The identification of uncultured microbial pathogens

Utility of investigation for suspected microbial keratitis: a diagnostic accuracy study

PURPOSE

The true disease status of a population with suspected microbial keratitis (MK) cannot be verified. There is not an accurate (gold) reference standard to confirm infection and inter-test comparisons of sensitivity and specificity therefore lead to bias with questionable estimates of test utility. We present an alternative method to report results.

METHODS

We used a decision to treat as the definition for MK. We retrospectively compared the results of corneal culture and polymerase chain reaction (PCR) as these are objective tests available for the three principal groups of pathogens. We then estimated the potential contribution of positive results, either alone or in combination, to support the working diagnosis.

RESULTS

We included 2021 (77.4%) eyes with suspected bacterial keratitis, 365 (14.0%) with suspected acanthamoeba keratitis, and 226 (8.6%) with suspected fungal keratitis, all treated between July 2013 and December 2019. In these groups, there were 51.6% positive culture and 6.5% positive PCR results for bacteria, 19.0% and 40.5% for acanthamoeba, and 28.3% and 15.0% for fungi. Between groups the differences in the proportions of positive results from culture and PCR was statistically significant (P < 0.001). The added benefit of PCR to the result of culture in identifying a potential pathogen was 1.4% for bacteria (P = 0.6292), 24.4% for acanthamoeba (P = 0.0001), and 5.8% for fungi (P = 0.3853).

CONCLUSIONS

For suspected MK a comparison of the test positivity rate is an easily comprehensible outcome measure of test utility.

Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database

Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.

The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis

The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.

Actinobacillus pleuropneumoniae serotypes in Hungary

A total of 255 Actinobacillus pleuropneumoniae isolates were collected from 634 lung samples representing 70 swine herds in Hungary between January 2012 and June 2016. On the basis of the indirect haemagglutination test 77 independent strains were included in the evaluation after the elimination of duplicate or multiple serotypes from the same herd. In the case of 7 herds strains of two different serotypes were identified. Fourteen Hungarian A. pleuropneumoniae isolates from the culture collection of the Department of Microbiology and Infectious Diseases, isolated before 2012, were also included in the evaluation (one each from 12 herds and two each from two herds, where two serotypes occurred). Out of the altogether 91 A. pleuropneumoniae strains 72 strains belonged to biotype I and 19 strains could be allocated to biotype II. In Hungary, the most common serotypes were serotype 2 (39.5%), 13 (15.4%), 8 (8.8%) and 16 (8.8%), but serotypes 9 (5.5%), 11 (3.3%) and 12 (3.3%) were also isolated. Twelve strains (13.2%) were untypable.

Integron Digestive Carriage in Human and Cattle: A "One Health" Cultivation-Independent Approach

Objectives: Dissemination of antimicrobial resistance (AMR) is a global issue that requires the adoption of a "One-Health" approach promoting integration of human and animal health. Besides culture-dependent techniques frequently used for AMR surveillance, cultivation-independent methods can give additional insights into the diversity and reservoir of AMR genetic determinants. Integrons are molecular markers that can provide overall and reliable estimation of AMR dissemination. In this study, considering the "One-Health" approach, we have analyzed the integron digestive carriage from stools of humans and cattle living in a same area and exposed to different antibiotic selection pressures. Methods: Three collections of human [general population (GP) and intensive care unit patients (ICUs)] and bovine (BOV) stool samples were analyzed. The three main classes of integrons were detected using a multiplex qPCR both from total DNA extracted from stools, and from Gram-negative bacteria obtained by culture after an enrichment step. Results: With the cultivation-independent approach, integron carriage was 43.8, 52.7, and 65.6% for GP, ICU, and BOV respectively, percentages being at least twofold higher to those obtained with the cultivation-dependent approach. Class 1 integrons were the most prevalent; class 2 integrons seemed more associated to cattle than to humans; no class 3 integron was detected. The integron carriage was not significantly different between GP and ICU populations according to the antibiotic consumption, whatever the approach. Conclusion: The cultivation-independent approach constitutes a complementary exploratory method to investigate the integron digestive carriage of humans and bovines, notably within subjects under antibiotic treatment. The high frequency of carriage of integrons in the gut is of clinical significance, integrons being able to easily acquire and exchange resistant genes under antibiotic selective pressure and so leading to the dissemination of resistant bacteria.

Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains

The repeated failures reported in cultivating some microbial lineages are a major challenge in microbial ecology and probably linked, in the case of Frankia microsymbionts to atypical patterns of auxotrophy. Comparative genomics of the so far uncultured cluster-2 Candidatus Frankia datiscae Dg1, with cultivated Frankiae has revealed genome reduction, but no obvious physiological impairments. A direct physiological assay on nodule tissues from Coriaria myrtifolia infected with a closely-related strain permitted the identification of a requirement for alkaline conditions. A high pH growth medium permitted the recovery of a slow-growing actinobacterium. The strain obtained, called BMG5.1, has short hyphae, produced diazovesicles in nitrogen-free media, and fulfilled Koch’s postulates by inducing effective nodules on axenically grown Coriaria spp. and Datisca glomerata. Analysis of the draft genome confirmed its close proximity to the Candidatus Frankia datiscae Dg1 genome with the absence of 38 genes (trehalose synthase, fumarylacetoacetase, etc) in BMG5.1 and the presence of 77 other genes (CRISPR, lanthionine synthase, glutathione synthetase, catalase, Na+/H+ antiporter, etc) not found in Dg1. A multi-gene phylogeny placed the two cluster-2 strains together at the root of the Frankia radiation.

Methods for Detecting the Environmental Coccoid Form of Helicobacter pylori

Helicobacter pylori is recognized as the most common pathogen to cause gastritis, peptic and duodenal ulcers, and gastric cancer. The organisms are found in two forms: (1) spiral-shaped bacillus and (2) coccoid. H. pylori coccoid form, generally found in the environment, is the transformed form of the normal spiral-shaped bacillus after exposed to water or adverse environmental conditions such as exposure to sub-inhibitory concentrations of antimicrobial agents. The putative infectious capability and the viability of H. pylori under environmental conditions are controversial. This disagreement is partially due to the fact of lack in detecting the coccoid form of H. pylori in the environment. Accurate and effective detection methods of H. pylori will lead to rapid treatment and disinfection, and less human health damages and reduction in health care costs. In this review, we provide a brief introduction to H. pylori environmental coccoid forms, their transmission, and detection methods. We further discuss the use of these detection methods including their accuracy and efficiency.

Neurologic melioidosis in an imported pigtail macaque (Macaca nemestrina)

Burkholderia pseudomallei is the cause of melioidosis in humans and other animals. Disease occurs predominately in Asia and Australia. It is rare in North America, and affected people and animals typically have a history of travel to (in human cases) or importation from (in animal cases) endemic areas. We describe the gross and histopathologic features and the microbiologic, molecular, and immunohistochemical diagnoses of a case of acute meningoencephalomyelitis and focal pneumonia caused by B. pseudomallei infection in a pigtail macaque that was imported from Indonesia to the United States for research purposes. This bacterium has been classified as a Tier 1 overlap select agent and toxin; therefore, recognition of pathologic features, along with accurate and timely confirmatory diagnostic testing, in naturally infected research animals is imperative to protect animals and personnel in the laboratory animal setting.

Utility of PCR amplification and DNA microarray hybridization of 16S rDNA for rapid diagnosis of bacteremia associated with hematological diseases

OBJECTIVES

The rapid diagnosis of bacteremia is crucial for patient management including the choice of antimicrobial therapy, especially in cases of hematological disease, because neutropenia occurs frequently during antineoplastic chemotherapy or disease progression. We describe a rapid detection and identification system that uses universal PCR primers to amplify a variable region of bacterial 16S ribosomal DNA (rDNA), followed by DNA microarray hybridization.

METHODS

Probes for 72 microorganisms including most causal clinical pathogens were spotted onto a microarray plate. The DNA microarray and conventional methods of identification were applied to 335 cultures from patients with hematological diseases.

RESULTS

Forty-one samples (12.2%) tested positive by conventional blood culture test in a few days, while 40 cases (11.9%) were identified by the new method within 24 h. The sensitivity and specificity of this new method were 93% and 99%, respectively, compared with conventional blood culture testing.

CONCLUSIONS

PCR combined with a DNA microarray is useful for the management of febrile patients with hematological diseases.

Evaluation of species-specific score cutoff values of routinely isolated clinically relevant bacteria using a direct smear preparation for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based bacterial identification

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was introduced a few years ago as a new method for bacterial identification. A variety of studies have been published concerning MALDI-TOF MS-based identification, most of them using culture collections for the validation of the respective databases in a retrospective manner in favor of a parallel investigation. The score cutoff value is of special importance for reliable species identification in the Biotyper database. The score cutoff values suggested by the manufacturer have been validated using a previously published formic acid extraction protocol. In most of the previously published studies investigating the Biotyper database, only little information was given concerning species-specific score values. In addition, the mass spectrometer instruments, the number of replicates, the number of spectra used to calculate a sum-spectrum by the supplied software, and the score cutoff values which have been applied varied within these studies. In this study, we compared a straightforward direct smear preparation and measurement without replicate testing to defined biochemical identifications in a parallel manner. In addition, we described new species-specific score cutoff values for the identification of certain bacteria.

Cyclomodulins in urosepsis strains of Escherichia coli

Determinants of urosepsis in Escherichia coli remain incompletely defined. Cyclomodulins (CMs) are a growing functional family of toxins that hijack the eukaryotic cell cycle. Four cyclomodulin types are actually known in E. coli: cytotoxic necrotizing factors (CNFs), cycle-inhibiting factor (Cif), cytolethal distending toxins (CDTs), and the pks-encoded toxin. In the present study, the distribution of CM-encoding genes and the functionality of these toxins were investigated in 197 E. coli strains isolated from patients with community-acquired urosepsis (n = 146) and from uninfected subjects (n = 51). This distribution was analyzed in relation to the phylogenetic background, clinical origin, and antibiotic resistance of the strains. It emerged from this study that strains harboring the pks island and the cnf1 gene (i) were strongly associated with the B2 phylogroup (P, <0.001), (ii) frequently harbored both toxin-encoded genes in phylogroup B2 (33%), and (iii) were predictive of a urosepsis origin (P, <0.001 to 0.005). However, the prevalences of the pks island among phylogroup B2 strains, in contrast to those of the cnf1 gene, were not significantly different between fecal and urosepsis groups, suggesting that the pks island is more important for the colonization process and the cnf1 gene for virulence. pks- or cnf1-harboring strains were significantly associated with susceptibility to antibiotics (amoxicillin, cotrimoxazole, and quinolones [P, <0.001 to 0.043]). Otherwise, only 6% and 1% of all strains harbored the cdtB and cif genes, respectively, with no particular distribution by phylogenetic background, antimicrobial susceptibility, or clinical origin.

Bacillary angiomatosis in an immunosuppressed dog

A dog being treated with immunosuppressive doses of prednisone and azathioprine for pancytopenia of unknown origin, developed, over a 2-week period, multiple erythematous nodular lesions in the skin including footpads. Skin samples revealed lesions identical to those of human bacillary angiomatosis (BA). The nodules were composed of multifocal proliferations of capillaries, each lined by protuberant endothelial cells. The capillary clusters were separated by an oedematous connective tissue, lightly infiltrated with degenerate inflammatory cells, including neutrophils and macrophages. Tissue sections stained with Warthin-Starry silver stain revealed large numbers of positively stained bacilli in the stromal tissue, most heavily concentrated around the proliferating capillaries. Lesions of vascular degeneration and inflammation were evident. Bartonella vinsonii subsp. berkhoffii genotype 1 was independently amplified and sequenced from the blood and the skin tissue. The pathognomonic nature of the histological lesions, demonstration of compatible silver-stained bacilli in the tissue, and identification of B. vinsonii subsp. berkhoffii in the blood and tissue indicates that this is most likely the aetiologic agent responsible for the lesions. Antibiotic therapy was successful in resolving the nodules. It would appear that B. vinsonii subsp berkhoffii, like Bartonella henselae and Bartonella quintana, has the rare ability to induce angioproliferative lesions, most likely in association with immunosuppression. The demonstration of lesions identical to those of human BA in this dog is further evidence that the full range of clinical manifestations of human Bartonella infection occurs also in canines.

Biomarkers for infants at risk for necrotizing enterocolitis: clues to prevention?

Necrotizing enterocolitis (NEC) is the most common severe gastrointestinal emergency that affects premature newborns. This disease often has a rapid onset with few, if any, antecedent signs that can be used to reliably predict its occurrence. Its rapid onset and progression to death, as well as its severe morbidity when the infant survives, begs for early diagnostic tools that may be used in determining those infants who would be at greatest risk for development of the disease and for whom early preventative measures could be targeted. Although studies have suggested efficacy of several techniques such as breath hydrogen, inflammatory mediators in blood, urine or stool, and genetic markers, these all have drawbacks limiting their use. The application of newly developed "omic" approaches may provide biomarkers for early diagnosis and targeted prevention of this disease.

A roadmap for understanding and preventing necrotizing enterocolitis

Necrotizing enterocolitis (NEC) is the most common severe gastrointestinal emergency that affects newborns. Its etiology is still undetermined. Most of our knowledge of this disease stems from epidemiologic studies, clinical experience, and studies using animal models that do not directly represent the disease in premature infants. An immature intestine that is colonized by bacteria is a prerequisite for the pathogenesis of NEC. Although causative microbes have not been found, newly developed analytic techniques now allow the detection of noncultivatable microbes and the determination of their overall diversity and metabolic capabilities. The National Institutes of Health Human Microbiome Roadmap Project is likely to generate new information highly germane to understanding NEC. Newly developed proteomic and metabolomic approaches also offer exciting new potential for early diagnosis and prevention of this disease in infants at highest risk.

Gastrointestinal microbiology enters the metagenomics era

PURPOSE OF REVIEW

Advances in DNA sequence-based technologies now permit genetic analysis of complex microbial populations without the need for prior cultivation. This review summarizes the molecular methods of culture-independent microbiology ('metagenomics') and their recent application to studies of the human gastrointestinal tract in both health and disease.

RECENT FINDINGS

Culture-independent metagenomic surveys reveal unprecedented microbial biodiversity in the human intestine. Upwards of 40,000 bacterial species are estimated to comprise the collective gastrointestinal microbiome, most of which have not been characterized by culture. Diverse conditions such as antibiotic-associated diarrhea, Crohn's disease, ulcerative colitis, obesity, and pouchitis have been correlated with large-scale imbalances in gastrointestinal microbiota, or 'dysbiosis'. These findings demonstrate the importance of commensal microorganisms in maintaining gastrointestinal health.

SUMMARY

Through technological and conceptual innovations in metagenomics, the complex microbial habitat of the human gastrointestinal tract is now amenable to detailed ecological analysis. Large-scale shifts in gut commensal populations, rather than occurrence of particular microorganisms, are associated with several gastroenterological conditions; redress of these imbalances may ameliorate the conditions.

New genus-specific primers for the PCR identification of novel isolates of the genus Streptomonospora

The halophilic actinomycete genus Streptomonospora, forming a distinct branch in the 16S rRNA gene phylogenetic tree adjacent to the genera Nocardiopsis and Thermobifida, was first proposed by Cui et al. to accommodate the species type Streptomonospora salina. During a biodiversity and taxonomic study on halophilic filamentous actinomycetes from a saline lake in western China, numerous new halophilic actinomycetes strains were isolated. To confirm whether they are members of the genus Streptomonospora, one set of genus-specific oligonucleotides was designed which allows rapid detection of members of the genus Streptomonospora by means of PCR amplification. The genus specificity of these primers was validated with reference strains as well as with wild-type isolates, which exhibited morphological characteristics common to this genus.

Clinical Applications of the Polymerase Chain Reaction: An Update

The development, in the past decade, of nucleic acid amplification and detection methods is useful in the study of the etiopathogenesis, diagnosis, and management of a variety of clinical (including rheumatologic) disorders. An association between infectious agents and rheumatic disorders has been established through such methods as polymerase chain reaction. This article describes the principles behind polymerase chain reaction-based diagnosis and updates its clinical applications. It is beyond the scope of this article, however, to describe other nucleic acid amplification methods or to include a complete list of all polymerase chain reaction assays that have been developed. Other recent reviews offer additional details.

Idiopathic granulomatous encephalitis mimicking malignant brain tumor

Idiopathic granulomatous encephalitis is a rare disorder of unknown etiology, undetermined treatment, and often grave prognosis. This article describes a 4-year-old female who presented with a single focal febrile convulsion followed a few weeks later by right-sided hemiparesis. A huge infiltrative cerebral mass tumor was found which proved to be a granuloma on histologic study. Despite a thorough evaluation, including tissue studies and search for an infectious agent, no etiology could be identified, and the final diagnosis was idiopathic granulomatous encephalitis. Recurrent resections and high-dose steroid treatment failed to control the process, and the patient died of disease 6 months after presentation. Evaluation and treatment of idiopathic granulomatous encephalitis should be aggressive, and the possibility of chemotherapy and perhaps even radiotherapy should be considered if there is no response to steroids.

Development of a multipathogen oligonucleotide microarray for detection of Bacillus anthracis

An oligonucleotide microarray system has been specifically designed to detect and differentiate Bacillus anthracis from other bacterial species present in clinical samples. The pilot-scale microarray initially incorporated probes to detect six common species of bacteria, which were fully evaluated. The microarray comprised long oligonucleotides (50--70-mer) designed to hybridise with the variable regions of the 16S rRNA genes. Probes which hybridised to virulence genes were also incorporated; for B. anthracis, these initially included the pag, lef, cap and vrrA (for partial genotyping) genes. Hybridisation conditions were initially optimised to be run using 5 x SSC, 0.1% SDS, 50 degrees C for 16 h. The detection limits of the microarray were determined under these conditions by titration of chromosomal DNA and unlabelled amplicons followed by hybridisation to determine the levels of sensitivity that could be obtained with the microarray. Two different amplification methodologies were also compared-specific-primer based PCR and random PCR (with the labelling stage incorporated). Higher sensitivity was obtained using specific PCR primers, however, since one of the desired outcomes of a microarray-based detection system was the high discrimination that it offered, random amplification and labelling was used as the amplification method of choice. The length of hybridisation was investigated using a time-course, and 1--2h was found to give optimal and higher signals than 16 h incubation. These results indicate that microarray technology can be employed in a diagnostic environment and moreover, results may be obtained in a similar time-scale to a standard PCR reaction, but with the advantage that no a priori knowledge of the infectious agent is required for detection.

Exploiting Molecular Methods to Explore Endodontic Infections: Part 1—Current Molecular Technologies for Microbiological Diagnosis

Endodontic infections have been traditionally studied by culture-dependent methods. However, as with other areas of clinical microbiology, culture-based investigations are plagued by significant problems, including the probable involvement of viable but uncultivable micro-organisms with disease causation and inaccurate microbial identification. Innumerous molecular technologies have been used for microbiological diagnosis in clinical microbiology, but only recently some of these techniques have been applied in endodontic microbiology research. This paper intended to review the main molecular methods that have been used or have the potential to be used in the study of endodontic infections. Moreover, advantages and limitations of current molecular techniques when compared to conventional methods for microbial identification are also discussed.

Blood culture-negative endocarditis in a reference center: etiologic diagnosis of 348 cases

To identify the current etiologies of blood culture-negative infective endocarditis and to describe the epidemiologic, clinical, laboratory, and echocardiographic characteristics associated with each etiology, as well as with unexplained cases, we tested samples from 348 patients suspected of having blood culture-negative infective endocarditis in our diagnostic center, the French National Reference Center for Rickettsial Diseases, between 1983 and 2001. Serology tests for Coxiella burnettii, Bartonella species, Chlamydia species, Legionella species, and Aspergillus species; blood culture on shell vial; and, when available, analysis of valve specimens through culture, microscopic examination, and direct PCR amplification were performed. Physicians were asked to complete a questionnaire, which was computerized. Only cases of definite infective endocarditis, as defined by the modified Duke criteria, were included. A total of 348 cases were recorded-to our knowledge, the largest series reported to date. Of those, 167 cases (48%) were associated with C. burnetii, 99 (28%) with Bartonella species, and 5 (1%) with rare, fastidious bacterial agents of endocarditis (Tropheryma whipplei, Abiotrophia elegans, Mycoplasma hominis, Legionella pneumophila). Among 73 cases without etiology, 58 received antibiotic drugs before the blood cultures. Six cases were right-sided endocarditis and 4 occurred in patients who had a permanent pacemaker. Finally, no explanatory factor was found for 5 remaining cases (1%), despite all investigations.Q fever endocarditis affected males in 75% of cases, between 40 and 70 years of age. Ninety-one percent of patients had a previous valvulopathy, 32% were immunocompromised, and 70% had been exposed to animals. Our study confirms the improved clinical presentation and prognosis of the disease observed during the last decades. Such an evolution could be related to earlier diagnosis due to better physician awareness and more sensitive diagnostic techniques. As for Bartonella species, B. quintana was recorded more frequently than B. henselae (53 vs 17 cases). For 18 patients with Bartonella endocarditis, the responsible species was not identified. Species determination was achieved through culture and/or PCR in 49 cases and through Western immunoblotting in 22. Comparison of B. quintana and B. henselae endocarditis revealed distinct epidemiologic patterns. The 2 cases due to T. whipplei reflect the emerging role of this agent as a cause of infective endocarditis. Because identification of the bacterium was possible only through analysis of excised valves by histologic examination, PCR, and culture on shell vial, the prevalence of the disease might be underestimated. Among patients who received antibiotic drugs before blood cultures, 4 cases (7%) were found to be associated with Streptococcus species (2 S. bovis and 2 S. mutans) through 16S rDNA gene amplification directly from the valve, which shows the usefulness of this technique in overcoming the limitations of previous antibiotic treatment. Right-sided endocarditis occurred classically in young patients (mean age, 36 yr), intravenous drug users in 50% of cases, and suffering more often from embolic complications. Finally, 5 cases without etiology or explaining factors were all immunocompetent male patients with previous aortic valvular lesions, and 3 of the 5 presented with an aortic abscess. Further investigations should be focused on this group to identify new agents 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.

[Etiology of bacterial infections in febrile neutropenic patients: the role of the laboratory in the diagnosis]

EPIDEMIOLOGICAL EVOLUTION: Until the mid-eighties, infectious complications (pneumonia, septicemia) observed in neutropenic patients were, in 70% of cases, of bacterial origin with Gram negative bacillae (Escherichia coli, Klebsiella sp, Pseudomonas aeruginosa) isolated 8 times out of 10. Among the Gram positive bacteria, Staphylococcus aureus predominated. The etiological profile of bacterial infections has since evolved with a predominance (60 to 70%) of Gram positive bacteria (coagulase-negative staphylococci, viridans streptococci) and a change in the epidemiology of the Gram positive bacteria notably with a lesser frequency of P. aeruginosa infections. THE GRAM POSITIVE BACTERIA: Coagulase-negative staphylococci are among the first germs responsible for nosocomial bacteremia (central venous catheters) and they are usually multiresistant. Viridans streptococci are a frequent cause of bacteremia; they are generally sensitive to antibiotics active on Gram positive bacteria, but the incidence of resistant strains is increasing. Enterococci are in majority responsible for colonisation in neutropenic patients and less frequently for infections; they raise the problem of resistance to antibiotics, notably to glycopeptides. Other Gram positive bacteria can be responsible for infections in neutropenic patients; it is crucial that they be identified because they require treatment with an appropriate antibiotic. GRAM NEGATIVE BACTERIA: Among the enterobacteria, Escherichia coli is predominantly isolated and raises the problem of the increasing incidence of resistance to fluoroquinolone. Pseudomonas aeruginosa, less frequently responsible today, remains associated with a far greater rate of mortality than that observed with the other microorganisms. Other Gram negative bacteria can be identified; they require an adapted antibiotherapy because they are often naturally multiresistant to antibiotics. THE ROLE OF THE LABORATORY: For the diagnosis of infections in neutropenic patients, the microbiology laboratory has a determinating role. The laboratory ensures the analysis of various biological examinations: blood cultures, methods permitting the diagnosis of an infection on a permanent catheter, copro-cultures (research for common enteropathogens, quantification in the case of digestive decontamination, screening for multiresistant bacteria), cytobacteriological examination of urine, samples of respiratory origin, cytobacteriological examination of cerebro-spinal fluid...).

Tropheryma whippelii as a cause of afebrile culture-negative endocarditis: the evolving spectrum of Whipple's disease

With the advent of molecular diagnostics culture-negative endocarditis caused by the organism Tropheryma whippelii is an increasingly described entity. We describe two patients with afebrile, culture-negative endocarditis caused by T. whippelii who had neither the gastrointestinal nor arthritic manifestations of Whipple's disease. Whipple's disease is a systemic illness caused by the organism Tropheryma whippelii and is typically characterized by diarrhea, weight loss, and arthropathy [Clin. Microbiol. Rev. 2001;14:561-583; Medicine (Baltimore) 1997;76:170-184]. Whipple's endocarditis is relatively common in autopsy studies [Can. J. Cardiol. 1996;12:831-834] but has rarely been diagnosed before death. With the advent of molecular diagnostic tools such as the polymerase chain reaction (PCR), Tropheryma whippelii as a cause of culture-negative endocarditis has become increasingly recognized [Clin. Infect. Dis. 2001;33:1309-1316; Ann. Intern. Med. 1999;131:112-116; Infection 2001;29:44-47; Ann. Intern. Med. 2000;132:595]. With this increased recognition has come the realization that Whipple's endocarditis can occur without other common manifestations of Whipple's disease [Ann. Intern. Med. 1999;131:112-116; Infection 2001;29:44-47; Ann. Intern. Med. 2000;132:595]. We report here two cases of Whipple's endocarditis without discrete febrile illness, gastrointestinal manifestations, or arthritic manifestations, diagnosed by PCR of resected valvular material.

Phylogenetic analysis identifies the 'megabacterium' of birds as a novel anamorphic ascomycetous yeast, Macrorhabdus ornithogaster gen. nov., sp. nov

An organism commonly referred to as 'megabacterium' colonizes the gastric isthmus of many species of birds. It is weakly gram-positive and periodic acid-Schiff-positive and stains with silver stains. Previous studies have shown that it has a nucleus and a cell wall similar to those seen in fungi. Calcofluor white M2R staining suggests that the cell wall contains chitin, a eukaryote-specific substance, and rRNA in situ hybridization demonstrates that it is a eukaryote. To characterize this organism phylogenetically, DNA was extracted from purified cells. rDNA was readily amplified by PCR with pan-fungal DNA primer sets and primer sets derived from the newly determined sequence, but not with bacteria-specific primer sets. Specific primer sets amplified rDNA from isthmus scrapings from an infected bird, but not from a non-infected bird or other control DNA. The sequence was confirmed to derive from the purified organism by in situ rRNA hybridization using a specific probe. Phylogenetic analysis of sequences of the 18S rDNA and domain D1/D2 of 26S rDNA showed the organism to be a previously undescribed anamorphic ascomycetous yeast representing a new genus. The name Macrorhabdus ornithogaster gen. nov., sp. nov. is proposed for this organism. The type material is CBS 9251T (= NRRL Y-27487T).

PCR methodology as a valuable tool for identification of endodontic pathogens

OBJECTIVES

This paper reviews the principles of polymerase chain reaction (PCR) methodology, its application in identification of endodontic pathogens and the perspectives regarding the knowledge to be reached with the use of this highly sensitive, specific and accurate methodology as a microbial identification test.

DATA SOURCES

Studies published in the medical, dental and biological literature.

STUDY SELECTION

Evaluation of published epidemiological studies examining the endodontic microbiota through PCR methodology.

CONCLUSIONS

PCR technology has enabled the detection of bacterial species that are difficult or even impossible to culture as well as cultivable bacterial strains showing a phenotypically divergent or convergent behaviour. Moreover, PCR is more rapid, much more sensitive, and more accurate when compared with culture. Its use in endodontics to investigate the microbiota associated with infected root canals has expanded the knowledge on the bacteria involved in the pathogenesis of periradicular diseases. For instance, Tannerella forsythensis (formerly Bacteroides forsythus), Treponema denticola, other Treponema species, Dialister pneumosintes, and Prevotella tannerae were detected in infected root canals for the first time and in high prevalence when using PCR analysis. The diversity of endodontic microbiota has been demonstrated by studies using PCR amplification, cloning and sequencing of the PCR products. Moreover, other fastidious bacterial species, such as Porphyromonas endodontalis, Porphyromonas gingivalis and some Eubacterium spp., have been reported in endodontic infections at a higher prevalence than those reported by culture procedures.

Microbial population diversity in the urethras of healthy males and males suffering from nonchlamydial, nongonococcal urethritis

Nonchlamydial, nongonococcal urethritis (NCNGU) is suggested to be a sexually transmitted disease in men. NCNGU patients were compared to control subjects with regard to the presence of potentially infectious bacteria in the first void urine. Patients' pre- and post-antibiotic-treatment urine samples and two samples obtained 2 weeks apart from healthy volunteers, who did not receive antibiotic therapy, were analyzed with broad-spectrum PCR tests aiming at eubacterial small subunit rRNA genes. Restriction fragment length polymorphism analysis of the amplicons cloned from the mixtures of PCR products revealed that many different species of microorganisms were found to be colonizing the male urethra. We document here clear differences in the composition of the resident urethral flora between samples obtained from various individuals and between samples obtained at various points in time for a single individual. No major changes in population complexity were found upon antimicrobial treatment. In two of five patients a previously suggested pathogen (Mycoplasma genitalium or Haemophilus parainfluenzae) was accurately identified on the basis of DNA sequencing. No ubiquitous, azithromycin-sensitive organism was identified as a common pathogen in all patients, but up to 40% of all clones represented as-yet-unclassified bacterial species. Relatively often Pseudomonas spp. or Pseudomonas-like organisms were identified in the bacterial flora of patients. Interestingly, an as-yet-uncharacterized microbial species was identified as a negative predictor of NCNGU. This species was identified in all control subjects and was absent from all of the patient' samples (5 of 5 versus 0 of 5, P = 0.0079). This suggests that NCNGU might also be diagnosed by assessing the absence rather than the presence of certain bacterial species.

Campylobacter gracilis and Campylobacter rectus in primary endodontic infections

AIM

A species-specific nested polymerase chain reaction (PCR) assay was used to investigate the occurrence of Campylobacter gracilis and C. rectus in primary root canal infections.

METHODOLOGY

Samples were collected from 57 single-rooted teeth with carious lesions, necrotic pulps and radiographic evidence of periradicular disease. Twenty-eight cases were diagnosed as chronic asymptomatic periradicular lesions, 12 cases as acute apical periodontitis, and 17 cases as acute periradicular abscess. DNA was extracted from the samples and initially amplified using universal 16S rDNA primers. A second round of amplification using the first PCR products was performed to specifically detect C. gracilis or C. rectus in the samples.

RESULTS

Campylobacter gracilis and C. rectus were, respectively, detected in 21.4 (6 of 28) and 30% (6 of 20) of the root canals associated with chronic asymptomatic periradicular lesions. Campylobacter gracilis was found in 16.7% (2 of 12) of the cases diagnosed as acute apical periodontitis, whilst C. rectus was found in 33.3% (two of six cases). In the abscessed cases, C. gracilis and C. rectus were detected in 23.5 (4 of 17) and 11.8% (2 of 17) of the cases, respectively. No association of these species with clinical symptoms was observed (P > 0.01) In general, species-specific nPCR allowed the detection of C. gracilis in 21.1% (12 of 57) and C. rectus in 23.3% (10 of 43)of the samples taken from primary endodontic infections.

CONCLUSIONS

Findings confirmed the assertion that both C. gracilis and C. rectus participate in infections of endodontic origin and suggest a pathogenetic role with regard to periradicular diseases.

Applications of polymerase chain reaction in rheumatology

Polymerase chain reaction (PCR) is a highly sensitive and specific method for detection and quantification of specific nucleic acids from a clinical sample. With its use, genetic, infectious, neoplastic, and autoimmune diseases can be diagnosed and managed with a high level of sensitivity, accuracy, and rapidity. This technique exactly reproduces unlimited copies of DNA, even if only a small amount are present initially. PCR assays can detect presence of fastidious and slow-growing microorganisms, such as chlamydia, mycoplasmas, mycobacterias, and viruses directly from clinical specimens and also can detect antimicrobial resistance. The value of viral load measurement by nucleic acid amplification in the management of patients with HIV infection or hepatitis C has also been well established. From the point of view of a clinician, the applications of PCR are focused mainly in the amplification and detection of diagnostic DNA segments from the genomes of both pathogens and patients.

Chronic prostatitis: epidemiology and role of infection

We review the epidemiology of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and the role of infectious agents, emphasizing critical data necessary to define current research issues. The epidemiologic literature is limited, but the worldwide prevalence appears to be in the range of 2% to 10%, indicating that CP/CPPS represents an important international health problem. Recent molecular studies have documented bacterial DNA sequences in prostate tissue from CP/CPPS patients. These data suggest that colonization and/or infection occurs in the prostates of many patients with CP/CPPS. Further molecular research is needed to define the role of bacteria in the etiology of CP/CPPS.

[Detection of bacterial contamination in platelet concentrates: perspectives]

Bacterial contamination of blood components represents today the highest infectious risk of blood transfusion, the risk is particularly high when it affects platelet concentrates. In France the prevention methods developed over the past six years (donor selection, phlebotomy site preparation, first 30 ml diversion, systematic leuko-reduction...) aimed at limiting the introduction of bacteria in blood and bacterial proliferation. Several methods have been tested for the detection of bacterial contamination in platelet concentrates but none have been generalised. Difficulties were met, due to the necessity of 1) detecting only the platelet concentrates presenting a real infectious risk, when the presence of bacteria is observed in 2.2% (2-4%) of donated blood and 2) guaranteeing the availability of platelet concentrates. New methods have been developed which seem able to bring responses to these difficulties. Several processes are being (or will be) assessed, including automated blood culture, bacterial genomic detection with or without amplification, flow cytometric methods. In parallel, an indirect method able to detect the presence of bacteria, based on oxygen consumption, will also be evaluated. One (or several) of these processes should allow, in the short-term, to detect platelet concentrates presenting an infectious risk. In the future, the interest of bio-chips for bacterial detection in biological fluids must be investigated.

A method for the detection and quantification of bacteria in human carious dentine using fluorescent in situ hybridisation

OBJECTIVES

Previous studies have evaluated bacterial numbers in carious dentine using conventional culturing methods, capable of detecting only a proportion of the total bacteria present within lesions. The aim of this study was to detect and enumerate the total bacterial population present in carious human dentine by means of fluorescent in situ hybridisation.

METHOD

Five freshly extracted carious molars were sequentially hand excavated under sterile conditions through four levels in the lesions. Replicate samples were probed with a rhodamine-tagged, 16S rRNA-directed probe (EUB338), specific for the bacterial domain. Two of the five original samples were examined using fluorescence microscopy and by using a systematic visual counting strategy; direct enumeration of the bacterial population in carious dentine was performed.

RESULTS

In the superficial, middle and deep/excavation front zones, a mean of 7.34 x 10(6) (standard error of the mean, SEM +/- 0.44), 5.23 x 10(6) (SEM +/- 0.18), and 1.69 x 10(6) (SEM +/- 0.15) total bacteria/mg dentine were found, respectively. In the advancing front zone (beyond the conventional clinical excavation boundary) a mean of 0.34 x 10(6) (SEM +/- 0.05) total bacteria/mg dentine was recorded.

CONCLUSION

A bacterial enumeration strategy was developed and detected greater numbers of bacteria through the depth of carious lesions that had been reported previously. The technique could be further developed using species-specific probes to determine the distribution, abundance and viability of all bacteria in carious dentine. This new information in turn will lead to a better understanding of the pathological process of caries and ultimately, its clinical treatment.

Endodontic infections: concepts, paradigms, and perspectives

Overwhelming evidence indicates that periradicular diseases are infectious disorders. The question now is no longer whether microorganisms are involved in the pathogenesis of such diseases, but which specific microbial species are. The list of microorganisms involved in periradicular diseases keeps expanding and has the potential to become increasingly more accurate during the next few years. Molecular methods have contributed significantly to the knowledge about the microbial species involved. Undoubtedly, a great deal of additional research is needed to define the specific role played by suspected endodontic pathogens in the etiology of each form of periradicular disease and to determine the best therapeutic measures for the pathogen's eradication. In addition, there is an emergent need to define markers that permit the clinician to know when he or she should conclude the treatment and to predict the outcome of the treatment. Although endodontic procedures and some acute endodontic infections can cause bacteremia, there is no clear evidence that microorganisms from the root canal can cause diseases in remote sites of the body. However, there is a risk in some compromised individuals, and prophylactic measures should be taken. Prescription of systemic antibiotics in endodontic therapy is rarely necessary. Because of the emergence of bacterial resistance against most known antibiotics, their use in endodontics should be highly limited and restricted to a few cases.

Characterization of the rRNA genes of Ehrlichia chaffeensis and Anaplasma phagocytophila

The rRNA genes of Ehrlichia chaffeensis and Anaplasma phagocytophila have been analyzed. The 16S rRNA genes were previously characterized for both of these agents. Southern hybridization was used to show that there are single copies of both the 16S and 23S rRNA genes in the genomes of each organism, and that the 16S rRNA genes were upstream from the 23S rRNA genes by at least 16 and 11 Kb for E. chaffeensis and A. phagocytophila, respectively. PCR amplification and gene walking was used to sequence the 23S and 5S rRNA genes, and show that these genes are contiguous and are likely expressed as a single operon. The level of homology between the E. chaffeensis and A. phagocytophila 23S and 5S rRNA genes, and 23S-5S spacers, was 91.8, 81.5, and 40%, respectively. To confirm the hybridization data, genome walking was used to sequence downstream of the 16S rRNA genes, and although no tRNA genes were identified, open reading frames encoding homologues of the Escherichia coli succinate dehydrogenase, subunit C, were found in both E. chaffeensis and A. phagocytophila. Phylogenetic analysis using the 23S rRNA gene suggests that reorganization of the phylum Proteobacteria by division of the class Alphaproteobacteria into two separate subclasses, may be appropriate.

[Bacteriological risks: detection and tracing]

Advances in molecular taxonomy of bacteria have generated many tools allowing identification of any bacteria, whether culturable or not. In addition to taxonomic identification, growing knowledge on pathogenicity mechanisms allows the detection of bacteria with given virulence genes. The problem is in asking the proper questions so that the most appropriate tools can be chosen. Some rapid identification tools (gene amplification, in situ hybridisation) require a starting hypothesis. Other tools (rrs gene amplification and sequencing) can be used without prior hypothesis, but take longer. To face the bioterrorist threat, particular attention should be given to laboratory and strain dispatch (within- and between-laboratory) organisation.

Temporal arteritis and Chlamydia pneumoniae: failure to detect the organism by polymerase chain reaction in ninety cases and ninety controls

OBJECTIVE

To examine the reported correlation between the presence of Chlamydia pneumoniae in temporal artery biopsy specimens and the diagnosis of temporal arteritis (TA).

METHODS

Among 90 possible cases of TA identified at our institution between 1968 and 2000, 79 of the positive biopsy specimens (88%) demonstrated giant cells and the other 11 cases (12%) had other histopathologic features compatible with TA; by chart review, all 90 patients were confirmed to have met the American College of Rheumatology classification criteria for TA. Controls had negative temporal artery biopsy specimens during the same 32-year time period and their postbiopsy disease courses were not compatible with TA. Controls were matched with each case by sex, year of biopsy, and age within 10 years. The biopsy specimens from all cases and controls were reevaluated and readings were confirmed in a masked manner by an experienced eye pathologist. Polymerase chain reaction (PCR) analyses for C pneumoniae were performed on the 180 samples using 2 different sets of PCR primers (which target 2 different genes). A primer set targeting the ompA gene (CP1-CP2/CPC-CPD) was used to perform a nested PCR, followed by confirmation of the findings with primers targeting the 16S ribosomal RNA (rRNA) gene (Cpn90/Cpn91) in a touchdown-enzyme time-release PCR. We used positive and negative controls, as well as controls made from infected and noninfected HEp-2 cells, suspended in a formalin-fixed, paraffin-embedded matrix.

RESULTS

Seventy-six percent of the 180 cases and controls were women. The mean age of the cases was 72.0 years (range 53-90), and that of the controls was 70.4 years (range 51-86). Eighty percent of the control samples were obtained by temporal artery biopsy performed within 1 year of the biopsies performed on the matched cases. Using the CP1-CP2/CPC-CPD primer set, only 1 TA case sample (1% of all case samples) was positive for the ompA gene. One control sample was also positive using these primers. With the Cpn90/Cpn91 primers, none of the cases and none of the controls were positive for the 16S rRNA gene.

CONCLUSION

The results of this study using sensitive and specific PCR analyses do not support a role for C pneumoniae in the pathogenesis of TA.

Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens

Advances in molecular technology show great potential for the rapid detection and identification of fungi for medical, scientific and commercial purposes. Numerous targets within the fungal genome have been evaluated, with much of the current work using sequence areas within the ribosomal DNA (rDNA) gene complex. This section of the genome includes the 18S, 5.8S and 28S genes which code for ribosomal RNA (rRNA) and which have a relatively conserved nucleotide sequence among fungi. It also includes the variable DNA sequence areas of the intervening internal transcribed spacer (ITS) regions called ITS1 and ITS2. Although not translated into proteins, the ITS coding regions have a critical role in the development of functional rRNA, with sequence variations among species showing promise as signature regions for molecular assays. This review of the current literature was conducted to evaluate clinical approaches for using the fungal ITS regions as molecular targets. Multiple applications using the fungal ITS sequences are summarized here including those for culture identification, phylogenetic research, direct detection from clinical specimens or the environment, and molecular typing for epidemiological investigations. The breadth of applications shows that ITS regions have great potential as targets in molecular-based assays for the characterization and identification of fungi. Development of rapid and accurate amplification-based ITS assays to diagnose invasive fungal infections could potentially impact care and improve outcome for affected patients.

Principles of molecular microbiology testing methods

Molecular testing methods have the potential to replace many conventional microbiology laboratory assays. Recent refinements in technology have resulted in more user-friendly testing platforms. These platforms are automated and have lowered risks for contamination, decreased costs, and are faster than older platforms. The success of these technologies depends on their successful application to patient care. Quality issues include appropriate specimens for analysis, performance characteristics of different analytical methods, optimal specimen processing, the effects of PCR inhibitors, and false-positive results caused by contaminating nucleic acids. Quality control guidelines for molecular microbiologic diagnostic assays are in their infancy and require further development. Additionally, the problem of "too much" sensitivity (brought on by the extreme sensitivity of these techniques coupled with the potential presence of small numbers of pathogenic organisms in asymptomatic individuals) should be considered. Potential problems when monitoring therapy (because molecular detection techniques do not generally have the ability to determine whether an organism is dead or alive) can also occur. Cost-effective test use, pathogen- or disease-targeted algorithms, and standardized methods will be necessary for the true value of these technologies to be realized. This is especially important, because, unlike traditional culture methods, most molecular microbiology methods are pathogen-specific. Clinicians familiar with the reasons why "pan-culture" (i.e., requesting all culture possibilities at once) is inadvisable should not use the same irrational approach when requesting molecular tests. The clinical usefulness of molecular testing will be maximized as targeted algorithms are developed and an understanding of molecular test ordering patterns is realized. Laboratory technicians and physicians must continue to apply and combine theories of traditional microbiology, clinical chemistry, and general medicine to the understanding and application of molecular diagnostics.

Evaluation and use of a nested polymerase chain reaction assay in cats experimentally infected with Bartonella henselae genotype I and Bartonella henselae genotype II

Cats have been shown to be infected with Bartonella henselae genotype I, B. henselae genotype II, and B. clarridgeiae. Feline bartonellosis infections and the strains involved in these infections are important in both veterinary and human medicine. Nucleic acid amplification methods such as polymerase chain reaction (PCR) are being used in both research and diagnostics as tools for understanding many infectious diseases. Bartonella bacteremia in cats is detected by blood culture; however, because of the limitations of culture (delayed turnaround time and sensitivity limits), PCR may be a more efficient method for identifying infected cats. Three distinct PCR assays that could differentiate among B. henselae genotype I, B. henselae genotype II. and B. clarridgeiae were developed and used to detect as few as 3.2 organisms. Fourteen cats experimentally infected with B. henselae genotype I and B. henselae genotype II were followed by bacterial culture and PCR through the course of infection, including periods of primary and relapsing bacteremia. The PCR assay was positive in 11 of the 14 cats for periods of 1-9 weeks after culture became negative. Of the 223 blood specimens that were culture negative, the PCR assay was positive in 38 (17%) of the specimens. Two of the 14 cats developed relapsing bacteremia. The 2 B. henselae genotypes were amplified in the cats and the bacteremic phase of these infections as determined by PCR lasted for a longer period than previously determined by culture. Using laboratory assays such as PCR to understand the strains involved in feline bartonellosis and the course of the infection is important in the understanding of these zoonotic agents.

Chromosomal DNA from a variety of bacterial species is present in synovial tissue from patients with various forms of arthritis

OBJECTIVE

We and others have reported the presence of Chlamydia and other bacterial species in joint specimens from patients with reactive arthritis (ReA). The present study was conducted to investigate whether bacteria other than those specified by diagnostic criteria for ReA could be identified in synovial fluid (SF) or tissue from patients with various arthritides, and whether the presence of such organisms corresponds to particular clinical characteristics in any patient set or subset.

METHODS

DNA in synovial biopsy samples and SF obtained from 237 patients with various arthritides, including ReA, rheumatoid arthritis, and undifferentiated oligoarthritis, was assayed by polymerase chain reaction (PCR) using "panbacterial" primers; we chose only samples known to be PCR negative for Chlamydia, Borrelia, and Mycoplasma species. PCR products were cloned, and cloned amplicons from each sample were sequenced; DNA sequences were compared against all others in GenBank for identification of bacterial species involved.

RESULTS

Ten percent of patient samples were PCR positive in panbacterial screening assays. Bacterial species identified belonged to the genera Neisseria, Acinetobacter, Moraxella, Salmonella, Pseudomonas, and others. Thirty-five percent of PCR-positive patients showed the presence of DNA from more than a single bacterial species in synovium; overall, however, we could identify no clear relationship between specific single or multiple bacterial species in the synovium and any general clinical characteristics of any individual or group of patients.

CONCLUSION

This analysis provides the first systematic attempt to relate bacterial nucleic acids in the synovium to clinical characteristics, joint findings, and outcomes. Many patients with arthritis have bacterial DNA in the joint, and, in some cases, DNA from more than a single species is present. However, except for 1 case of a control patient with staphylococcal septic arthritis, it is not clear from the present study whether the synovial presence of such organisms is related to disease pathogenesis or evolution in any or all cases.

Endocarditis due to rare and fastidious bacteria

The etiologic diagnosis of infective endocarditis is easily made in the presence of continuous bacteremia with gram-positive cocci. However, the blood culture may contain a bacterium rarely associated with endocarditis, such as Lactobacillus spp., Klebsiella spp., or nontoxigenic Corynebacterium, Salmonella, Gemella, Campylobacter, Aeromonas, Yersinia, Nocardia, Pasteurella, Listeria, or Erysipelothrix spp., that requires further investigation to establish the relationship with endocarditis, or the blood culture may be uninformative despite a supportive clinical evaluation. In the latter case, the etiologic agents are either fastidious extracellular or intracellular bacteria. Fastidious extracellular bacteria such as Abiotrophia, HACEK group bacteria, Clostridium, Brucella, Legionella, Mycobacterium, and Bartonella spp. need supplemented media, prolonged incubation time, and special culture conditions. Intracellular bacteria such as Coxiella burnetii cannot be isolated routinely. The two most prevalent etiologic agents of culture-negative endocarditis are C. burnetti and Bartonella spp. Their diagnosis is usually carried out serologically. A systemic pathologic examination of excised heart valves including periodic acid-Schiff (PAS) staining and molecular methods has allowed the identification of Whipple's bacillus endocarditis. Pathologic examination of the valve using special staining, such as Warthin-Starry, Gimenez, and PAS, and broad-spectrum PCR should be performed systematically when no etiologic diagnosis is evident through routine laboratory evaluation.

Bacteria-related sequences in a simian cytomegalovirus-derived stealth virus culture

Extensive sequencing of cloned DNA isolated from the culture of an African green monkey simian cytomegalovirus-derived stealth virus has identified multiple regions of highly significant homology to various bacterial genes. The apparent acquisition of bacterial sequences extends the potential role of stealth viruses as natural vectors in the transfer of genetic information. The findings highlight the dynamic interface between viral and bacterial genomes and the potential of this interaction in the emergence and spread of novel pathogens. The term viteria is proposed for microorganisms that contain both eukaryotic-viral and prokaryotic-bacterial genetic sequences.

Methods for the differentiation of microorganisms

Advances in analytical and diagnostic assays based on novel nucleic acid analyses techniques have revolutionized the application of molecular differentiation of microorganisms. Phenotypic typing schemes are now broadly supplemented by new genotyping methods which allow a more refined and detailed differentiation of closely related microorganisms, bacterial strains, isolates and pathogens on the DNA level. Bio-, sero- and phagetyping, antibiotic susceptibility tests, immunoblotting as well as multilocus enzyme- or polyacrylamide gel electrophoresis are now supported by the analysis of plasmid or chromosomal DNA restriction profiles, ribotyping, pulsed-field gel electrophoresis and polymerase- or ligase-chain reaction-based methods or direct sequencing technique to differentiate microorganisms. Some of these molecular techniques are also used in the field of virology to analyse and differentiate closely related sub- or genotypes. Few examples for the analysis and investigation of these usually small genomes will also be given.