Bacterial diversity in suspected prosthetic joint infections: an exploratory study using 16S rRNA gene analysis

Subacute osteomyelitis due to Staphylococcus caprae in a teenager: A case report and review of the literature

BACKGROUND

Staphylococcus caprae (S. caprae) is a human commensal bacterium which can be detected in the nose, nails, and skin. It can be responsible for heterogeneous infections such as bacteremia, endocarditis, pneumonia, acute otitis externa, peritonitis, and urinary tract infections. Bone and joint infections due to S. caprae have also been reported, but most of them resulted from the infection of orthopedic devices, especially joint prostheses and internal osteosynthesis devices. Rare cases of primary osteoarticular infections caused by S. caprae have been described, including osteitis, arthritis, or spondylodiscitis.

CASE SUMMARY

We report an unusual case of subacute osteomyelitis in a toe phalanx caused by S. caprae in a 14.5-year-old girl.

CONCLUSION

Subacute S. caprae osteomyelitis is a little-known and probably underestimated community-acquired infectious disease. This microorganism’s pathogenicity should be seen as more than a classic nosocomial orthopedic device infection.

Subacute osteomyelitis due to Staphylococcus caprae in a teenager: A case report and review of the literature

BACKGROUND

Staphylococcus caprae (S. caprae) is a human commensal bacterium which can be detected in the nose, nails, and skin. It can be responsible for heterogeneous infections such as bacteremia, endocarditis, pneumonia, acute otitis externa, peritonitis, and urinary tract infections. Bone and joint infections due to S. caprae have also been reported, but most of them resulted from the infection of orthopedic devices, especially joint prostheses and internal osteosynthesis devices. Rare cases of primary osteoarticular infections caused by S. caprae have been described, including osteitis, arthritis, or spondylodiscitis.

CASE SUMMARY

We report an unusual case of subacute osteomyelitis in a toe phalanx caused by S. caprae in a 14.5-year-old girl.

CONCLUSION

Subacute S. caprae osteomyelitis is a little-known and probably underestimated community-acquired infectious disease. This microorganism's pathogenicity should be seen as more than a classic nosocomial orthopedic device infection.

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.

Challenges in the Microbiological Diagnosis of Implant-Associated Infections: A Summary of the Current Knowledge

Implant-associated infections are characterized by microbial biofilm formation on implant surface, which renders the microbiological diagnosis challenging and requires, in the majority of cases, a complete device removal along with a prolonged antimicrobial therapy. Traditional cultures have shown unsatisfactory sensitivity and a significant advance in the field has been represented by both the application of the sonication technique for the detachment of live bacteria from biofilm and the implementation of metabolic and molecular assays. However, despite the recent progresses in the microbiological diagnosis have considerably reduced the rate of culture-negative infections, still their reported incidence is not negligible. Overall, several culture- and non-culture based methods have been developed for diagnosis optimization, which mostly relies on pre-operative and intra-operative (i.e., removed implants and surrounding tissues) samples. This review outlines the principal culture- and non-culture based methods for the diagnosis of the causative agents of implant-associated infections and gives an overview on their application in the clinical practice. Furthermore, advantages and disadvantages of each method are described.

In vitro polymicrobial inter-kingdom three-species biofilm model: influence of hyphae on biofilm formation and bacterial physiology

Biofilms are an important medical burden, notably for patients with orthopaedic device-related infections. When polymicrobial, these infections are more lethal and recalcitrant. Inter-kingdom biofilm infections are poorly understood and challenging to treat. Here, an in vitro three-species model including Staphylococcus aureus, Escherichia coli and Candida albicans was developed, to represent part of the diversity observed in orthopaedic infections or other clinical contexts. The importance of fungal hyphae for biofilm formation and virulence factor expression was explored. Two protocols were set up, allowing, or not, for hyphal formation. Culturable cells and biomass were characterised in both models, and biofilms were imaged in bright-field, confocal and electron microscopes. The expression of genes related to virulence, adhesion, exopolysaccharide synthesis and stress response was analysed in early-stage and mature biofilms. It was found that biofilms enriched in hyphae had larger biomass and showed higher expression levels of genes related to bacterial virulence or exopolysaccharides synthesis.

Sampling challenges in diagnosis of chronic bacterial infections

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

Do Mixed-Species Biofilms Dominate in Chronic Infections?-Need for in situ Visualization of Bacterial Organization

Chronic infections present a serious economic burden to health-care systems. The severity and prevalence of chronic infections are continuously increasing due to an aging population and an elevated number of lifestyle related diseases such as diabetes. Treatment of chronic infections has proven difficult, mainly due to the presence of biofilms that render bacteria more tolerant toward antimicrobials and the host immune response. Chronic infections have been described to harbor several different bacterial species and it has been hypothesized that microscale interactions and mixed-species consortia are present as described for most natural occurring biofilms i.e., aquatic systems and industrial settings, but also for some commensal human biofilms i.e., the mouth microbiota. However, the presence of mixed-species biofilms in chronic infections is most often an assumption based on culture-based methods and/or by means of molecular approaches, such as PCR and sequencing performed from homogenized bulk tissue samples. These methods disregard the spatial organization of the bacterial community and thus valuable information on biofilm aggregate composition, spatial organization, and possible interactions between different species is lost. Hitherto, only few studies have made visual in situ presentations of mixed-species biofilms in chronic infections, which is pivotal for the description of bacterial composition, spatial distribution, and interspecies interaction on the microscale. In order for bacteria to interact (synergism, commensalism, mutualism, competition, etc.) they need to be in close proximity to each other on the scale where they can affect e.g., solute concentrations. We argue that visual proof of mixed species biofilms in chronic infections is scarce compared to what is seen in e.g., environmental biofilms and call for a debate on the importance of mixed-species biofilm in chronic infections.

Comparison of Three Commercial Tools for Metagenomic Shotgun Sequencing Analysis

Metagenomic shotgun sequencing for the identification of pathogens is being increasingly utilized as a diagnostic method. Interpretation of large and complicated data sets is a significant challenge, for which multiple commercial tools have been developed. Three commercial metagenomic shotgun sequencing tools, CosmosID, One Codex, and IDbyDNA, were compared to determine whether they result in similar interpretations of the same sequencing data. We selected 24 diverse samples from a previously characterized data set derived from DNA extracted from biofilms dislodged from the surfaces of resected arthroplasties (sonicate fluid). Sequencing data sets were analyzed using the three commercial tools and compared to culture results and prior metagenomic analysis interpretation. Identical interpretations from all three tools occurred for 6 samples. The total number of species identified included 28 by CosmosID, 59 by One Codex, and 41 by IDbyDNA. All of the tools performed similarly in detecting those microorganisms identified by culture, including polymicrobial mixes. These data show that while all of the tools performed well overall, there were some differences, particularly in their predilection for identifying low-abundance or contaminant organisms as present.

Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods

Introduction. Prosthetic joint infections (PJIs) are challenging to treat therapeutically because the infectious agents often are resistant to antibiotics and capable of abundant growth in surface-attached biofilms. Though infection rates are low, ca. 1-2 %, the overall increase in the sheer number of joint replacement surgeries results in an increase in patients at risk.Aims. This study investigates the consensus of microbial species comprising PJI ecology, which is currently lacking.Methodology. In this study, PJI populations from seven patients were analysed using combined culturing and whole-genome shotgun sequencing (WGSS) to establish population profiles and compare WGSS and culture methods for detection and identification of the PJI microbiome.Results. WGSS detected strains when culture did not, notably dormant, culture-resistant and rare microbes. The CosmosID algorithm was used to predict micro-organisms present in the PJI and discriminate contaminants. However, culturing indicated the presence of microbes falling below the WGSS algorithm threshold. In these instances, microbes cultured are believed to be minor species. The two strategies were combined to build a population profile.Conclusions. Variability between and among PJIs showed that most infections were distinct and unique. Comparative analysis of populations revealed PJIs to form clusters that were related to, but separate from, vaginal, skin and gut microbiomes. Fungi and protists were detected by WGSS, but the role of fungi is just beginning to be understood and for protists it is unknown. These micro-organisms and their novel and strain-specific microbial interactions remain to be determined in current clinical tests.

Comparative study of cultures and next-generation sequencing in the diagnosis of shoulder prosthetic joint infections

BACKGROUND

Serum and synovial markers used to diagnose lower extremity prosthetic joint infection (PJI) have performed poorly for shoulder PJI. As a result, diagnosis is commonly reliant on the accuracy of positive or negative cultures. Next-generation sequencing (NGS) can sequence an entire bacterial genome. This study was conducted to determine the correlation between NGS and routine cultures in revision shoulder arthroplasty.

METHODS

All patients undergoing revision shoulder arthroplasty were prospectively enrolled. In a standardized manner, tissue samples were transferred immediately into sterile specimen containers and transported for culture and NGS (MicroGen Dx, Lubbock, TX, USA). Infection definitions using culture and NGS were analyzed for concordance.

RESULTS

There were 44 total revision arthroplasty cases included. There were no cases of polymicrobial culture results. Cutibacterium (formerly Propionibacterium) acnes was the most common bacterial species cultured (8 of 13 [61.5%]) and identified by NGS (12 of 17 [70.1%]) in cases of definite and probable infection. The concordance (κ) between the 2 diagnostic criteria for defining infection that included culture or NGS was 0.333 (fair). There were significantly more cases of probable contaminants when cultures (10 of 44 [22.7%]) were used in the definition of infection compared with NGS (0 of 44 [0%]; P = .001).

DISCUSSION

Culture data from revision shoulder arthroplasty cases commonly yields monomicrobial results; whereas, NGS data suggests that bacterial loads in revision arthroplasty are most commonly polymicrobial. In addition, a definition of infection that uses cultures is more prone to "probable contaminants" than NGS. Significant uncertainty remains about our current methods of diagnosing shoulder PJI.

Activities of Combinations of Antistaphylococcal Antibiotics with Fusidic Acid against Staphylococcal Biofilms in In Vitro Static and Dynamic Models

Staphylococcal biofilms are a major cause of therapeutic failure, especially when caused by multiresistant strains. Oral fusidic acid is currently being redeveloped in the United States for skin, skin structure, and orthopedic infections, in which biofilms play a major role. The aim of this study was to examine the activity of fusidic acid alone or combined with other antistaphylococcal drugs against biofilms made by a reference strain and five clinical isolates of Staphylococcus aureus or Staphylococcus epidermidis in in vitro static and dynamic models (microtiter plates and a CDC reactor) exposed to clinically relevant concentrations. In microtiter plates, antibiotics alone were poorly active, with marked differences among strains. At concentrations mimicking the free-drug human maximum concentration of drug in serum (C_max), the combination of fusidic acid with linezolid, daptomycin, or vancomycin resulted in increased activity against 4 to 5 strains, while the combination with doxycycline, rifampin, or moxifloxacin increased activity against 1 to 3 strains only. In the CDC reactor, biofilms were grown under constant flow and antibiotic concentrations decreased over time according to human elimination rates. A bactericidal effect was obtained when fusidic acid was combined with daptomycin or linezolid, but not with vancomycin. The higher tolerance of biofilms to antibiotics in the CDC reactor is probably attributable to the more complex architecture they adopt when growing under constant flow. Because biofilms grown in the CDC reactor are considered more similar to those developing in vivo, the data support further testing of combinations of fusidic acid with daptomycin or linezolid in models pertinent to chronic skin, skin structure, or orthopedic infections.

Differential Contributions of Specimen Types, Culturing, and 16S rRNA Sequencing in Diagnosis of Prosthetic Joint Infections

Prosthetic joint failure is mainly caused by infection, aseptic failure (AF), and mechanical problems. Infection detection has been improved with modified culture methods and molecular diagnostics. However, comparisons between modified and conventional microbiology methods are difficult due to variations in specimen sampling. In this prospective, multidisciplinary study of hip or knee prosthetic failures, we assessed the contributions of different specimen types, extended culture incubations, and 16S rRNA sequencing for diagnosing prosthetic joint infections (PJI). Project specimens included joint fluid (JF), bone biopsy specimens (BB), soft-tissue biopsy specimens (STB), and swabs (SW) from the prosthesis, collected in situ, and sonication fluid collected from prosthetic components (PC). Specimens were cultured for 6 (conventional) or 14 days, and 16S rRNA sequencing was performed at study completion. Of the 156 patients enrolled, 111 underwent 114 surgical revisions (cases) due to indications of either PJI (n = 43) or AF (n = 71). Conventional tissue biopsy cultures confirmed PJI in 28/43 (65%) cases and refuted AF in 3/71 (4%) cases; one case was not evaluable. Based on these results, minor diagnostic adjustments were made. Fourteen-day cultures of JF, STB, and PC specimens confirmed PJI in 39/42 (93%) cases, and 16S rRNA sequencing confirmed PJI in 33/42 (83%) cases. One PJI case was confirmed with 16S rRNA sequencing alone and five with cultures of project specimens alone. These findings indicated that JF, STB, and PC specimen cultures qualified as an optimal diagnostic set. The contribution of sequencing to diagnosis of PJI may depend on patient selection; this hypothesis requires further investigation.

Diagnosis of Periprosthetic Joint Infection: The Potential of Next-Generation Sequencing

BACKGROUND

Next-generation sequencing is a well-established technique for sequencing of DNA and has recently gained attention in many fields of medicine. Our aim was to evaluate the accuracy of next-generation sequencing in identifying the causative organism(s) in patients with periprosthetic joint infection.

METHODS

In this prospective study, samples were collected from 65 revision arthroplasties (39 knees and 26 hips) and 17 primary arthroplasties (9 hips and 8 knees). Synovial fluid, deep tissue, and swabs were obtained at the time of the surgical procedure and were shipped to the laboratory for next-generation sequencing. Deep-tissue specimens were also sent to the institutional laboratory for culture. Sensitivity and specificity were calculated for next-generation sequencing, using the Musculoskeletal Infection Society (MSIS) definition of periprosthetic joint infection as the standard.

RESULTS

In 28 revisions, the cases were considered to be infected; cultures were positive in 17 cases (60.7% [95% confidence interval (CI), 40.6% to 78.5%]), and next-generation sequencing was positive in 25 cases (89.3% [95% CI, 71.8% to 97.7%]), with concordance between next-generation sequencing and culture in 15 cases. Among the 11 cases of culture-negative periprosthetic joint infection, next-generation sequencing was able to identify an organism in 9 cases (81.8% [95% CI, 48.2% to 97.7%]). Next-generation sequencing identified microbes in 9 (25.0% [95% CI, 12.1% to 42.2%]) of 36 aseptic revisions with negative cultures and in 6 (35.3% [95% CI, 14.2% to 61.7%]) of 17 primary total joint arthroplasties. Next-generation sequencing detected several organisms in most positive samples. However, in the majority of patients who were infected, 1 or 2 organisms were dominant.

CONCLUSIONS

Next-generation sequencing may be a useful adjunct in identification of the causative organism(s) in culture-negative periprosthetic joint infection. Our findings suggest that some cases of monomicrobial periprosthetic joint infection may have additional organisms that escape detection when culture is used. Further study is required to determine the clinical implications of isolated organisms in samples from patients who are not thought to be infected.

LEVEL OF EVIDENCE

Diagnostic Level I. See Instructions for Authors for a complete description of levels of evidence.

Prevention of Propionibacterium acnes biofilm formation in prosthetic infections in vitro

BACKGROUND

The role of Propionibacterium acnes in shoulder arthroplasty and broadly in orthopedic prosthetic infections has historically been underestimated, with biofilm formation identified as a key virulence factor attributed to invasive isolates. With an often indolent clinical course, P acnes infection can be difficult to detect and treat. This study investigates absorbable cements loaded with a broad-spectrum antibiotic combination as an effective preventive strategy to combat P acnes biofilms.

METHODS

P acnes biofilm formation on an unloaded synthetic calcium sulfate (CaSO₄) bone void filler cement bead was evaluated by scanning electron microscopy over a period of 14 days. Beads loaded with tobramycin alone or vancomycin alone (as comparative controls) and beads loaded with a vancomycin-tobramycin dual treatment were assessed for their ability to eradicate planktonic P acnes, prevent biofilm formation, and eradicate preformed biofilms using a combination of viable-cell counts, confocal microscopy, and scanning electron microscopy.

RESULTS

P acnes surface colonization and biofilm formation on unloaded CaSO₄ beads was slow. Beads loaded with antibiotics were able to kill planktonic cultures of 10⁶ colony-forming units/mL, prevent bacterial colonization, and significantly reduce biofilm formation over periods of weeks. Complete eradication of established biofilms was achieved with a contact time of 1 week.

CONCLUSIONS

This study demonstrates that antibiotic-loaded CaSO₄ beads may represent an effective antibacterial and antibiofilm strategy to combat prosthetic infections in which P acnes is involved.

Advancements in Diagnosing Periprosthetic Joint Infections after Total Hip and Knee Arthroplasty

Periprosthetic joint infection (PJI) is a complication of total joint arthroplasty that is challenging to diagnose. Currently, there is no "gold standard" for definite diagnosis of PJI. A multi-criteria definition has been described for PJI based on microbiology cultures, serum markers, such as erythrocyte sedimentation rate and C-reactive protein (CRP), synovial fluid biomarkers, such as leukocyte esterase and histopathology assessment of the periprosthetic tissue. The conventional serum markers are generally nonspecific and can be elevated in inflammatory conditions. Therefore, they cannot be relied on for definite diagnosis of PJI. Hence, with the use of proteomics, synovial fluid biomarkers such as α-defensin, IL-6, and CRP have been proposed as more accurate biomarkers for PJI. Current methods to culture micro-organisms have several limitations, and can be false-negative and false-positive in a considerable number of cases. In an attempt to improve culture sensitivity, diagnostic methods to target biofilms have recently been studied. The understanding of the concept of biofilms has also allowed for the development of novel techniques for PJI diagnosis, such as visualizing biofilms with fluorescent in-situ hybridization and detection of bacteria via DNA microarray. Lastly, the use of amplification-based molecular techniques has provided methods to identify specific species of bacteria that cause culture-negative PJI. While diagnosing PJI is difficult, these advances could be valuable tools for clinicians.

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections

Background

Necrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold standard for identification of pathogens is culture; however molecular methods for identification of microorganisms may provide a more rapid result and may be able to identify additional microorganisms that are not detected by culture.

Methods

In this study, tissue samples (n = 20) obtained after debridement of 10 patients with NSTI were analyzed by standard culture, fluorescence in situ hybridization (FISH) and multiple molecular methods. The molecular methods included analysis of microbial diversity by 1) direct 16S and D2LSU rRNA gene Microseq 2) construction of near full-length 16S rRNA gene clone libraries with subsequent Sanger sequencing for most samples, 3) the Ibis T5000 biosensor and 4) 454-based pyrosequencing. Furthermore, quantitative PCR (qPCR) was used to verify and determine the relative abundance of Streptococcus pyogenes in samples.

Results

For 70 % of the surgical samples it was possible to identify microorganisms by culture. Some samples did not result in growth (presumably due to administration of antimicrobial therapy prior to sampling). The molecular methods identified microorganisms in 90 % of the samples, and frequently detected additional microorganisms when compared to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods.

Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also made including infection by a) Acinetobacter baumannii, b) Streptococcus pneumoniae, and c) fungi, mycoplasma and Fusobacterium necrophorum.

Conclusion

The study emphasizes that many pathogens can be involved in NSTIs, and that no specific “NSTI causing” combination of species exists. This means that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially for fulminant life-threatening infections such as NSTI.

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing

Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing.

In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study

Background

Staphylococcus aureus gene expression has been sparsely studied in deep-sited infections in humans. Here, we characterized the staphylococcal transcriptome in vivo and the joint fluid metabolome in a prosthetic joint infection with an acute presentation using deep RNA sequencing and nuclear magnetic resonance spectroscopy, respectively. We compared our findings with the genome, transcriptome and metabolome of the S. aureus joint fluid isolate grown in vitro.

Result

From the transcriptome analysis we found increased expression of siderophore synthesis genes and multiple known virulence genes. The regulatory pattern of catabolic pathway genes indicated that the bacterial infection was sustained on amino acids, glycans and nucleosides. Upregulation of fermentation genes and the presence of ethanol in joint fluid indicated severe oxygen limitation in vivo.

Conclusion

This single case study highlights the capacity of combined transcriptome and metabolome analyses for elucidating the pathogenesis of prosthetic infections of major clinical importance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0695-6) contains supplementary material, which is available to authorized users.

Bacterial and fungal DNA extraction from blood samples: manual protocols

A critical point of molecular diagnosis of systemic infections is the method employed for the extraction of microbial DNA from blood. A DNA isolation method has to be able to fulfill several fundamental requirements for optimal performance of diagnostic assays. First of all, low- and high-molecular-weight substances of the blood inhibitory to downstream analytical reactions like PCR amplification have to be removed. This includes human DNA which is a known source of false-positive results and factor decreasing the analytical sensitivity of PCR assays by unspecific primer binding. At the same time, even extremely low amounts of microbial DNA need to be supplied to molecular diagnostic assays in order to detect low pathogen loads in the blood. Further, considering the variety of microbial etiologies of sepsis, a method should be capable of lysing Gram-positive, Gram-negative, and fungal organisms. Last, extraction buffers, reagents, and consumables have to be free of microbial DNA which leads to false-positive results. Here, we describe manual methods which allow the extraction of microbial DNA from small- and large-volume blood samples for the direct molecular analysis of pathogen.

Treating periprosthetic joint infections as biofilms: key diagnosis and management strategies

Considerable evidence suggests that microbial biofilms play an important role in periprosthetic joint infection (PJI) pathogenesis. Compared to free-floating planktonic bacteria, biofilm bacteria are more difficult to culture and possess additional immune-evasive and antibiotic resistance mechanisms, making infections harder to detect and eradicate. This article reviews cutting-edge advances in biofilm-associated infection diagnosis and treatment in the context of current PJI guidelines and highlights emerging technologies that may improve the efficacy and reduce costs associated with PJI. Promising PJI diagnostic tools include culture-independent methods based on sequence comparisons of the bacterial 16S ribosomal RNA gene, which offer higher throughput and greater sensitivity than culture-based methods. For therapy, novel methods based on disrupting biofilm-specific properties include quorum quenchers, bacteriophages, and ultrasound/electrotherapy. Since biofilm infections are not easily detected or treated by conventional approaches, molecular diagnostic techniques and next-generation antibiofilm treatments should be integrated into PJI clinical practice guidelines in the near future.

'All in a box' a concept for optimizing microbiological diagnostic sampling in prosthetic joint infections

Background

Accurate microbial diagnosis is crucial for effective management of prosthetic joint infections. Culturing of multiple intraoperative tissue samples has increased diagnostic accuracy, but new preparatory techniques and molecular methods hold promise of further improvement. The increased complexity of sampling is, however, a tough challenge for surgeons and assistants in the operation theatre, and therefore we devised and tested a new concept of pre-packed boxes with a complete assortment of swabs, vials and additional tools needed in the operating theatre for non-standard samples during a clinical study of prosthetic joint infections.

Findings

The protocol for the clinical study required triplicate samples of joint fluid, periprosthetic tissue, bone tissue, and swabs from the surface of the prosthesis. Separate boxes were prepared for percutaneous joint puncture and surgical revision; the latter included containers for prosthetic components or the entire prosthesis. During a 2-year project period 164 boxes were used by the surgeons, 98 of which contained a complete set of samples. In all, 1508 (89%) of 1685 scheduled samples were received.

Conclusion

With this concept a high level of completeness of sample sets was achieved and thus secured a valid basis for evaluation of new diagnostics. Although enthusiasm for the project may have been a contributing factor, the extended project period suggests that the ‘All in a box’ concept is equally applicable in routine clinical settings with standardized but complex diagnostic sampling.

Diversity of patients microflora on orthopaedic and dental implants

The aim of this study was to compare the diversity of microbial colonization on implant material from different individuals. Eubacterial DNA was extracted, separated and sequenced from orthopaedic metallic implant material, tissues or body fluids, and skin of 4 patients as well as from identical dental cement material from 10 individuals after revision and routine removal. Additionally, the composition of the bacterial population of the dental cement and the oral swab sample from one individual after direct extraction of bacterial DNA was compared to extraction after conventional microbiological enrichment. The latter investigation proved that the commonly used cultivation technique gave different results than direct extraction of DNA, especially as regards the detection of anaerobes. Comparing the bacterial colonization of implant materials from different patients showed significant individual diversity. The common focus on a constricted pathogen spectrum may have to be expanded toward a multispecies population. Moreover, the dependence of the bacterial population on the individual host has to be integrated in discussing implant colonization and infection.

Ribosomal PCR and DNA sequencing for detection and identification of bacteria: experience from 6 years of routine analyses of patient samples

The use of broad range PCR and DNA sequencing of bacterial 16S ribosomal RNA genes for routine diagnostics of bacterial infections was evaluated. Here, the results from more than 2600 analyses during a 6-year period (2003-2009) are presented. Almost half of the samples were from joints and bones, and the second most frequent origin of samples was from the central nervous system. Overall, 26% of all samples were positive for bacterial DNA and bacterial identification was obtained in 80% of the PCR-positive samples by subsequent DNA sequencing. Ambiguous species identification was noticed among non-haemolytic streptococci, especially within the mitis group. The data show that ribosomal PCR with subsequent DNA sequencing of the PCR product is a most valuable supplement to culture for identifying bacterial agents of both acute and prolonged infections. However, some bacteria, including non-haemolytic streptococci, may not be precisely identified.