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

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

16S rRNA Gene PCR/Sequencing of Heart Valves for Diagnosis of Infective Endocarditis in Routine Clinical Practice

Sequencing is increasingly used for infective endocarditis (IE) diagnosis. Here, the performance of 16S rRNA gene PCR/sequencing of heart valves utilized in routine clinical practice was compared with conventional IE diagnostics. Subjects whose heart valves were sent to the clinical microbiology laboratory for 16S rRNA gene PCR/sequencing from August 2020 through February 2022 were studied. A PCR assay targeting V1 to V3 regions of the 16S rRNA gene was performed, followed by Sanger and/or next-generation sequencing (NGS) (using an Illumina MiSeq), or reported as negative, depending on an algorithm that included the PCR cycle threshold value. Fifty-four subjects, including 40 with IE, three with cured IE, and 11 with noninfective valvular disease, were studied. Thirty-one positive results, 11 from NGS and 20 from Sanger sequencing, were generated from analysis of 16S rRNA gene sequence(s). Positivity rates of blood cultures and 16S rRNA gene PCR/sequencing of valves were 55% and 75%, respectively (P = 0.06). In those with prior antibiotic exposure, positivity rates of blood cultures and 16S rRNA gene PCR/sequencing of valves were 11% and 76%, respectively (P < 0.001). Overall, 61% of blood culture-negative IE subjects had positive valve 16S rRNA gene PCR/sequencing results. 16S rRNA gene-based PCR/sequencing of heart valves is a useful diagnostic tool for pathogen identification in patients with blood culture-negative IE undergoing valve surgery in routine clinical practice.

Updates in Culture-Negative Endocarditis

Blood culture-negative infective endocarditis (BCNE) is a challenging condition associated with significant morbidity and mortality. This review discusses the epidemiology, microbiology, diagnosis, and treatment of BCNE considering advancements in molecular diagnostics and increased access to cardiac surgery. BCNE can be categorized into bacterial endocarditis with sterilized blood cultures due to previous antibiotic treatment, endocarditis caused by fastidious microorganisms, and true BCNE caused by intracellular organisms that cannot be cultured using traditional techniques. Non-infectious causes such as nonbacterial thrombotic endocarditis should also be considered. Diagnostic approaches involve thorough patient history; blood and serum testing, including appropriate handling of blood cultures; serological testing; and molecular techniques such as targeted and shotgun metagenomic sequencing. Where available, evaluation of explanted cardiac tissue through histopathology and molecular techniques is crucial. The therapy for BCNE depends on the likely causative agent and the presence of prosthetic material, with surgical intervention often required.

Native Valve Endocarditis Caused by Nocardia asteroides in an Immunocompetent Host: A Case Report and a Review of the Literature

Nocardia species are a rare cause of infective endocarditis (IE). We describe a case of native valve endocarditis caused by Nocardia asteroides in a 38-year-old Hispanic male with no apparent environmental exposures or risk factors for IE. Transesophageal echocardiography revealed severe mitral regurgitation, prompting emergent replacement of the valve. Nocardia asteroides were isolated from the tissue culture of the mitral valve. MRI of the brain also demonstrated innumerable micronodular intra-axial lesions throughout the brain, consistent with disseminated nocardiosis. The patient was treated with intravenous trimethoprim/sulfamethoxazole, meropenem, and amikacin for a six-week course, followed by oral trimethoprim/sulfamethoxazole and minocycline for 12 months. Follow-up after 18 months revealed no evidence of relapse. Although several cases of endocarditis due to Nocardia asteroides have been reported in immunocompromised hosts, to the best of our knowledge we believe the present case is the first to describe native valve endocarditis by Nocardia asteroides in an immunocompetent host with no apparent risk factors for IE.

Blood Culture Negative Endocarditis: A Review of Laboratory Diagnostic Approaches

Infective endocarditis is a potentially fatal condition, and identifying the pathogen is crucial to optimizing antibiotic treatment. While a blood culture takes time and may yield negative results, it remains the gold standard for diagnosis, blood culture-negative endocarditis, which accounts for up to 20% of infective endocarditis cases, poses a clinical challenge with increasing mortality. To better understand the etiology of blood culture-negative infective endocarditis, we reviewed non-culture-based strategies and compared the results. Serology tests work best in limited pathogens, such as Coxiella burnetii and Bartonella infections. Most of the pathogens identified by broad-range PCR tests are Streptococcus spp, Staphylococcus spp and Propionibacterium spp. adding specific real-time PCR assays to the systematic PCR testing of patients with blood culture-negative endocarditis will increase the efficiency of diagnosis. Recently, metagenomic next-generation sequencing has also shown promising results.

Native valve, prosthetic valve, and cardiac device-related infective endocarditis: A review and update on current innovative diagnostic and therapeutic strategies

Infective endocarditis (IE) is a life-threatening microbial infection of native and prosthetic heart valves, endocardial surface, and/or indwelling cardiac device. Prevalence of IE is increasing and mortality has not significantly improved despite technological advances. This review provides an updated overview using recent literature on the clinical presentation, diagnosis, imaging, causative pathogens, treatment, and outcomes in native valve, prosthetic valve, and cardiac device-related IE. In addition, the experimental approaches used in IE research to improve the understanding of disease mechanisms and the current diagnostic pipelines are discussed, as well as potential innovative diagnostic and therapeutic strategies. This will ultimately help towards deriving better diagnostic tools and treatments to improve IE patient outcomes.

Infective endocarditis by HACEK: a review

Infective endocarditis (IE) is a severe disease that is still associated with high mortality despite recent advances in diagnosis and treatment. HACEK organisms (Haemophilus spp., Aggregatibacter actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella kingae) are gram-negative bacteria that are part of the normal flora of the mouth and upper respiratory tract in humans. These organisms cause a wide range of infections, of which IE is one of the most notable. In order to control and prevent endocarditis caused by HACEK, measures such as oral hygiene and the use of prophylactic drugs should be used for people at risk, including people with underlying heart disease and people with artificial valves. This review is a summary of the main aspects of IE focusing on HACEK organisms.

Molecular Analysis With 16S rRNA PCR/Sanger Sequencing and Molecular Antibiogram Performed on DNA Extracted From Valve Improve Diagnosis and Targeted Therapy of Infective Endocarditis: A Prospective Study

BACKGROUND

Molecular analysis (MA) on heart valve (HV) improves the microbiologic diagnosis of infectious endocarditis (IE). The main drawback of MA is the lack of antimicrobial susceptibility information.

METHODS

We conducted a prospective cohort observational study of consecutive adult patients from April 2012 to May 2021 who underwent valve surgery at our hospital. The performance of MA, blood cultures (BC) and valve cultures (VC), and the diagnostic and therapeutic impact of MA were evaluated. Molecular antibiogram results were compared to culture-based antimicrobial susceptibility testing (AST).

RESULTS

A total of 137 patients with definite IE and 52 patients with no IE were enrolled in the study. Among IE cases BC, VC, and MA were positive in 75 (55%), 30 (22%), and 120 (88%) of IE cases, respectively. Among 62 cases of BC-negative IE (BCNE), 57 achieved diagnosis with MA. MA led to a change of antimicrobial therapy in 92% of BCNE. MA was negative in 100% of patients with no IE. Molecular antibiogram performed on 17 valve specimens that resulted positive for pathogens potential carrier of genes encoding for multidrug resistant mechanisms showed 100% concordance with AST.

CONCLUSIONS

MA showed a high specificity and sensitivity in etiological diagnosis of IE. Molecular antibiogram could overcome the major limitation of MA that is the lack of susceptibility testing. We advocate for the inclusion of MA among diagnostic criteria for IE and for a more extensive use of molecular antibiogram when the culture result is negative, and MA is the only positive test.

Utility of Plasma Microbial Cell-Free DNA Decay Kinetics After Aortic Valve Replacement for Bartonella Endocarditis: Case Report

Background

Detection and sequencing of circulating microbial cell-free DNA (mcfDNA) in plasma is an increasingly popular tool for diagnosing many infectious diseases, but could also be used to monitor the progress of infection. However, the decay of this microbial cell-free DNA in blood following treatment has not been previously characterized.

Case Presentation

A 53 year-old male was diagnosed with Bartonella quintana bioprosthetic aortic valve endocarditis by sequencing of the mcfDNA in the blood (Karius, Redwood City, CA). We then monitored the kinetics of decay of mcfDNA after parenteral antibiotics and valve resection in this individual. We measured plasma mcfDNA (Karius) in serial samples obtained in the operating room to calculate mcfDNA half-life after valve resection. After four weeks of parenteral antibiotics, Bartonella mcfDNA signal decreased by 78%. The signal subsequently rose during operative manipulation of the infected valve but dropped 81-fold over four hours following valve resection. The half-life of mcfDNA between the time shortly following resection of the infected valve and 24 to 48 hours post-operatively was between 35 and 115 minutes. The trend in mcfDNA signal was characterized by rapid and then slower phases of decay within 24 hours, and little change between 24 and 48 hours.

Conclusions

This study is one of the first to characterize decay kinetics of mcfDNA and highlights the potential of monitoring mcfDNA in addressing major challenges in infective endocarditis management, including monitoring the response to therapy, and as an early screen for recurrence.

Clinical features, diagnosis and treatment outcome of fungal endocarditis: A systematic review of reported cases

The landscape of fungal endocarditis (FE) has constantly been evolving in the last few decades. Despite the advancement in diagnostic methods and the introduction of newer antifungals, mortality remains high in FE. This systematic review aimed to evaluate the epidemiology, clinical features, diagnostic and therapeutic interventions in patients with FE. We also aim to examine the aforementioned factors as a determinant of mortality in FE. A literature search was performed in PubMed, Google Scholar and Scopus, and all patients ≥18 years with proven fungal endocarditis were included. A total of 220 articles (250 patients) were included in the final analysis. Candida was the commonest aetiology (49.6%), followed by Aspergillus (30%) and Scedosporium species (3.2%). The proportion of prosthetic valve endocarditis (PVE) and intravenous drug users was 35.2% and 16%, respectively. The overall mortality rate was 40%. On multivariate analysis, Aspergillus endocarditis (HR 3.7, 95% CI 1.4-9.7; p = .009) and immunocompromised state (HR 2.8, 95% CI 1.24-6.3; p = .013) were independently associated with mortality. Patients treated with surgery along antifungals had better survival (HR 0.20, 95% CI 0.09-0.42; p < .001) compared to those treated with antifungals alone. Recurrence of FE was reported in 10.4% of patients. In conclusion, FE carries significant mortality, particularly in immunodeficient and Aspergillus endocarditis. We advocate the use of surgery combined with antifungals to improve clinical outcomes.

16S rDNA PCR for the aetiological diagnosis of culture-negative infective endocarditis

INTRODUCTION

Culture-negative infective endocarditis (IE) accounts for 7-31% of all cases. Metagenomics has contributed to improving the aetiological diagnosis of IE patients undergoing valve surgery. We assessed the impact of 16S ribosomal DNA gene polymerase chain reaction (16S rDNA PCR) in the aetiological diagnosis of culture-negative IE.

METHODS

Between January 2016 and January 2020, clinical data from culture-negative IE patients were reviewed retrospectively. Identification of bacteria was performed using 16S rDNA PCR in heart valve specimens.

RESULTS

36 out of 313 patients (12%) with culture-negative IE had their valve tissue specimens submitted for 16S rDNA PCR. 16S rDNA PCR detected and identified bacterial nucleic acid in heart valve tissue significantly more frequently compared to valve culture alone 25(70%) vs 5(12%); p < 0.05. Mean age was 57 years (SD 18) and 80% were male. Native and aortic valve were involved in 76% and 52% of cases, respectively. Streptococcus spp. (n 15) were the most commonly detected organisms, followed by bacteria of the HACEK group (Haemophilus parainfluenzae 2, Aggregatibacter actinomycetemcomitans 1), nutritionally variant streptococci (Abiotrophia defectiva 2), and one each of Staphylococcus aureus, Corynebacterium pseudodiphtheriticum, Helcococcus kunzii, Neisseria gonorrhoeae, Tropheryma whipplei.

CONCLUSION

16S rDNA PCR may be a useful diagnostic tool for the identification of the causative organism in culture-negative IE. Efforts towards a shorter turnaround time for results should be consider and further studies assessing the clinical impact of this technique in culture-negative IE are needed.

Comparison of traditional methods and high-throughput genetic sequencing in the detection of pathogens in pulmonary infectious diseases

Background

The major causes of pulmonary infections are various microorganisms. This study aimed to compare the positive rates of pathogenic microorganism DNA/RNA high-throughput genetic sequencing (PMseq), which is an emerging technique, with traditional methods for pulmonary disease detection, and to investigate the differences in different sample types.

Methods

Bronchoalveolar lavage fluid (BALF) and venous blood samples from 104 patients were collected for detection.

Results

The positive rates of PMseq in BALF and venous blood were both significantly higher than those of traditional methods in the same sample (P<0.001). For BALF, the detection sensitivities were 96.9% for non-febrile patients and 100% for febrile patients. For venous blood, the detection sensitivities were 50.0% for non-febrile patients and 81.3% for febrile patients. There was no statistical difference in the sensitivity of venous blood samples with or without fever (P=0.075). For patients without fever, the sensitivity of BALF was much higher than venous blood samples (P<0.001). In patients with fever, there were no significant differences between different samples.

Conclusions

This study showed that PMseq has a higher positive rate for the detection of pulmonary diseases. For patients without fever, it is recommended to use BALF instead of venous blood samples because of the higher sensitivity. However, for patients with fever, venous blood samples can be used when bronchoalveolar lavage is inconvenient.

Infective endocarditis caused by Nocardia nova: A case report and literature review of nocardial endocarditis

Although a variety of microorganisms have caused infective endocarditis, Nocardia species have rarely been reported as a causative agent of the disease. We describe a case of nocardial endocarditis, occurring to a 22-year-old Japanese woman during long-term corticosteroid therapy for adult-onset Still's disease and diagnosed after the rupture of cerebral mycotic aneurysm. Echocardiography showed that the causative organism, isolated from the blood and identified as Nocardia nova with an analysis of 16S ribosomal RNA sequences, affected the posterior papillary muscle of the left ventricle. Nocardia-like organisms were also detected in the pus around the raptured aneurysm. After treatment with imipenem/cilastatin plus amikacin for 3 months followed by oral trimethoprim/sulfamethoxazole for 1 year, no relapse of nocardiosis occurred during a follow-up for 3 years. To our knowledge, the present case is the first reported endocarditis due to N. nova.

Next-Generation Sequencing for the Diagnosis of Challenging Culture-Negative Endocarditis

Diagnosis of culture-negative infective endocarditis usually implies indirect pathogen identification by serologic or molecular techniques. Clinical metagenomics, relying on next-generation sequencing (NGS) is an emerging approach that allows pathogen identification in challenging situations, as evidenced by a clinical case. We sequenced the DNA extracted from the surgically-removed frozen valve tissue from a patient with suspected infective endocarditis with negative blood and valve cultures. Mapping of the sequence reads against reference genomic sequences, a 16S rRNA gene database and clade-specific marker genes suggested an infection caused by Cardiobacterium hominis.

Broad-range PCR Application in a Large Academic Pediatric Center: Clinical Value and Challenges in Diagnosis of Infectious Diseases

BACKGROUND

Broad-range polymerase chain reaction (BR-PCR) detects infectious pathogens from clinical specimens using targets for bacteria (16S rRNA), fungi (28S rDNA), and mycobacteria (fluorescence resonance energy transfer and heat shock protein 65 gene) with reported diagnostic sensitivity and specificity ranging from 43% to 100% and 100%, respectively. We describe our experience when applying BR-PCR to clinical samples submitted for conventional infectious disease testing [conventional testing (CT)] from pediatric patients with concern for infection.

METHODS

Retrospective analysis of clinical samples obtained from Nationwide Children's Hospital microbiology laboratory from January 2011 to December 2014 and sent for BR-PCR. Medical record review collected data on patient characteristics, clinical manifestations, laboratory results and antimicrobials prescribed, and a determination of clinical value of BR-PCR was assigned.

RESULTS

There were 247 clinical samples from 163 patients identified; 71 (44%) patients were immunocompromised and 192 (78%) samples reflected pretreatment with antimicrobials. A clinically significant putative organism was identified for 59 samples (24%) between all diagnostic modalities. Conventional testing identified organisms in 41 (17%) samples, 17 of which were corroborated by BR-PCR. Broad-range polymerase chain reaction identified an organism in an additional 18 samples with negative CT results and was considered to provide additional important clinical information. Broad-range polymerase chain reaction detected a bacterial or fungal organism more frequently from tissue samples than from bronchoalveolar lavage or other fluid samples (P = 0.0096, χ).

CONCLUSIONS

In our cohort, BR-PCR was an important adjunctive diagnostic in identifying bacteria and fungi in complex clinical situations. Additional data are needed to define the optimal clinical circumstances and specimen type in which BR-PCR can provide the highest diagnostic yield.

Zoonotic multidrug-resistant microorganisms among non-hospitalized horses from Germany

Colonization with multidrug-resistant organisms (MDROs) belonging to the genus Staphylococcus and the order Enterobacterales poses a particular threat to populations at risk. While previous studies focused on MDRO carriage among livestock or companion animals, respective epidemiological data on the general equine population are limited. Here, carriage of methicillin-resistant Staphylococcus aureus (MRSA) and extended spectrum beta-lactamase (ESBL) producing Enterobacteriaceae (ESBL-E) in non-hospitalized horses living on private farms in the rural area in Northwest Germany was assessed. Intranasal and perianal swab samples were cultured on solid chromogenic media directly and after enrichment in tryptic soy broth, respectively. S. aureus isolates were spa-typed, MRSA and ESBL-E were further classified by phenotypic and molecular methods. Additionally, a subgroup of the first 20 samples was used to isolate and characterize staphylococci other than S. aureus. Among 223 horses, fifteen (6.8%) carried S. aureus. Two isolates were identified as MRSA (0.9% of all horses, mecA-positive) and classified as spa types t011 and t6867, both known as members of the livestock-associated MRSA MLST clonal complex 398. Nine horses (4.0%) were colonized by ESBL-Escherichia coli positive for bla_CTX-M and/or bla_TEM. ESBL-E carriage was associated with prior antibiotic treatment (4/31 vs. 5/183; p = 0.0362) and veterinary examinations (4/31 vs. 5/183; p = 0.0362). In the subgroup, nine different staphylococcal species other than S. aureus were found. The high prevalence of ESBL-E. coli in non-hospitalized horses underlines the necessity to raise awareness for strain dissemination across different hosts in order to do justice to the “One Health” concept.

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The prevalence of equine ESBL-E carriage is 4.0%.

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0.9% of horses carry MRSA.

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Risk factors for ESBL-E carriage: antibiotic treatment and veterinary examinations.

Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

BACKGROUND

Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases.

METHODS

To assess the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients, we employed both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for pathogens and antimicrobial resistance detection in seven culture-negative IE patients. Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both platforms for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria.

RESULTS

Our results showed both metagenomics methods can be applied for the causative pathogen detection in all IE samples. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features.

CONCLUSION

Metagenomic methods for IE detection can provide clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery. However, more efforts should be made to optimize protocols for sample processing, sequencing and bioinformatics analysis.

Zoonotic multidrug-resistant microorganisms among small companion animals in Germany

Antimicrobial multidrug-resistant microorganisms (MDRO) can be transmitted between companion animals and their human owners. Aim of this study was to determine the prevalence of extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) and Staphylococcus aureus including methicillin-resistant S. aureus (MRSA) in different companion animal species. Dogs (n = 192), cats (n = 74), and rabbits (n = 17), treated in a veterinary practice and hospital or living in an animal shelter and private households, were sampled. All facilities were located in a region characterized by a high density of pig production. Nasal, buccal and perianal swabs were enriched and cultured on solid chromogenic selective media. A subgroup of 20 animals (13 dogs, 3 cats, 4 rabbits) was analyzed for the presence of staphylococci other than S. aureus. Amongst all animals (n = 283), twenty dogs (10.4%) and six cats (8.1%) carried S. aureus. MRSA was found in five dogs (2.6%) and two cats (2.7%). Isolates were of spa types t011, t034, t108 (all mecA-positive, ST398), and t843 (mecC-positive, ST130), typical for livestock-associated (LA)-MRSA. Except for one dog, MRSA-positive animals did not have direct contact to husbandry. ESBL-Escherichia coli (bla_CTX-M/bla_TEM/bla_SHV genes) were present in seven dogs (3.6%), one cat (1.4%) possessed a cefotaxime-resistant Citrobacter freundii isolate (bla_TEM/bla_CMY-2 genes). MDRO carriage was associated with animals from veterinary medical settings (p<0.05). One dog and one rabbit carried methicillin-resistant coagulase-negative staphylococci. The exclusive occurrence of MRSA lineages typically described for livestock stresses the impact of MDRO strain dissemination across species barriers in regional settings. Presence of ESBL-E and LA-MRSA among pets and probable dissemination in clinical settings support the necessity of a “One Health” approach to address the potential threats due to MDRO-carrying companion animals.

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.

A broad-range PCR technique for the diagnosis of infective endocarditis

Infective endocarditis (IE) remains a severe and potentially fatal disease demanding sophisticated diagnostic strategies for detection of the causative microorganisms. The aim of the present study was to develop a broad-range 16S ribosomal RNA gene polymerase chain reaction in the routine diagnostic of IE for the early diagnosis of fatal disease. A broad-range PCR technique was selected and evaluated in terms of its efficiency in the diagnosis of endocarditis using 19 heart valves from patients undergoing cardiovascular surgeries at the Habib Bourguiba Hospital of Sfax, Tunisia, on the grounds of suspected IE. The results demonstrated the efficiency of this technique particularly in cases involving a limited number of bacteria since it helped to increase detection sensitivity. The technique proved to be efficient, particularly, in the bacteriological diagnosis of IE in contexts involving negative results from conventional culture methods and other contexts involving bacterial species that were not amenable to identification by phenotypic investigations. Indeed, the sequencing of the partial 16S ribosomal RNA gene revealed the presence of Bartonella henselae, Enterobacter sp., and Streptococcus pyogenes in three heart valves with the negative culture. It should be noted that the results obtained from the polymerase chain reaction-sequencing identification applied to the heart valve and the strain isolated from the same tissue were not consistent with the ones found by the conventional microbiological methods in the case of IE caused by Gemella morbillorum. In fact, the results from the molecular identification revealed the presence of Lactobacillus jensenii. Overall, the results have revealed that the proposed method is sensitive, reliable and might open promising opportunities for the early diagnosis of IE.

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.

Persistent extra-axial post-surgical collections and Propionibacterium acnes infection. Presentation of two cases and literature review

OBJECTIVES

It is common to observe the persistence of extra-axial collections after craniotomies. Most of these disappear in weeks or months but some remain. The onset of focal symptoms or the growth of these persistent collections months or years after surgery may indicate the presence of a chronic and latent infection by germs of low virulence such as Propionibacterium acnes (P. acnes).

METHODS

We present two clinical cases with persistent extra-axial collections, which required surgery years after diagnosis, in which P. acnes was isolated as an aetiological agent and we reviewed the literature published in this regard.

RESULTS

These are two patients who, following surgical procedures (decompressive craniectomy for severe TBI and craniotomy for right parietal meningioma) and extra-axial collections were kept, which were monitored over time and then were infected and required emergency evacuation. In these collections P. acnes grew as a causal agent and required targeted antibiotics.

CONCLUSIONS

We must consider P. acnes as an infectious agent of post-surgical collections of long evolution. Atypical presentation and radiological changes may be helpful in diagnosis.

Laboratory Diagnosis of Infective Endocarditis

Infective endocarditis is life-threatening; identification of the underlying etiology informs optimized individual patient management. Changing epidemiology, advances in blood culture techniques, and new diagnostics guide the application of laboratory testing for diagnosis of endocarditis. Blood cultures remain the standard test for microbial diagnosis, with directed serological testing (i.e., Q fever serology, Bartonella serology) in culture-negative cases. Histopathology and molecular diagnostics (e.g., 16S rRNA gene PCR/sequencing, Tropheryma whipplei PCR) may be applied to resected valves to aid in diagnosis. Herein, we summarize recent knowledge in this area and propose a microbiologic and pathological algorithm for endocarditis diagnosis.

New insights into valve-related intramural and intracellular bacterial diversity in infective endocarditis

Aims

In infective endocarditis (IE), a severe inflammatory disease of the endocardium with an unchanged incidence and mortality rate over the past decades, only 1% of the cases have been described as polymicrobial infections based on microbiological approaches. The aim of this study was to identify potential biodiversity of bacterial species from infected native and prosthetic valves. Furthermore, we compared the ultrastructural micro-environments to detect the localization and distribution patterns of pathogens in IE.

Material and methods

Using next-generation sequencing (NGS) of 16S rDNA, which allows analysis of the entire bacterial community within a single sample, we investigated the biodiversity of infectious bacterial species from resected native and prosthetic valves in a clinical cohort of 8 IE patients. Furthermore, we investigated the ultrastructural infected valve micro-environment by focused ion beam scanning electron microscopy (FIB-SEM).

Results

Biodiversity was detected in 7 of 8 resected heart valves. This comprised 13 bacterial genera and 16 species. In addition to 11 pathogens already described as being IE related, 5 bacterial species were identified as having a novel association. In contrast, valve and blood culture-based diagnosis revealed only 4 species from 3 bacterial genera and did not show any relevant antibiotic resistance. The antibiotics chosen on this basis for treatment, however, did not cover the bacterial spectra identified by our amplicon sequencing analysis in 4 of 8 cases. In addition to intramural distribution patterns of infective bacteria, intracellular localization with evidence of bacterial immune escape mechanisms was identified.

Conclusion

The high frequency of polymicrobial infections, pathogen diversity, and intracellular persistence of common IE-causing bacteria may provide clues to help explain the persistent and devastating mortality rate observed for IE. Improved bacterial diagnosis by 16S rDNA NGS that increases the ability to tailor antibiotic therapy may result in improved outcomes.

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.

Histopathology of valves in infective endocarditis, diagnostic criteria and treatment considerations

BACKGROUND

Infective endocarditis (IE) is a severe disease. Pathogen isolation is fundamental so as to treat effectively and reduce morbidity and mortality. Blood and valve culture and histopathology (HP) are routinely employed for this purpose. Valve HP is the gold standard for diagnosis.

OBJECTIVES

To determine the sensitivity and specificity of clinical criteria for IE (the modified Duke and the St Thomas' minor modifications, STH) of blood and valve culture compared to valve HP, and to evaluate antibiotic treatment duration.

METHODS

Prospective case series of patients, from 2006 to 2014 with surgically treated IE. Statistical analysis was done by the R software.

RESULTS

There were 136 clinically definite episodes of IE in 133 patients. Mean age ± SD was 43 ± 15.6 years and IE was left sided in 81.6 %. HP was definite in 96 valves examined, which were used as gold standard. Sensitivity of blood culture was 61 % (CI 0.51, 0.71) and of valve culture 15 % (CI 0.07, 0.26). The modified Duke criteria were 65 % (CI 0.55, 0.75) sensitive and 33 % specific, while the STH's sensitivity was 72 % (CI 0.61, 0.80) with similar specificity. In multivariate analysis and logistic regression, the only variable with statistical significance was duration of antibiotic therapy postoperatively.

CONCLUSIONS

Valve HP had high sensitivity and valve culture low sensitivity in the diagnosis of IE. The STH's criteria were more sensitive than the modified Duke criteria. Valve HP should guide duration of postoperative antibiotic treatment.

An unusual case of thoracic empyema caused by Granulicatella elegans (nutritionally variant streptococci) in a patient with pulmonary tuberculosis and human immunodeficiency virus infection

INTRODUCTION

Nutritionally variant streptococci (NVS) are an infrequent cause of human infection with Granulicatella elegans being the least encountered species in clinical specimens. The most common infection caused by NVS is infective endocarditis.

CASE PRESENTATION

We report an unusual case of thoracic empyema due to G. elegans in a patient with pulmonary tuberculosis (TB) and human immunodeficiency virus infection. The patient responded favourably to drainage and penicillin.

CONCLUSION

This case illustrates that even though TB is responsible for the majority of pleural effusions in this setting, other rare opportunistic bacteria may cause infection in susceptible patients. Therefore, microbiological investigations should be performed in all patients presenting with pleural effusion.

Case series of Bartonella quintana blood culture-negative endocarditis in Washington, DC

Introduction:

Prior studies (predominantly from Europe) have demonstrated blood culture-negative endocarditis due to Bartonella. Our objective was to describe three cases of Bartonella quintana endocarditis identified within one year at a large hospital in Washington, DC, USA.

Case presentation:

We constructed a descriptive case series from a retrospective review of medical records from April to December 2013 at an 800-bed urban hospital. All three patients (ages: 52, 55 and 57 years) were undomiciled/homeless men with a history of alcoholism. Although they had negative blood cultures, echocardiography demonstrated aortic/mitral valve perforation and regurgitation in one patient, aortic/mitral valve vegetation with mitral regurgitation in the second patient, and aortic valve vegetation with regurgitation in the third patient. The patients had positive Bartonella quintana serum immunoglobulin G (IgG) with negative immunoglobulin M (IgM). PCR on DNA extracted from cardiac valves was positive for Bartonella, and DNA sequencing of PCR amplicons identified Bartonella quintana. Patients received treatment with doxycycline/rifampin or doxycycline/gentamicin.

Conclusion:

Clinicians should consider Bartonella endocarditis as a differential diagnosis in patients who fit elements of the Duke Criteria, as well as having a history of homelessness and alcoholism.

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.

Polymicrobial Infective Endocarditis: Clinical Features and Prognosis

To describe the profile of left-sided polymicrobial endocarditis (PE) and to compare it with monomicrobial endocarditis (ME).Among 1011 episodes of left-sided endocarditis consecutively diagnosed in 3 tertiary centers, between January 1, 1996 and December 31, 2014, 60 were polymicrobial (5.9%), 821 monomicrobial (81.7%), and in 123 no microorganism was detected (12.2%). Seven patients (0.7%) were excluded from the analysis because contamination of biologic tissue could not be discarded. The authors described the clinical, microbiologic, echocardiographic, and outcome of patients with PE and compared it with ME.Mean age was 64 years SD 16 years, 67% were men and 30% nosocomial. Diabetes mellitus (35%) were the most frequent comorbidities, fever (67%) and heart failure (43%) the most common symptoms at admission. Prosthetic valves (50%) were the most frequent infection location and coagulase-negative Staphylococci (48%) and enterococci (37%) the leading etiologies. The most repeated combination was coagulase-negative Staphylococci with enterococci (n = 9). Polymicrobial endocarditis appeared more frequently in patients with underlying disease (70% versus 56%, P = 0.036), mostly diabetics (35% versus 24%, P = 0.044) with previous cardiac surgery (15% versus 8% P = 0.049) and prosthetic valves (50% versus 37%, P = 0.038). Coagulase-negative Staphylococci, enterococci, Gram-negative bacilli, anaerobes, and fungi were more frequent in PE. No differences on age, sex, symptoms, need of surgery, and in-hospital mortality were detected.Polymicrobial endocarditis represents 5.9% of episodes of left-sided endocarditis in our series. Despite relevant demographic and microbiologic differences between PE and ME, short-term outcome is similar.

Bartonella endocarditis

Blood culture-negative endocarditis presents a clinical and diagnostic challenge. Here, we describe a patient with a delayed diagnosis of Bartonella henselae endocarditis. <Learning objective: The aim of this report is to highlight the importance of Bartonella species as a cause of culture-negative endocarditis and to illustrate the challenges it poses in diagnosis and treatment.>.

Innovative qPCR using interfacial effects to enable low threshold cycle detection and inhibition relief

Molecular diagnostics offers quick access to information but fails to operate at a speed required for clinical decision-making. Our novel methodology, droplet-on-thermocouple silhouette real-time polymerase chain reaction (DOTS qPCR), uses interfacial effects for droplet actuation, inhibition relief, and amplification sensing. DOTS qPCR has sample-to-answer times as short as 3 min 30 s. In infective endocarditis diagnosis, DOTS qPCR demonstrates reproducibility, differentiation of antibiotic susceptibility, subpicogram limit of detection, and thermocycling speeds of up to 28 s/cycle in the presence of tissue contaminants. Langmuir and Gibbs adsorption isotherms are used to describe the decreasing interfacial tension upon amplification. Moreover, a log-linear relationship with low threshold cycles is presented for real-time quantification by imaging the droplet-on-thermocouple silhouette with a smartphone. DOTS qPCR resolves several limitations of commercially available real-time PCR systems, which rely on fluorescence detection, have substantially higher threshold cycles, and require expensive optical components and extensive sample preparation. Due to the advantages of low threshold cycle detection, we anticipate extending this technology to biological research applications such as single cell, single nucleus, and single DNA molecule analyses. Our work is the first demonstrated use of interfacial effects for sensing reaction progress, and it will enable point-of-care molecular diagnosis of infections.

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.

Mycoplasma hominis, a Rare but True Cause of Infective Endocarditis

Mycoplasma spp. are rarely recognized agents of infective endocarditis. We report a case of Mycoplasma hominis prosthetic valve endocarditis diagnosed by 16S ribosomal DNA (rDNA) PCR and culture of valves in a 74-year-old man. We reviewed the literature and found only 8 other cases reported.

The culturome of the human nose habitats reveals individual bacterial fingerprint patterns

The complex anatomy of the human nose might offer distinct microbial niches. Microbiota composition may affect nose inflammatory diseases and Staphylococcus aureus carriage. Considering different nasal cavity locations, microbial colonization was analysed across individuals exhibiting chronic nasal inflammatory diseases (n = 18) and those without local inflammation signs (n = 16). Samples were collected systematically during surgery and examined by an extensive culture-based approach and, for a subset, by 16S rRNA gene community profiling. Cultivation yielded 141 taxa with members of Staphylococcus, Corynebacterium and Propionibacterium as most common isolates comprising the nasal core culturome together with Finegoldia magna. Staphylococcus aureus was most frequently found in association with Staphylococcus epidermidis and Propionibacterium acnes, and the posterior vestibules were redefined as S. aureus' principle habitat. Culturome analysis revealed host-specific bacterial 'fingerprints' irrespective of host-driven factors or intranasal sites. Comparisons between cultivable and molecular fingerprints demonstrated that only a small fraction of phylotypes (6.2%) was correlated. While the total number of different phylotypes was higher in the molecular dataset, the total number of identifications down to the species level was higher in the culturomic approach. To determine host-specific microbiomes, the advantages of molecular approaches should be combined with the resolution and reliability of species identification by culturomic analyses.

Randomized controlled clinical trial evaluating multiplex polymerase chain reaction for pathogen identification and therapy adaptation in critical care patients with pulmonary or abdominal sepsis

OBJECTIVE

To determine whether a multiplex polymerase chain reaction (PCR)-based test could reduce the time required for initial pathogen identification in patients in an intensive care unit (ICU) setting.

METHODS

This double-blind, parallel-group randomized controlled trial** enrolled adults with suspected pulmonary or abdominal sepsis caused by an unknown pathogen. Both the intervention and control groups underwent the standard blood culture (BC) testing, but additional pathogen identification, based on the results of a LightCycler® SeptiFast PCR test, were provided in the intervention group.

RESULTS

The study enrolled 37 patients in the control group and 41 in the intervention group. Baseline clinical and demographic characteristics were similar in both groups. The PCR-based test identified a pathogen in 10 out of 41 (24.4%) patients in the intervention group, with a mean duration from sampling to providing the information to the ICU of 15.9 h. In the control group, BC results were available after a significantly longer period (38.1 h).

CONCLUSION

The LightCycler® SeptiFast PCR test demonstrated a significant reduction in the time required for initial pathogen identification, compared with standard BC.

[Infective endocarditis]

Colonization of native cardiac valves or polymer implants, e.g. valves, conduits, rings, electrode leads and polymer-associated endocarditis (PIE), by microorganisms, primarily gram-positive bacteria (infective endocarditis), constitutes a severe, prognostically unfavorable disease. Fever and in the majority of cases development of a valve regurgitant murmur are clinical landmark findings. The white blood cell count, erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) are regularly elevated. With a normal CRP level, infective endocarditis is extremely unlikely. Irrespective of body temperature, at least three blood cultures (aerobic and anaerobic) should be taken and if initiation of antimicrobial therapy is urgent, 1 h apart before therapy is initiated. Identification of the pathogen to the species level and testing antimicrobial susceptibility to antibiotics by a quantitative hemodilution test, not with agar diffusion tests, are obligatory. A minimum inhibitory concentration should be administered for antibiotics and usual combinations of antibiotics with an expected synergistic potential. Streptococci, staphylococci and enterococci are the most frequent causative organisms. Immediate initiation of transthoracic echocardiography (TTE) is mandatory followed by transesophageal echocardiography if imaging quality is poor, involvement of intracardiac implants is possible or TTE is insufficient to establish the diagnosis. An insufficiently long antimicrobial therapy promotes recurrent infections, thus a 4-week treatment is standard, while in special cases (e.g. PIE) treatment for 6 weeks should be the rule. If typical complications of infective endocarditis, such as uncontrolled local infection, systemic thromboembolism, central nervous involvement, development of a severe valve incompetence or mitral kissing vegetation in primary aortic valve endocarditis occur, urgent surgical intervention should be considered. If cardiac implants are involved, early surgical removal followed by a 6-week antimicrobial treatment is the rule. Adequate and timely diagnosis and treatment are the key to improve the overall prognosis.

Salvage microbiology: opportunities and challenges in the detection of bacterial pathogens following initiation of antimicrobial treatment

Broad-range 16S ribosomal RNA gene PCR coupled with Sanger sequencing was originally employed by soil scientists and was subsequently adapted for clinical applications. PCR coupled with electrospray ionization mass spectrometry has also progressed from initial applications in the detection of organisms from environmental samples into the clinical realm and has demonstrated promise in detection of pathogens in clinical specimens obtained from patients with suspected infection but negative cultures. We review studies of multiplex PCR, 16S ribosomal RNA gene PCR and sequencing and PCR coupled with electrospray ionization mass spectrometry for detection of bacteria in specimens that were obtained from patients during or after administration of antibiotic treatment, and examine the role of each for assisting in antimicrobial treatment and stewardship efforts. Following an exploration of the available data in this field, we discuss the opportunities that the preliminary investigations reveal, as well as the challenges faced with the implementation of these strategies in clinical practice.

Incidence and outcome of documented fungal endocarditis

BACKGROUND

Fungal endocarditis, the most severe form of infective endocarditis, is characterized by excessive mortality and morbidity.

OBJECTIVES

The present study aimed to analyze the characteristics of fungal endocarditis to improve the management of these patients.

MATERIALS AND METHODS

In this cross-sectional study, vegetations on the mitral or tricuspid valves and embolic material surgically removed from the patients with suspected infective endocarditis between December 2009 and November 2011 were examined for fungal infection by direct smear and culture, and the susceptibility patterns of the isolated species were determined. Then, blood samples were cultured on BACTEC media and real-time PCR was done with blood and tissue samples.

RESULTS

Of the 31 patients with suspected infective endocarditis who did not respond to antibacterial therapy, 11 had confirmed fungal endocarditis. The most frequent predisposing risk factors were previous surgery and drug abuse. The organisms isolated were Aspergillus spp. and Candida albicans. Resistance to amphotericin B and itraconazole was observed in Aspergillus species, and to fluconazole in Candida albicans. Positive PCR results were obtained in blood and tissue samples.

CONCLUSIONS

Fungal endocarditis should be considered in the patients not responsive to antimicrobials. Moreover, management of these patients can be improved with molecular diagnostic methods and by determining the susceptibility patterns of the etiologic agents.

A case of culture-negative endocarditis due to Streptococcus tigurinus

Culture-negative endocarditis remains a diagnostic and therapeutic challenge despite recent medical advances. Streptococcus tigurinus, a novel member of the Streptococcus mitis group, was first identified in Zurich. S. tigurinus possesses virulence determinants and causes invasive infections. We report a case of culture-negative endocarditis with serious complications due to S. tigurinus, which was identified by 16S ribosomal RNA gene sequence analysis of excised valve tissue specimens. This technique is useful for identification of the causative microorganism in patients with culture-negative endocarditis and may facilitate early diagnosis and appropriate antimicrobial treatment.