after ACLR and potential risk factors in a large single-system analysis.

STUDY DESIGN

Cohort study; Level of evidence, 3.

METHODS

All ACLR cases performed by 10 high-volume sports medicine fellowship-trained ACL surgeons between January 2000 and January 2022 were retrospectively analyzed. Minimum follow-up was 90 days after ACLR, and all multiligament reconstructions were excluded. Demographic information, surgical variables, infection characteristics, and rate of ACL graft retention were collected for all included patients. Independent samples t test, chi-square test, or Fisher exact tests with adjusted Benjamini-Hochberg post hoc procedure were used for group comparisons.

RESULTS

In total, 6652 patients were included in this study. The most commonly used graft was allograft (n = 2491; 37.4%), followed by HT (n = 1743; 26.2%), BTB (n = 1478; 22.2%), and QT (n = 940; 14.1%). The overall postoperative rate of septic arthritis was 0.34% (n = 23). Septic arthritis rates based on graft type were 0.74% (n = 13) for HT, 0.24% (n = 6) for allograft, 0.20% (n = 3) for BTB, and 0.10% (n = 1) for QT. While a statistically significant difference with regard to graft type (P = .01) was observed, no significant relationships were found between postoperative septic arthritis and age, sex, revision ACLR, ACLR surgical technique, and accompanying intra-articular procedures for all septic arthritis patients (P > .05). The average time from the onset of the symptoms of infection to surgical irrigation and debridement (I&D) was 2 days (minimum, 0; maximum, 6). ACL grafts were retained during I&D procedures in all patients with postoperative septic arthritis.

CONCLUSION

The postoperative rate of septic arthritis was 0.1% after use of the QT autograft. While graft choice may affect rates of septic arthritis after ACLR, patient characteristics, ACLR technique, revision ACLR, and accompanying intra-articular procedures during ACLR were not associated with postoperative septic arthritis with the numbers available for analysis.