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Prion diseases in humans and their relevance to other neurodegenerative diseases.

Molecular genetics has led to considerable advances in our understanding of the transmissible spongiform encephalopathies. The identification of pathogenic mutations in the prion protein gene has enabled a molecular reclassification of the familial forms of these diseases, which may now be referred to as inherited prion diseases. Prion diseases of both humans and animals are associated with deposition of an abnormal isoform of a host-encoded protein, the prion protein (PrP). Human prion diseases have inherited, sporadic and acquired forms. A considerable body of evidence now supports the idea that the transmissible agent in these diseases may be an abnormal isoform of the prion protein. The identification of pathogenic mutations in the PrP gene has enabled the identification of cases of inherited prion disease that would not have been recognised using existing clinical and pathological diagnostic criteria. Since marked clinical and neuropathological overlap between the different neurodegenerative disorders is well recognised, PrP gene analysis is of increasing importance in differential diagnosis. Frontal lobe dementia of non-Alzheimer type and Pick's disease share a number of important clinical and pathological features with prion diseases, and could be considered as candidate prion diseases. However, we have not been able to demonstrate either PrP mutations or the presence of the disease-associated isoform of prion protein in several well-characterised families with these disorders.

Humans↗

Development of a polymerase chain reaction test for specific identification of the urinary tract pathogen Aerococcus urinae.

A polymerase chain reaction test was developed for identification of the gram-positive urinary tract pathogen Aerococcus urinae. Oligonucleotide primers were based on highly specific sequences within the small-subunit rRNA gene. A confirmatory test based on hybridization of the amplified products to a highly specific internal probe was also developed.

Bacteriological Techniques↗

Identification of cardiac myosin peptides capable of inducing autoimmune myocarditis in BALB/c mice.

Immunization with cardiac myosin induces T cell-mediated myocarditis in genetically predisposed mice and serves as a model for autoimmune heart disease. This study was undertaken to identify pathogenic epitopes on the myosin molecule. Our approach was based on the comparison of the pathogenicity between cardiac (alpha-)myosin and soleus muscle (beta-)myosin. We show that alpha-myosin is the immunodominant isoform and induces myocarditis at high severity and prevalence whereas beta-myosin induces little disease. Therefore the immunodominant epitopes of alpha-myosin must reside in regions of different amino acid sequence between alpha- and beta-myosin isoforms. Cardiac myosin peptides corresponding to these regions of difference were synthesized and tested for their ability to induce inflammatory heart disease. Three pathogenic peptides were identified. One peptide that is located in the head portion of the molecule induced severe myocarditis, whereas two others that reside in the rod portion possessed only minor pathogenicity. The identification of pathogenic epitopes on the cardiac myosin molecule will allow detailed studies on the recognition of this antigen by the immune system and might be used to downmodulate ongoing heart disease.

Amino Acid Sequence↗

Rapid presumptive identification of entero-pathogenic Escherichia coli in faecal smears by means of fluorescent antibody. 1. Preparation and testing of reagents.

In outbreaks of infantile diarrhoea caused by enteropathogenic Escherichia coli, rapid detection of the etiological agent is essential for specific and adequate therapy. Fluorescent antibody techniques have proved advantageous for rapid identification of many microorganisms. The development of fluorescein-labelled antibodies specific for nine serogroups of E. coli and the testing of these reagents for specificity are described in this paper. Results of testing pure cultures of various Enterobacteriaceae as well as faecal specimens from cases of diarrhoea are reported. These data show excellent correlation between the fluorescent antibody technique and conventional serological methods for identifying enteropathogenic types of E. coli. The immunofluorescent technique is more rapid than the usual bacteriological and serological methods in that smears from faecal specimens can be stained directly with the labelled antibodies. Details of the procedures for carrying out the technique are given in annexes.

Antibodies↗

DNA microarray for discrimination between pathogenic 0157:H7 EDL933 and non-pathogenic Escherichia coli strains.

The primary technique currently used to detect biological agents is based on immunoassays. Although sensitive and specific, currently employed immunoassays generally rely on the detection of a single epitope, and therefore often cannot discriminate subtle strain-specific differences. Since DNA microarrays can hybridize hundreds to thousands of genomic targets simultaneously and do not rely on phenotypic expression of these genetic features for identification purposes, they have enormous potential to provide inexpensive, flexible and specific strain-specific detection and identification of pathogens. In this study, pathogenic Escherichia coli O157:H7-specific genes, non-pathogenic K12-specific genes, common E. coli genes, and negative control genes were polymerase chain reaction-amplified and spotted onto the surface of treated glass slides. After labeled bacterial cDNA samples were hybridized with probes on the microarray, specific fluorescence patterns were obtained, enabling identification of pathogenic E. coli O157:H7 and non-pathogenic E. coli K12. To test the utility of this microarray device to detect genetically engineered bacteria, E. coli BL21 (a B strain derivative with antibiotic resistance gene, ampR) and E. coli JM107 (a K12 strain derivative lacking the gene ompT) were also employed. The array successfully confirmed the strain genotypes and demonstrated that antibiotic resistance can also be detected. The ability to assess multiple data points makes this array method more efficient and accurate than a typical immunoassay, which detects a single protein product.

Colony Count, Microbial↗

Direct amplification of rRNA gene sequences for identification of selected oral pathogens in root canal infections.

AIM: The purpose of this study was to assess the prevalence of selected oral pathogens in root canal infections and their relationship with symptoms using a highly sensitive technique, the polymerase chain reaction. METHODOLOGY: Samples were obtained from 91 infected teeth associated with periradicular lesions, including cases of acute periradicular abscesses. DNA was extracted from the samples and analysed for the presence of target microbial species using a PCR-based identification assay. RESULTS: All samples were positive for the presence of bacteria. Streptococcus anginosus group was detected in 16.7%, Fusobacterium nucleatum in 14.3%, and Bacteroides forsythus in 7.1% of the abscess samples. No pus sample yielded Actinomyces israelii, Actinobacillus actinomycetemcomitans or fungal species. In general, B. forsythus was found in 20% of the cases (16 of 80), S. anginosus in 12% (6 of 50), F. nucleatum in 10% (6 of 60) and A. israelii in 5% (two of 40). A. actinomycetemcomitans was not detected in any case. Fungi were present in only one of 50 cases (2%). There was no correlation between the species and symptoms. CONCLUSIONS: Direct molecular approaches appear to be a valuable tool for the rapid and reliable diagnosis of infectious diseases, as well as for research purposes. There was no correlation between target microbial species and symptoms.

Actinomyces↗

Species specific identification of the Neofabraea pathogen complex associated with pome fruits using PCR and multiplex DNA amplification.

Five species of pathogenic fungi belong to Neofabraea. One of these, N. krawtzewii (syn. N. populi), is responsible for bark lesions on poplar (Populus) trees. The other four species cause post-harvest bull's eye rot of pome fruits, and at least two of these also cause bark cankers on pome fruit trees. Morphological variation among these species is slight, and overlap in geographic range sometimes occurs. As a consequence, identification based on conventional criteria can be tenuous. PCR primers with putative species specificity were developed following genetic analysis of the beta-tubulin gene for isolates of each of the five species of Neofabraea. PCR conditions required to achieve specificity of the primer sets were determined, and a multiplex PCR protocol was developed to optimize their diagnostic utility on apple fruits. A protocol with higher annealing temperatures in the initial PCR cycles followed by lower temperatures in later cycles gave complete species-specificity when the primer sets were used individually and in multiplex, resulting in successful detection of the pathogens from axenic culture and infected apple fruits.

Ascomycota↗

A PCR-based assay for the identification of the fish pathogen Renibacterium salmoninarum.

By means of a one-step one-tube extraction from less than 1 mg of tissue it is possible to identify, via the polymerase chain reaction, Renibacterium salmoninarum in salmon with bacterial kidney disease. A 149-bp DNA sequence unique to R. salmoninarum was specifically amplified and its nature confirmed by Southern hybridization using a non-isotopically labelled probe. The sensitivity of the approach allowed the detection of 22 R. salmoninarum cells. The procedure was successfully applied in the identification of the causative agent of bacterial kidney disease in kidney tissue from infected fishes.

Animals↗

Detection and identification of multiple mycobacterial pathogens by DNA amplification in a single tube.

A comparison of the DNA sequence of the 16S rRNA revealed a region in which there was a minor variation between the species of mycobacteria. This information was used to develop a multiplex amplification system that could identify the genus Mycobacterium and then distinguish between M. avium and M. intracellulare, two commonly encountered mycobacteria other than tuberculosis. The combination of these rRNA gene primers together with primers aimed at the MPB70 gene of M. tuberculosis complex organisms permits the detection and identification of clinically significant mycobacteria in a single tube. An amplification product of 1030 bp is indicative of the genus Mycobacterium and smaller fragments of 850, 372, and 180 bp are the positive signals for M. intracellulare, M. tuberculosis complex, and M. avium, respectively.

Base Sequence↗

Use of PCR with universal primers and restriction endonuclease digestions for detection and identification of common bacterial pathogens in cerebrospinal fluid.

We have designed a universal PCR capable of amplifying a portion of the 16S rRNA gene of eubacteria, including Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus pneumoniae, Enterococcus faecium, Enterococcus faecalis, Mycobacterium tuberculosis, Legionella pneumophila, Escherichia coli, Klebsiella pneumoniae, Serratia marcescens, Enterobacter cloacae, Pseudomonas aeruginosa, Acinetobacter baumannii, Proteus mirabilis, Haemophilus influenzae, and Neisseria meningitidis. The sizes of the amplified products from various bacteria were the same (996 bp), but the restriction patterns of most PCR products generated by HaeIII digestion were different. PCR products from S. aureus and S. epidermidis could not be digested by HaeIII but yielded different patterns when they were digested with MnlI. PCR products from S. pneumoniae, E. faecium, and E. faecalis yielded the same HaeIII digestion pattern but could be differentiated by AluI digestion. PCR products from E. coli, K. pneumoniae, S. marcescens, and E. cloacae also had the same HaeIII digestion pattern but had different patterns when digested with DdeI or BstBI. This universal PCR could detect as few as 10 E. coli or 250 S. aureus organisms. Compared with culture, the sensitivity of this universal PCR for detection and identification of bacteria directly from 150 cerebrospinal fluids was 92.3%. These results suggest that this universal PCR coupled with restriction enzyme analysis can be used to detect and identify bacterial pathogens in clinical specimens.

Aged↗

Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species.

BACKGROUND: Leptospira are the parasitic bacterial organisms associated with a broad range of mammalian hosts and are responsible for severe cases of human Leptospirosis. The epidemiology of leptospirosis is complex and dynamic. Multiple serovars have been identified, each adapted to one or more animal hosts. Adaptation is a dynamic process that changes the spatial and temporal distribution of serovars and clinical manifestations in different hosts. Serotyping based on repertoire of surface antigens is an ambiguous and artificial system of classification of leptospiral agents. Molecular typing methods for the identification of pathogenic leptospires up to individual genome species level have been highly sought after since the decipherment of whole genome sequences. Only a few resources exist for microbial genotypic data based on individual techniques such as Multiple Locus Sequence Typing (MLST), but unfortunately no such databases are existent for leptospires. RESULTS: We for the first time report development of a robust MLST method for genotyping of Leptospira. Genotyping based on DNA sequence identity of 4 housekeeping genes and 2 candidate genes was analyzed in a set of 120 strains including 41 reference strains representing different geographical areas and from different sources. Of the six selected genes, adk, icdA and secY were significantly more variable whereas the LipL32 and LipL41 coding genes and the rrs2 gene were moderately variable. The phylogenetic tree clustered the isolates according to the genome-based species. CONCLUSION: The main advantages of MLST over other typing methods for leptospires include reproducibility, robustness, consistency and portability. The genetic relatedness of the leptospires can be better studied by the MLST approach and can be used for molecular epidemiological and evolutionary studies and population genetics.

Animals↗

Detection and identification of Bartonella species pathogenic for humans by PCR amplification targeting the riboflavin synthase gene (ribC).

Several Bartonella species have now been implicated as human pathogens. The recovery of these fastidious organisms in the clinical microbiology laboratory remains difficult, and current methods are still relatively insensitive. Thus, the bartonellae are good candidates for detection by PCR. We have developed a PCR assay which uses a single primer pair targeting the riboflavin synthase gene (ribC) and detected six Bartonella species that have been implicated in human disease, B. henselae, B. quintana, B. bacilliformis, B. clarridgeiae, B. elizabethae, and B. vinsonii subsp. berkhoffii. Species identification is achieved simply by restriction enzyme digestion of the amplicon. This PCR assay appears to be specific for the Bartonella genus because it failed to amplify DNA from several other bacterial species.

Bacterial Proteins↗

Direct identification of major blood culture pathogens, including Pseudomonas aeruginosa and Escherichia coli, by a panel of fluorescence in situ hybridization assays using peptide nucleic acid probes.

Rapid identification of four major pathogens from 1,231 positive blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes (AdvanDx Inc., Woburn, Mass.) was evaluated. For Escherichia coli, Staphylococcus aureus, and Candida albicans results agreed with conventional identification. The lower sensitivity of the Pseudomonas aeruginosa assay should not compromise the utility of the four assays.

Adult↗

Identification and characterization of bacterial pathogens causing bloodstream infections by DNA microarray.

Bloodstream infections are potentially life-threatening and require rapid identification and antibiotic susceptibility testing of the causative pathogen in order to facilitate specific antimicrobial therapy. We developed a prototype DNA microarray for the identification and characterization of three important bacteremia-causing species: Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. The array consisted of 120 species-specific gene probes 200 to 800 bp in length that were amplified from recombinant plasmids. These probes represented genes encoding housekeeping proteins, virulence factors, and antibiotic resistance determinants. Evaluation with 42 clinical isolates, 3 reference strains, and 13 positive blood cultures revealed that the DNA microarray was highly specific in identifying S. aureus, E. coli, and P. aeruginosa strains and in discriminating them from closely related gram-positive and gram-negative bacterial strains also known to be etiological agents of bacteremia. We found a nearly perfect correlation between phenotypic antibiotic resistance determined by conventional susceptibility testing and genotypic antibiotic resistance by hybridization to the S. aureus resistance gene probes mecA (oxacillin-methicillin resistance), aacA-aphD (gentamicin resistance), ermA (erythromycin resistance), and blaZ (penicillin resistance) and the E. coli resistance gene probes blaTEM-106 (penicillin resistance) and aacC2 (aminoglycoside resistance). Furthermore, antibiotic resistance and virulence gene probes permitted genotypic discrimination within a species. This novel DNA microarray demonstrates the feasibility of simultaneously identifying and characterizing bacteria in blood cultures without prior amplification of target DNA or preidentification of the pathogen.

Acetyltransferases↗

[Current state and problems in the microbiology laboratory--organizing the laboratory].

The microbiological laboratory in the hospital has many roles including the rapid and precise identification of pathogenic bacteria in specimens, their antimicrobial susceptibility tests, microbial antigen detection using immunological methods and DNA hybridization methods, surveillance of bacterial milieu of the hospital environment, monitoring quality control of microbiological methods, to educate microbiological skills of staffs, the economical management of laboratory and so on. The last two issues are our major concerns. Improvement of the microbiological skills of the staff is most important in the laboratory, but is a time-consuming. From our experience, a technical expert, intermediately skilled technicians and beginners should always work in the laboratory, together. On the other hand, the economical management of the microbiological laboratory is also another concern. Although the mechanization of procedures comes to mind, it is hard to improve the economical conditions in the laboratory. Because of the control of the machines is not completely automatic and requires the knowledges and decisions of technical experts, the work force and running cost can not be reduced. As the technical expert can economize in the use of media or tests for identification of pathogens, good training of beginners into skillful successors, is important.

Humans↗

Silkworm pathogenic bacteria infection model for identification of novel virulence genes.

Silkworms are killed by injection of pathogenic bacteria, such as Staphylococcus aureus and Streptococcus pyogenes, into the haemolymph. Gene disruption mutants of S. aureus whose open reading frames were previously uncharacterized and that are conserved among bacteria were examined for their virulence in silkworms. Of these 100 genes, three genes named cvfA, cvfB, and cvfC were required for full virulence of S. aureus in silkworms. Haemolysin production was decreased in these mutants. The cvfA and cvfC mutants also had attenuated virulence in mice. S. pyogenes cvfA-disrupted mutants produced less exotoxin and had attenuated virulence in both silkworms and mice. These results indicate that the silkworm-infection model is useful for identifying bacterial virulence genes.

Animals↗

Mitochondrial telomeres as molecular markers for identification of the opportunistic yeast pathogen Candida parapsilosis.

Recent studies have demonstrated that a large number of organisms carry linear mitochondrial DNA molecules possessing specialized telomeric structures at their ends. Based on this specific structural feature of linear mitochondrial genomes, we have developed an approach for identification of the opportunistic yeast pathogen Candida parapsilosis. The strategy for identification of C. parapsilosis strains is based on PCR amplification of specific DNA sequences derived from the mitochondrial telomere region. This assay is complemented by immunodetection of a protein component of mitochondrial telomeres. The results demonstrate that mitochondrial telomeres represent specific molecular markers with potential applications in yeast diagnostics and taxonomy.

Candida↗

Mutational analysis of BRCA1 and BRCA2 in Mediterranean Spanish women with early-onset breast cancer: identification of three novel pathogenic mutations.

In Spain, the contribution of BRCA mutations to the population incidence of early-onset breast cancer was unknown. We carried out a mutational analysis of the BRCA1 and BRCA2 genes in 124 Spanish women diagnosed with breast cancer before the age 41 and who were not selected for a family history of this disease. The genetic study was performed by PCR-SSCP analysis and DNA sequencing. We identified 6 pathogenic BRCA mutations in 7 unrelated probands (5.6%; 95% CI=2.3% to 11.3%): 1 BRCA1 (c.2080delA) and 5 BRCA2 (p.Y3006X, p.Q1994X, c.9204_9217del14, c.9254_9258del5 and c.295+2T>C). Three out of 6 mutations were novel (BRCA2 p.Y3006X, c.9204_9217del14, and c.295+2T>C), and two further mutations had not been previously found in Spain (BRCA1 c.2080delA and BRCA2 p.Q1994X). The one remaining (BRCA2 c.9254_9258del5) was detected in two probands of our sample. Additionally, we identified two new missense mutations: BRCA1 p.P1812A and BRCA2 p.G2044A. Our data support the notion that Spaniards represent a heterogeneous population with its own spectrum of BRCA mutations, some of which appear as founding mutations. We categorized patients into familial or non-familial groups on the basis of her family history of breast/ovarian cancer; this analysis indicated that among Spanish women with early-onset breast cancer, an even moderate family history is a good predictor of being a BRCA mutation carrier.

Adult↗