Impact of a molecular approach to improve the microbiological diagnosis of infective heart valve endocarditis

Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood

Background

The introduction of benchtop sequencers has made adoption of whole genome sequencing possible for a broader community of researchers than ever before. Concurrently, metagenomic sequencing (MGS) is rapidly emerging as a tool for interrogating complex samples that defy conventional analyses. In addition, next-generation sequencers are increasingly being used in clinical or related settings, for instance to track outbreaks. However, information regarding the analytical sensitivity or limit of detection (LoD) of benchtop sequencers is currently lacking. Furthermore, the specificity of sequence information at or near the LoD is unknown.

Results

In the present study, we assess the ability of three next-generation sequencing platforms to identify a pathogen (viral or bacterial) present in low titers in a clinically relevant sample (blood). Our results indicate that the Roche-454 Titanium platform is capable of detecting Dengue virus at titers as low as 1X10^2.5 pfu/mL, corresponding to an estimated 5.4X10⁴ genome copies/ml maximum. The increased throughput of the benchtop sequencers, the Ion Torrent PGM and Illumina MiSeq platforms, enabled detection of viral genomes at concentrations as low as 1X10⁴ genome copies/mL. Platform-specific biases were evident in sequence read distributions as well as viral genome coverage. For bacterial samples, only the MiSeq platform was able to provide sequencing reads that could be unambiguously classified as originating from Bacillus anthracis.

Conclusion

The analytical sensitivity of all three platforms approaches that of standard qPCR assays. Although all platforms were able to detect pathogens at the levels tested, there were several noteworthy differences. The Roche-454 Titanium platform produced consistently longer reads, even when compared with the latest chemistry updates for the PGM platform. The MiSeq platform produced consistently greater depth and breadth of coverage, while the Ion Torrent was unequaled for speed of sequencing. None of the platforms were able to verify a single nucleotide polymorphism responsible for antiviral resistance in an Influenza A strain isolated from the 2009 H1N1 pandemic. Overall, the benchtop platforms perform well for identification of pathogens from a representative clinical sample. However, unlike identification, characterization of pathogens is likely to require higher titers, multiple libraries and/or multiple sequencing runs.

Molecular diagnosis of bacterial infective endocarditis in tabriz, azerbaijan

INTRODUCTION

The aim of this study was to analyze a PCR based approach for detection of infective endocarditis in Azerbaijan.

METHODS

Ten aortic valves, 8 mitral valves and 2 tricuspid valves, were analyzed for the presence of bacterial infective endocarditis using Gram staining, culture and PCR methods.

RESULTS

Of the 20 valves, 5 and 4 cases were positive by Gram staining and culture assay, respectively. Bacterial DNA was positive in 12 of the 20 valves (60%) by broad-spectrum PCR. Direct sequencing for species identification was possible in 10 cases.

CONCLUSION

PCR and direct molecular identification of the etiological agents responsible for infective endocarditis may enable specific treatment to begin at an earlier phase of the disease.

Advantages and limitations of ribosomal RNA PCR and DNA sequencing for identification of bacteria in cardiac valves of danish patients

Studies on the value of culture-independent molecular identification of bacteria in cardiac valves are mostly restricted to comparing agreement of identification to what is obtained by culture to the number of identified bacteria in culture-negative cases. However, evaluation of the usefulness of direct molecular identification should also address weaknesses, their relevance in the given setting, and possible improvements.

In this study cardiac valves from 56 Danish patients referred for surgery for infective endocarditis were analysed by microscopy and culture as well as by PCR targeting part of the bacterial 16S rRNA gene followed by DNA sequencing of the PCR product. PCR and DNA sequencing identified significant bacteria in 49 samples from 43 patients, including five out of 13 culture-negative cases. No rare, exotic, or intracellular bacteria were identified. There was a general agreement between bacterial identity obtained by ribosomal PCR and DNA sequencing from the valves and bacterial isolates from blood culture. However, DNA sequencing of the 16S rRNA gene did not discriminate well among non-haemolytic streptococci, especially within the Streptococcus mitis group.

Ribosomal PCR with subsequent DNA sequencing is an efficient and reliable method of identifying the cause of IE, but exact species identification of some of the most common causes, i.e. non-haemolytic streptococci, may be improved with other molecular methods.

Comparison of MALDI-TOF MS and VITEK 2 system for laboratory diagnosis of Granulicatella and Abiotrophia species causing invasive infections

Granulicatella and Abiotrophia spp. were known as nutritionally variant streptococci (NVS). Such strains have caused major diagnostic difficulties due to fastidious culturing and unspecific colony morphology. The present study is aimed at comparing the performance of laboratory available diagnostic methods for NVS isolates and determining the antimicrobial susceptibility of these isolates. Fourteen clinical invasive isolates, consisting of 10 Granulicatella adiacens, 1 Granulicatella elegans, and 3 Abiotrophia defectiva were in parallel analyzed by 2 matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems, i.e., Bruker MS and Vitek MS, as well as Vitek 2 for the species determination. 16S rRNA gene sequencing was applied as a reference method. The Vitek MS gave correct identification for all 14 isolates. The Bruker MS could correctly identify 8/10 G. adiacens, 0/1 G. elegans, and 3/3 A. defectiva isolates at the first analysis occasion, and all 14 isolates became identifiable after repeated tests. The Vitek 2 system could identify 6/10 G. adiacens, 1/1 G. elegans, and 2/3 A. defectiva isolates at the species level. Antimicrobial susceptibilities of 11 antibiotics were determined by Etest. Resistance against ciprofloxacin, ceftriaxone, rifampicin, and tetracycline were observed in 4, 10, 4, and 1 isolates, respectively. In conclusion, MALDI-TOF MS is a useful tool for the rapid diagnosis of NVS. Phenotypic testing by Vitek 2 is only partially effective for the accurate identification of such strains. The emergence of resistant NVS isolates indicates the necessity of monitoring antimicrobial susceptibilities of such uncommon pathogens.

Contemporary drug treatment of infective endocarditis

Infective endocarditis (IE) occurs at a rate of approximately 0.9-6.2 per 100,000 people per year and is associated with a high morbidity and mortality despite advancements in antibiotic and surgical treatments. The general approach to the treatment of IE is initial clinical stabilization, early acquisition of blood cultures, and definitive medical and/or surgical treatment. Surgical consultation should be obtained early when indicated in order to determine the best treatment approach for each individual patient. Surgery is indicated in most cases of prosthetic valve endocarditis, Staphylococcus aureus endocarditis, fungal endocarditis, and endocarditis associated with large vegetations (≥10 mm). Initial antibiotic therapy for IE should be targeted to the culprit microorganism; however, in some cases, empiric therapy must be initiated prior to definitive culture diagnosis. Empiric antibiotics should be targeted toward the most likely pathogens, including staphylococci, streptococci, and enterococci species. Here we discuss the recommended antibiotic regimens for the most common causes of IE as indicated by the American Heart Association and European Society of Cardiology. In 2008, the ACC/AHA published guideline updates on the treatment of valvular heart disease, which included a focused update on endocarditis prophylaxis. According to the most recent guidelines, the number of patients who require antibiotic prophylaxis has decreased substantially. Treatment of IE should be targeted toward the causative microorganism and must be based on the type and location of valve involved (native, prosthetic, left or right sided), the clinical status of the patient, and the likelihood for clinical success. This requires a collaborative effort from multiple medical specialties including infectious disease specialists, cardiologists, and cardiothoracic surgeons.

PCR-electrospray ionization time-of-flight mass spectrometry: a new tool for the diagnosis of infective endocarditis from heart valves

A polymerase chain reaction with an injection of the amplicons in an electrospray ionization mass spectrometry (PCR-ESI-MS) technique was evaluated for the diagnosis of bacterial and yeast pathogens on 13 cardiac valves with suspected endocarditis. At the moment of surgery, 3/13 PCR-ESI-MS results matched with microbiological documentation. Nine PCR-ESI-MS results correlated with Duke's criteria, leukocytes, C-reactive protein and blood cultures before surgery. The PCR-ESI-MS result of the last valve failed to confirm the blood culture result obtained fifteen days before. With speed and accuracy, this method may be useful to assert microbiological identification and adapt treatment.

Pacemaker lead infection and related bacteraemia caused by normal and small colony variant phenotypes of Bacillus licheniformis

Here, we report what we believe to be the first case of bacteraemia with small colony variants of Bacillus licheniformis related to a pacemaker lead infection by B. licheniformis displaying the normal phenotype. Arbitrarily primed PCR analysis showed a clonal strain. The infection was cured after the removal of the infected device.

Are histopathological findings of diagnostic value in native valve endocarditis?

BACKGROUND

Optimal management of infective endocarditis (IE) depends on the early detection of IE-causing pathogens and on appropriate antimicrobial and surgical therapy. The current guidelines of the European Society of Cardiology (ESC) recommend histopathological examination as the gold standard for diagnosing IE Habib et al. (Eur Heart J 30:2369-2413, 2005). We hypothesize that histopathological findings do not provide additional information relevant to clinical decision-making.

METHODS

We retrospectively reviewed a cohort of patients who had undergone surgery for native valve endocarditis (NVE) at the University Hospital Regensburg between September 1994 and February 2005. All episodes of intraoperatively confirmed endocarditis during this period were included in the study. Data were retrieved from surgical records, microbiological and histopathological reports, and medical files of the treating as well as admitting hospital. Pathogens were correlated with the site of manifestation of the affected heart valve and with clinical and histopathological findings.

RESULTS

A total of 163 episodes of NVE were recorded and entered into our study for analysis. The valves affected were the aortic valve (45 %), the mitral valve (28 %), the aortic and mitral valve (22 %), and other valves (5 %). IE-causing pathogens were Staphylococcus aureus (22 %), viridans streptococci (18 %), enterococci (10 %), streptococci other than Streptococcus viridans (9 %), coagulase-negative staphylococci (5 %), miscellaneous pathogens (4 %), and culture-negative endocarditis (33 %). Infection with S. aureus was associated with high rates of sepsis, septic foci, and embolic events, while patients with enterococcal IE showed the highest rate of abscesses. Mortality rate in all subgroups was low without significant differences. However, histopathological findings correlated poorly with the pathogen involved and showed only few significant associations that were without clinical relevance.

CONCLUSIONS

The clinical presentation of IE depends on the pathogen involved. Among the episodes of NVE examined, the histopathological examination of resected heart valves did not show any pathogen-specific morphological patterns and therefore did not provide any additional information of clinical value. Based on our findings, we recommend complementary cultures of the resected materials (valve tissue, thrombotic material, pacer wire) and implementation of molecular diagnostic methods (e.g., broad-range PCR amplification techniques) instead of histopathological analyses of resected valve tissue.

Differential recovery of phylogenetically disparate microbes from spacecraft-qualified metal surfaces

Universal and species-specific quantitative polymerase chain reaction-based methods were employed to compare the effectiveness of four distinct materials used to collect biological samples from metal surfaces. Known cell densities of a model microbial community (MMC) were deposited onto metal surfaces and subsequently collected with cotton and nylon-flocked swabs for small surface areas and biological sampling kits (BiSKits) and polyester wipes for large surface areas. Ribosomal RNA gene-based quantitative PCR (qPCR) analyses revealed that cotton swabs were superior to nylon-flocked swabs for recovering nucleic acids (i.e., DNA) from small surface areas. Similarly, BiSKits outperformed polyester wipes for sampling large surface areas. Species-specific qPCR results show a differential recovery of rRNA genes of the various MMC constituents, seemingly dependent on the type of sampling device employed. Both cotton swabs and BiSKits recovered the rDNA of all nine of the MMC constituent microbes assayed, whereas nylon-flocked swabs and polyester wipes recovered the rDNA of only six and four of these MMC strains, respectively. The findings of this study demonstrate the importance and proficiency of molecular techniques in gauging the effectiveness and efficiency of various modes of biological sample collection from metal surfaces.

New approaches to sepsis: molecular diagnostics and biomarkers

Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies.

Evaluating treatment options for patients with infective endocarditis: when is it the right time for surgery?

Infective endocarditis remains a life-threatening condition with an unchanging incidence and mortality of nearly 30% at 1 year. Surgery is required in 25–50% of acute infections and 20–40% of patients during convalescence. Operative procedures are often technically challenging and high-risk, often due to coexistent multisystem disease. However, international guidelines provide clear indications for surgical intervention, which are applicable for the majority of patients. These are not, however, supported by particularly robust clinical evidence and decision-making often needs to be tailored to the advancing age of the overall patient cohort, the presence of multisystem disease, comorbidities, prior antibiotic therapy of varying duration and the availability of surgical expertise. Native valve endocarditis will be the initial focus of this article, along with subgroups including prosthetic valve endocarditis. We present the treatment options for patients with infective endocarditis, evaluate the evidence-base that supports current clinical practice and attempt to provide an insight and subsequent recommendations for the timing of surgery.

Rapidly progrediating aortic valve infective endocarditis in an intravenous drug user treated by antibiotics and surgery

We report the case of a 22-year old male, a self-confessed recreational drug user who developed cardiogenic shock because of severe destruction of the aortic valve by rapidly progressive aortic valve endocarditis. The disease progression was acute; in a matter of days, the clinical manifestations were life-threatening necessitating urgent aortic valve replacement surgery. Cultivation revealed Streptococcus viridans as the microbial agent. Subsequent recovery with antibiotic treatment was without complication. This case report shows that immediately performed transoesophageal echocardiography and early consultation with a cardiac surgeon has fundamental importance in diagnosis and management of acute infective endocarditis in haemodynamically instable patients.

A combination of clinical and microbiological management of generalized aggressive periodontitis in primary teeth. A case report

BACKGROUND

Generalized aggressive periodontitis (GAP) in primary teeth is a rare periodontal disease that occurs during or soon after eruption of the primary teeth. An association with systemic diseases is a possibility.

CASE REPORT

A 4-year-old Brazilian girl presented with GAP involving the entire primary dentition. The patient and her parents and sister were subjected to microbiological testing to identify the microorganisms involved in the disease. The patient underwent tooth extraction to eradicate the disease and received a prosthesis for the restoration of masticatory function. After the permanent teeth erupted, fixed orthodontic appliances were place to restore dental arch form and occlusion.

CONCLUSIONS

The results show the importance of an early diagnosis of GAP and of a multidisciplinary approach involving laboratory and clinical management to treat the disease and to restore masticatory function, providing a better quality of life for patients.

Native Cardiac Valve Pathology

Anatomy of the native cardiac valves, reasons for surgical excision and examination, and a summary of the gross examination and documentation are presented. Aortic stenosis, aortic valve regurgitation, tricuspid and pulmonary valve pathology, mitral stenosis, and mitral insufficiency are each presented with an overview, focused anatomy, and discussion of pathologic diagnosis by gross examination and histology.

Improvement of detection of bacterial pathogens in normally sterile body sites with a focus on orthopedic samples by use of a commercial 16S rRNA broad-range PCR and sequence analysis

A new commercially available universal 16S and 18S rRNA gene PCR test, which is followed by sequence analysis of amplicons (SepsiTest), was evaluated for rapid identification of pathogens in the diagnosis of bone and joint infections. Eighty-three orthopedic samples and 21 specimens from other normally sterile body sites collected from 84 patients were analyzed in parallel by culture and PCR for detection of bacteria and fungi. Compared to culture, the diagnostic sensitivity and specificity of PCR were 88.5% and 83.5%, respectively. The detection rate of PCR (34.6%) was higher than that of bacterial culture (25.0%) as a consequence of the presence of fastidious and noncultivable species in samples and antibiotic treatment of patients. Thirteen culture-negative infections were identified by PCR, and PCR was able to detect culture-proven polymicrobial infections. On the other hand, three samples were culture positive but PCR negative. SepsiTest was demonstrated to be a valuable supplemental tool in the rapid detection of bacteria, especially for fastidious and noncultivable organisms, allowing earlier initiation of pathogen-adapted therapy in patients with bone and joint infections.

Granulicatella infection: diagnosis and management

Granulicatella species, along with the genus Abiotrophia, were originally known as 'nutritionally variant streptococci'. They are a normal component of the oral flora, but have been associated with a variety of invasive infections in man and are most noted as a cause of bacterial endocarditis. It is often advised that Granulicatella endocarditis should be treated in the same way as enterococcal endocarditis. We review here the published data concerning diagnosis and treatment of Granulicatella infection, and include some observations from local cases, including four cases of endocarditis.

Management of infective endocarditis: challenges and perspectives

Despite improvements in medical and surgical therapies, infective endocarditis is associated with poor prognosis and remains a therapeutic challenge. Many factors affect the outcome of this serious disease, including virulence of the microorganism, characteristics of the patients, presence of underlying disease, delays in diagnosis and treatment, surgical indications, and timing of surgery. We review the strengths and limitations of present therapeutic strategies and propose future directions for better management of endocarditis according to the most recent research. Novel perspectives on the management of endocarditis are emerging and offer hope for decreasing the rate of residual deaths by accelerating the process of diagnosis and risk stratification, reducing delays in starting antimicrobial therapy, rapid transfer of high-risk patients to specialised medico-surgical centres, development of new surgical methods, and close long-term follow-up.

Molecular diagnosis of sepsis

INTRODUCTION

Current management of sepsis relies on the early detection and early administration of antimicrobials. This requires detection of pathogens earlier than conventional blood cultures and recognition of the immune status of the host earlier than the conventional biomarkers. This can be achieved by molecular techniques.

AREAS COVERED

Molecular diagnosis of pathogens is based on either rapid detection of pathogens grown in blood cultures or direct use of whole blood and blood products. Molecular diagnosis of the constellation of activations and inhibitions of pathways implicated in cellular processes can be achieved by gene profiling of a large array of genes.

EXPERT OPINION

Molecular microbial diagnosis enables rapid identification and precedes results obtained by conventional culture methods. Its role can be proved more useful in sepsis caused by specific microorganisms such as fungi performed by PMA-FISH and MALDI-TOF MS. Molecular techniques using blood aim for rapid pathogen identification. However, the provided information regarding the antimicrobial susceptibility of the pathogen is limited. Gene profiling in sepsis provides individualized information for the activation or inhibition of pathways of a variety of cellular processes. The transcriptome information is difficult to interpret in everyday clinical practice particularly on how information translates to patient needs.

Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology

Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.

Guidelines for the diagnosis and antibiotic treatment of endocarditis in adults: a report of the Working Party of the British Society for Antimicrobial Chemotherapy

The BSAC guidelines on treatment of infectious endocarditis (IE) were last published in 2004. The guidelines presented here have been updated and extended to reflect developments in diagnostics, new trial data and the availability of new antibiotics. The aim of these guidelines, which cover both native valve and prosthetic valve endocarditis, is to standardize the initial investigation and treatment of IE. An extensive review of the literature using a number of different search criteria has been carried out and cited publications used to support any changes we have made to the existing guidelines. Publications referring to in vitro or animal models have only been cited if appropriate clinical data are not available. Randomized, controlled trials suitable for the development of evidenced-based guidelines in this area are still lacking and therefore a consensus approach has again been adopted for most recommendations; however, we have attempted to grade the evidence, where possible. The guidelines have also been extended by the inclusion of sections on clinical diagnosis, echocardiography and surgery.

Comparative molecular and microbiological diagnosis of 19 infective endocarditis cases in which causative microbes were identified by PCR-based DNA sequencing from the excised heart valves

Infective endocarditis (IE) is traditionally diagnosed by microbiological analysis of blood cultures, following which therapeutic antibiotics are chosen based on antimicrobial sensitivity tests. However, such conventional techniques do not always lead to an accurate etiological diagnosis. Recently, PCR analysis of the 16S rRNA gene has been employed to identify organisms isolated from excised heart valves. In this study, we analyzed 19 valve samples from patients with confirmed IE, as identified by Duke's criteria. Using broad-range PCR amplification, followed by direct gene sequencing, pathological agents were identified in all samples. Although blood cultures yielded negative results in 4 cases, PCR analysis of valve samples showed positive identification of causative organisms. In 3 cases, there was a difference between blood culture and PCR in identification of pathological agents, which are likely to be misidentified by the conventional method based on the phenotypic database. Postoperative antibiotics were chosen considering the severity of lesions and the results of PCR, Gram staining, and valve cultures. All patients were cured without relapse. The broad-range PCR method was therefore beneficial for the management of IE because it enabled us to identify pathogens directly from the site of infection, even organisms that were difficult to culture or likely to be misidentified by the conventional culture method. Identification of the agents provided precise knowledge of the microbiological spectrum involved in the cases of IE.

Molecular methods for diagnosis of infective endocarditis

Infective endocarditis (IE) is a life-threatening disease associated with high mortality. Conventional microbiologic diagnosis is based mainly on culture-dependent methods that often fail because of previous antibiotic therapy or the involvement of fastidious or slowly growing microorganisms. In recent years, molecular techniques entered the field of routine diagnostics. Amplification-based methods proved useful for detection of microorganisms in heart valve tissue. More recently, they were applied to blood samples from patients with IE. Direct detection of microorganisms in valve specimens by fluorescence in situ hybridization allowed identification of the causative agent and simultaneous visualization of complex microbial communities. These techniques will gain more importance in the near future, provided that procedures are standardized and results are interpreted with caution. With this review, we intend to give an overview of the impact and limitations of molecular techniques for the diagnosis of IE, including a focus on recent developments.

Real-time PCR assays compared to culture-based approaches for identification of aerobic bacteria in chronic wounds

Chronic wounds cause substantial morbidity and disability. Infection in chronic wounds is clinically defined by routine culture methods that can take several days to obtain a final result, and may not fully describe the community of organisms or biome within these wounds. Molecular diagnostic approaches offer promise for a more rapid and complete assessment. We report the development of a suite of real-time PCR assays for rapid identification of bacteria directly from tissue samples. The panel of assays targets 14 common, clinically relevant, aerobic pathogens and demonstrates a high degree of sensitivity and specificity using a panel of organisms commonly associated with chronic wound infection. Thirty-nine tissue samples from 29 chronic wounds were evaluated and the results compared with those obtained by culture. As revealed by culture and PCR, the most common organisms were methicillin-resistant Staphylococcus aureus (MRSA) followed by Streptococcus agalactiae (Group B streptococcus) and Pseudomonas aeruginosa. The sensitivities of the PCR assays were 100% and 90% when quantitative and qualitative culture results were used as the reference standard, respectively. The assays allowed the identification of bacterial DNA from ten additional organisms that were not revealed by quantitative or qualitative cultures. Under optimal conditions, the turnaround time for PCR results is as short as 4-6 h. Real-time PCR is a rapid and inexpensive approach that can be easily introduced into clinical practice for detection of organisms directly from tissue samples. Characterization of the anaerobic microflora by real-time PCR of chronic wounds is warranted.

A case of brain abscess caused by Propionibacterium acnes 13 months after neurosurgery and confirmed by 16S rRNA gene sequencing

Propionibacterium acnes is a gram-positive anaerobic bacillus and a normal inhabitant of the skin. Although it is often considered a contaminant of blood cultures, it can occasionally cause serious infections, including postoperative central nervous system infections. Here, we report the case of a 70-yr-old man who developed a large cerebral abscess caused by P. acnes 13 months after neurosurgery. Immediate gram staining of the pus from his brain revealed the presence of gram-positive coccobacilli. However, colony growth was observed only after 5 days of culture. Therefore, we performed 16S rRNA gene sequencing of the pus specimen. The isolate was identified as P. acnes. The colonies developed 9 days after the initial culture. The API Rapid ID 32A test (bioMérieux, France) was performed using a colony, but an unacceptable profile was obtained. Then, the pus was transferred into the enrichment broths of the BACTEC FX (Becton Dickinson, USA) and BacT/Alert 3D (bioMérieux, Organon Teknika, USA) systems, but only the BACTEC FX system could detect growth after 5 days. We performed 16S rRNA gene sequencing and API Rapid 32A profiling with a colony recovered from Brucella agar, which was inoculated with the microbial growth in the enrichment broth from the BACTEC FX system. The organism was identified as P. acnes by both methods. This case suggests that 16S rRNA gene sequencing may be a useful alternative for identifying slowly growing P. acnes from specimens that do not show growth after 5 days of culture.

Culture negative mitral valve endocarditis caused by Neisseria gonorrhoeae confirmed by 16S rDNA sequence analysis of resected valvular tissue

Infective endocarditis is a dynamic disease with changing epidemiology and diagnostic strategies. Culture negative endocarditis poses a particular problem for clinicians regarding appropriate antimicrobial therapy and adequate duration of therapy. Utilization of nucleic acid amplification techniques and subsequent sequencing has provided clinicians an alternative to traditional phenotypic microbial identification which has been extremely useful in identification of fastidious organisms. We report a case of a young male with culture negative native mitral valve endocarditis and subsequent 16S rDNA sequencing of Neisseria gonorrhoeae from excised valvular tissue and embolic material. Identification of this organism with novel nucleic acid amplification and 16S rDNA sequence analysis techniques permitted targeted antibiotic therapy and successful treatment of this potentially fatal disease.

Evaluation of a multiplex real-time PCR assay for detecting pathogens in cardiac valve tissue in patients with endocarditis

With a novel real-time multiplex polymerase chain reaction test, the LightCycler SeptiFast® test, 25 bacterial and fungal species can be identified directly in blood. The SeptiFast® test has been used for rapid etiologic diagnosis in infectious endocarditis using blood samples but has not been evaluated directly on cardiac vegetations in patients being treated for infectious endocarditis. We prospectively analyzed 15 samples of heart valve tissue with active infectious endocarditis using the SeptiFast® test and compared the test's sensitivity with that of blood culture, valve tissue culture, and the SeptiFast® test in blood. The sensitivity of the SeptiFast test in heart valve tissue was 100%. The test results confirmed the diagnosis obtained using blood culture in 13 cases and identified the pathogen in 2 cases where blood culture tested negative. The sensitivity of the SeptiFast® test in heart valve tissue was greater than that obtained with conventional culture of vegetations or with the SeptiFast test in blood.

Staphylococcus aureus invades the epithelium in nasal polyposis and induces IL-6 in nasal epithelial cells in vitro

BACKGROUND

Staphylococcus aureus has been associated with chronic rhinosinusitis with nasal polyps (CRSwNP) pathogenesis but its role is still controversially discussed. Here, we demonstrate S. aureus detection in the mucosa of CRSwNP. In addition, intracellular residency of S. aureus in nasal polyp epithelial cells (NPECs) and its capability to induce TH-2 cytokines were analyzed in vitro.

METHODS

Staphylococcus aureus detection in CRSwNP (n = 25), CRS without polyps (CRSsNP, n = 5), and turbinate mucosa (TM, n = 10) was performed by peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) and microbial cultivation from tissue biopsies. Intracellular residency was examined by intracellular persistence assay and electron microscopy. IL-6 and IL-13 responses to S. aureus infection and supernatants were quantified by ELISA.

RESULTS

Peptide nucleic acid-fluorescence in situ hybridization positive bacterial cells were significantly increased in the epithelium of CRSwNP (17/25) compared to CRSsNP (0/5) and TM (1/10). Good concordance of PNA-FISH results and S. aureus cultivation was found applying Cohen's κ for CRSwNP (κ = 0.841) and TM (κ = 1.0). Intracellular persistence assay with S. aureus strain Newman and its corresponding small-colony variant mutant strain III33 demonstrated intracellular survival and replication of S. aureus within NPECs. Both S. aureus strains significantly induced IL-6 but not IL-13 in infected NPECs and in NPECs challenged with corresponding staphylococcal supernatants.

CONCLUSION

Invasion of the epithelium by S. aureus was a phenomenon seen predominantly in CRSwNP. Regardless of an intra- or extracellular localization in the epithelium, S. aureus is capable to induce IL-6 synthesis in vitro and thus may contribute to the TH-2 cytokine pattern in CRSwNP.

Incidence of staphylococcal colonization and of the 753Q Toll-like receptor 2 variant in nasal polyposis

BACKGROUND

The impact of Staphylococcus aureus on the development of chronic sinusitis with nasal polyps (nasal polyposis [NP]) is a controversial discussion because different S. aureus colonization rates have been reported. Aside from the presence of a microbial stimulus, elements of innate immunity such as Toll-like receptors (TLRs) and/or impaired TLR function could be relevant for the development of this disease. Because the 753Q TLR2 variant may predispose to staphylococcal infection, we simultaneously analyzed staphylococcal colonization and the R753Q TLR2 single nucleotide polymorphism (SNP) in NP.

METHODS

Sixty-eight patients with NP (47 men and 21 women; mean age [+/-SD], 51.8 years [16.3]) and 51 controls (32 men and 19 women; mean age [+/-SD], 36.3 years [12.2]) were included. Patient characteristics studied included status of allergy, asthma, aspirin intolerance, and endoscopic and CT polyp score. For detection of bacteria, standard procedures of bacteriology and 16S rRNA gene sequencing were used. The R753Q TLR2 polymorphism was studied by allelic discrimination assay.

RESULTS

Overall, 128 isolates were cultured from 68 NP specimens, with Staphylococcus epidermidis and S. aureus being the most frequent bacterial isolates. Other bacterial species were infrequently detected. Fifty-nine isolates were cultured from 51 controls. Similarly, S. epidermidis and S. aureus were the most frequent bacterial isolates. S. aureus colonization was significantly increased in NP (p < 0.05). However, SNP genotyping results showed no association of the 753Q TLR2 variant with NP.

CONCLUSION

Although S. aureus detection was increased in NP, nasal polyp pathology is not related to the 753Q TLR2 variant.

The era of molecular and other non-culture-based methods in diagnosis of sepsis

Sepsis, a leading cause of morbidity and mortality throughout the world, is a clinical syndrome with signs and symptoms relating to an infectious event and the consequent important inflammatory response. From a clinical point of view, sepsis is a continuous process ranging from systemic inflammatory response syndrome (SIRS) to multiple-organ-dysfunction syndrome (MODS). Blood cultures are the current "gold standard" for diagnosis, and they are based on the detection of viable microorganisms present in blood. However, on some occasions, blood cultures have intrinsic limitations in terms of sensitivity and rapidity, and it is not expected that these drawbacks will be overcome by significant improvements in the near future. For these principal reasons, other approaches are therefore needed in association with blood culture to improve the overall diagnostic yield for septic patients. These considerations have represented the rationale for the development of highly sensitive and fast laboratory methods. This review addresses non-culture-based techniques for the diagnosis of sepsis, including molecular and other non-culture-based methods. In particular, the potential clinical role for the sensitive and rapid detection of bacterial and fungal DNA in the development of new diagnostic algorithms is discussed.

Nocardia cyriacigeorgica: a case of endocarditis with disseminated soft-tissue infection

Nocardia cyriacigeorgica is a common environmental organism. It has been isolated from clinical samples in Europe, Asia and North America, predominantly from respiratory samples but also from samples from several other sites. We present a case report of an 85-year-old female patient in the UK who was found to have a multi-focal soft-tissue infection from which N. cyriacigeorgica was isolated. She had a background history of chronic obstructive pulmonary disease and corticosteroid use for polymyalgia rheumatica. During the course of her treatment echocardiography showed the presence of a mobile heart mass attached to a valve leaflet, a major Dukes criterion for endocarditis. We suggest that in cases of disseminated Nocardia infection, endocarditis should be tested for, particularly in cases failing to respond to treatment. We also review previous reports of both N. cyriacigeorgica infection, and of endocarditis due to Nocardia species and related genera.

23S rDNA real-time polymerase chain reaction of heart valves: a decisive tool in the diagnosis of infective endocarditis

AIMS

A new diagnostic strategy to improve the detection of pathogens in heart valves (HVs) from patients with infective endocarditis (IE) was evaluated.

METHODS AND RESULTS

Three hundred and fifty seven HVs surgically removed from 326 patients with proven IE or suspicious intra-operative findings, examined by 16S rDNA polymerase chain reaction (PCR) and culture were retrospectively analysed according to the predictive value of various PCR methods. Patients were classified into four categories: active IE, IE with ambiguous infective status, healed IE, and valve diseases but no IE. Retained samples of 200 HVs were analysed by real-time PCR targeting bacterial 23S rDNA, fungal 28S rDNA, and mycoplasmal tuf gene. 16S rDNA PCR revealed 80.6% sensitivity, 100% specificity, 100% positive predictive value, and 71% negative predictive value (NPV), compared with cultivation with 33.4, 96.6, 95.5, and 40.9%, respectively. The use of real-time PCR increased diagnostic sensitivity to 96.4%, and NPV to 92.5%. Bacterial load, C-reactive protein, and white blood cell counts (WBCs) decreased during antibiotic treatment. Bacterial load showed no correlation to C-reactive protein or WBCs, whereas C-reactive protein and WBCs were significantly correlated.

CONCLUSION

23S rDNA real-time PCR of surgically removed HVs improves the diagnosis of IE. Polymerase chain reaction analysis of explanted HVs allow the optimization of the antimicrobial therapy, especially in patients with culture-negative IE.

[PCR rDNA 16S used for the etiological diagnosis of blood culture negative endocarditis]

We report the case of a 55 year-old man presenting with a double aortic and mitral endocarditis for which resected valve culture was repeatedly negative. Specific PCR made on valves because of highly positive blood tests for Bartonella henselae remained negative. A molecular approach was made with 16S rDNA PCR, followed by sequencing. Bartonella quintana was identified as the etiology of endocarditis. B. quintana, "fastidious" bacteria, even if hard to identify in a laboratory, is often reported as a blood culture negative endocarditis (BCNE) agent. Molecular biology methods have strongly improved the diagnosis of BCNE. We propose a review of the literature focusing on the interest of broad-spectrum PCR on valve for the etiological diagnosis of BCNE.