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PubMed2001

Rapid identification of pathogenic bacteria by single-enzyme amplified fragment length polymorphism analysis.

Despite major progress in their treatment and prevention, bacterial infections remain a significant cause of morbidity and mortality worldwide. In responding to a disease outbreak, rapid and accurate identification of the bacterial species involved is of paramount importance. Strain level discrimination is desirable to allow selection of treatment modalities, and in the case of a deliberate release, for identification of the source. Single-enzyme amplified fragment length polymorphism (SE-AFLP) analysis was used to perform species and strain identification of subgroup I Bacilli, Yersinia, Staphylococci and Escherichia coli. By careful selection of AFLP primers, it was possible to obtain reproducible and sensitive identification to strain level, even within the highly monomorphic species Bacillus anthracis. SE-AFLP fragments can be analyzed using standard gel electrophoresis, and can be easily scored by visual inspection, due to the low complexity of the fingerprint obtained by this method. These features make SE-AFLP suitable for use in either field or laboratory applications.

Bacillus↗
PubMed1982

Comparison of a rapid micromedia method to cystine trypticase agar (CTA) and fluorescent methods for the identification of pathogenic Neisseria.

A four-hour micromedia method which detects enzymes formed by bacteria for the degradion of carbohydrates was compared to the utilization of carbohydrates was compared to the utilization of carbohydrates in cystine tyrpticase agar (CTA) for the identification of Neisseria gonorrhoeae and Neisseria meningitidis. This rapid micromedia method (RMM) correlated 100% with the utilization of carbohydrates in CTA. Identification of N. gonorrhoeae by RMM was compared to the identification achieved by a commercially available coagglutination method and a fluorescent antibody (FA) technique. Of 144 isolates identified as N. gonorrhoeae by RMM, 122 (84.7%) were identified by coagglutination and 141 (97.9%) were identified by FA as N. gonorrhoeae. Five (13%) of 40 isolates identified as N. meningitidis by RMM were identified as N. gonorrhoeae by coagglutination while eleven (28%) were identified as N. gonorrhoeae by the FA technique. One (14%) and four (57%) of seven isolates identified as Neisseria species were identified as N. gonorrhoeae by coagglutination and the FA technique respectively. The rapid micromedia method was found to be a quick, sensitive, specific and economic way of identifying N. gonorrhoeae and N. meningitidis.

Cheilitis↗
PubMed2006

Sphingolipid biosynthesis in pathogenic fungi: identification and characterization of the 3-ketosphinganine reductase activity of Candida albicans and Aspergillus fumigatus.

An early step in sphingolipid biosynthesis, the reduction of 3-ketosphinganine, is catalyzed in the yeast Saccharomyces cerevisiae by Tsc10p (TSC10 (YBR265W)). We have identified orthologs of TSC10 in two clinically important fungal pathogens, Candida albicans and Aspergillus fumigatus. The translated sequences of the putative C. albicans ortholog, KSR1 (orf6.5112), and the putative A. fumigatus ortholog, ksrA, show significant homology to the yeast protein. All three proteins contain the signature motifs of NAD(P)H-dependent oxidoreductases in the short-chain dehydrogenase/reductase family and a conserved putative substrate-binding domain. Despite being essential in S. cerevisiae, we demonstrate that the C. albicans ortholog, KSR1, is not required for cell viability. However, ksr1 null mutants produce lower levels of inositolphosphorylceramides, are significantly more sensitive than the wildtype to an inhibitor of a subsequent step in sphingolipid biosynthesis, and are defective for the transition from yeast to filamentous growth, a key virulence determinant. Recombinant, purified Ksr1p and KsrA can carry out the reduction of 3-ketosphinganine in an NADPH-dependent manner. Molecular modeling of Ksr1p with bound substrates suggests that a significant portion of the aliphatic chain of 3-ketosphinganine protrudes from the enzyme. Guided by this molecular model, we developed shorter, water-soluble derivatives of 3-ketosphinganine that are substrates for 3-ketosphinganine reductase.

Alcohol Oxidoreductases↗
PubMed1997

[Evaluation of the usefulness of the agglutination test with Mangifera indica extract for the identification of pathogenic Yersinia enterocolitica strains].

The study was performed on 137 Y. enterocolitica strains belonging to various serological groups, including 75 03 group strains isolated form human clinical material. The agglutination test on slides was carried out on this strains using Mangifera indica extract of own production. Agglutinating preparation obtained from the seeds of M. indica agglutinated Y. enterocolitica organisms possessing the pVY plasmid and CRMOX+ phenotype in dilutions to 1.56 micrograms/ml. In identification tests conducted parallelly agglutination solution was used in concentrations of 100 and 10 micrograms/ml. All clones of Y. enterocolitica from O3 group from cultures at 37 degrees C and with CRMOX+ phenotype possessing the pVY plasmid were agglutinated by the extract. Agglutination failed to develop in the cultures of these clones incubated at 25 degrees C. Yersinia clones not containing the pVY plasmid with CRMOX- phenotype were resistant to agglutination. The virulence plasmid was found in 44 out of 75 strains of Y. enterocolitica O3 and was identified by restriction analysis after plasmid DNA digestion with Eco RI enzyme. The obtained results agreed with those of Wauters et al. in 1995 and confirmed the opinion of these authors on the usefulness of the test with M. indica agglutinin for the identification of virulent Y. enterocolitica strains.

Agglutination Tests↗
PubMed2001

Bioinformatics in medical practice: what is necessary for a hospital?

Building bioinformatic facilities for a university hospital is pretty similar to using standardized building blocks to construct a house. Starting with the intention to built a dwelling house, a factory or just a shelter the architect draws a construction plan and determines the material to be used. In general, the building is then constructed by the workmen following exactly the plan. However, for particular reasons, minor alterations may be needed to improve the construction of the building. Here we use the metaphor of constructing a "bio-informatics building" to describe the steps needed to support the daily tasks of a university hospital medical microbiology department which uses genomic methods quite extensively for pathogen identification. Today the Giessen "bioinformatics building" is not yet complete but we have been able to lay solid foundations and erect the ground floor which is functional already. Using a combination of standard tools, internet accessible genomic databases and some own software tools we can support genome sequencing from the raw sequence to pathogen identification.

Computational Biology↗
PubMed2000

Phosphorylcholine decoration of lipopolysaccharide differentiates commensal Neisseriae from pathogenic strains: identification of licA-type genes in commensal Neisseriae.

Phosphorylcholine (ChoP) is a potential candidate for a plurispecific vaccine, because it is present on surface components of many mucosal organisms, including Haemophilus influenzae, Streptococcus pneumoniae and Pseudomonas aeruginosa. In addition, ChoP has been detected on pili of Neisseria meningitidis and Neisseria gonorrhoeae. In this study, we demonstrate the presence of the phosphorylcholine epitope on the lipopolysaccharides (LPSs) of several species of commensal Neisseriae (Cn), a property that differentiates commensal from the pathogenic strains of Neisseriae. In an extended survey of 78 strains, we confirmed the exclusive expression of the ChoP epitope on pili of pathogenic Neisseriae. Despite the presence of pili on Cn, which are homologous to Class II pili of N. meningitidis, they did not react with anti-ChoP antibody. This observation was further supported by the fact that 14C-labelled choline was incorporated only in the LPSs of Cn. Analysis of the LPS of N. lactamica strain NL4 revealed two distinct and interconvertible molecular species of LPS with high and low levels of reactivity with anti-ChoP antibody. In addition, on/off phase variation gave rise to frequent modulation in the levels of antibody reactivity. A concurrent modulation was also observed in the binding of C-reactive protein, CRP, a ChoP-binding reactant that is implicated in bacterial clearance. Genetic analysis showed the presence of a gene in several Cn spp. with significant sequence identity to H. influenzae licA. This gene encodes choline kinase and is also involved in phase variation of the LPS-associated ChoP in H. influenzae. In contrast, licA-like genes were not identified in the pathogenic Neisseria strains tested. They are absent from N. meningitidis strain Z2491 genome database. These data suggest that the genetic basis for ChoP incorporation in Cn LPS resembles that in H. influenzae spp. and may be distinct from that generating the ChoP epitope on pili of pathogenic Neisseriae. Further, the modulation of ChoP expression on Cn LPS, and corresponding modulation of CRP binding, has the potential to confer the property of immune avoidance and thus of persistence on mucosa.

Amino Acid Sequence↗
PubMed1990

Superoxol and aminopeptidase tests for identification of pathogenic Neisseria species and Moraxella (Branhamella) catarrhalis.

The superoxol test, and prolyl aminopeptidase and gammaglutamyl aminopeptidase tests were evaluated for the detection of pathogenic Neisseria spp. using 317 strains of Neisseria-ceae. The superoxol test was positive for all 116 gonococci and 62 Moraxella (Branhamella) catarrhalis strains, but also for three strains of Neisseria meningitidis, one strain of Neisseria lactamica and eight saprophytic neisseriae. When using strains grown on Thayer-Martin medium, the positive and negative predictive values of the superoxol test for the identification of Neisseria gonorrhoeae were 96.7% and 100% respectively. Meningococci were the only neisseriae growing on Thayer-Martin medium that showed gamma-glutamyl aminopeptidase activity. The prolyl aminopeptidase test showed low specificity.

Aminopeptidases↗
PubMed1980

Evaluation of rapid carbohydrate degradation tests for identification of pathogenic Neisseria.

A total of 156 clinical isolates were tested by the modified rapid fermentation test, the BACTEC Neisseria differentiation kit, and the cystine-Trypticase agar method. The modified rapid fermentation test and BACTEC methods accurately identified at least 95% of 101 strains of N. gonorrhoeae tested and at least 91% of 45 strains of N. meningitidis tested within 4 h. Overall, the cystine-Trypticase agar method was the most accurate (97%) but required as long as 48 h of incubation. The data presented appear to show that rapid carbohydrate degradation tests can provide reliable and specific identification results.

Bacteriological Techniques↗
PubMed1988

Evaluation of eight methods for identification of pathogenic Neisseria species: Neisseria-Kwik, RIM-N, Gonobio-Test, Minitek, Gonochek II, GonoGen, Phadebact Monoclonal GC OMNI Test, and Syva MicroTrak Test.

The performance of eight methods in identifying Neisseria species, particularly N. gonorrhoeae, was evaluated. These methods included four rapid carbohydrate utilization tests (Gonobio-Test, Neisseria-Kwik, RIM-N, and Minitek); the Gonochek II, a test which is based on the utilization of chromogenic substrates; and three monoclonal antibody tests (Syva MicroTrak, GonoGen, and Phadebact Monoclonal GC OMNI Test). In all, 182 isolates comprised in six species of Neisseria as well as Branhamella catarrhalis and Moraxella sp. were tested. Cystine-tryptic digest agar supplemented with sugars was included for reference purposes. In the carbohydrate utilization tests, the sensitivity and specificity of the Neisseria-Kwik and Minitek tests for the identification of N. gonorrhoeae were 100%. This compared with sensitivities and specificities, respectively, of 100 and 99.1% for the Gonobio-Test and 99.1 and 100% for cystine-tryptic digest agar sugars and the RIM-N test. The sensitivity and specificity of the Gonochek II test were 99.0 and 86.7%, respectively. Although most test kits did not claim to identify all Neisseria species, in several cases isolates of N. subflava were misidentified or could be misinterpreted as N. gonorrhoeae or N. meningitidis. With the monoclonal reagents, the Syva MicroTrak system was 100% sensitive and 100% specific. The GonoGen test was both 99.1% sensitive and specific, while the Phadebact Monoclonal GC OMNI Test was 99.1% sensitive but 91.2% specific. With this latter test, cross-reactions were observed with strains of B. catarrhalis, N. cinerea, and N. lactamica.

Agglutination Tests↗
PubMed2005

Molecular identification of pathogenic house dust mites using 12S rRNA sequences.

House dust mites are microarthropods implicated in the cause of allergic diseases. Currently, there is no phylogenetic analysis of dust mites based on genomic or mitochondrial DNA (mtDNA) evidence. For the first time, we report evolutionary relationships based on partial mtDNA 12S rRNA sequences among the four dust mite families Pyroglyphidae (Dermatophagoides pteronyssinus), Glycyphagoidea (Glycyphagus privatus), Acaridae (Aleuroglyphus ovatus), and Echimyopodidae (Blomia tropicalis). Thirteen sequence variants were obtained and phylogenetic analysis showed two monophyletic clades composed of two species each. Contrary to current taxonomic classification, the Acaridae clustered in a monophyletic group with the Pyroglyphidae. Considering the current difficulties in identifying these medically important species for the purpose of eradication and treatment, it is significant that sequence data are capable of discriminating between species belonging to different families of dust mites.

Acaridae↗
PubMed1995

Rheumatoid factor avidity in patients with rheumatoid arthritis: identification of pathogenic RFs which correlate with disease parameters and with the gal(0) glycoform of IgG.

The standard ELISA for measuring rheumatoid factor (RF) binding was modified by treatment after the RF-Fc interaction with 2 M guanidine, which allowed a measurement of the avidity of the interaction. Incubation with 4 M guanidine eliminated RF binding. There was a direct correlation (r = 0.99) between the avidity as measured by the modified guanidine ELISA, and the dissociation constant for monoclonal RFs, as measured by competitive ELISA. Of the seropositive rheumatoid arthritis (RA) patients tested, 47% had high-avidity RFs (> or = 8% RF binding remaining after guanidine treatment). Tender joint count scores were significantly higher in the high avidity group (p = 0.05), whereas there was no significant difference in the ages, disease duration, sedimentation rate, RF titer or serum Ig levels compared to those with low-avidity RFs. Additionally 58% of those with high-avidity RFs had subcutaneous nodules, compared to 40% of the low-avidity group. A significantly higher number of nodules was present in the high-avidity RF group compared to those with low-avidity RFs (p = 0.03). Interestingly, the RF avidity was significantly higher in isolated immune complexes (IC), compared to that in circulating IgM RFs (p = 0.01). The RF avidity correlated with the presence of the glycoform of IgG lacking galactose in both circulating and IC-derived IgG (p = 0.003 and 0.009 respectively). Information about the strength of binding to Fc identifies a subgroup of IgM RFs that are likely pathological in patients with RA, as well as a specific glycoform of the target antigen.

Antibodies↗
PubMed2003

Molecular identification of pathogenic and nonpathogenic strains of Vibrio harveyi using PCR and RAPD.

Fifteen environmental samples of Vibrio spp. isolated from healthy and diseased shrimps were tested for pathogenicity to juvenile shrimps. Two isolates, strains Z2 and Z3, were observed to be pathogenic, causing 100% mortality of the target host compared to the control strain Vibrio harveyi ATCC 14126. Environmental and type strains were subjected to molecular characterization by restriction fragment length polymorphism (RFLP) and PCR using primers targeted to different virulence, transcriptional regulator, or quorum sensing genes from V. harveyi. Primers designed for luxN were specific and identified all the environmental strains as V. harveyi. The random amplified polymorphic DNA (RAPD) method was used to differentiate between pathogenic and nonpathogenic strains of V. harveyi. These methodologies allowed us to detect and distinguish strains virulent and avirulent to juvenile shrimp.

Animal Diseases↗
PubMed2003

Identification of pathogenic mutations in the human rapsyn gene.

Rapsyn, a complex postsynaptic protein of the striated muscle, assembles acetylcholine receptors (AChR) at high density at the motor endplate (EP). Neuromuscular junctions of mice lacking rapsyn show no clusters of AChRs or other structural postsynaptic proteins such as beta-dystroglycan and utrophin. Humans with mutations in the rapsyn gene ( RAPSN) are affected with a postsynaptic form of congenital myasthenic syndrome (CMS) characterized by impairment of the morphologic development of the postsynaptic region. We have identified four patients from four different families with RAPSNmutations and CMS, confirmed in two cases by microelectrode and electron microscopy studies. The N88K mutation was present in all patients. One patient who was homozygous for N88K was only mildly affected, while the other three patients who were heterozygous for N88K and a second mutation (either L14P, 46insC, or Y269X) were severely affected. Mutations 46insC and Y269X predicts truncation of the protein. L14P predicts a conformational change at the N-terminus that may disrupt membrane association. N88K occurs within the putative leucine zipper motif potentially important for AChR clustering. These findings may explain the severe clinical involvement of compound heterozygous patients.

Adolescent↗
PubMed2025

Identification of pathogenic variants in six Chinese families with keratoconus of autosomal dominant inheritance: pathogenicity analysis and variable phenotype.

PURPOSE: Keratoconus (KC) is a bilateral, asymmetric disease causing corneal thinning, irregular astigmatism, and vision decline, with unclear etiology. This study aims to investigate pathogenic variants of candidate genes in Chinese KC families via whole exome sequencing (WES). METHODS: The Pentacam 3D anterior segment analysis system was applied for keratectasia detection, and the Corvis ST was used for corneal biomechanics measurement. Probands from KC families were screened via WES and further verified in other family members through Sanger sequencing. Additionally, qPCR was used to validate copy number variants and identify pathogenic gene loci. The identified variants were then classified according to the Standards and Guidelines for the Interpretation of Sequence Variants published by the American College of Medical Genetics and Genomics (ACMG). Finally, STRING protein-protein interaction (PPI) networks analysis was performed to investigate interactions among candidate gene-related proteins. RESULTS: Using WES, four heterozygous missense variants were detected in the ZNF469, KRT12, COL8A2, and COL18A1 genes: c.4384G > A: p.Asp1462Asn, c.1229T > G:p.Val410Gly, c.505A > G:p.Ile169Val, and c.1159G > A:p.Gly387Arg. Additionally, a heterozygous frameshift variant was detected in the PMS2 gene: c.1551_1572del:p.Ser517Argfs*71. The affected parents carried the same variants as the probands verified by Sanger sequencing. A copy number variant was detected in the DPP6 gene: seq[GRCh38] dup(7)(q36.2q36.2) chr7:g.153782360_ 153982491dup. According to ACMG guidelines, ZNF469, KRT12, COL8A2, and COL18A1 gene variants are Likely Pathogenic; PMS2 and DPP6 gene variants are Pathogenic. STRING analysis highlights a tightly interconnected network centered on COL8A2, involving COL18A1, FN1, ZNF469, and KRT12. DPP6 was involved in KC via affecting FN1. In four of six autosomal dominant KC (adKC) families, affected parents had the same variants as probands but milder phenotypes. CONCLUSION: In this study, six novel variants in ZNF469, KRT12, COL8A2, COL18A1, PMS2, and DPP6 were linked to adKC. Family phenotypes showed variable expressivity with irregular dominance inheritance. Abnormal KC-related gene protein expression may contribute to corneal structural instability. This study broadened KC genetic screening candidates and suggested genetic testing could aid early KC diagnosis and intervention.

Adult↗
PubMed2005

Identification and pathogenic characterization of endophytic Fusarium species from cowpea seeds.

Isolates of Fusarium were obtained and identified from seeds of cowpea, Vigna unguiculata (L.) Walp., by means of blotter tests and slide cultures. Species were differentiated according to the morphology of the macroconidia, microconidia and their arrangement in chains or false heads, the size and type of conidiophore, and the presence or absence of chlamydospores. The species were identified as F. semitectum, F. equiseti, F. oxysporum, F. solani, F. anthophilum, F. sporotrichioides, F. moniliforme, and Fusarium sp. Among the species, F. semitectum was the most frequently detected. None of these species were pathogenic when inoculated in susceptible cowpea cultivar (BR 17-Gurgueia). But, an isolate of F. oxysporum f. sp. tracheiphilum used as a standard of comparison for pathogenicity (control) induced symptoms of yellowing, vascular wilting, and death of a susceptible cowpea cultivar under the same environmental conditions.

Brazil↗