Use of the polymerase chain reaction and DNA sequencing for detection of Bartonella quintana in the aortic valve of a patient with culture-negative infective endocarditis

Molecular characterization and toxin quantification of Microcystis panniformis: A microcystin producer in Lake Taihu, China

Microcystis panniformis is a bloom forming species with flat panniform-like colonies. This species was recently found in Lake Taihu, China. To specifically characterize M. panniformis based on isolated strains, morphological examination on colonial transition and genetic examination are needed. Three M. panniformis strains isolated from a water bloom sample in Lake Taihu were characterized by molecular analysis and toxin quantification. Phylogenetic analysis based on both 16S rRNA gene and internal transcribed spacer (ITS) between 16S and 23S rRNA genes were performed and compared to facilitate easy identification of the species. Relatively high similarities (98%-99%) were shown in 16S rDNA sequences between the strains of M. panniformis and those of other Microcystis species, whereas the similarities for ITS sequences were 88%-95%. In the phylogenetic tree based on the 16S rDNA sequences, the M. panniformis and M. aeruginosa strains were intermixed together with no clear division, whereas all of the M. panniformis strains were clustered together in a single clade based on the ITS sequences based phylogenyetic tree. The mcyE gene was detected in all three strains, and microcystin was determined by high-performance liquid chromatography. The molecular detection and toxin production of M. panniformis strains are of great significance for the environmental risk assessment of Microcystis blooms.

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.

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.

A population-based study of aerococcal bacteraemia in the MALDI-TOF MS-era

The purpose of this study was to determine the incidence of aerococcal bacteraemia in the MALDI-TOF MS-era, to describe the clinical presentation and to determine the MIC values of aerococci for ten antibiotics. Aerococci in blood cultures were identified through searches in the laboratory database for the years 2012-2014. MALDI-TOF MS, sequencing of the 16S rRNA gene and a PYR test were used for species identification. Patients' medical charts were systematically reviewed. Etests were used to determine MIC values. Seventy-seven patients were identified (Aerococcus urinae n = 49, Aerococcus viridans n = 14, Aerococcus sanguinicola n = 13 and Aerococcus christensenii n = 1) corresponding to incidences of 14 cases per 1,000,000 inhabitants per year (A. urinae) and 3.5 cases per 1,000,000 inhabitants per year (A. sanguinicola and A.viridans). A. urinae was in pure culture in 61 %, A. sanguinicola in 46 % and A. viridans in 36 % of the cases. The A. urinae and A. sanguinicola patients were old and many had urinary tract disorders, and a majority had a suspected urinary tract focus of the bacteraemia. Eighty percent of the A. urinae patients were men. Five A. urinae patients were diagnosed with infective endocarditis. Six patients died within 30 days. Most isolates had low MICs to penicillins and carbapenems. MALDI-TOF MS has led to an increased identification of aerococcal bacteremia. A. urinae remains the most common Aerococcus in blood cultures and in aerococcal IE.

Culture negative endocarditis: a diagnostic and therapeutic challenge!

Infective endocarditis remains a diagnostic and therapeutic challenge. The authors report an older male who presented with a lower extremities rash and signs of cardiac failure. Echocardiography showed vegetations attached to the bio-prosthetic aortic valve, however, with negative blood cultures. Further investigation revealed positive Bartonella serologies. The patient was diagnosed with Bartonella endocarditis affecting the prosthetic valve and started on appropriate antibiotics. Valvular surgery was refused by patient secondary to age and medical co-morbidities. The patient presented 10 days later with intracerebral haemorrhage and progression of the endocarditis as demonstrated on echocardiogram. Valve replacement was contraindicated at this occasion due to the intracerebral bleed. The patient had poor prognosis and a decision to withdraw care was made by the family. The authors demonstrate a case of complicated infective endocarditis caused by Bartonella species leading to multisystem involvement. This case highlights the need for urgent valve replacement in the setting of Bartonella endocarditis.

The ail gene is present in some Yersinia enterocolitica biotype 1A strains

One chromosomal virulence marker of Yersinia is the gene ail, which encodes Ail, an outer membrane protein that promotes attachment and invasion. A high correlation has been found between the ail gene and the virulence of Yersinia. Here, we report two Yersinia enterocolitica biotype 1A strains that are usually nonpathogenic and carry the ail gene. The ail gene sequences of biotype 1A strains displayed similarity to the bioserotype 1B/O:8 strain 8081. The finding suggests that ail-based detection methods for Y. enterocolitica alone are insufficient to detect real pathogenic strains.

Mycobacteria are hidden endophytes in the shoots of rock plant [Pogonatherum paniceum (Lam.) Hack.] (Poaceae)

A mycobacterium was isolated from micropropagated Pogonatherum paniceum and identified as a close relative of Mycobacterium cookii. The endophyte diversity in the shoots of potted and micropropagated P. paniceum plants was studied by culture-independent techniques. Group- and strain-specific PCR demonstrated that the P. paniceum plants harboured the isolated Mycobacterium strain as a minority. Altogether 101 clones of the PCR products were sequenced. The shoots of potted P. paniceum plants harboured unculturable endophytes in the families Phyllobacteriaceae, Hyphomicrobiaceae, Sphingobacteriaceae, Enterobacteriaceae, Alcaligenaceae and Mycobacteriaceae. Among the unculturable Mycobacteriaceae strains related to Mycobacterium chubuense, M. poriferae, M. obuense, M. fortuitum, M. neoaurum, M. diernhoferi, M. intracellulare and M. cookii were identified. Three unique sequences that clustered with M. llatzarense and M. mucogenicum were identified in micropropagated plants. According to the results, the shoots and micropropagated tissues of rock plant are inhabited by mycobacteria, which should stimulate further studies on the diversity of unculturable mycobacteria in edible crop plants.

Medicinal properties, in vitro protocols and secondary metabolite analyses of scots pine

Scots pine (Pinus sylvestris L.) is known as an economically important forest tree with a wide distribution throughout the Northern hemisphere. Recently, the species has also become recognized as a novel source of functional food and bioactive compounds with medicinal properties. The present paper provides up-to-date information on protocols for somatic embryogenesis (i.e., the most promising in vitro method for vegetative propagation of Scots pine). Endophyte protocols cover the topics of endophyte isolation, identification and elimination from in vitro cultures. Moreover, the protocols for secondary metabolite analyses are described in order to emphasize the emerging role of Scots pine as a medicinal plant.

Validation criteria for nucleic acid amplification techniques for bacterial infections

Nucleic acid techniques (NATs), such as species-specific and universal polymerase chain reactions (PCRs), are finding ever wider use in the diagnosis of bacterial infection. However, although universal PCR assays, in particular, approach a type of modern Petri dish, they have a number of limitations which restrict their applicability. The sensitivity of universal PCR is lower than that of many species-specific PCRs, and the contamination of samples and PCR reagents with irrelevant DNA from various sources remains a problem. Thus, NATs in general and universal PCR assays in particular require careful validation to be of value for the diagnosis of infection. Validation includes sampling, DNA extraction/isolation, template amplification and visualisation of the results. Furthermore, it implies the establishment of measures of asepsis, the inclusion of positive and negative controls, techniques to optimise the release of DNA from bacterial cells, adequate repetition of the amplification reaction, and routine testing of reagent negative and inhibition controls. Finally, it entails the comparison of results obtained by NATs with those obtained by conventional microbiological methods and matching with clinical evidence of infection. Validation of NATs in clinical diagnosis remains an ongoing challenge. Because of these limitations, NATs can only serve as adjunct tools for the diagnosis of infection in selected cases; they cannot replace conventional culturing techniques.

Usefulness of broad-range PCR for the diagnosis of osteoarticular infections

PURPOSE OF REVIEW

Conventional methods such as microbiological cultures may lack the sensitivity and specificity to establish definitive diagnosis of osteoarticular infections. Herein, we review the general principles and the usefulness of broad-range PCR to improve the etiological diagnosis of osteoarticular infections.

RECENT FINDINGS

Broad-range PCR followed by sequencing has been successfully developed to identify microorganisms involved in infections when patients have previously received antibiotics or in the presence of slow-growing or intracellular microorganisms. For osteoarticular infections, the studies have shown that the use of this molecular tool increased mainly the identification of Kingella kingae, anaerobic bacteria, and Streptococcus spp. However, it is very important to underline that the interpretation of this molecular tool is critical because of several pitfalls, including contamination causing false-positive results.

SUMMARY

Broad-range PCR followed by sequencing offers several advantages when used to complement culture results for the diagnosis of fastidious bacteria and for patients taking antibiotics. However, its use should be restricted mainly for culture-negative cases when infection is suspected on the basis of clinical signs and symptoms or inflammatory syndrome. Future developments will include the use of real-time PCR in a closed system and pathogen-specific PCR for the molecular diagnosis of osteoarticular infections.

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.

Identification of alpha-hemolytic streptococci by pyrosequencing the 16S rRNA gene and by use of VITEK 2

Alpha-hemolytic streptococci are very difficult to identify by phenotypic methods. In this study, a pyrosequencing method for the identification of streptococcal species based on two variable regions of the 16S rRNA gene is described. Almost all studied streptococcal species (n = 51) represented by their type strains could be differentiated except for some closely related species of the Streptococcus bovis or S. salivarius group. The pyrosequencing results of alpha-hemolytic streptococci isolated from blood (n = 99) or from the normal pharyngeal microbiota (n = 25) were compared to the results obtained by the VITEK 2 with GP card (bioMérieux, Marcy l'Etoile, France). As expected, the results of the two methods did not completely agree, but 93 (75.0%) of the isolates assigned to the same streptococcal group by both methods and 57 (46.0%) reached consistent results at the species level. However, 10 strains remained unidentified by VITEK 2, and 4 isolates could not be assigned to any streptococcal group by pyrosequencing. Identification of members of the S. mitis and S. sanguinis groups proved difficult for both methods. Furthermore, the pyrosequencing analysis revealed great sequence variation, since only 43 (32.3%) of the 133 isolates analyzed by pyrosequencing had sequences identical to a type strain. The variation was greatest in the pharyngeal isolates, slightly lower in the blood culture isolates, and nonexistent in invasive pneumococcal isolates (n = 17) that all had the S. pneumoniae type strain sequence. The resolution of the results obtained by the two methods is impeded by the lack of a proper gold standard.

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

BACKGROUND/AIMS

The aetiology of infective endocarditis (IE) can be determined directly from surgically removed valve tissue using broad-range bacterial rDNA polymerase chain reaction (PCR) followed by sequencing. We sought to assess the value of this methodology in a routine clinical setting.

METHODS

Broad-range PCR with primers targeting conserved bacterial rDNA sequences was applied to directly analyse valve samples from 56 patients operated on for diagnosed or suspected IE. Identification of the aetiological agent was performed by partial DNA sequencing of the 16S and 23S rDNA genes.

RESULTS

The final diagnosis was definite IE in 36 patients and possible IE in 2 patients, while the diagnosis of IE was rejected in 18 patients. PCR analysis from removed valve tissue was positive in 25 patients with IE. Molecular identification was consistent with the blood culture finding in 20 of these patients. The PCR approach was the only method to yield the aetiological diagnosis in additional 4 patients (2 Staphylococcus species, 1 Streptococcus bovis, 1 Bartonella quintana), all of whom had received antimicrobials before blood cultures were taken. The mean duration of preoperative antimicrobial treatment for the patients with PCR-positive valves was 19.6 (range 1-58) days.

CONCLUSIONS

Bacterial DNA may persist during treatment in infected valves for long periods. The PCR method is especially useful when the causative agent of IE is fastidious or when the specimen is taken during antimicrobial treatment.

Comparison between cultured small-intestinal and fecal microbiotas in beagle dogs

The microbiota of the small intestine is poorly known because of difficulties in sampling. In this study, we examined whether the organisms cultured from the jejunum and feces resemble each other. Small-intestinal fluid samples were collected from 22 beagle dogs with a permanent jejunal fistula in parallel with fecal samples. In addition, corresponding samples from seven of the dogs were collected during a 4-week period (days 4, 10, 14, and 28) to examine the stability of the microbiota. In the jejunal samples, aerobic/facultative and anaerobic bacteria were equally represented, whereas anaerobes dominated in the fecal samples. Despite lower numbers of bacteria in the jejunum (range, 10(2) to 10(6) CFU/g) than in feces (range, 10(8) to 10(11) CFU/g), some microbial groups were more prevalent in the small intestine: staphylococci, 64% versus 36%; nonfermentative gram-negative rods, 27% versus 9%; and yeasts, 27% versus 5%, respectively. In contrast, part of the fecal dominant microbiota (bile-resistant Bacteroides spp., Clostridium hiranonis-like organisms, and lactobacilli) was practically absent in the jejunum. Many species were seldom isolated simultaneously from both sample types, regardless of their overall prevalence. In conclusion, the small intestine contains a few bacterial species at a time with vastly fluctuating counts, opposite to the results obtained for the colon, where the major bacterial groups remain relatively constant over time. Qualitative and quantitative differences between the corresponding jejunal and fecal samples indicate the inability of fecal samples to represent the microbiotas present in the upper gut.

Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections

We developed a diagnostic array of oligonucleotide probes targeting species-specific variable regions of the genes encoding topoisomerases GyrB and ParE of respiratory bacterial pathogens. Suitable broad-range primer sequences were designed based on alignment of gyrB/parE sequences from nine different bacterial species. These species included Corynebacterium diphtheriae, Fusobacterium necrophorum, Haemophilus influenzae, Legionella pneumophila, Moraxella catarrhalis, Mycoplasma pneumoniae, Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes. Specific probe sequences were selected by comparative analysis against the European Bioinformatics Database, as well as gyrB/parE sequences generated for this study. To verify specificity, at least six initial oligonucleotide probe sequences per bacterial species were tested by hybridization on a solid glass support using culture collection strains as templates. Finally, three oligonucleotide probes per bacterial species were utilized to examine 65 middle ear fluid and 29 throat swab samples. The sensitivities of the developed assay compared to classic culture from middle ear fluid samples for H. influenzae, M. catarrhalis, and S. pneumoniae were 96 (93 for culture), 73 (93 for culture), and 100% (78% for culture), respectively. No cross-reactivity with bacterial species belonging to the normal oral flora was observed when the 29 throat swab samples were studied. The sensitivity of the assay to detect S. pyogenes from these samples was 93% (80% for culture). These results provide a proof of concept for the diagnostic use of microarray technology based on broad-range topoisomerase gene amplification, followed by hybridization and specific detection of bacterial species.

Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases

The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.

Bartonella koehlerae, a new cat-associated agent of culture-negative human endocarditis

Bartonella koehlerae is reported for the first time to be a human pathogen that causes culture-negative endocarditis. It is also shown that this species, isolated twice before from domestic cats, can be recovered as well from a stray cat population in Israel. This work follows a recent report of the same case in which the causative agent was misidentified as B. henselae, based on serology and PCR-restriction fragment length polymorphism (RFLP) analysis (A. Schattner, O. Zimhony, B. Avidor, and M. Gilad, Lancet 361:1786, 2003). B. koehlerae was identified in the valvular tissue of an endocarditis patient by DNA sequencing of the PCR products of two Bartonella genes: the genes for citrate synthase (gltA) and riboflavin synthase (ribC). The commonly used PCR-RFLP analysis of the TaqI-digested gltA PCR product did not distinguish between B. koehlerae and B. quintana or between B. elizabethae and B. clarridgeiae. PmlI digestion of the gltA amplification product failed to differentiate between B. quintana, B. clarridgeiae, and B. elizabethae. RFLP analysis of the heat shock protein (htrA) gene by TaqI digestion misidentified B. koehlerae as B. henselae. However, RFLP analysis of the ribC PCR product, digested with TaqI, was able to distinguish between the human endocarditis-associated Bartonella species tested, B. henselae, B. quintana, B. elizabethae, and B. koehlerae, as well as between the cat-associated Bartonella species, B. henselae and B. clarridgeiae. Given the expanding number of Bartonella species emerging as human pathogens, it is suggested that PCR-RFLP analysis for the diagnosis of Bartonella infections target several genes and be coupled with DNA sequencing to avoid species identification.

Molecular Methods in the Diagnosis of Endocarditis

Advances in molecular microbiologic diagnostics have yielded new tools to diagnose infective endocarditis. These tools can detect microorganisms that are difficult to grow or are uncultivable, because of prior antimicrobial therapy or because of innate characteristics of the microorganisms. This paper reviews molecular microbiologic diagnostic techniques and their role in the diagnosis of infective endocarditis.

Causative organisms of infective endocarditis according to host status

A prospective study of infective endocarditis (IE) was conducted between 1994 and 2000 in Marseilles, France, and included 170 definite cases diagnosed with the use of modified Duke criteria. Classification of IE based on the aetiological agent was related to epidemiological characteristics, including age, gender and the nature of the injured valve. Enterococci and Streptococcus bovis were identified more frequently in older subjects (p 0.02), and S. bovis was also associated with mitral valve infection (p 0.03). Streptococcus spp. were found to be associated with native valves (p < 10(-3)), whereas coagulase-negative staphylococci and Coxiella burnetii were associated with intracardiac prosthetic material (p < 0.05). S. bovis and Staphylococcus aureus were the predominant species associated with presumably healthy valves (p < 0.05), whereas oral streptococci caused IE exclusively in patients with previous valve damage. The basic host status of IE patients has been linked to specific microorganisms, and this may be of value when empirical treatment is needed in patients who have received previous antibiotic therapy and whose blood cultures are negative.

Semiquantitative detection by real-time PCR of Aspergillus fumigatus in bronchoalveolar lavage fluids and tissue biopsy specimens from patients with invasive aspergillosis

A real-time PCR method was developed and used to detect Aspergillus fumigatus mitochondrial DNA (mtDNA) in bronchoalveolar lavage (BAL) fluids and tissue biopsy specimens. The analytical sensitivity of the assay was one A. fumigatus conidium per reaction, and the assay was linear at least over 4 orders of magnitude above the detection limit. BAL fluids from 66 immunocompromised patients at risk of invasive pulmonary aspergillosis (IPA) and 33 immunocompetent controls and tissue biopsy specimens from 10 immunocompromised patients were analyzed. The results were related to the clinical diagnosis established according to recently published consensus criteria. A. fumigatus mtDNA positivity was encountered in 16 of 81 (20%) BAL fluid specimens from patients at risk and 1 of 33 (3%) specimens from immunocompetent controls. PCRs were positive in six of seven, two of four, and four of five of the patients with proven, probable, and possible IPA, respectively, as well as in four patients at risk but without any other evidence of IPA. With qualitative detection, the diagnostic sensitivity of PCR was 73%, specificity was 93%, and predictive values of positive (PPV) and negative (NPV) results were 73 and 95%, respectively. Using a threshold cycle of <35 as a limit for positive PCR, the specificity and PPV of PCR in the diagnosis of invasive aspergillosis were 100%, but its sensitivity was only 45% and NPV was 92%. PCR was positive in tissue biopsy specimens from all patients with invasive aspergillosis caused by A. fumigatus. Semiquantitative detection of A. fumigatus mtDNA in BAL fluid may be helpful in the diagnosis of IPA. PCR is well suited for the verification of the presence of A. fumigatus in tissue biopsy specimens.

Etiologic diagnosis of infective endocarditis by broad-range polymerase chain reaction: a 3-year experience

We analyzed surgically resected endocardial specimens from 49 patients by broad-range PCR. PCR results were compared with (1) results of previous blood cultures, (2) results of culture and Gram staining of resected specimens, and (3) clinical data (Duke criteria). Molecular analyses of resected specimens and previous blood cultures showed good overall agreement. However, in 18% of patients with sterile blood cultures, bacterial DNA was found in the resected materials. When data from patients with definite or rejected cases of infective endocarditis (IE) were included, the sensitivity, specificity, and positive and negative predictive values of broad-range PCR were 82.6%, 100%, 100%, and 76.5%, respectively, overall, and 94.1%, 100%, 100%, and 90%, for cases of native valve endocarditis. The sensitivity, specificity, and positive and negative predictive values of culture of resected specimens from patients with native valve endocarditis were 17.6%, 88.9%, 75%, and 36.4%. We recommend broad-range PCR of surgically resected endocardial material in cases of possible IE, in cases of suspected IE in which blood cultures are sterile, and in cases in which organisms grow in blood cultures but only Duke minor criteria are met. We propose to add molecular techniques to the pathologic criteria of the Duke classification scheme.

Detection by immunofluorescence assay of Bartonella henselae in lymph nodes from patients with cat scratch disease

Laboratory diagnosis of Bartonella henselae infections can be accomplished by serology or PCR assay on biopsy samples. The purpose of our work was to assess immunofluorescence detection (IFD) in lymph node smears using a specific monoclonal antibody directed against B. henselae and a commercial serology assay (IFA) compared with PCR detection. Among 200 lymph nodes examined from immunocompetent patients, 54 were positive for B. henselae by PCR, of which 43 were also positive by IFD. Among the 146 PCR-negative lymph nodes, 11 were positive by IFD. Based on PCR results, the specificity of this new technique was 92.5%, the sensitivity was 79.6%, and the positive predictive value was 79.6%. At a cutoff titer of 64, the sensitivity of the IFA was 86.8% and the specificity was 74.1%. Diagnosis of cat scratch disease (CSD) may be improved, with a specificity of 100%, when the two tests (IFD and IFA) were negative; the sensitivity was 97.4% if one of the two tests was positive. Since PCR-based detection with biopsy samples is available only in reference laboratories, we suggest using IFD coupled with the commercial serology test for the diagnosis of CSD.

A clinical study of culture-negative endocarditis

Culture-negative infective endocarditis (CNE) is a diagnostic problem in spite of improved echocardiographic and blood culturing techniques. We conducted the present study to estimate the proportion of CNE in patients with infective endocarditis, to investigate data regarding risk factors, and to evaluate the Duke and the modified Beth Israel criteria in patients with CNE. We evaluated 820 consecutive suspected episodes of infective endocarditis in adults at the Departments of Infectious Diseases in Göteborg and Borås, Sweden (1984-1996). All patients were diagnosed and treated according to a protocol; 487 episodes were identified as infective endocarditis. Episodes with absence of bacterial growth at blood culture were defined as CNE and were classified with the Duke and the modified Beth Israel criteria. We identified 116 CNE episodes (median age, 67 yr). Mortality was 7%, and in 15%, cardiac surgery was performed. The Duke criteria classified 20 definite, 80 possible, and 16 reject episodes. The modified Beth Israel criteria distinguished 13 definite, 15 probable, 27 possible, and 61 reject episodes. The proportion of CNE among patients with infective endocarditis varied from 19% to 27% at the 2 departments. Antibiotic treatment preceded blood culture in 45% of the CNE episodes. About 20% in a Scandinavian population of infective endocarditis patients have CNE. Antibiotic pretreatment explains less than 50% of all CNE episodes. The Duke criteria are more sensitive but less specific than the modified Beth Israel criteria in classifying patients with CNE.

Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources

During studies on the bacteriology of appendicitis in children, we often isolated from inflamed and non-inflamed tissue samples, an unusual bile-resistant pigment-producing strictly anaerobic gram-negative rod. Phenotypically this organism resembles members of Bacteroides fragilis group of species, as it is resistant to bile and exhibits a special-potency-disk pattern (resistance to vancomycin, kanamycin and colistin) typical for the B. fragilis group. However, the production of brown pigment on media containing haemolysed blood and a cellular fatty acid composition dominated by iso-C15:0, suggests that the organism most closely resembles species of the genus Porphyromonas. However, the unidentified organism differs from porphyromonads by being bile-resistant and by not producing butyrate as a metabolic end-product. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism represents a distinct sub-line, associated with but distinct from, the miss-classified species Bacteroides putredinis. The clustering of the unidentified bacterium with Bacteroides putredinis was statistically significant, but they displayed > 4% sequence divergence with each other. Chromosomal DNA-DNA pairing studies further confirmed the separateness of the unidentified bacterium and Bacteroides putredinis. Based on phenotypic and phylogenetic considerations, it is proposed that Bacteroides putredinis and the unidentified bacterium from human sources be classified in a new genus Alistipes, as Alistipes putredinis comb. nov. and Alistipes finegoldii sp. nov., respectively. The type strain of Alistipes finegoldii is CCUG 46020(T) (= AHN243(T)).

Aetiological diagnosis of brain abscesses and spinal infections: application of broad range bacterial polymerase chain reaction analysis

OBJECTIVE

To evaluate the usefulness of the broad range bacterial rDNA polymerase chain reaction (PCR) method combined with DNA sequencing in the aetiological diagnosis of intracranial or spinal infections in neurosurgical patients.

METHODS

In addition to conventional methods, the broad range bacterial PCR approach was applied to examine pus or tissue specimens from cerebral or spinal lesions in patients treated in a neurosurgical unit for a clinical or neuroradiological suspicion of bacterial brain abscess or spondylitis.

RESULTS

Among the 44 patients with intracranial or spinal lesions, the final diagnosis suggested bacterial disease in 25 patients, among whom the aetiological agent was identified in 17. A causative bacterial species was identified only by the rDNA PCR method in six cases, by both the PCR methodology and bacterial culture in six cases, and by bacterial culture alone in five. All samples in which a bacterial aetiology was identified only by the PCR approach were taken during antimicrobial treatment, and in three patients the method yielded the diagnosis even after >/= 12 days of parenteral treatment. One case also identified by the PCR approach alone involved a brain abscess caused by Mycoplasma hominis, which is not readily cultured by routine methods.

CONCLUSIONS

In patients with brain abscesses and spinal infections, the broad range bacterial rDNA PCR approach may be the only method to provide an aetiological diagnosis when the patient is receiving antimicrobial treatment, or when the causative agent is fastidious.

Negative bacterial polymerase chain reaction (PCR) findings in prostate tissue from patients with symptoms of chronic pelvic pain syndrome (CPPS) and localized prostate cancer

BACKGROUND

The etiology of chronic pelvic pain syndrome (CPPS) remains obscure. Although, bacterial etiology has frequently been suggested, evidence of both bacterial involvement in CPPS and the presence of normal bacterial flora in the prostate remain uncertain.

MATERIALS AND METHODS

We investigated the presence of bacterial DNA using polymerase chain reaction (PCR) techniques on prostatic tissue samples obtained in radical prostatectomy from 10 patients with moderate to severe symptoms of CPPS and 10 nonsymptomatic patients with localized prostate cancer. For symptom evaluation we used the National Institutes of Health-Chronic Prostatitis Symptom Index (NIH-CPSI).

RESULTS

All but one sample were negative for bacterial DNA. The PCR from a symptomatic patient was reproducibly positive in 16S rDNA PCR but negative in 23S rDNA PCR. Bacterial DNA was found in only one out of two sample aliquots and cloning yielded different sequences in two PCR products.

CONCLUSIONS

A bacterial etiology for CPPS symptoms could not be demonstrated in patients with prostate cancer. The results also suggest that the prostate is unlikely to harbor bacterial normal flora.

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

IE is a serious, life-threatening disease. Because treatment must often be adapted to the pathogen involved, rapid identification of the etiologic agent is critical to successful management of each patient. When difficult-to-culture pathogens are involved, routine microbiologic tests, including blood culture, may remain negative. Because such cases may account for up to 31% of all IE cases, alternative diagnostic approaches are necessary. Among the etiologic agents of culture-negative endocarditis, C burnetii and Bartonella spp play a major role; each is responsible for up to 3% of episodes of IE. The authors therefore recommend the systematic use of specific serologies in all cases of clinically suspected endocarditis. The cross-reactivity between C burnetii, Bartonella spp, and Chlamydia spp is of diagnostic importance because all are potential etiologic agents of endocarditis. However, given that the levels of specific antibodies observed in Bartonella endocarditis are extremely high, low-level cross-reactions with other antigens should not lead to misdiagnosis, provided serology for all suspected agents is performed. When serologic test results are negative for both Bartonella spp and C burnetii, special staining by the Gram, Giemsa, Gimenez, PAS, Warthin-Starry, and Grocott methods may guide the use of new diagnostic tools such as PCR and tissue culture for isolation and identification of the causative agent. Such novel approaches may lead to more comprehensive patient evaluations and the discovery of new etiologic agents of IE.

Identification of the bacterial etiology of culture-negative endocarditis by amplification and sequencing of a small ribosomal RNA gene

We report two cases of culture-negative bacterial endocarditis in which the organisms were identified by amplification and sequencing of the bacterial 16S rRNA gene. These results support an important role for polymerase chain reaction followed by direct sequencing to determine the etiology of culture-negative bacterial endocarditis and to guide appropriate antimicrobial therapy.

Cure of bartonella endocarditis of a prosthetic aortic valve without surgery: value of serologic follow-up

Bartonella species are emerging as an important cause of blood culture-negative endocarditis, but the optimal management of this disease has not been fully defined. We describe a case of subacute Bartonella henselae endocarditis of a prosthetic aortic valve in an immunocompetent woman that was cured with long-term antibiotic therapy alone. In addition, we demonstrate that follow-up of serologic titers against B. henselae was helpful in assessing definitive cure of the infection.

Diagnosis of Bartonella endocarditis by a real-time nested PCR assay using serum

Bartonella endocarditis is a severe disease for which blood cultures frequently remain negative. We tested three PCR assays by using specimens of serum sampled early during the disease from 43 patients diagnosed in our laboratory as having Bartonella endocarditis on the basis of serological, culture, and/or valvular molecular detection. We tested a two-step nested PCR (TSN-PCR), a one-step nested PCR (OSN-PCR) with a regular thermal cycler, and a one-step nested PCR with the LightCycler (LCN-PCR). These assays were performed with primers derived from the riboflavin synthase-encoding gene ribC, never before amplified in our laboratory. Due to contamination of negative controls, the results of the TSN-PCR were not interpretable, and this technique was no longer considered. The LCN-PCR had a specificity of 100% and a sensitivity of 58.1%, higher than those of the OSN-PCR (18.6%; P < 0.01) and prolonged blood culturing (7.1%; P < 0.01). The LCN-PCR results correlated strictly with those of other direct diagnostic tests, when available, and identified the causative species for six patients previously diagnosed on the basis of serological analysis only. The efficacy of the LCN-PCR was not influenced by antibiotics (P = 0.96) but was altered by prolonged storage of serum specimens at -20 degrees C (P = 0.04). Overall, the LCN-PCR is specific and more sensitive than traditional methods (i.e., culturing and/or PCR with EDTA-treated blood). It can easily be applied to the diagnosis of patients with suspected Bartonella endocarditis, especially when only serum is available.

Laboratory diagnosis of Bartonella infections

Bartonella species are pathogens of emerging and reemerging significance, causing a wide array of clinical syndromes. In North America and Europe, they are increasingly recognized as a cause of culture negative endocarditis, neuroretinitis, and disease among homeless, HIV-infected, and other immunosuppressed individuals. In South America, bartonellosis continues to plague those in endemic regions and poses a significant threat to travelers in these areas. As the clinician is increasingly faced with these illnesses, which may be difficult to diagnose, laboratory techniques to confirm or refute the diagnosis are becoming increasingly important. Culture methods have improved over the past decade demonstrating increased sensitivity, but still require prolonged periods before isolation of the organism. Specimen handling, media selection, and growth conditions all may affect results and must be optimized in order to provide the highest likelihood of recovering the organism. Pure culture of the bacteria not only provides morphologic information, but also provides material for further diagnostic testing. Work with liquid media, which may provide a more rapid means of cultivation has shown some promise and should continue to be pursued. Improved blood culture techniques were a primary factor in the discovery of Bartonella endocarditis and continued improvements will likely demonstrate further clinical insights. Serologic testing for B henselae infections has become the cornerstone of clinical diagnosis, replacing the skin test that was poorly standardized and posed a potential risk to the patient. Immunofluorescence assays have been well characterized and validated in clinical trials, however they are not universally available. Vero cell cocultivated antigens appear to provide higher sensitivity and specificity when compared with agar-derived antigens. IFA assays are inherently difficult to perform, requiring significant expertise to provide reproducible results. On the contrary, enzyme immunoassays offer ease of use and a high level of reproducibility, however ideal antigens for use in the diagnosis of Bartonella infections have not been clearly identified. Continued work to define antigenic targets of the human response to infection and incorporation of these into a widely available EIA will provide a cost-effective tool for the clinician and epidemiologist alike. Due to the close phylogenetic relationship of B henselae and B quintana, differentiation between these species by serologic means may prove difficult. Molecular techniques including PCR offer high sensitivity and specificity, rapid availability of information, and the ability to differentiate Bartonella organisms at the highest level. Results of studies to date are promising and as methods are refined it will be important to conduct clinical studies to define the role of these assays. In disseminated Bartonella infections such as bacillary angiomatosis, peliosis, endocarditis, and urban trench fever, PCR currently offers the ability to establish the diagnosis when other tests may be unrevealing. For CSD, this technique should be used as a confirmatory technique when the diagnosis is unclear by other means. PCR analysis of blood specimens offers a minimally invasive approach to diagnosis, but clinical data are scarce and further studies are needed. As DNA microarrays move into the clinical arena, specific hybridization probes may allow improved identification and differentiation of Bartonellae at the molecular level.

Optimal DNA isolation method for detection of bacteria in clinical specimens by broad-range PCR

Broad-range amplification of bacterial DNA from clinical specimens has proved useful for the diagnosis of various bacterial infections, especially during antimicrobial treatment of the patient. Optimal sample processing protocols for diagnostic broad-range bacterial PCR should release DNA from an array of target organisms with equal efficiencies and wash out inhibitory factors from various sample types without introducing bacterial DNA contamination to the amplification reaction. In the present study, two physical cell wall disintegration methods, bead beating and sonication, for enhanced detection of organisms with difficult-to-lyse cell walls were studied. The analytical sensitivities of several commercially available DNA purification kits, which were used with and without additional cell disintegration steps, were compared by using dilution series of model bacteria. Selected purification methods were used to process routine clinical specimens in parallel with the standard phenol-ether DNA extraction, and the results obtained by bacterial PCR and sequencing with the two template preparations were compared. The method with the DNA isolation kit with the lowest detection limits from the bacterial suspensions (Masterpure) did not prove to be superior to the standard method when the two methods were applied to 69 clinical specimens. For another set of 68 clinical specimens, DNA purified with a glass fiber filter column (High Pure) with an additional sonication step yielded results well in accord with those obtained by the standard method. Furthermore, bacterial DNA was detected in four samples that remained PCR negative by the standard method, and three of these contained DNA from gram-positive pathogens. Three samples were positive by the standard method only, indicating the limitations of applying any single method to all samples.

Comparison of in-house and commercial slides for detection by immunofluorescence of immunoglobulins G and M against Bartonella henselae and Bartonella quintana

We compared the sensitivities and specificities of indirect fluorescent antibody tests developed in our laboratory and commercially available from Focus Technologies (FT; formerly MRL Diagnostic) for detection of serum antibodies to Bartonella spp. Serum samples tested were from patients with culture- or PCR-confirmed Bartonella quintana or B. henselae infections causing cat scratch disease (CSD), chronic bacteremia, or endocarditis. At a cutoff titer of 64, the FT test had higher sensitivity than our in-house test in detecting anti-B. henselae immunoglobulin G (IgG) antibodies in CSD patients (91.2 versus 52.9%; P < 0.001). The specificity in serum samples from 85 control patients was, however, lower with the FT test (87%) than with the in-house test (98.8%) (P = 0.002). A cutoff titer of 128 improves the specificity for the FT test but lowers the sensitivity to 85%. For patients infected with B. henselae, our in-house test, but not the FT test, enabled endocarditis to be detected more reliably. With the in-house test, titers of IgG against B. henselae of >/=1,024 were found only in endocarditis patients and not in CSD patients. With the FT test, 19.1% of CSD patients had titers of IgG against B. henselae of >/=1,024 (P < 0.001). Our in-house technique also improved detection of anti-B. quintana antibodies in homeless patients with endocarditis. IgG titers of >/=1,024 were present in 75% of serum samples, but only in 16.7% of serum samples with the FT test (P = 0.004). Since each test has advantages over the other, the serological diagnosis of Bartonella infections would benefit if both tests were used concurrently.

Value of microimmunofluorescence for diagnosis and follow-up of Bartonella endocarditis

Bartonella endocarditis is a disease of emerging importance that causes serious complications and high rates of mortality. Due to the fastidious nature of Bartonella species and their high degrees of antibiotic susceptibility, cultures of clinical samples most often remain sterile and valvular biopsy specimens, the best specimens for PCR amplification, are seldom available. Therefore, serology appears to be the easiest diagnostic tool. In order to determine the best cutoff value for serology and its predictive values for the detection of Bartonella endocarditis, we studied 48 patients with culture- and/or PCR-confirmed Bartonella endocarditis. We also applied these serological criteria to 156 patients with blood culture-negative endocarditis. Furthermore, we compared the kinetics of the antibody responses to Bartonella spp. in order to estimate the value of serology for prediction of the occurrence of relapses. A titer of > or = 1:800 for immunoglobulin G antibodies to either Bartonella henselae or B. quintana has a positive predictive value of 0.810 for the detection of chronic Bartonella infections in the general population and a value of 0.955 for the detection of Bartonella infections among patients with endocarditis. When this cutoff was applied to 156 patients with blood culture-negative endocarditis, we were able to diagnose Bartonella infections in an additional 45 patients with definite endocarditis for whom a positive Bartonella serology was the only evidence of infection. On follow-up, the kinetics of the decrease in antibody titers were significantly delayed in two patients with relapses. In conclusion, we recommend the determination of antibodies to both B. quintana and B. henselae and the use of a cutoff value of 1:800 for the diagnosis of Bartonella endocarditis. We propose that this criterion, which may also help with the detection of late relapses, be included as a major criterion in the Duke criteria for the diagnosis of infective endocarditis.

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.

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

Culture-negative endocarditis currently represents a diagnostic challenge for physicians. Traditional methods such as histology, serology, and culture have been improved and new molecular techniques have been developed to improve the detection of difficult-to-culture agents. Serologic tests for the two most frequent etiologic agents, Coxiella burnetii and Bartonella spp, should be performed first because they can usually be identified easily in this way. The sensitivity of culture for intracellular bacteria has been improved by inoculation of samples in shell vials and by the use of novel tissue cell lines. Recently, universal and species-specific primers have been designated to amplify bacterial DNA directly from resected valves, allowing positive identification.

Detection of Bartonella quintana from body lice (Anoplura: Pediculidae) infesting homeless people in Tokyo by molecular technique

We report detection of Bartonella quintana Brenner, the pathogenic agent of trench fever, from body lice, Pediculus humanus L., infesting homeless people in Tokyo by polymerase chain reaction. Two of 12 (16.7%) homeless were infested with Bartonella-positive body lice. From the current status of the recent increase of homeless people in many large cities of the developed countries, a medical examination of homeless people should be carefully performed in the consideration of trench fever. Sampling of body lice from clothing of homeless people is recommended for quick and accurate diagnosis of trench fever through the detection of B. quintana DNA.

Clinical "pneumococcal pneumonia" due to Moraxella osloensis: case report and a review

A previously healthy 6-y-old girl presented with a disease very similar to pneumococcal pneumonia. However, Moraxella osloensis was isolated by lung tap. The patient responded well to a course of parenteral penicillin. This is probably the first documented case of community-acquired pneumonia associated with this agent. Clinical isolates of M. osloensis are rare and its pathogenesis has not been delineated; however, a literature review suggests that the organism is more common than is generally recognized.

Broad-range bacterial detection and the analysis of unexplained death and critical illness

Broad-range rDNA polymerase chain reaction (PCR) provides an alternative, cultivation-independent approach for identifying pathogens. In 1995, the Centers for Disease Control and Prevention initiated population-based surveillance for unexplained life-threatening infections (Unexplained Death and Critical Illness Project [UNEX]). To address the causes of UNEX cases, we examined 59 specimens from 46 cases by using broad-range bacterial 16S rDNA PCR and phylogenetic analysis of amplified sequences. Specimens from eight cases yielded sequences from Neisseria meningitidis (cerebrospinal fluid from two patients with meningitis), Streptococcus pneumoniae (cerebrospinal fluid from one patient with meningitis2 and pleural fluid from two patients with pneumonia), or Stenotrophomonas maltophilia (bone marrow aspirate from one patient with pneumonia). Streptococcus pneumoniae rDNA sequence microheterogeneity was found in one pleural fluid specimen, suggesting the presence of multiple strains. In conclusion, known bacterial pathogens cause some critical illnesses and deaths that fail to be explained with traditional diagnostic methods.