Diagnostic methods. Current best practices and guidelines for identification of difficult-to-culture pathogens in infective endocarditis

A retrospective analysis of blood culture-negative endocarditis at a tertiary care centre in Switzerland

AIMS OF THE STUDY

Numerous studies from different countries have contributed to an improved understanding of blood culture-negative infective endocarditis. However, little is known about its epidemiology and microbiology in Switzerland. We aimed to assess the epidemiology and microbiology of blood culture-negative endocarditis at the University Hospital Zurich, Switzerland.

METHODS

We screened all patients hospitalised between 1997 and 2020 with possible or definite endocarditis at our institution. Thereof, we identified all cases with blood culture-negative endocarditis and retrospectively retrieved patient characteristics, microbiological, histopathological, radiographic and surgical data from medical records.

RESULTS

Among 861 patients screened, 66 (7.7%) cases of blood culture-negative endocarditis were identified. Thereof, 31 cases could be microbiologically documented or not documented (n = 30), and in five cases a non-infectious aetiology was confirmed. Endocarditis predominantly affected men (77%) and the left heart (79%); predisposing factors were prosthetic valves (42%), congenital heart disease (35%) and prior endocarditis (14%). The most common reasons for negative blood cultures were antibiotic treatment prior to blood culture sampling (35%), fastidious and slow growing microorganisms (30%) and definite non-infective endocarditis (8%). Coxiella burnetii and Bartonella spp. were the most common fastidious bacteria identified. In addition to serology, identification of causative microorganisms was possible by microbiological and/or histopathological analysis of tissue samples, of which polymerase chain reaction testing (PCR) of the 16S ribosomal RNA proved to be most successful.

CONCLUSIONS

The present study provides a detailed analysis of blood culture-negative endocarditis over a time span of more than 20 years in Zurich, Switzerland. Antibiotic treatment prior to blood collection, and fastidious and slow growing organisms were identified as main reasons for sterile blood cultures. Typical culture-negative bacteria were mainly found by PCR and/or culture of tissue samples.

Pathogenesis, Diagnosis, Antimicrobial Therapy, and Management of Infective Endocarditis, and Its Complications

Infective endocarditis in the adult is life-threatening. Bacterial endocarditis is an inner infection lining the heart muscle (endocardium). The scientific study of the causes of diseases is known as etiology. The agents that cause disease fall into five groups: bacteria, viruses, protozoa, fungi, and helminths (worms). Risk factors are past heart defects, damaged or abnormal heart valves, new valves after surgery, chronic hemodialysis, and immunosuppressed state (chemotherapy, HIV, etc.). Infective endocarditis is categorized into two clinical forms: bacterial acute and subacute endocarditis. Acute bacterial endocarditis is usually caused by staphylococci (staph) and streptococci (strep). And occasionally by listeria and brucella bacterial strains. Invasive medical technology has increased the responsibility of healthcare-associated infective endocarditis (HAIE). Microscopy of the disease is the chronic aggressive cells in the deeper zone of nonspecific, composed of fibrin and platelets covering colonies of bacteria. Tuberculous valvular endocarditis due to mycobacterium tuberculosis is a rare clinical entity. Syphilitic endocarditis is pathologically the cutaneous lesions of secondary syphilis. It is caused by infection with the microorganismTreponema pallidum. Fungal endocarditis is a rare and fatal condition. They are infected with fungi such as Candida albicans, Histoplasma capsulatum, and Aspergillus species. Fatal endocarditis associated with Q fever (query fever). Q fever is a chronic or prolonged disease caused by the rickettsial-like bacillus Coxiella burnetii, a rare form of rickettsia in the endocarditis. Varicella-zoster virus (VZV) infection causes chronic and repeated febrile illness. They are followed by pharyngitis, malaise, and a vesicular rash. Chronic Q fever usually manifests as endocarditis or hepatitis. The therapy given to simplify the complications is antimicrobial therapy. The medicines prescribed are ampicillin, cefazolin, ceftazidime, gentamicin, vancomycin, metronidazole, and tobramycin. High medicinal antibiotics are used to control the spread of infective endocarditis.

Rapid and Visual Detection of Coxiella burnetii Using Recombinase Polymerase Amplification Combined with Lateral Flow Strips

Coxiella burnetii, a global-distributed biological warfare agent, is the causative agent of Q fever. Correct diagnosis of Q fever is challenging and developing a fast, simple, and reliable detection method is necessary. In this study, recombinase polymerase amplification (RPA) assay combined with lateral flow (LF) test was developed targeting 23S rRNA gene of C. burnetii Xinqiao strain. Primers and probe were designed and synthesized, with one set with high amplification efficiency screened for establishment of the method. Reaction conditions were optimized. Sensitivity, specificity, and accuracy were evaluated. The established RPA-LF reaction could be completed in 30 minutes by combining RPA at 37°C with LF at room temperature, with visually judged results. The method showed good specificity without recognizing other bacteria evaluated. It detected positive plasmid and genomic DNA at levels of 10 copies/reaction and 7 copies/reaction, respectively, levels comparable to that of real-time quantitative PCR (RT-qPCR) targeting 23S rRNA gene established previously. Both RPA-LF and RT-qPCR were used to detect C. burnetii-infected mouse samples and the results were fully consistent. The method showed superior detection performance and will provide technical support against C. burnetii in resources-limited areas.

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.

Bartonella Species, an Emerging Cause of Blood-Culture-Negative Endocarditis

Since the reclassification of the genus Bartonella in 1993, the number of species has grown from 1 to 45 currently designated members. Likewise, the association of different Bartonella species with human disease continues to grow, as does the range of clinical presentations associated with these bacteria. Among these, blood-culture-negative endocarditis stands out as a common, often undiagnosed, clinical presentation of infection with several different Bartonella species. The limitations of laboratory tests resulting in this underdiagnosis of Bartonella endocarditis are discussed. The varied clinical picture of Bartonella infection and a review of clinical aspects of endocarditis caused by Bartonella are presented. We also summarize the current knowledge of the molecular basis of Bartonella pathogenesis, focusing on surface adhesins in the two Bartonella species that most commonly cause endocarditis, B. henselae and B. quintana. We discuss evidence that surface adhesins are important factors for autoaggregation and biofilm formation by Bartonella species. Finally, we propose that biofilm formation is a critical step in the formation of vegetative masses during Bartonella-mediated endocarditis and represents a potential reservoir for persistence by these bacteria.

Comparison of PCR-Electrospray Ionization Mass Spectrometry with 16S rRNA PCR and Amplicon Sequencing for Detection of Bacteria in Excised Heart Valves

Identification of the causative pathogen of infective endocarditis (IE) is crucial for adequate management and therapy. A broad-range PCR-electrospray ionization mass spectrometry (PCR-ESI-MS) technique was compared with broad-spectrum 16S rRNA PCR and amplicon sequencing (16S rRNA PCR) for the detection of bacterial pathogens in 40 heart valves obtained from 34 definite infective endocarditis patients according to the modified Duke criteria and six nonendocarditis patients. Concordance between the two molecular techniques was 98% for being positive or negative, 97% for concordant identification up to the genus level, and 77% for concordant identification up to the species level. Sensitivity for detecting the causative pathogen (up to the genus level) in excised heart valves was 88% for 16S rRNA PCR and 85% for PCR-ESI-MS; the specificity was 83% for both methods. The two molecular techniques were significantly more sensitive than valve culture (18%) and accurately identified bacteria in excised heart valves. In eight patients with culture-negative IE, the following results were obtained: concordant detection of Coxiella burnetii (n = 2), Streptococcus gallolyticus (n = 1), Propionibacterium acnes (n = 1), and viridans group streptococci (n = 1) by both molecular tests, detection of P. acnes by PCR-ESI-MS whereas the 16S rRNA PCR was negative (n = 1), and a false-negative result by both molecular techniques (n = 2). In one case of IE caused by viridans streptococci, PCR-ESI-MS was positive for Enterococcus spp. The advantages of PCR-ESI-MS compared to 16S rRNA PCR are its automated workflow and shorter turnaround times.

Development of a serum-free liquid medium for Bartonella species

The genus Bartonella comprises numerous species with at least 13 species pathogenic for humans. They are fastidious, aerobic, Gram negative, and facultative intracellular bacteria which cause a variety of human and non-human diseases. This study focused on the development of a serum-free liquid medium for culture of Bartonella species. Some liquid media are available commercially but all of them use undefined supplements such as fetal calf serum or defibrinated sheep blood. Our intention was to create a reproducible liquid medium for Bartonella species that can simply be prepared. We tested several supplements that could potentially support the growth of Bartonella species. Slight growth improvement was achieved with glucose and sucrose. However, hemin in particular improved the growth rate. At a temperature of 37 °C, a CO₂ concentration of 5 %, a humidified atmosphere, and the use of the supplements glucose, sucrose, and hemin, we developed a medium that does not need serum as an undefined supplement any more. In conclusion, the newly developed medium supports growth of Bartonella species equal to the commercially available media but with the advantage that it has a serum-free formulation. It can be prepared fast and easy and is a useful tool in studying these bacteria.

Serological characterization of surface-exposed proteins of Coxiella burnetii

The obligate intracellular Gram-negative bacterium Coxiella burnetii causes Q fever, a worldwide zoonosis. Here we labelled Cox. burnetii with biotin and used biotin-streptavidin affinity chromatography to isolate surface-exposed proteins (SEPs). Using two-dimensional electrophoresis combined with mass spectrometry, we identified 37 proteins through bioinformatics analysis. Thirty SEPs expressed in Escherichia coli (recombinant SEPs, rSEPs) were used to generate microarrays, which were probed with sera from mice experimentally infected with Cox. burnetii or sera from Q fever patients. Thirteen rSEPs were recognized as seroreactive, and the majority reacted with at least 50 % of the sera from mice infected with Cox. burnetii but not with sera from mice infected with Rickettsia rickettsii, R. heilongjiangensis, or R. typhi. Further, 13 proteins that reacted with sera from patients with Q fever did not react with sera from patients with brucellosis or mycoplasma pneumonia. Our results suggest that these seroreactive SEPs have potential as serodiagnostic antigens or as subunit vaccine antigens against Q fever.

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.

Q fever endocarditis in Romania: the first cases confirmed by direct sequencing

Infective endocarditis (IE) is a serious, life-threatening disease with highly variable clinical signs, making its diagnostic a real challenge. A diagnosis is readily made if blood cultures are positive, but in 2.5 to 31% of all infective endocarditis cases, routine blood cultures are negative. In such situations, alternative diagnostic approaches are necessary. Coxiella burnetii and Bartonella spp. are the etiological agents of blood culture-negative endocarditis (BCNE) most frequently identified by serology. The purpose of this study is to investigate the usefulness of molecular assays, as complementary methods to the conventional serologic methods for the rapid confirmatory diagnostic of Q fever endocarditis in patients with BCNE. Currently, detection of C. burnetii by culture or an antiphase I IgG antibody titers >800 represents a major Duke criterion for defining IE, while a titers of >800 for IgG antibodies to either B. henselae or B. quintana is used for the diagnosis of endocarditis due to Bartonella spp. We used indirect immunofluorescence assays for the detection of IgG titers for C. burnetii, B. henselae and B. quintana in 57 serum samples from patients with clinical suspicion of IE. Thirty three samples originated from BCNE patients, whereas 24 were tested before obtaining the blood cultures results, which finally were positive. The results of serologic testing showed that nine out of 33 BCNE cases exhibited antiphase I C. burnetii IgG antibody titer >800, whereas none has IgG for B. henselae or B. quintana. Subsequently, we used nested-PCR assay for the amplification of C. burnetii DNA in the nine positive serum samples, and we obtained positive PCR results for all analyzed cases. Afterwards we used the DNA sequencing of amplicons for the repetitive element associated to htpAB gene to confirm the results of nested-PCR. The results of sequencing allowed us to confirm that C. burnetii is the causative microorganism responsible for BCNE. In conclusion, the nested PCR amplification followed by direct sequencing is a reliable and accurate method when applied to serum samples, and it may be used as an additional test to the serological methods for the confirmatory diagnosis of BCNE cases determined by C. burnetii.

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.

An evaluation of extended incubation time with blind subculture of blood cultures in patients with suspected endocarditis

BACKGROUND

In a small proportion of patients, bacterial endocarditis is due to organisms that grow slowly and may not be recovered in conventional blood cultures incubated for five days. This has led to recommendations for prolonged incubation and routine subculture of negative cultures.

OBJECTIVE

The above-mentioned approach is evaluated.

METHOD

The microbiology of all blood cultures subjected to prolonged incubation and the charts of individuals who had organisms recovered after five days were evaluated to determine their clinical significance.

RESULTS

In all, 507 blood cultures were handled using an extended incubation and blind subculture protocol. Fifty-three blood cultures in 27 patients were positive. Blood cultures were positive after five days in only five cases; patient outcomes were not affected by the results in any of these cases, although several fastidious organisms (ie, Haemophilus paraphrophilus and Haemophilus parainfluenzae) were recovered in the first five days of incubation.

CONCLUSION

Prolonged incubation and blood subcultures in patients with suspected endocarditis or infections due to fastidious organisms do not represent a wise use of increasingly scarce resources.

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.

Endocarditis in cattle caused by Bartonella bovis

This study aimed to determine the role of Bartonella as an endocarditis agent in cattle. Bartonella bovis was identified by PCR, gene sequences analysis, and specific internal transcribed spacer amplicon product size in 2 bovine endocarditis cases with high antibody titers, which demonstrates that B. bovis is a pathogen for cattle.

Microarray for serotyping of Bartonella species

Background

Bacteria of the genus Bartonella are responsible for a large variety of human and animal diseases. Serological typing of Bartonella is a method that can be used for differentiation and identification of Bartonella subspecies.

Results

We have developed a novel multiple antigenic microarray to serotype Bartonella strains and to select poly and monoclonal antibodies. It was validated using mouse polyclonal antibodies against 29 Bartonella strains. We then tested the microarray for serotyping of Bartonella strains and defining the profile of monoclonal antibodies.

Bartonella strains gave a strong positive signal and all were correctly identified. Screening of monoclonal antibodies towards the Gro EL protein of B. clarridgeiae identified 3 groups of antibodies, which were observed with variable affinities against Bartonella strains.

Conclusion

We demonstrated that microarray of spotted bacteria can be a practical tool for serotyping of unidentified strains or species (and also for affinity determination) by polyclonal and monoclonal antibodies. This could be used in research and for identification of bacterial strains.

DNA sequence-based detection of group B Streptococcus directly from heart valve tissue in a patient with culture-negative endocarditis

A human case of culture-negative bacterial endocarditis is presented where conventional methods failed to determine a microbial aetiology. DNA sequencing performed directly on autopsy heart valve tissue revealed Streptococcus agalactiae (group B streptococcus). To our knowledge, this is the first report of DNA sequence-based detection of this organism directly from a heart valve.

New insight into the diagnosis of fastidious bacterial endocarditis

Sterile blood cultures are noted in one third of patients with infectious endocarditis. Although in half of cases this is due to previous antibiotic therapy, in the other half, the aetiology of culture-negative endocarditis is intracellular bacteria such as Coxiella burnetii or fastidious growing bacteria. Although it was previously considered that the prevalence of such organisms was identical throughout the world, recent investigations on Bartonella endocarditis clearly showed that the aetiology of culture-negative endocarditis is likely to be strongly related to epidemiology of the agent in each country. During the past decade the use of molecular techniques such as PCR with subsequent sequencing to detect or to identify bacteria in valves from patients with infectious endocarditis have considerably improved the aetiological diagnosis. This is especially true in the case of culture-negative endocarditis following earlier antibiotic therapy. However, the fact that DNA remnants of past endocarditis can be detected some time after the acute episode, when the patient has been cured, suggests that the predictive value of these techniques along with the traditional histology and culture need to be evaluated closely.

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

The BSAC Guidelines on Endocarditis were last published in 1998. The Guidelines presented here have been updated and extended to reflect changes in both the antibiotic resistance characteristics of causative organisms and the availability of new antibiotics. 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. The Guidelines cover diagnosis and laboratory testing, suitable antibiotic regimens and causative organisms. Special emphasis is placed on common causes of endocarditis, such as streptococci and staphylococci, however, other bacterial causes (such as enterococci, HACEK organisms, Coxiella and Bartonella) and fungi are considered. The special circumstances of prosthetic endocarditis are discussed.

Simplified serological diagnosis of endocarditis due to Coxiella burnetii and Bartonella

We tested a single-step serological assay against Coxiella burnetii and Bartonella species and found a sensitivity of 100%, and a positive predictive value of 98% for the diagnosis of blood culture-negative endocarditis (BCNE). This assay should be considered as a possible commercial test for the diagnosis of BCNE.

Culture-negative endocarditis due to Houston Complex Bartonella henselae acquired in Noumea, New Caledonia

A 44-year-old man with a bioprosthetic aortic valve suffered destructive endocarditis with severe embolic disease due to Bartonella henselae infection. Multilocus sequence typing was successfully performed with crude preparations of operative tissue as templates, and the infecting organism was determined to be typical of the Houston clonal group, although it was never cultured from blood or tissue. This is the first report of B. henselae infection in the South Pacific, and it reminds one that B. henselae is a cause of potentially lethal culture-negative endocarditis which may respond poorly to conventional empirical therapy. Nothing is known of the epidemiology of the infection in this region, but it is likely to be common and to contain representatives of both major clonal complexes. This study emphasizes the ease with which multilocus sequence typing can be used directly with tissue, which is important because of suggestions of strain-dependent clinical outcomes.

Peroneal Neuropathy due to a Popliteal Aneurysm in a Patient with Infectious Endocarditis

We present an 18-year-old young man with the diagnosis of infective endocarditis who also suffered from concomitant knee pain. The clinical examination revealed right homonymous hemianopsia and left peroneal neuropathy. Magnetic resonance imaging studies of the knee demonstrated a lobulated saccular aneurysm in the left popliteal fossa. We diagnosed this patient as having peripheral mononeuropathy due to an aneurysm compressing the peroneal nerve in the left poplitea.

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.