Analysis of 525 samples to determine the usefulness of PCR amplification and sequencing of the 16S rRNA gene for diagnosis of bone and joint infections

Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification

PURPOSE

Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration coordinated by Genomic Medicine Sweden.

METHODS

Thirteen mock samples comprised of various bacterial strains and an External Quality Assessment (EQA) panel from QCMD (Quality Control for Molecular Diagnostics) were analysed by 20 microbiological laboratories across Sweden, using the recent v14 chemistry. Most laboratories generated full-length 16S rRNA sequencing libraries using an optimized protocol for the 16S Barcoding Kit 24, while two laboratories employed in-house PCR coupled with the Ligation Sequencing Kit. The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).

RESULTS

Seventeen out of 20 laboratories successfully sequenced and analysed the samples. Laboratories that used sodium acetate-containing elution buffers faced compatibility issues during library construction, resulting in reduced read count. High bacterial load samples were generally well-characterized, whereas hard-to-lyse bacteria such as Gram-positive strains were detected at lower abundance. The GMS-16S tool provided improved species-level identification compared to the 1928-16S pipeline, particularly for closely related taxa within the Streptococcus and Staphylococcus genera.

CONCLUSION

Nanopore sequencing demonstrated promising potential for bacterial identification in a clinical setting. The results prompt further optimization of the protocol to improve detection of a broader range of species. This multicentre study highlights the feasibility of implementing Nanopore sequencing into clinical microbiological laboratories, for improved national precision diagnostics.

Septic arthritis - symptoms, diagnosis and new therapy

Septic arthritis (SA) is an infection of one or more joints caused mainly by Staphylococcus aureus, to a lesser extent by streptococci and Gram-negative bacilli. It poses a huge medical problem due to its high mortality rate of 2-15%. Disease symptoms are often vague, resulting in a risk that SA may be diagnosed too late. This shows the urgency of finding a rapid diagnostic method for SA and an effective therapy. Basic treatment of SA including joint drain or empirical antimicrobial therapy does not always provide the desired results. Hence, new therapies are being sought, including the use of antimicrobial peptide or phage therapy.

Wide variability of the definitions used for native vertebral osteomyelitis: walking the path for a unified diagnostic framework with a meta-epidemiological approach

BACKGROUND CONTEXT

Native Vertebral Osteomyelitis (NVO) has seen a rise in incidence, yet clinical outcomes remain poor with high relapse rates and significant long-term sequelae. The 2015 IDSA Clinical Practice Guidelines initiated a surge in scholarly activity on NVO, revealing a patchwork of definitions and numerous synonyms used interchangeably for this syndrome.

PURPOSE

To systematically summarize these definitions, evaluate their content, distribution over time, and thematic clustering.

STUDY DESIGN/SETTING

Meta-epidemiological study with a systematic review of definitions.

PATIENTS SAMPLE

An extensive search of multiple databases was conducted, targeting trials and cohort studies dating from 2005 to present, providing a definition for NVO and its synonyms.

OUTCOME MEASURES

Analysis of the diagnostic criteria that composed the definitions and the breaking up of the definitions in the possible combinations of diagnostic criteria.

METHODS

We pursued a thematic synthesis of the published definitions with Boolean logic, yielding single or multiple definitions per included study. Using 8 predefined diagnostic criteria, we standardized definitions, focusing on the minimum necessary combinations used. Definition components were visualized using Sankey diagrams.

RESULTS

The literature search identified 8,460 references, leading to 171 studies reporting on 21,963 patients. Of these, 91.2% were retrospective, 7.6% prospective, and 1.2% RCTs. Most definitions originated from authors, with 29.2% referencing sources. We identified 92 unique combinations of diagnostic criteria across the literature. Thirteen main patterns emerged, with the most common being clinical features with imaging, followed by clinical features combined with imaging and microbiology, and lastly, imaging paired with microbiology.

CONCLUSIONS

Our findings underscore the need for a collaborative effort to develop standardized diagnostic criteria. We advocate for a future Delphi consensus among experts to establish a unified diagnostic framework for NVO, emphasizing the core components of clinical features and MRI while incorporating microbiological and histopathological insights to improve both patient outcomes and research advancements.

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.

A prospective multicentre evaluation of BioFire® Joint Infection Panel for the rapid microbiological documentation of acute arthritis

OBJECTIVES

To assess the performance of the rapid syndromic BioFire® Joint Infection Panel (BF-JIP) to detect bacterial and fungal pathogens, as well as antibiotic resistance genes, directly in synovial fluid specimens collected from patients with acute arthritis.

METHODS

The study was conducted in six French bacteriological laboratories. To assess the performances of BF-JIP, results were compared with those of synovial fluid 14-day culture and, in case of discrepancy, with those of complementary molecular methods and intraoperative samples. A total of 308 synovial fluid specimens were tested after collection from 308 adults and children presenting with clinical and biological suspicion of acute arthritis; patients presenting with acute periprosthetic joint infection were included according to the European Bone and Joint Infection Society 2021 criteria.

RESULTS

Only one specimen failed (no result). On the basis of the consolidated data, the BF-JIP was concordant with the 14-day culture in 280 (91.2%) of the 307 specimens finally included in the study. The positive percentage agreement was 84.9% (95% CI, 78.8-89.8%) and the negative percentage agreement was 100% (95% CI, 97.2-100%). The positive predictive value was extremely high (100%; 95% CI, 97.6-100%), whereas the negative predictive value was lower (82.6%; 95% CI, 75.7-88.2%), partially explained by the missing target species in the panel.

DISCUSSION

The BF-JIP showed high performances to detect pathogens involved in acute arthritis.

Update on the role of pathology and laboratory medicine in diagnosing periprosthetic infection

Technological and implant design advances have helped reduce the frequency of aseptic total joint arthroplasty failure, but periprosthetic joint infections (PJI) remain a clinical important problem with high patient morbidity. Misinterpreting PJI as aseptic mechanical loosening commonly leads to unsatisfactory revision arthroplasty, persistent infection, and poor long-term results. While there is no single "gold standard" diagnostic test for PJI, recent collaborative efforts by Orthopaedic and Infectious Disease Societies have developed algorithms for diagnosing PJI. However, the efficacy of individual tests as well as diagnostic thresholds are controversial. We review the recommended thresholds for commonly used screening tests as well as tissue histopathology and confirmatory tests to diagnose periprosthetic infection. We also update lesser-known laboratory tests, and we briefly summarize rapidly evolving molecular tests to diagnose periprosthetic infection. Pathologists hold a critical role in assisting with PJI diagnosis, maintaining laboratory test quality and interpreting test results. Collaboration between clinicians and pathologists is essential to provide optimal patient care and reduce the burden of PJI.

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

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

Fracture related Infection - Challenges in definition and diagnosis

In the field of orthopedics and trauma surgery, the rise of periprosthetic joint infections following joint replacement and fracture-related infections (FRI) has become a growing concern. The recent establishment of a definitive definition for FRI aimed to standardize diagnosis and treatment approaches while considering unique aspects of implant-associated infections in the presence of concomitant bone fractures. Diagnosing FRI can be challenging due to the varied clinical symptoms, and confirmatory criteria may not always be evident, necessitating additional diagnostic measures. Blood markers like leukocyte count, C-reactive protein (CRP), and erythrocyte sedimentation rate (ESR) have limited specificity. Although novel biomarkers such as D-dimer and interleukin-6 (IL-6) show potential, they require further investigation. The use of microbiological diagnostics with tissue samples and sonication has improved pathogen detection. Cross-sectional imaging techniques like CT scans and MRI scans help evaluate bone status, soft tissue infiltration, and abscesses. Nuclear medicine techniques are accurate but may not always be practical in routine clinical practice. Histopathological interpretation for FRI remains less standardized compared to periprosthetic joint infections (PJI). FRI diagnosis requires the identification of visible microorganisms in deep tissue specimens and the quantification of polymorphonuclear neutrophils (PMNs). The defined concept of FRI has opened doors for better diagnostic and treatment approaches. However, challenges persist, especially in preoperative diagnosis, particularly for cases with unclear clinical presentations. Future endeavors aimed at optimizing diagnostic procedures and establishing a histopathological classification for FRI could lead to improved treatment recommendations and outcomes.

Universal PCR for bacteria, mycobacteria, and fungi: a 10-year retrospective review of clinical indications and patient outcomes

IMPORTANCE

Our work provides a retrospective analysis of universal PCR orders for bacteria, mycobacteria, and fungi across our institution across a 10-year period. We assessed the positivity rates for this diagnostic tool by test type and specimen type and, critically, studied whether and how the results influenced the outcomes from treatment change, to readmission, to death.

Development of a scoring system to identify high-yield specimens for bacterial broad-range 16S rRNA gene PCR with sequencing at a tertiary care medical center

OBJECTIVES

Broad-range bacterial polymerase chain reaction with sequencing (BRBPS) provides valuable diagnostic data, especially in cases of culture-negative infections. However, as BRBPS testing demonstrates generally low positivity, cost per impactful result can be high and commonly involves longer turnaround times compared with other methods, targeting use of this assay to high-yield situations remains a challenging goal. Diagnostic stewardship can help alleviate these challenges and increase clinical utility, yet not all laboratories have a dedicated stewardship team, and little formal guidance exists on identifying high-yield samples outside of specific clinical syndromes. In this study, we performed a retrospective review of 86 BRBPS orders from a tertiary care medical center, with a focus on identifying high-yield cases using an infectious markers scoring system, visualized inflammation or organism (VIO) score, to predict return of actionable diagnostic data.

METHODS

Using chart review, we evaluated how results from high VIO score or low VIO score specimens contributed to clinical management.

RESULTS

Testing low VIO score samples identified an organism in only 10% of samples, and of these positive results, 33% were considered to represent contamination. Despite negative routine workup and no identified pathogen via BRBPS, broad antimicrobial treatment was continued in 85% of cases with a low VIO score. In contrast, specimens with high VIO scores were more predictably positive by BRBPS, identified organisms that were universally considered pathogens, and provided opportunities to target or de-escalate antimicrobial therapy.

CONCLUSIONS

This study describes the VIO scoring system to guide the identification of high-yield samples and steward the appropriate use of BRBPS testing.

Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management.

AREAS COVERED

A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance.

EXPERT OPINION

Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.

Fluorescence In Situ Hybridization as Diagnostic Tool for Implant-associated Infections: A Pilot Study on Added Value

Implant-associated infections are a devastating complication in surgery. Especially in infections with biofilm-forming microorganisms, the identification of the causing microorganism remains a challenge. However, the classification as biofilm is not possible with conventional polymerase chain reaction or culture-based diagnostics. The aim of this study was to evaluate the additional value of fluorescence in situ hybridization (FISH) and nucleic acid amplification technique (FISHseq) to discuss a diagnostic benefit of the culture-independent methods and to map spatial organization of pathogens and microbial biofilms in wounds.

Methods

In total, 118 tissue samples from 60 patients with clinically suspected implant-associated infections (n = 32 joint replacements, n = 24 open reduction and internal fixation, n = 4 projectiles) were analyzed using classic microbiological culture and culture-independent FISH in combination with polymerase chain reaction and sequencing (FISHseq).

Results

In 56 of 60 wounds, FISHseq achieved an added value. FISHseq confirmed the result of cultural microbiological examinations in 41 of the 60 wounds. In 12 wounds, one or more additional pathogens were detected by FISHseq. FISHseq could show that the bacteria initially detected by culture corresponded to a contamination in three wounds and could exclude that the identified commensal pathogens were a contamination in four other wounds. In five wounds, a nonplanktonic bacterial life form was detected.

Conclusions

The study revealed that FISHseq gives additional diagnostic information, including therapy-relevant findings that were missed by culture. In addition, nonplanktonic bacterial life forms could also be detected with FISHseq, albeit less frequently than previously indicated.

Advances in the Microbiological Diagnosis of Prosthetic Joint Infections

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

Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens

16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S rRNA gene sequencing from direct clinical specimens on antimicrobial management. Adult inpatients whose attending physician requested 16S rRNA gene sequencing and corresponding bacterial culture from a direct clinical specimen between January and December 2021 in a university hospital were prospectively included in this study. A total of 434 specimens from 374 patients were requested. Of these, 253 (58.3%) specimens were collected from patients whose final diagnosis indicated a bacterial infection, whereas 181 (41.7%) specimens were from nonbacterial infections. Using the final diagnosis as a "gold standard," the sensitivity and specificity of 16S rRNA gene sequencing were 38.3% and 93.9%, respectively. Among the bacterial infection cases, the proportion of 16S rRNA gene sequencing-positive and culture-positive cases was 32.4%, and the proportion of sequencing-positive and culture-negative cases was 5.9%. The impact on antimicrobial management was evident in 10 (2.3%) specimens, which all resulted in the continuation of antibiotics. The impact on antimicrobial management was highest in skin and soft tissue infections, followed by bone and joint infections. In this study, the long turnaround time of 16S rRNA gene sequencing of clinical specimens was a limiting factor. In conclusion, the overall diagnostic yield of 16S rRNA gene sequencing in bacterial infection cases was fair, being useful in selected cases. Restrictions on test requests may improve test utilization in this setting. IMPORTANCE 16S rRNA gene sequencing has been increasingly used in clinical practice. Using the final diagnosis as a gold standard, the sensitivity of 16S rRNA gene sequencing was fair. In the setting with no 16S rRNA gene sequencing test ordering restrictions, only small percentages of the test results had an impact on antimicrobial management. Restrictions on test requests should be developed to maximize the benefit of the test.

Diagnosis and Treatment of Culture-Negative Periprosthetic Joint Infection

Identification of the causative organism(s) in periprosthetic joint infection (PJI) is a challenging task. The shortcomings of traditional cultures have been emphasized in recent literature, culminating in a clinical entity known as "culture-negative PJI." Amidst the growing burden of biofilm infections that are inherently difficult to culture, the field of clinical microbiology has seen a paradigm shift from culture-based to molecular-based methods. These novel techniques hold much promise in the demystification of culture-negative PJI and revolutionization of the microbiology laboratory. This article outlines the clinical implications of culture-negative PJI, common causes of this diagnostic conundrum, established strategies to improve culture yield, and newer molecular techniques to detect infectious organisms.

Involvement of Bacteria in the Pathological Changes Before Achilles Tendon Rupture: A Case Series Investigating 16S rDNA in 20 Consecutive Ruptures

Background

The source of the pathological changes that occur before an acute Achilles tendon rupture (ATR) is not fully understood. Bacterial DNA has previously been detected in samples from ruptured Achilles tendons, suggesting a pathogenic role of bacteria in ATR.

Purpose/Hypothesis

The purpose of this study was to investigate if DNA from bacteria was present in acutely ruptured Achilles tendons. We hypothesized that 20% to 30% of the samples from the rupture site and no samples from healthy tissue would be positive for bacterial DNA.

Study Design

Case series; Level of evidence, 4.

Methods

This study included 20 consecutive patients scheduled for surgical repair of an acute ATR. Tendon biopsy specimens were taken from the rupture site and from the healthy tendon tissue proximal to the rupture to act as a control. Samples were blinded to the technician and analyzed using polymerase chain reaction targeted to the bacterial 16S rDNA gene and Sanger sequencing to identify the bacterial species present. McNemar test for paired proportions was performed to test for statistically significant differences in the number of samples positive for bacterial DNA between the ruptured and control regions of the Achilles tendon.

Results

Of the 20 patients, 1 (5%) had a positive sample with bacterial DNA from the ruptured part of the Achilles tendon. The same patient also had a positive control sample, although with different bacterial DNA. An additional patient had a positive control sample. There was no statistically significant difference in the number of bacterial DNA-positive samples between the ruptured and control regions of the Achilles tendon. The bacteria found (Staphylococcus sp, Micrococcus sp, and Staphylococcus epidermidis) were normal commensal organisms on the human skin.

Conclusion

Bacterial DNA was infrequent in tissue from ruptured Achilles tendons and, if identified, likely was a result of contamination. This suggests that bacteria are not involved in the pathological changes occurring before rupture of the Achilles tendon.

Improving the Diagnosis of Bacterial Infections: Evaluation of 16S rRNA Nanopore Metagenomics in Culture-Negative Samples

While 16S rRNA PCR-Sanger sequencing has paved the way for the diagnosis of culture-negative bacterial infections, it does not provide the composition of polymicrobial infections. We aimed to evaluate the performance of the Nanopore-based 16S rRNA metagenomic approach, using both partial and full-length amplification of the gene, and to explore its feasibility and suitability as a routine diagnostic tool for bacterial infections in a clinical laboratory. Thirty-one culture-negative clinical samples from mono- and polymicrobial infections based on Sanger-sequencing results were sequenced on MinION using both the in-house partial amplification and the Nanopore dedicated kit for the full-length amplification of the 16S rRNA gene. Contamination, background noise definition, bacterial identification, and time-effectiveness issues were addressed. Cost optimization was also investigated with the miniaturized version of the flow cell (Flongle). The partial 16S approach had a greater sensitivity compared to the full-length kit that detected bacterial DNA in only 24/31 (77.4%) samples. Setting a threshold of 1% of total reads overcame the background noise issue and eased the interpretation of clinical samples. Results were obtained within 1 day, discriminated polymicrobial samples, and gave accurate bacterial identifications compared to Sanger-based results. We also found that multiplexing and using Flongle flow cells was a cost-effective option. The results confirm that Nanopore technology is user-friendly as well as cost- and time-effective. They also indicate that 16S rRNA targeted metagenomics is a suitable approach to be implemented for the routine diagnosis of culture-negative samples in clinical laboratories.

Identification of Peptoniphilus vaginalis-Like Bacteria, Peptoniphilus septimus sp. nov., From Blood Cultures in a Cervical Cancer Patient Receiving Chemotherapy: Case and Implications

A 39-year-old woman with a 3-year human papillomavirus (HPV) 18 infection history was admitted to the hospital for a 16-day history of vaginal bleeding after sex. She was diagnosed with cervical cancer based on the results of the electronic colposcopy, cervical cytology, microscopy, and magnetic resonance imaging (MRI). Then, she received chemotherapy, with paclitaxel 200 mg (day 1), cisplatin 75 mg (day 2), and bevacizumab 700 mg (day 3) twice with an interval of 27 days. During the examination for the diagnosis and treatment, many invasive operations, including removal of intrauterine device, colposcopy, and ureteral dilatation, were done. After that, the patient was discharged and entered the emergency department about 2.5 months later with a loss of consciousness probably caused by septic shock. The patient finally died of multiple organ failure and bacterial infection, although she has received antimicrobial therapy. The blood cultures showed a monobacterial infection with an anaerobic Gram-positive bacterial strain, designated as SAHP1. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI–TOF MS) indicated that the patient was infected with Peptoniphilus asaccharolyticus, while molecular analysis and genome-based taxonomy confirmed the infection with a novel Peptoniphilus species that has a close genetic relationship with Peptoniphilus vaginalis and proposed provisionally as Peptoniphilus septimus sp. nov., which may also act as a commensal of the human vagina. Genomic features of SAHP1 have been fully described, and comparative genomic analysis reveals the known prokaryote relative of Peptoniphilus septimus sp. nov. in the genus Peptoniphilus. The invasive operations on the genital tract during the diagnosis and treatment of the patient and the tumor tissue damage and bleeding may have a certain role in the bloodstream infection. This study casts a new light on the Peptoniphilus bacteria and prompts clinicians to include anaerobic blood cultures as part of their blood culture procedures, especially on patients with genital tract tumors. Furthermore, due to the incomplete database and unsatisfying resolution of the MALDI–TOF MS for Peptoniphilus species identification, molecular identification, especially whole-genome sequencing, is required for those initially identified as bacteria belonging to Peptoniphilus in the clinical laboratory.

Culture-negative endocarditis caused by Stenotrophomonas maltophilia: a report of two cases

Stenotrophomonas maltophilia, an aerobic, non-fermenting, Gram-negative bacterium, is an emerging nosocomial pathogen. It is considered to be a low-grade pathogen, and infections due to S. maltophilia are uncommon. However, in the recent past, S. maltophilia infections have been on the rise, particularly in patients who are either immunocompromised, aged or on long-term antibiotic therapy. Endocarditis due to S. maltophilia is extremely rare. This is a report of two patients with S. maltophilia endocarditis who were diagnosed by 16S rRNA gene sequencing.

Detection of bacterial DNA in synovial fluid in dogs with arthritis: a comparison between bacterial culture and 16S rRNA polymerase chain reaction

Background

Septic arthritis (SA) is a serious condition in dogs that requires a prompt diagnosis and treatment to minimize long-term joint pathology. Although bacterial detection in synovial fluid (SF) through culture or cytology is often performed to confirm diagnosis, the sensitivity of these tests is low. The need for a reliable diagnostic tool to confirm the presence of bacteria in SF in humans has led to the increased use of 16S rRNA (i.e., ribosomal RNA) gene sequencing by polymerase chain reaction (16S rRNA PCR). The aim of this prospective clinical study was to compare the sensitivity and specificity of 16S rRNA PCR with bacterial culture on blood agar plates after pre-incubation of SF in paediatric blood bacterial culture bottles to identify bacteria in dogs with clinical signs of SA and to investigate the usefulness of these methods as diagnostic tools.

Results

Ten dogs with clinical signs of SA, nine with osteoarthritis (OA, control group) and nine with clinical signs of immune-mediated polyarthritis (IMPA, second control group) were examined. Bacterial culture was positive in seven of 10 dogs with clinical SA, of which only two were positive by 16S rRNA PCR. The sensitivity of 16S rRNA PCR and bacterial culture analysis for dogs with clinical SA were 20% and 70%, respectively. All SF samples collected from control group (n = 9) and second control group (n = 14) animals were negative on culture, and 16S rRNA PCR rendered a specificity of 100%.

Conclusions

Our study showed a lower sensitivity of 16S rRNA PCR than bacterial culture for dogs with clinical SA. Our findings suggest that there is currently no advantage in using 16S rRNA PCR as a diagnostic tool for dogs with clinical SA. Furthermore, our study indicates that pre-incubation in paediatric blood bacterial culture bottles before bacterial cultivation on blood agar plates might enhance bacterial culture sensitivity compared to other culture methods.

Serum and Synovial Biomarkers for the Diagnosis of Implant-Associated Infection After Orthopedic Surgery

Implant-associated infection is one of the most devastating complications following orthopedic surgery. Early identification is crucial for treatment. Currently, however, a reliable diagnostic tool is lacking, partly due to disparate bacteria colonies (virulent vs non-virulent), difficulty in distinguishing infection from inflammatory disease, and highly diverse diagnostic thresholds and testing methods. Given the importance of biomarkers in the initial screening for the infection, an extensive effort has been made to develop serum and synovial biomarkers. In this review, the authors summarize the results from the most relevant studies to provide comprehensive information on biomarkers for the diagnosis of implant-associated infection. [Orthopedics. 2021;44(2):e158-e166.].

Diagnosing fracture related infections: Where are we now?

Accurate diagnosis of fracture related infection (FRI) is critical for preventing poor outcomes such as loss of function or amputation. Due to the multiple variables associated with FRI, however, accurate diagnosis is challenging and complicated by a lack of standardized diagnostic criteria. Limitations with the current gold standard for diagnosis, which is routine microbiology culture, further complicate the diagnostic and management process. Efforts to optimize the process rely on a foundation of data derived from prosthetic joint infections (PJI), but differences in PJI and FRI make it clear that unique approaches for these distinct infections are required. A more concerted effort focusing on FRI has dominated more recent investigations and publications leading to a consensus definition by the American Orthopedics (AO) Foundation and the European Bone and Joint Infection Society (EBJIS). This has the potential to better standardize the diagnostic process, which will not only improve patient care but also facilitate more robust and reproducible research related to the diagnosis and management of FRI. The purpose of this review is to explore the consensus definition, describe the foundation of data supporting current FRI diagnostic techniques, and identify pathways for optimization of clinical microbiology-based strategies and data.

Diagnostic performance of Ion 16S metagenomics kit and Ion reporter metagenomics workflow for bacterial pathogen detection in culture-negative clinical specimens from sterile sources

PCR-based deep sequencing of 16S rRNA gene allows for detection of a wide array of bacterial pathogens in culture-negative specimens. Ion 16S metagenomics kit and Ion Reporter metagenomics workflow (Ion 16S mNGS) provides an end-to-end solution with integrated workflow. Ninety-eight clinical samples with the diagnosis generated with 16S rRNA gene PCR/chain termination (Sanger) sequencing (16S CS) was used to assess the performance of Ion 16S mNGS. Compared to species level detection of 16S CS, the Ion 16S mNGS had 88% sensitivity and 76% specificity. When accounting for genus level of detection, the Ion 16S mNGS had 100% sensitivity. Notably, Ion 16S mNGS generated diagnosis in 13% of 16S CS and culture-negative samples. In addition, Ion 16S mNGS had the advantage of detecting more than 1 pathogen in 16S CS positive samples. We showed that the workflow had high reproducibility.

Cutibacterium acnes in shoulder surgery: a scoping review of strategies for prevention, diagnosis, and treatment

BACKGROUND

Cutibacterium acnes is a commensal, gram-positive, facultatively anaerobic bacillus that resides in the dermis. Historically thought to be a contaminant when identified on cultured specimens, recent advances in diagnostic technology have now implicated it as the most common organism responsible for postoperative shoulder infections. Despite a recognition of the role of this organism and a significant research interest in recent years, there is clear lack of consensus guideline on strategies to prevent, diagnose, and treat postoperative shoulder infection.

METHOD

The electronic databases PubMed, MEDLINE, CINAHL, Scopus, and Web of Science were searched in March 2020. All experimental and nonexperimental studies that investigate C acnes in shoulder surgery were included. Inclusion was limited to articles published after 2000 and written in English; reviews, gray literature, or abstracts were excluded. A total of 70 studies were included in this review. This scoping review was performed in accordance with the Extended Preferred Reporting Items of Systematic Reviews and Meta-Analyses Statement for Scoping Reviews (PRISMA-ScR).

RESULTS

Standard surgical prophylactic regimens such as intravenous antibiotics and topical chlorhexidine are ineffective at removing C acnes from the deep layer of the dermis, and there is a shift toward using topical benzoyl peroxide with significantly improved efficacy. An improved understanding of the bacteria has demonstrated that a prolonged culture time of up to 14 days is needed, especially in cases of established infection. Advances in diagnostics such as sonication and molecular-based testing are promising. Although usually thought to be susceptible to a broad range of antibiotics, resistance is emerging to clindamycin. An improved understanding of its ability to form a biofilm highlights the difficulty in treating an established infection.

CONCLUSION

The role of C acnes causing postoperative infection following shoulder surgery is being increasingly recognized. Strategies for prevention, diagnosis, and treatment have been outlined from both an antimicrobial and surgical perspective. A number of these strategies are emerging and require further research to demonstrate efficacy before implementation into clinical guidelines.

Molecular characterization of bacterial communities of two neotropical tick species (Amblyomma aureolatum and Ornithodoros brasiliensis) using rDNA 16S sequencing

Ticks are one of the main vectors of pathogens for humans and animals worldwide. However, they harbor non-pathogenic microorganisms that are important for their survival, facilitating both their nutrition and immunity. We investigated the bacterial communities associated with two neotropical tick species of human and veterinary potential health importance from Brazil: Amblyomma aureolatum and Ornithodoros brasiliensis. In A. aureolatum (adult ticks collected from wild canids from Southern Brazil), the predominant bacterial phyla were Proteobacteria (98.68%), Tenericutes (0.70%), Bacteroidetes (0.14%), Actinobacteria (0.13%), and Acidobacteria (0.05%). The predominant genera were Francisella (97.01%), Spiroplasma (0.70%), Wolbachia (0.51%), Candidatus Midichloria (0.25%), and Alkanindiges (0.13%). The predominant phyla in O. brasiliensis (adults, fed and unfed nymphs collected at the environment from Southern Brazil) were Proteobacteria (90.27%), Actinobacteria (7.38%), Firmicutes (0.77%), Bacteroidetes (0.44%), and Planctomycetes (0.22%). The predominant bacterial genera were Coxiella (87.71%), Nocardioides (1.73%), Saccharopolyspora (0.54%), Marmoricola (0.42%), and Staphylococcus (0.40%). Considering the genera with potential importance for human and animal health which can be transmitted by ticks, Coxiella sp. was found in all stages of O. brasiliensis, Francisella sp. in all stages of A. aureolatum and in unfed nymphs of O. brasiliensis, and Rickettsia sp. in females of A. aureolatum from Banhado dos Pachecos (BP) in Viamão municipality, Brazil, and in females and unfed nymphs of O. brasiliensis. These results deepen our understanding of the tick-microbiota relationship in Ixodidae and Argasidae, driving new studies with the focus on the manipulation of tick microbiota to prevent outbreaks of tick-borne diseases in South America.

Detection of synovial sepsis in horses using enzymes as biomarker

Background

Synovial sepsis is a commonly occurring, potentially career‐ending or even life‐threatening orthopaedic emergency. Diagnosis of synovial sepsis is currently primarily based on synovial fluid analysis, which often leaves diagnostic ambiguity due to overlap of clinicopathological parameters between septic and aseptic inflammatory synovitis.

Objectives

To evaluate the reliability of lysozyme (LYS), myeloperoxidase (MPO) and elastase (ELT) as biomarkers for synovial sepsis in horses using a photometric assay to measure increased enzyme activity.

Study design

Prospective, single‐blinded, analytical, clinical study.

Methods

Equine synovial samples were assigned to one of three groups: (1) healthy controls (n = 10), (2) aseptic (n = 27) and (3) septic synovitis (n = 30). The enzyme activity assays (LYS, MPO and ELT) were compared with standard synovial fluid parameters and broad‐range bacterial 16S rDNA PCR.

Results

LYS and MPO activities were significantly different between septic synovial samples, and both aseptic and control samples (P < .001, LYS: confidence interval [CI]: 2.25‐3.41, resp., 2.21‐3.8, MPO: CI 0.752‐1.6, resp., 0.639‐1.81). LYS achieved a 100% sensitivity and 100% specificity in differentiating between septic and aseptic (cut‐off value 751.4) or control (cut‐off: 484.6) samples (P < .001). MPO reached 93.33% sensitivity, 100% specificity for distinguishing septic from control (cut‐off value: 0.1254) synovial samples and 93.33% sensitivity, 81.48% specificity for discriminating between septic and aseptic (cut‐off value: 0.1305) synovial samples (P < .001). ELT activity could not be measured in any synovial sample. Both the LYS and the MPO measurements showed a highly significant correlation with PCR (LYS r = .79, MPO r = .69), synovial leukocyte count (LYS r = .752, MPO r = .571), % neutrophils (LYS r = .751, MPO r = 0.663) and each other (r = .744, all P < .001).

Main limitations

Variation in horses’ signalment, affected synovial structures and synovial fluid freezing times may have affected the discriminative power of this study.

Conclusions

Increased MPO and LYS activities allow reliable, rapid diagnosis of synovial sepsis with high sensitivity and specificity.

Revised version (INFD-D-20-00242): impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study

Background

PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types.

Methods

From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive.

Results

Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001).

Conclusion

In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05892-4.

Age-Associated Tooth Loss and Oral Microbial Dysbiosis in a Mouse Genetic Model of Chronic Nicotine Exposure

Nicotine acts as a potent modulator of normal cellular responses through the nicotinic acetylcholine receptor subtype alpha7. In a mouse genetic model of alpha7 receptor dysfunction, alpha7^E260A:G, 85 percent of 18 month-old mice exhibit an age-associated spontaneous loosening or complete loss of 3rd molars that was not present in the control mice. The adjacent soft tissues appeared largely unaffected. Further analysis including micro-CT revealed evidence of bone loss surrounding the 3rd molars with areas of cavitation and/or sponge-like (cancellous) bone remodeling in the mandible. The mandible microbiome was examined using 16S-rRNA sequencing. The results show the alpha7^E260A:G oral microbiome included increased landscape complexity indicative of dysbiosis, and a significant increase of some bacteria, particularly Staphylococcus. These results suggest that normal alpha7 function plays a relevant role in maintaining normal gene expression and oral microbiome stasis. Consequently, this mouse model suggests there are consequences to ongoing alpha7 receptor dysfunction and oral health, as can occur from chronic exposure to nicotine as expected from electronic nicotine delivery systems (ENDS or "vaping"), that may not be seen until older age.

Prosthetic joint infection after total hip arthroplasty caused by Sneathia sanguinegens: A case report (CARE-complaint)

INTRODUCTION

Sneathia sanguinegens(S sanguinegens) is a gram-negative rod-shaped bacterium mostly reported to cause a perinatal infection, and there are no reports of S sanguinegens in prosthetic joint infection (PJI). The purpose of this report is to describe a very rare case of PJI after total hip arthroplasty (THA) caused by S sanguinegens.

PATIENT CONCERNS

A 79-year-old woman presented with right coxalgia, inability to walk, and a fever of 39°C. She had undergone THA 28 years earlier for osteoarthritis of the hip.

DIAGNOSES

The diagnosis was acute late-onset PJI, because blood tests revealed marked inflammatory reaction and computed tomography showed an abscess at the right hip joint; synovial fluid analysis resulted in detection of a gram-negative bacillus.

INTERVENTION

Surgical debridement with retention of the implant and antibiotic therapy was performed.

OUTCOMES

One month after surgery, polymerase chain reaction (PCR) assay showed that the pathogen was 99.9% likely to be S sanguinegens. There has been no recurrence of infection or loosening of the implant in the 2 years since her surgery.

LESSONS

PCR should facilitate detection of previously unknown pathogens and potentially novel bacterial species.

Polymicrobial infections and microbial patterns in infected nonunions - a descriptive analysis of 42 cases

BACKGROUND

Frequencies of polymicrobial infection and pathogens evidenced in course of infected nonunion treatment are largely unknown. Therefore, this study aims at investigating microbial patterns in infected nonunions.

METHODS

Surgically treated patients with long bone infected nonunion admitted between January 2010 and March 2018 were included in the study. Microbiological culture and polymerase-chain-reaction results of tissue samples of initial and follow-up revision surgeries were assessed and compared with patient and treatment characteristics.

RESULTS

Forty two patients with a mean age of 53.9 ± 17.7 years were included. In six patients (14.3%) polymicrobial infection was evident. A change of pathogens evidenced in course of the treatment occurred in 21 patients (50%). In 16 patients (38.1%) previously detected bacteria could be determined by microbial testing after further revision surgery. Staphylococcus aureus was most often detected (n = 34, 30.6%), followed by Enterococcus spp. (n = 25, 22.5%) and Staphylococcus epidermidis (n = 18, 16.2%). Five Staphylococcus aureus were resistant to methicillin (MRSA). In patients without polymicrobial infection or further germ detection in course of the treatment, 86.4% of the infections were due to Staphylococcus spp.. Infections due to Streptococcus spp. and gram-negative bacteria were only present in patients with polymicrobial infection and germ-change in course of the treatment.

CONCLUSION

A low rate of polymicrobial infections was evidenced in the present study. Germ-change often occurs in course of revision surgeries. Prospective studies with more sensitive diagnostic tools are necessary to elucidate the therapeutical relevance of microbiological testing results for surgical as well as medical treatment in infected nonunions.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Detecting the presence of bacteria in low-volume preoperative aspirated synovial fluid by metagenomic next-generation sequencing

OBJECTIVES

Preoperative diagnosis is important for patients who need revision surgery due to PJI. Microbial culture plays an important role in PJI diagnosis, but the sensitivity of cultures is low when the sample amount is limited or when a patient is treated with antibiotics before sample collection. In this study, metagenomic next-generation sequencing (mNGS) was used to detect bacteria in preoperative puncture synovial fluid samples from patients with suspected PJI, and the preoperative and intraoperative culture results were compared to estimate its diagnostic efficiency.

METHODS

From July 2016 to December 2018, patients with suspected PJI who underwent prosthetic joint revision surgery were included, and the results of those who had been tested by preoperative synovial fluid culture and mNGS were obtained. The demographic characteristics, medical history, laboratory test results, culture results, and mNGS results of each patient were recorded. Then, the efficiency of preoperative synovial fluid mNGS was compared to that of synovial fluid culture for diagnosing PJI.

RESULTS

A total of 37 patients were included, and 24 patients (25 joints) were diagnosed with PJI. The sensitivity, specificity, and accuracy of preoperative synovial fluid mNGS were 92%, 91.7%, and 83.7%, respectively. The sensitivity, specificity, and accuracy of preoperative synovial fluid culture were 52%, 91.7%, and 43.7%, respectively.

CONCLUSIONS

With a low volume of synovia (1 ml), mNGS can be performed with higher sensitivity and specificity compared to synovial culture. Thus, mNGS can be a useful supplemental method to improve diagnostic efficiency during the preoperative period.

Diagnosis of Culture-Negative Septic Arthritis with Polymerase Chain Reaction in an Immunosuppressed Patient: A Case Report

CASE

We present a 23-year-old woman on immunosuppressive therapy with polyarticular, culture-negative septic arthritis. She underwent irrigation and debridement with empiric antibiotic therapy but had recurrence of septic arthritis despite treatment. Polymerase chain reaction testing eventually identified Ureaplasma as the causative organism. She was successfully treated with an extended course of organism-specific antibiotics.

CONCLUSION

More patients are being treated with immune modulating therapies. Immunosuppressed patients are at risk for atypical infections and may have different presentations than immunocompetent patients. Newer diagnostic modalities can help identify causative organisms and direct treatment in the case of negative cultures.

Detecting the presence of bacterial RNA by polymerase chain reaction in low volumes of preoperatively aspirated synovial fluid from prosthetic joint infections

Aims

Preoperative diagnosis is important for revision surgery after prosthetic joint infection (PJI). The purpose of our study was to determine whether reverse transcription-quantitative polymerase chain reaction (RT-qPCR), which is used to detect bacterial ribosomal RNA (rRNA) preoperatively, can reveal PJI in low volumes of aspirated fluid.

Methods

We acquired joint fluid samples (JFSs) by preoperative aspiration from patients who were suspected of having a PJI and failed arthroplasty; patients with preoperative JFS volumes less than 5 ml were enrolled. RNA-based polymerase chain reaction (PCR) and bacterial culture were performed, and diagnostic efficiency was compared between the two methods.According to established Musculoskeletal Infection Society (MSIS) criteria, 21 of the 33 included patients were diagnosed with PJI.

Results

RNA-based PCR exhibited 57.1% sensitivity, 91.7% specificity, 69.7% accuracy, 92.3% positive predictive value, and 55.0% negative predictive value. The corresponding values for culture were 28.6%, 83.3%, 48.5%, 75.0%, and 40.0%, respectively. A significantly higher sensitivity was thus obtained with the PCR method versus the culture method.

Conclusion

In situations in which only a small JFS volume can be acquired, RNA-based PCR analysis increases the utility of preoperative puncture for patients who require revision surgery due to suspected PJI.

Cite this article:Bone Joint Res. 2020;9(5):219–224.

A novel intraoperative technique seeding morselized bone tissue into pediatric blood culture bottles improves microbiological diagnosis in patients with foot and ankle osteomyelitis

BACKGROUND

Osteomyelitis, particularly cases involving the foot and ankle, is a challenging situation that frequently leads to amputations and major sequelae. Targeted antibiotics treating an identified pathogen are key to a successful outcome; however, traditional culture methods for bone tissue have poor sensitivity. This study prospectively compared a novel method for obtaining and processing infected bone tissue with the standard technique.

METHODS

107 patients presenting with a diagnosis of osteomyelitis of the foot and ankle between 2008 and 2017 were prospectively included. Diagnosis was done according to clinical, laboratory and imaging findings. We obtained paired samples of bone tissue from all patients; they were processed through a usual culture method (UCM), but they were also morselized and seeded into pediatric blood culture bottles (PBCBs). We compared the culture yield and the number of agents detected using both the McNemar and the Mann-Whitney tests, respectively.

RESULTS

We studied 107 patients (63 with diabetic foot infection and 44 with nondiabetic osteomyelitis). The causative agent was identified in 60.7% of cases using the UCM and in 97.2% of cases using PBCBs (p < 0.001). We detected a mean of 1.05 ± 1.03 bacteria using the UCM and 1.67 ± 0.92 bacteria using PBCBs (p < 0.01).

CONCLUSION

Cultures using morselized bone seeded in PBCBs identified the causative agent in a significantly larger percentage than the UCM. Additionally, this method identified a larger number of pathogen agents. A better agent identification method has advantages such as identifying more specific antibiotic treatment in these cases.

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

Background

The microbiological diagnosis of bone and joint infections (BJI) currently relies on cultures, and the relevance of molecular methods is still debated. The aim of this study was to determine whether polymerase chain reaction (PCR) could improve the etiological diagnosis of BJI.

Methods

A prospective study was conducted during a 4-year period at Lariboisiere University Hospital (Paris, France), including patients with suspicion of infectious spondylodiscitis, septic arthritis, prosthetic joint infections, and respective noninfected groups. Clinical and radiological data were collected at inclusion and during follow-up. All samples were analyzed by conventional cultures and 16S ribosomal deoxyribonucleic acid (rDNA) gene (16S-PCR). Specific cultures and PCR targeting Mycobacterium tuberculosis were also performed for spondylodiscitis samples. Case records were subsequently analyzed by an independent expert committee to confirm or invalidate the suspicion of infection and definitively classify the patients in a case or control group. The sensitivity of the combination of culture and PCR was compared with culture alone.

Results

After expert committee analysis, 105 cases of BJI cases and 111 control patients were analyzed. The most common pathogens of BJI were staphylococci (30%), M tuberculosis (19%), and streptococci (14%). Adding PCR enhanced the sensitivity compared with culture alone (1) for the diagnosis of M tuberculosis spondylodiscitis (64.4% vs 42.2%; P < .01) and (2) for nonstaphylococci BJI (81.6% vs 71.3%; P < .01). It is interesting to note that 16S-PCR could detect BJI due to uncommon bacteria such as Mycoplasma and fastidious bacteria.

Conclusions

Our study showed the benefit of 16S-PCR and PCR targeting M tuberculosis as add-on tests in cases of suspected BJI.

[The value of mucosal small intestine microbiota in digestion and absorption disorders in metabolic syndrome]

AIM

To evaluate the qualitative and quantitative composition of the parietal microbiota of the small intestine (SI) and its significance in the disturbance of the digestive and absorption functions of the small intestine in metabolic syndrome (MS).

MATERIALS AND METHODS

67 patients with metabolic syndrome were examined. In addition to clinical data, a comprehensive study of the digestive and absorption function of SI was carried out using exercise tests with carbohydrates. The compositional characteristics of mucosal SI microbiota in MS patients were determined by gas chromatography mass spectrometry. The relationship of enteric disorders with changes in small intestinal microbiocenosis was assessed by correlation analysis.

RESULTS

The majority (82.9%) of patients with metabolic syndrome showed clinical local and general signs of small intestinal lesions. Violations of all stages of the hydrolysis - resorption process were revealed against the background of changes in the quantitative and qualitative composition of the parietal microbiota of the small intestine. In patients with MS, excessive bacterial growth is observed in the small intestine mainly due to conditionally pathogenic microbiota strains, and, in comparison with the control group, there is a significant increase in the growth of aerobes, microscopic fungi and viruses. The relationship between the severity of excess bacterial growth and impaired digestion and absorption in the small intestine in MS.

CONCLUSION

The results of our research suggest that the identified changes in the functional state of SI in combination with a violation of mucosal enteral microbiocenosis are an important link in the complex pathogenesis of the MS.

Rapid analysis of bacterial composition in prosthetic joint infection by 16S rRNA metagenomic sequencing

Objectives

Prosthetic joint infection (PJI) is the most common cause of arthroplasty failure. However, infection is often difficult to detect by conventional bacterial cultures, for which false-negative rates are 23% to 35%. In contrast, 16S rRNA metagenomics has been shown to quantitatively detect unculturable, unsuspected, and unviable pathogens. In this study, we investigated the use of 16S rRNA metagenomics for detection of bacterial pathogens in synovial fluid (SF) from patients with hip or knee PJI.

Methods

We analyzed the bacterial composition of 22 SF samples collected from 11 patients with PJIs (first- and second-stage surgery). The V3 and V4 region of bacteria was assessed by comparing the taxonomic distribution of the 16S rDNA amplicons with microbiome sequencing analysis. We also compared the results of bacterial detection from different methods including 16S metagenomics, traditional cultures, and targeted Sanger sequencing.

Results

Polymicrobial infections were not only detected, but also characterized at different timepoints corresponding to first- and second-stage exchange arthroplasty. Similar taxonomic distributions were obtained by matching sequence data against SILVA, Greengenes, and The National Center for Biotechnology Information (NCBI). All bacteria isolated from the traditional culture could be further identified by 16S metagenomics and targeted Sanger sequencing.

Conclusion

The data highlight 16S rRNA metagenomics as a suitable and promising method to detect and identify infecting bacteria, most of which may be uncultivable. Importantly, the method dramatically reduces turnaround time to two days rather than approximately one week for conventional cultures.

Cite this article: M-F. Chen, C-H. Chang, C. Chiang-Ni, P-H. Hsieh, H-N. Shih, S. W. N. Ueng, Y. Chang. Rapid analysis of bacterial composition in prosthetic joint infection by 16S rRNA metagenomic sequencing. Bone Joint Res 2019;8:367–377. DOI: 10.1302/2046-3758.88.BJR-2019-0003.R2.

Effectiveness of 16S ribosomal DNA real-time PCR and sequencing for diagnosing bacterial keratitis

PURPOSE

To evaluate the efficacy of real-time PCR for 16S ribosomal DNA (16S r-DNA) and sequencing for diagnosing microbial keratitis.

METHODS

We studied 272 eyes of 272 patients with keratitis. Eyes with keratitis were classified as "definite" (N = 118), "likely" (N = 71), or "non-bacterial" (N = 83) to have bacterial keratitis. The diagnostic efficacy of real-time PCR and conventional testing was determined by receiver operating characteristic analysis. The copy numbers of bacterial DNA and clinical characteristics were retrospectively analyzed for association with concordant culture results in the "definite" cases.

RESULTS

The level of bacterial DNA was significantly associated with the diagnostic probability of the three diagnostic categories. The level of bacterial DNA had comparable diagnostic efficacy with the area under the curve (AUC) at 0.67, by culture at 0.65, and by smear testing at 0.73. The efficacy was significantly improved by combining the DNA level with the conventional culture testing with an AUC of 0.81. Analysis of the "definite" cases showed culture positivity in 51.8% (58 eyes), and of these, 41 eyes (70.7%) were higher than the cutoff PCR values and 40 eyes were identified by 16S r-DNA sequencing. In the culture-negative eyes, the level of bacterial DNA was significantly lower (P = 0.0008). Eyes with higher bacterial DNA levels had significantly concordant outcomes with sequencing and culture results (P = 0.006). Previous antibiotic treatments decreased the bacterial DNA amount by 0.09-fold, and it was a significant factor for discordance (P = 0.006).

CONCLUSION

Quantification of the bacterial DNA level and conventional testing improves the diagnostic efficacy of infectious bacterial keratitis.

Joint EANM/ESNR and ESCMID-endorsed consensus document for the diagnosis of spine infection (spondylodiscitis) in adults

PURPOSE

Diagnosis of spondylodiscitis (SD) may be challenging due to the nonspecific clinical and laboratory findings and the need to perform various diagnostic tests including serologic, imaging, and microbiological examinations. Homogeneous management of SD diagnosis through international, multidisciplinary guidance would improve the sensitivity of diagnosis and lead to better patient outcome.

METHODS

An expert specialist team, comprising nuclear medicine physicians appointed by the European Association of Nuclear Medicine (EANM), neuroradiologists appointed by the European Society of Neuroradiology (ESNR), and infectious diseases specialists appointed by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID), reviewed the literature from January 2006 to December 2015 and proposed 20 consensus statements in answer to clinical questions regarding SD diagnosis. The statements were graded by level of evidence level according to the 2011 Oxford Centre for Evidence-based Medicine criteria and included in this consensus document for the diagnosis of SD in adults. The consensus statements are the result of literature review according to PICO (P:population/patients, I:intervention/indicator, C:comparator/control, O:outcome) criteria. Evidence-based recommendations on the management of adult patients with SD, with particular attention to radiologic and nuclear medicine diagnosis, were proposed after a systematic review of the literature in the areas of nuclear medicine, radiology, infectious diseases, and microbiology.

RESULTS

A diagnostic flow chart was developed based on the 20 consensus statements, scored by level of evidence according to the Oxford Centre for Evidence-based Medicine criteria.

CONCLUSIONS

This consensus document was developed with a final diagnostic flow chart for SD diagnosis as an aid for professionals in many fields, especially nuclear medicine physicians, radiologists, and orthopaedic and infectious diseases specialists.

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

OBJECTIVE

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Polymerase Chain Reaction Assay Using the Restriction Fragment Length Polymorphism Technique in the Detection of Prosthetic Joint Infections: A Multi-Centered Study

BACKGROUND

PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) techniques have been used for the diagnosis of bacteria in some infections. In this study, we aimed to evaluate the diagnostic accuracy of PCR for the diagnosis of prosthetic joint infections (PJI) and to identify isolated microorganisms, using the RFLP method.

METHODS

During January 2015 to January 2018, patients who were suspected of having PJI after arthroplasty surgery or were candidates for revision surgery due to loosening of implant entered the study. Patients who had 1 major criterion or 3 minor criteria for PJI based on the Philadelphia Consensus Criteria (PCC) on Periprosthetic Joint Infection were considered as cases of PJI. Both culture results and PCR findings, were cross compared with results of the PCC (as the gold standard criteria).

RESULTS

Overall, 76 samples were included in the study. Mean (standard deviation) age of patients was 66.72 ± 11.82 years. Overall, 57.9% of patients were females. Prevalence of PJI was 50% based on the PCC. Sensitivity, specificity, positive predictive value, negative predictive value, and general efficacy of PCR for detection of PJI was 97.4%, 100%, 100%, 97.4%, and 98.7%, respectively. Sensitivity, specificity, positive predictive value, negative predictive value, and general efficacy of culture was 31.6%, 100%, 65.7%, 100%, and 59.4%, respectively. We isolated a broad range of bacteria using PCR-RFLP including Gram-positive cocci such as Staphylococcus sp., Streptococcus sp., and Enterococcus sp., and Gram-negative bacilli such as Enterobacteriaceae sp., Pseudomonas sp. Citrobacter sp., as well as Chlamydophila pneumonia, Stenotrophomonas maltophilia, Brucella melitensis, non-gonococcal Neisseria, Kingella kingae, Bacteroides ovatus, and Proteus mirabilis from PJI patients.

CONCLUSION

Inhere, for the first time, we showed that PCR-RFLP is a powerful tool for identifying the type of bacteria involved in PJI, and can be used for follow-up of patients suspected of PJI and those with a history of antibiotic use. PCR-RFLP may be able to substantially decrease detection time of PJI among PCR-based methods, while allowing more accurate identification of the bacteria involved.

Low-grade infections as a possible cause of arthrofibrosis after total knee arthroplasty

Purpose

Arthrofibrosis after total knee arthroplasty represents a considerable burden for the patient and a therapeutic challenge for the practitioner. One possible cause discussed in the literature is a low-grade infection. This hypothesis should be examined within the scope of this retrospective study.

Patients and methods

Nineteen patients with clinical symptoms of arthrofibrosis after primary total knee arthroplasty were examined between January, 1999 and January, 2012. Incorrect positioning was radiologically ruled out. All patients were examined clinically (score of Freeman as well as Blauth and Jäger), radiologically (component and leg alignment, patella height according to Insall and Salvati), microbiologically (culture-based procedures), molecular biologically (PCR) and histologically in the course of an open revision of the prosthesis.

Results

According to the score of Freeman et al. (1977), a highly significant improvement in pain (p = 0.007) and in the overall score (p = 0.003) was shown. The knee joint mobility did not change significantly (p = 0.795). PCR was negative in 17 patients. One patient showed a PCR-positive result of the synovial membrane for Corynebacterium spp., while Staphylococcus warneri was detected in the culture. Another patient had a positive result of synovia PCR for Enterococcus cecorum as well as Corynebacterium spp. However, this culture was sterile. In 16 patient samples, no bacterial growth was detectable. Two samples were not evaluable. The main histopathological findings were synovialitis and fibrosis.

Conclusion

The hypothesis of low-grade-infection-induced arthrofibrosis after total knee arthroplasty could not be confirmed in this study. However, based on this small study population the conclusion needs to be confirmed by new and larger studies, ideally prospectively designed including a control group.

A Clinico-Microbiological Study of Prosthetic Joint Infections in an Indian Tertiary Care Hospital: Role of Universal 16S rRNA Gene Polymerase Chain Reaction and Sequencing in Diagnosis

BACKGROUND

We determined the magnitude and clinico-microbiological profile of prosthetic joint infection (PJI) at a tertiary hospital. The diagnostic potential of 16S rRNA gene polymerase chain reaction (PCR) and sequencing on periprosthetic tissue samples was evaluated for the diagnosis of PJI.

MATERIALS AND METHODS

This ambispective cohort study consisted of patients who underwent primary or revision hip or knee arthroplasty from June 2013 to June 2017. The patients were classified as either infected or noninfected according to criteria set out by the musculoskeletal infection society (MSIS). Three to five periprosthetic tissue samples were collected from each patient for culture and 16S rRNA gene PCR sequencing.

RESULTS

Hundred and six patients were diagnosed to have PJI as per the MSIS Criteria. The cumulative incidence of PJI at our Institute at the end of 36 months was 1.1% (95% confidence interval [CI]: 0.59-2.91). Microorganisms were isolated by periprosthetic tissue culture (PTC) in 84 patients (sensitivity: 79% and specificity: 100%). Gram-negative aerobes were most frequently isolated (61%). Polymicrobial infections were present in 8.3% of cases. The most common infecting microorganism was Staphylococcus aureus (19.5%). Multidrug resistance and methicillin resistance were noted in 54% and 34% of bacterial isolates, respectively. The sensitivity and specificity of 16S rRNA PCR of periprosthetic tissue was 86% (95% CI: 74.9-89.9) and 100% (95% CI: 94.7-100), respectively. Periprosthetic tissue 16S rRNA PCR was more sensitive than PTC (P = 0.008), although both were 100% specific (P = 0.99).

CONCLUSIONS

The incidence of PJI at our Institute compares well with other published reports. Contrary to previous reports, a predominance of Gram-negative PJI's was found. The preponderance of multidrug-resistant organisms in PJI's is worrisome. The high sensitivity and specificity of the 16S PCR assay used in our study support its use in culture-negative PJI suspected cases.

Antibiotics for amniotic-fluid colonization by Ureaplasma and/or Mycoplasma spp. to prevent preterm birth: A randomized trial

Objective

To assess whether antibiotics used for treatment in asymptomatic second-trimester women positive for Mycoplasma or Ureaplasma spp. detected by amniotic-fluid PCR prevents preterm delivery.

Design

A randomized, double-blind, placebo-controlled trial.

Setting

10 maternal fetal medicine centers in France.

Population

Women with a singleton pregnancy who underwent amniocentesis between 16 and 20 weeks’ gestation (weeks) for Down syndrome screening. A sample of 238 women with PCR-positive findings per treatment group was needed to show a 50% reduction in the preterm delivery rate.

Methods

Amniotic fluid was tested. Women with positive findings on real-time PCR of amniotic fluid for Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum and Ureaplasma parvum were randomized to receive josamycin or placebo. Amniotic fluid was also tested for 16S PCR.

Main outcome measures

The primary outcome was delivery before 37 weeks.

Results

In total, 1043 women underwent amniotic-fluid screening with specific PCR detection between July 2008 and July 2011: PCR detection failed in 27 (2.6%), and 20 (1.9%) underwent termination of pregnancy. Among the 1016 women with PCR results, 980 had available data for the primary outcome (delivery before 37 weeks) and 29 (3.0%) were positive for Ureaplasma and/or Mycoplasma spp. Because of the low rate of women with PCR-positive findings, the trial was stopped prematurely. In total, 19 women were randomized to receive placebo (n = 8) or josamycin (n = 11) and their characteristics were comparable, as was the rate of preterm delivery and secondary outcomes. In comparing all PCR-positive and -negative women regardless of treatment, PCR positivity for Ureaplasma and/or Mycoplasma spp. was not associated with any adverse pregnancy or neonatal outcome. Amniotic-fluid screening by 16S PCR showed no other bacterial colonization associated with preterm birth.

Conclusions

Because of a low amniotic fluid colonization rate, the trial was interrupted. Maternal amniotic-fluid colonization by Mycoplasma and/or Ureaplasma spp. at 16–20 weeks in asymptomatic women is rare and not associated with adverse pregnancy outcomes.

Trial registration

ClinicalTrials.gov NCT00718705