Aetiological diagnosis of infective endocarditis by direct amplification of rRNA genes from surgically removed valve tissue. An 11-year experience in a Finnish teaching hospital

Effect of Antibiotic Therapy on the Sensitivity of Etiological Diagnostic Methods in Patients with Infective Endocarditis after Surgery

Aim. Assessment of impact  of the duration  of preoperative  antimicrobial  therapy  (AMT) on the sensitivity  of microbiological examination and polymerase  chain reaction (PCR) of blood/tissues of resected valves in operated patients with infective endocarditis  (IE).

Materials and methods. 52 operated patients with active IE were included prospectively (Duke criteria, 2015). All patients underwent microbiological examination of blood  before  admission  to the cardiac  surgery  hospital,  as well as parallel  simultaneous microbiological examination and  PCR  of blood/tissues of excised  valves,  followed  by Sanger  sequencing. The duration  of preoperative  treatment  was  calculated  from the first day of AMT according to IE diagnosis to the day of surgery.

Results. The causative agent of IE was established in 84.6% (n=44) patients by means of complex etiological diagnosis. A significant  decrease in the sensitivity of microbiological examination of venous blood was revealed when performed  in the period before and after hospitalization to a surgical hospital (up 44.2% to 17.3%, p<0.05). When comparing microbiological examination of blood/tissues of resected valves and PCR of blood/tissues of resected valves, molecular biological  methods demonstrated the greatest sensitivity, with a great advantage when examining the tissues of resected valves (17.3% and 19.2% vs. 38.5% and 75.0%, respectively;  p<0.001). The microbiological examination of venous blood performed  at an early date before admission  to the cardiac  surgery  hospital was comparable in sensitivity to the PCR blood test performed  at a later date after prolonged AMT,  and significantly less sensitive in relation to the PCR of resected valve tissues [44.2% and 38.5% (p>0.05) vs. 75.0% (p<0.05)]. In course of AMT 1-28 days,  there were comparable results of microbiological examination with PCR blood examination and significantly better results of PCR of resected valve tissues [31.0% and 34.5% and 41.4% (p>0.05) vs 72.4% (p<0.001), respectively], and with AMT ≥ 29 days, microbiological examination of any biological  material was negative  in all patients,  and PCR of blood/tissues of resected valves retained high sensitivity (0% and 0% vs. 34.8% and 78.3%, respectively; p<0.01).

Conclusion. Long-term preoperative AMT significantly reduced the sensitivity of microbiological examination of resected valve blood/tissue in operated patients with IE, whereas PCR of resected valve blood/tissue was highly sensitive even with preoperative AMT for more than 29 days.

Impact of pre-operative antimicrobial treatment on microbiological findings from endocardial specimens in infective endocarditis

Treatment of infective endocarditis (IE) should be initiated promptly. This might hamper the chances to identify the causative organism in blood cultures. Microbiological sampling of infected valve in patients undergoing surgery might identify the causative organism. The impact of pre-operative antimicrobial treatment on the yield of valve samples is not known. This study evaluated the impact of the duration of the pre-operative antibiotic treatment on valve culture and 16S rRNA PCR findings from resected endocardial samples. Patients meeting the modified Duke criteria of definite or possible IE and undergoing valve surgery due to IE during 2011–2016 were included from Southern Finland. Eighty-seven patients were included. In patients with shorter than 2 weeks of pre-operative antimicrobial treatment, PCR was positive in 91% (n = 42/46) and valve culture in 41% (n = 19/46) of cases. However, in patients who had 2 weeks or longer therapy before operation, PCR was positive in 53% (n = 18/34) and all valve cultures were negative. In 14% of patients, PCR had a diagnostic impact. In blood-culture negative cases (n = 13), PCR could detect the causative organism in ten patients (77%). These included five cases of Bartonella quintana, one Tropheryma whipplei, and one Coxiella burnetii. Long pre-operative antimicrobial treatment was shown to have a negative impact on microbiological tests done on resected endocardial material. After 2 weeks of therapy, all valve cultures were negative, but PCR was positive in half of the cases. PCR aided in diagnostic work-up, especially in blood culture negative cases.

Utility of a Direct 16S rDNA PCR and Sequencing for Etiological Diagnosis of Infective Endocarditis

Background

Cases of infective endocarditis (IE) require prompt etiological diagnosis for effective treatment. Molecular methods can aid in rapid and reliable diagnosis of culture-negative IE cases. We evaluated the utility of 16S rDNA PCR and sequencing in determining the causative agents of IE in valve tissues, especially when specimens were obtained after initiation of antimicrobial therapy.

Methods

We performed 16S rDNA PCR and sequencing in heart valve specimens and medical records review of 80 patients who underwent protocol-based cardiac surgery from 2013 to 2015. One patient did not meet the criteria for IE. Sixty-five (81.3%) and 14 pa-tients (17.5%) were diagnosed as having definite IE and possible IE, respectively. Blood and heart valve biopsy tissue were examined by using routine microbiological methods.

Results

Blood cultures in our hospital were IE-positive for 33 patients (41.8%), whereas 49 patients (62.0%) showed positive blood cultures when initial blood cultures performed at the referring hospital were included. Eighteen (22.8%) and 40 patients (50.6%) were IE-positive in valve tissue cultures and 16S rDNA PCR, respectively. Bacteria in the Streptococcus mitis group (n=26) were the most common etiological agents of IE. Eight (10.1%) culture-negative specimens tested positive by 16S rDNA PCR. In five of eight PCR-positive and culture-negative cases, fastidious or anaerobic organisms were the cause of IE.

Conclusions

Direct 16S rDNA PCR and sequencing can be used as a supplementary method to conventional blood and biopsy culture testing, especially in culture-negative IE cases that are negative for IE by culture.

Molecular Diagnosis of Bacterial Definite Infective Endocarditis by Real-Time Polymerase Chain Reaction

Infective endocarditis (IE) can be diagnosed using the Duke criteria, which cannot be conclusive especially when the results of blood cultures are negative. This study aimed at using real-time polymerase chain reaction (PCR) technique to isolate bacteria present in whole blood samples of patients with definitive IE on the basis of the method designed in this study. This laboratory and test study was conducted on 20 whole blood samples taken from patients with definitive IE. Real-time PCR of the 16s rRNA was utilized to directly analyze whole blood samples to diagnose bacterial IE. Of 20 whole blood samples with definitive IE, only one blood culture (5%) was positive and the isolated bacterium belonged to Streptococci viridans group. Also, 13 whole blood samples were positive using real-time PCR technique. The isolated bacteria were Enterococcus faecalis with seven (35%) cases, Streptococcus gallolyticus with two (10%) cases, Streptococcus mutans with one (5%) case, Streptococcus sanguinis with one (5%) case, Streptococcus salivarius with one (5%) case, and Staphylococcus aureus with one (5%) case. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) using real-time PCR technique were 65%, 100%, 100%, and 74%, respectively. The developed real-time PCR method allows us to detect bacteria in whole blood samples and is much more sensitive than culturing method. It also permits the differentiation of the main group of bacteria within a few hours for IE.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.

The diagnosis of microorganism involved in infective endocarditis (IE) by polymerase chain reaction (PCR) and real-time PCR: A systematic review

Broad-range bacterial rDNA polymerase chain reaction (PCR) followed by sequencing may be identified as the etiology of infective endocarditis (IE) from surgically removed valve tissue; therefore, we reviewed the value of molecular testing in identifying organisms' DNA in the studies conducted until 2016. We searched Google Scholar, Scopus, ScienceDirect, Cochrane, PubMed, and Medline electronic databases without any time limitations up to December 2016 for English studies reporting microorganisms involved in infective endocarditis microbiology using PCR and real-time PCR. Most studies were prospective. Eleven out of 12 studies used valve tissue samples and blood cultures while only 1 study used whole blood. Also, 10 studies used the molecular method of PCR while 2 studies used real-time PCR. Most studies used 16S rDNA gene as the target gene. The bacteria were identified as the most common microorganisms involved in infective endocarditis. Streptococcus spp. and Staphylococcus spp. were, by far, the most predominant bacteria detected. In all studies, PCR and real-time PCR identified more pathogens than blood and tissue cultures; moreover, the sensitivity and specificity of PCR and real-time PCR were more than cultures in most of the studies. The highest sensitivity and specificity were 96% and 100%, respectively. The gram positive bacteria were the most frequent cause of infective endocarditis. The molecular methods enjoy a greater sensitivity compared to the conventional blood culture methods; yet, they are applicable only to the valve tissue of the patients undergoing cardiac valve surgery.

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.

Efficacy of Antibiotic Prophylactic Regimens for the Prevention of Bacterial Endocarditis of Oral Origin

Despite the controversy about the risk of individuals developing bacterial endocarditis of oral origin, numerous Expert Committees in different countries continue to publish prophylactic regimens for the prevention of bacterial endocarditis secondary to dental procedures. In this paper, we analyze the efficacy of antibiotic prophylaxis in the prevention of bacteremia following dental manipulations and in the prevention of bacterial endocarditis (in both animal models and human studies). Antibiotic prophylaxis guidelines remain consensus-based, and there is scientific evidence of the efficacy of amoxicillin in the prevention of bacteremia following dental procedures, although the results reported do not confirm the efficacy of other recommended antibiotics. The majority of studies on experimental models of bacterial endocarditis have verified the efficacy of antibiotics administered after the induction of bacteremia, confirming the efficacy of antibiotic prophylaxis in later stages in the development of bacterial endocarditis. There is no scientific evidence that prophylaxis with penicillin is effective in reducing bacterial endocarditis secondary to dental procedures in patients considered to be "at risk". It has been suggested that there is a high risk of severe allergic reactions secondary to prophylactically administered penicillins, but, in reality, very few cases have been reported in the literature. It has been demonstrated that antibiotic prophylaxis could contribute to the development of bacterial resistance, but only after the administration of several consecutive doses. Future research on bacterial endocarditis prophylactic protocols should involve the re-evaluation of the time and route of administration of antibiotic prophylaxis, and a search for alternative antimicrobials.

Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review

Background

The study aimed to explore the sensitivity and specificity of a novel fast 16S rDNA PCR and sequencing assay for the improved diagnosis of infective endocarditis (IE) in patients with suspected native or prosthetic heart valve (HV) infection over a multi-year period at our cardiovascular center.

Methods

Sixty-eight patients were prospectively enrolled who underwent HV replacement for suspected or confirmed IE between February 1, 2009 and September 1, 2014. Patient demographics, medical co-morbidities, Duke’s criteria, culture results, and antibiotic therapy were collected by detailed chart reviews. Dual-priming oligonucleotide primers targeted to 500 bps of the V1-V3 region of the 16S rRNA gene were used to perform fast broad-range 16S rDNA PCR and Sanger sequencing on ribosomal DNA extracted from HV tissues. The performance/diagnostic efficiency of the molecular test was evaluated against blood cultures and Gram stain and culture of HV tissue in patients’ with definite IE according to Duke’s criteria.

Results

Fifty patients (73.5 %) had definite IE and another 8 (11.8 %) had possible IE according to Duke’s criteria. Cardiac surgery was delayed an average of 15.4 days from the time of the patient’s last positive blood culture, and appropriate antibiotic therapy was given in the pre-operative period. While 44/50 (88 %) patients had a positive blood culture, HV tissue culture was only positive in 23 (46 %) of them. Molecular testing of all HV tissues had sensitivity, specificity, NPV and PPV of 92, 77.8, 77.8 and 92 % compared to 44, 100, 39.1 and 100 % respectively for culture for diagnosis of definite IE. For prosthetic HV tissue, 16S rDNA PCR had sensitivity of 93 % and specificity of 83 % compared to 35 and 100 % respectively for culture. A literature review showed that the diagnostic accuracy of our novel fast broad-range 16S rDNA PCR assay was similar or better than that of previously published studies.

Conclusions

This novel fast broad-range 16S rDNA PCR/sequencing test had superior sensitivity compared to tissue Gram stain and culture for identifying underlying bacterial pathogen in both native and prosthetic valve endocarditis.

Advantages and Limitations of Direct PCR Amplification of Bacterial 16S-rDNA from Resected Heart Tissue or Swabs Followed by Direct Sequencing for Diagnosing Infective Endocarditis: A Retrospective Analysis in the Routine Clinical Setting

Infective endocarditis (IE) is a life-threatening disease that is associated with high morbidity and mortality. Its long-term prognosis strongly depends on a timely and optimized antibiotic treatment. Therefore, identification of the causative pathogen is crucial and currently based on blood cultures followed by characterization and susceptibility testing of the isolate. However, antibiotic treatment starting prior to blood sampling or IE caused by fastidious or intracellular microorganisms may cause negative culture results. Here we investigate the additional diagnostic value of broad-range PCR in combination with direct sequencing on resected heart tissue or swabs in patients with tissue or swab culture-negative IE in a routine clinical setting. Sensitivity, specificity, and positive and negative predictive values of broad-range PCR from diagnostic material in our patients were 33.3%, 76.9%, 90.9%, and 14.3%, respectively. We identified a total of 20 patients (21.5%) with tissue or culture-negative IE who profited by the additional application of broad-range PCR. We conclude that broad-range PCR on resected heart tissue or swabs is an important complementary diagnostic approach. It should be seen as an indispensable new tool for both the therapeutic and diagnostic management of culture-negative IE and we thus propose its possible inclusion in Duke's diagnostic classification scheme.

What to expect from molecular tools for non-documented pediatric infectious diseases

OBJECTIVE

Evaluation of the contribution of molecular tools to the overall diagnosis of infectious diseases in children.

METHODS

Results of 16S rDNA analysis (179 children; 228 specimens), combined to specific amplification of Kingella kingae (126 children; 166 osteoarticular specimens), were retrospectively analyzed for samples with inconclusive cultures.

RESULT

The overall positive yield in diagnosis was 12.8% of the patients for 16S rDNA PCR, 40.5% for K. kingae PCR and 45.2% for combined use of both methods. Results were related to clinical and biological data (direct examination, certainty/uncertainty of clinical diagnosis, fever, biological markers, previous antibiotics), and to the number of samples analyzed per patient, allowing the identification of specific situations with significant contribution of PCR methods.

CONCLUSION

Molecular techniques constitute valuable tools to improve the bacterial infection diagnosis in children; however, specific indications, dedicated samples, and number of analyzed samples per patient are key points to optimize their contribution.

Infective endocarditis: does a new 16S rDNA set of primers improve the microbiological diagnosis?

BACKGROUND

In infective endocarditis (IE), blood cultures are negative in 2.5-31% of cases because of a previously prescribed antimicrobial treatment. Molecular methods may represent an alternative to conventional microbiological techniques to identify the causative agent. The aim of this prospective study was to evaluate the performance of a new primer pair (341F/785R) for 16S rDNA amplification in heart valves compared with primers 91E/13BS already used for the diagnosis of IE. The primer pair 341F/785R was previously selected in silico to allow 16S rDNA amplification for a large coverage of bacterial species.

RESULTS

A total of 74 patients suspected of having IE were included in this study. IE was diagnosed in 55 of these patients using the modified Duke criteria, which was the gold standard here. 91E/13BS primers were more sensitive than 341F/785R primers: 38/55 (69.1%) samples were positive using 91E/13BS primers against 28/55 (50.9%) with 341F/785R (p = 0.013). When at least one of the two molecular methods was positive, the sensitivity and specificity of 16S rDNA amplification was 72.7% and 94.7%, respectively.

CONCLUSION

Even if the new primer pair 341F/785R seemed promising in silico, it was less sensitive for 16S rDNA amplification in heart valves than the 91E/13BS pair already used. This study underlines a lack of standardization for 16S rDNA amplification for clinical samples.

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.

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.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past two decades due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation and user-friendly software have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, have benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods has lagged somewhat behind. The purpose of this chapter is to review and discuss the interpretation and relevance of results produced by these advanced molecular techniques. Moreover, this chapter will address the “myths” of NAATs, as these myths can markedly influence the interpretation and relevance of these results.

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.

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.

The human microbiome and surgical disease

OBJECTIVE

The purpose of this review article is to summarize what is currently known about microbes associated with the human body and to provide examples of how this knowledge impacts the care of surgical patients.

BACKGROUND

Pioneering research over the past decade has demonstrated that human beings live in close, constant contact with dynamic communities of microbial organisms. This new reality has wide-ranging implications for the care of surgical patients.

METHODS AND RESULTS

Recent advances in the culture-independent study of the human microbiome are reviewed. To illustrate the translational relevance of these studies to surgical disease, we discuss in detail what is known about the role of microbes in the pathogenesis of obesity, gastrointestinal malignancies, Crohn disease, and perioperative complications including surgical site infections and sepsis. The topics of mechanical bowel preparation and perioperative antibiotics are also discussed.

CONCLUSIONS

Heightened understanding of the microbiome in coming years will likely offer opportunities to refine the prevention and treatment of a wide variety of surgical conditions.

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.

[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.

Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria

This study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and 40 % of medically important Gram-positive cocci (GPC), and 21 and 34 % of medically important Gram-positive rods (GPR) confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15 and 34 % of medically important GPC and 14 and 25 % of medically important GPR confidently to the species level. Among staphylococci, streptococci, enterococci, mycobacteria, corynebacteria, nocardia and members of Bacillus and related taxa (Paenibacillus, Brevibacillus, Geobacillus and Virgibacillus), the methods and databases are least useful for identification of staphylococci and nocardia. Only 0–2 and 2–13 % of staphylococci, and 0 and 0–10 % of nocardia, can be confidently and doubtfully identified, respectively. However, these methods and databases are most useful for identification of Bacillus and related taxa, with 36–56 and 11–14 % of Bacillus and related taxa confidently and doubtfully identified, respectively. A total of 15 medically important GPC and 18 medically important GPR that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. A total of 9 medically important GPC and 21 medically important GPR that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. 16S rRNA gene sequence results of Gram-positive bacteria should be interpreted with basic phenotypic tests results. Additional biochemical tests or sequencing of additional gene loci are often required for definitive identification. To improve the usefulness of the MicroSeq databases, bacterial species that can be confidently identified by 16S rRNA gene sequencing but are not found in the MicroSeq databases should be included.

Molecular analyses of bacterial DNA in extirpated heart valves from patients with infective endocarditis

BACKGROUND/AIMS

Infective endocarditis (IE) is caused by a microbial infection of the endothelial surface of the heart. Although blood culture examinations are commonly used to determine the associated bacterial species, molecular techniques, which enable rapid identification of targeted bacterial species, have recently been applied in clinical cases.

METHODS

Nine heart valve specimens from IE patients (six subacute cases and three acute cases) were extirpated and collected, then bacterial DNA was extracted. Bacterial species in the specimens were determined by two different molecular methods and the results were compared with those from a conventional blood culture technique. In addition, a comparison between the two molecular methods was carried out using known numbers of six streptococcal species.

RESULTS

The conventional blood culture method revealed the bacterial species in eight cases, while one was found to be negative. Multiple species were identified in most of the cases by both molecular methods; however, those specified by one method were not always consistent with those specified by the other. Furthermore, the species determined by the blood culture technique were not always identified by the molecular methods. We also found that the two molecular methods used in the present study were extremely sensitive to detect from 1 to 100 cells of individual oral streptococcal species.

CONCLUSION

Our results suggest that species specified by molecular methods may have disseminated incidentally into the bloodstream, so interpretation of such results should be carefully undertaken in clinical situations.

Getting to the heart of the problem: serological and molecular techniques in the diagnosis of infective endocarditis

Infective endocarditis is diagnosed using the Duke criteria, which rely predominantly on cardiac imaging and recovery of a causative organism from the bloodstream. These criteria can be inconclusive, particularly when blood cultures remain sterile either due to the fastidious nature of the infecting organism or prior antibiotic therapy. Serology and, more recently, molecular techniques have been investigated as a solution to the problematic negative blood culture. The detection of elevated antibody levels has proved particularly useful in the diagnosis of those patients infected with organisms that cannot be cultured using standard laboratory methods, whilst molecular methods have been successfully used in the detection of both fastidious pathogens and those inhibited by prior antibiotic therapy. In view of recent and ongoing developments in the field of molecular diagnostics, these techniques will become increasingly important not only in the routine investigation of infectious disease, but specifically the diagnosis of endocarditis.

Long-term outcome of infective endocarditis: a study on patients surviving over one year after the initial episode treated in a Finnish teaching hospital during 25 years

Background

Only a few previous studies have focused on the long-term prognosis of the patients with infective endocarditis (IE). Our purpose was to delineate factors potentially associated with the long-term outcome of IE, recurrences of IE and requirement for late valve surgery.

Methods

A total of 326 episodes of IE in 303 patients were treated during 1980–2004 in the Turku University Hospital. We evaluated the long-term outcome and requirement for late valve surgery for 243 of these episodes in 226 patients who survived longer than 1 year after the initial admission. Factors associated with recurrences were analysed both for the 1-year survivors and for all 303 patients.

Results

The mean (SD) follow-up time for the 1-year survivors was 11.5 (7.3) years (range 25 days to 25.5 years). The overall survival was 95%, 82%, 66%, 51% and 45% at 2, 5, 10, 15 and 20 years. In age and sex adjusted multivariate analyses, significant predictors for long-term overall mortality were heart failure within 3 months of admission (HR 1.97, 95% CI 1.27 to 3.06; p = 0.003) and collagen disease (HR 2.54, 95% CI 1.25 to 5.19; p = 0.010) or alcohol abuse (HR 2.39, 95% CI 1.30 to 4.40; p = 0.005) as underlying conditions, while early surgery was significantly associated with lower overall mortality rates (HR 0.31, 95% CI 0.17 to 0.58; p < 0.001). Heart failure was also significantly associated with the long-term cardiac mortality (p = 0.032). Of all 303 patients, 20 had more than 1 disease episode. Chronic dialysis (p = 0.002), intravenous drug use (p = 0.002) and diabetes (p = 0.015) were significant risk factors for recurrent episodes of IE, but when analysed separately for the 1-year survivors, only chronic dialysis remained significant (p = 0.017). Recurrences and late valve surgery did not confer a poor prognosis.

Conclusion

Heart failure during the index episode of IE was the complication, which significantly predicted a poor long-term outcome. Patients who underwent surgery during the initial hospitalisation for IE faired significantly better than those who did not.

Microbiologic investigations for head and neck infections

A variety of methods, including direct examination of stained smears, antigen detection, routine and special cultures, and histopathologic evaluation are available for investigation of head and neck infections. Newer rapid molecular techniques with increased sensitivity and specificity are becoming available at many centers. Evaluation of specific causes in head and neck infections is complicated by the tendency for polymicrobial infections, difficulty in obtaining adequate specimens, and the presence of a diverse endogenous microflora at various mucosal sites that also can include true pathogens. These aspects of laboratory investigation for head and neck infections are reviewed in this article.

Molecular methods for diagnosis of infective endocarditis

The culture of viable microorganisms from the blood or from cardiac tissue is currently the most important test for diagnosis of IE. This is followed by phenotypic identification methods used for taxonomic positioning of isolates. However, in those cases where the invading microorganism is difficult or impossible to culture (including instances of prior antimicrobial treatment), molecular methods provide the best means for detection. Molecular identification methods, either nucleic acid target or signal amplification alone or in combination with sequence analysis can offer a more specific and in some cases a more rapid alternative to the phenotypic methods. We propose revised Duke criteria of IE, including positive identification of an organism by molecular biology methods.