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PubMed1983

Exoantigen tests for the immunoidentification of fungal cultures.

Exoantigen tests for the immunoidentification of fungal pathogens are playing a new and significant role in the diagnostic laboratory. Properly performed and controlled exoantigen tests lead to rapid, accurate identification of cultures of many fungal pathogens. The tests are particularly valuable in identifying dimorphic pathogens that are difficult to convert or with atypical cultures. We review the value of exoantigen tests for identifying mycelial form fungi: Aspergillus spp. Blastomyces dermatitidis, Coccidioides immitis, Exophiala jeanselmei, Histoplasma spp., Paracoccidioides brasiliensis, Penicillium marneffei, Pseudallescheria boydii, Sporothrix schenckii, Wangiella dermatitidis and certain dermatophytes. We discuss procedures for performing the tests and sources of error.

Antigens, Fungal↗
PubMed2006

Bacterial identification, clinical significance, and antimicrobial susceptibilities of Acinetobacter ursingii and Acinetobacter schindleri, two frequently misidentified opportunistic pathogens.

The species belonging to the Acinetobacter genus are currently reported as opportunistic pathogens in hospitalized patients with underlying predispositions. However, except for the Acinetobacter calcoaceticus-Acinetobacter baumannii complex, the identification of other species is frequently unreliable, especially for Acinetobacter ursingii and Acinetobacter schindleri, newly described in 2001. Thus, the clinical significance, phenotypic features, and antimicrobial susceptibilities of these two misidentified species remain unclear. Of 456 Acinetobacter sp. clinical strains isolated from 2002 to 2005 in Henri Mondor Hospital, 15 isolates (10 A. ursingii and 5 A. schindleri isolates) were studied. They were characterized using a phenotypic approach (API 20 NE and VITEK 2 systems), 16S rRNA gene sequencing, and susceptibility to antimicrobial agents with evaluation of impact in clinical relevance. The two corresponding type strains were also included for comparison. All isolates were identified to the species level using molecular tools, whereas the phenotypic methods remained unreliable due to the absence of these two species in the manufacturers' databases. However, the API 20 NE system appeared to be a reasonably reliable phenotypic alternative for the identification of A. ursingii when the numerical code 0000071 was found. Conversely, no discriminative phenotypic alternative existed for A. schindleri isolates. Concerning antimicrobial susceptibility, A. ursingii strains appeared to be more resistant to antibiotics than A. schindleri strains, which could imply therapeutic consequences. Finally, the prevalence of infections caused by A. ursingii and A. schindleri (representing 9.7% and 4.8% of non-A. calcoaceticus-A. baumannii complex strains, respectively) seems to be underestimated.

Acinetobacter↗
PubMed1996

Artificial feeding of ixodid ticks.

Ixodid ticks are economically important as they cause direct damage to livestock and are vectors of several pathogens that cause diseases in humans and animals. Some of the important tick-borne pathogens of livestock are Theileria parva, T. annulata, Babesia bigemina, B. bovis, Anaplasma marginale and Cowdria ruminantium. These pathogens are responsible for causing enormous losses in livestock. Identification of factors that influence transmission and development of these pathogens in ticks will greatly facilitate development of rational strategies for control of tick-borne diseases. This research has been hampered by the lack of suitable artificial feeding methods. In this paper, Sam Waladde, Aian Young and Subhash Morzaria review recent developments in the artificial feeding of ixodid ticks and evaluate how this method can potentially be exploited. They use an example the transmission of an important livestock pathogen, T. parva, by Rhipicephalus appendiculatus.

Journal Article↗
PubMed2001

The use of 16S and 16S-23S rDNA to easily detect and differentiate common Gram-negative orchard epiphytes.

The identification of Gram-negative pathogenic and non-pathogenic bacteria commonly isolated from an orchard phylloplane may result in a time consuming and tedious process for the plant pathologist. The paper provides a simple "one-step" protocol that uses the polymerase chain reaction (PCR) to amplify intergenic spacer regions between 16S and 23S genes and a portion of 16S gene in the prokaryotic rRNA genetic loci. Amplified 16S rDNA, and restriction fragment length polymorphisms (RFLP) following EcoRI digestion produced band patterns that readily distinguished between the plant pathogen Erwinia amylovora (causal agent of fire blight in pear and apple) and the orchard epiphyte Pantoea agglomerans (formerly E. herbicola). The amplified DNA patterns of 16S-23S spacer regions may be used to differentiate E. amylovora at the intraspecies level. Isolates of E. amylovora obtained from raspberries exhibited two major fragments while those obtained from apples showed three distinct amplified DNA bands. In addition, the size of the 16S-23S spacer region differs between Pseudomonas syringae and Pseudomonas fluorescens. The RFLP pattern generated by HaeIII digestion may be used to provide a rapid and accurate identification of these two common orchard epiphytes.

DNA, Bacterial↗
PubMed2004

Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens.

MOTIVATION: Processing and presentation of major histocompatibility complex class I antigens to cytotoxic T-lymphocytes is crucial for immune surveillance against intracellular bacteria, parasites, viruses and tumors. Identification of antigenic regions on pathogen proteins will play a pivotal role in designer vaccine immunotherapy. We have developed a system that not only identifies high binding T-cell antigenic epitopes, but also class I T-cell antigenic clusters termed immunological hot spots. METHODS: MULTIPRED, a computational system for promiscuous prediction of HLA class I binders, uses artificial neural networks (ANN) and hidden Markov models (HMM) as predictive engines. The models were rigorously trained, tested and validated using experimentally identified HLA class I T-cell epitopes from human melanoma related proteins and human papillomavirus proteins E6 and E7. We have developed a scoring scheme for identification of immunological hot spots for HLA class I molecules, which is the sum of the highest four predictions within a window of 30 amino acids. RESULTS: Our predictions against experimental data from four melanoma-related proteins showed that MULTIPRED ANN and HMM models could predict T-cell epitopes with high accuracy. The analysis of proteins E6 and E7 showed that ANN models appear to be more accurate for prediction of HLA-A3 hot spots and HMM models for HLA-A2 predictions. For illustration of its utility we applied MULTIPRED for prediction of promiscuous T-cell epitopes in all four SARS coronavirus structural proteins. MULTIPRED predicted HLA-A2 and HLA-A3 hot spots in each of these proteins.

Algorithms↗
PubMed1982

[Identification of yeast-like fungi in the hospital laboratory].

Although Candida albicans is a major pathogen yeast, various similar species and genus are responsible for illness in human beings. Therefore, it is necessary to find a practical and efficient system for the identification of these pathogenic microorganisms. The authors propose a valid scheme for this purpose.

Candidiasis↗
PubMed2004

Microtechnique for identification of lactic acid bacteria.

Certain gut species are pathogens, but a number of other resident bacteria may be of some benefit to host health. Examples include enterococci, lactobacilli, propionibacteria, and bifidobacteria, which are present in the colon in significant numbers. Identification and classification are not identical. A group can be identified only after it has been classified, based on a pattern of properties shown by all the members of the group that other groups do not possess. The properties used in identification are often different from those used in classification. Biochemical, nutritional, and physiological characterization tests (usually carried out in bottles and tubes of solid and liquid media and on plates) have been developed and modified since the earliest days of bacteriology. Generally, the characteristics chosen for an identification plan should be easily determinable, whereas those used for classification (such as DNA homology) may be quite difficult to determine. Genera and species identification might not be based on only a few tests, but rather on the pattern given by a whole battery of tests. The members of the family Lactobacillaceae represent one example of this. Some probiotic strains can be selected for their benefical properties as active antimicrobial agents against pathogenic microorganisms, hydrophobic ability, presence of substances with a capacity for adherence to epithelium, and so on. After isolation, identification is an important step before selecting probiotic strains. These identifications can be facilitated through microtechniques. To alleviate the need to inoculate large numbers of tubes with media (conventional test), some rapid multitest systems have been devised and are commercially available (such as the API or Biolog systems). Although they are expensive for large studies and not always sufficiently versatile, these kits do offer the advantages of convenience, miniaturization, rapidity, and, above all, strict standardization. Other methods such as ribotyping or randomly amplified polymorphic DNA do not take into account the phenotypic characteristics (biotyping). In this chapter, we describe a simple, rapid, and economical microplates technique to identify lactic acid bacteria and enterobacteria based on general metabolic characteristics, adapted for routine study of a large number of strains.

Bacteriological Techniques↗
PubMed1999

Identification of genes in a KG- phenotype of Lactococcus garvieae, a fish pathogenic bacterium, whose proteins react with antiKG- rabbit serum.

Five different clones (SA1B05, SA1B10, SA2F01, SA8A11 and SA9H10) were isolated from the gene library of the Lactococcus garvieae SA8201 (KG-) strain by immunological screening using rabbit serum against L. garvieae (KG-) phenotype cells. A Western blot analysis indicated that the molecular sizes of immunologically detected proteins of SA1B05, SA1B10, SA2F01, SA8A11 and SA9H10, which were fused with LacZ protein, were 25, 30, 28, 26 and 13 kDa, respectively. The amino acid sequences of the immunologically detected proteins of SA1B05, SA1B10, SA2F01 and SA8A11 were homologous to a processing protease of Bacillus subtilis (36.6%), dihydropteroate synthase of Escherichia coli (34.6%), trigger factor of B. subtilis (45.8%) and N-acetylglucosamine-6-phosphate deacetylase of Vibrio furnissii (37.1%), respectively. There was no significant homologous sequence of SA9H10 in DDBJ/EMBL/GenBank and SwissProt. We cloned and sequenced a longer DNA fragment (SA9H10L) of SA9H10 from the gene library. The predicted amino acid sequence of this clone was weak homology to M protein of Streptococcus pyogenes (22.7%). Five genes were specifically expressed in the KG- phenotype strains. However, SA8A11 and SA9H10 was expressed in the mutated strain SA8201-TTC, whose serological phenotype was changed from KG- to KG+ by 2,3,5-triphenyltetrazolium chloride.

Amino Acid Sequence↗
PubMed2004

[Identification of geophilic and zoophilic dermatophytes in siblings with tinea capitis. A pathogenic factor or contamination?].

Two siblings of African origin presented with multiple scaling patches and alopecia on the scalp four weeks after returning from a vacation in Eritrea. Direct KOH examination revealed fungal elements; Trichophyton mentagrophytes and Trichophyton terrestre were identified in the fungal culture. We discuss the putative pathogenic role of both microorganisms in causing disease. Although infection with Microsporum canis currently accounts for almost fifty percent of all cases of tinea capitis in Germany, other fungi have gained importance due to tourism and increasing migration.

Alopecia↗
PubMed2004

Proteomic approach: identification of Medicago truncatula proteins induced in roots after infection with the pathogenic oomycete Aphanomyces euteiches.

The legume root rot disease caused by the oomycete pathogen Aphanomyces euteiches is one major yield reducing factor in legume crop production. A comparative proteomic approach was carried out in order to identify proteins of the model legume Medicago truncatula which are regulated after an infection with A. euteiches . Several proteins were identified by two dimensional gel electrophoresis to be differentially expressed after pathogen challenge. Densitometric evaluation of expression values showed different regulation during the time-course analysed. Proteins regulated during the infection were identified by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). Among the differentially expressed proteins, two encoded putative cell wall proteins and two were designated as small heat shock proteins. Furthermore, an isoform of the chalcone-O-methyltransferase was found to be increased in infected roots. The majority of induced proteins belonged to the family of class 10 of pathogenesis related proteins (PR10). Previously, various PR10-like proteins have been shown to be regulated by general stress or abscisic acid (ABA). Therefore, these proteins were further investigated concerning their regulation in response to drought stress and exogenous ABA-application. Complex regulation patterns were identified: three of the A. euteiches -induced PR10-like proteins were also induced by exogenous ABA- but none of them is induced after drought stress. In contrast, three of these proteins are down-regulated by drought stress. Hence, the strong expression of different PR10-family members and their regulation profiles indicates that this set of proteins plays a major role during root adaptations to various stress conditions.

Abscisic Acid↗
PubMed2026

Clade-dependent antifungal resistance and susceptibility in Candidozyma auris: A global scoping review.

BACKGROUND: Candidozyma auris (formerly Candida auris) is an emerging multidrug-resistant fungal pathogen that has spread globally since its first identification in 2009 and is now classified as a critical-priority pathogen by the World Health Organization. Distinct genetic clades are associated with variations in geographic distribution, antifungal susceptibility, and resistance mechanisms; however, clade-specific evidence remains fragmented. AIMS: To systematically map global evidence on clade diversity, antifungal susceptibility patterns, resistance mechanisms, and clinical implications of C. auris. METHODS: A scoping review was conducted following PRISMA-ScR guidelines. Peer-reviewed primary studies published between 2009 and September 2025 were included if they reported clade attribution and antifungal susceptibility or resistance data. PubMed/MEDLINE, Scopus, and Web of Science were searched. Two reviewers independently screened studies and extracted data using a standardized form. RESULTS: Of 2050 records identified, 105 studies met inclusion criteria, representing 29 countries and diverse study designs. Whole-genome sequencing was the most common typing method. Antifungal susceptibility varied substantially across clades. High fluconazole resistance was consistently reported (MIC 4 to >256μg/mL). Echinocandins generally retained activity, although reduced susceptibility associated with FKS1 mutations was observed. Resistance mechanisms primarily involved mutations in ERG11, FKS1, and efflux-related genes. Studies also reported challenges in healthcare-associated transmission, environmental persistence, and diagnostic misidentification. CONCLUSIONS: C. auris exhibits marked clade-dependent variability in antifungal susceptibility and resistance mechanisms. These findings support the need for clade-informed interpretation of susceptibility data, standardized surveillance, improved diagnostics, and development of novel antifungal therapies.

Antifungal Agents↗
PubMed2002

Identification of a second proliferating cell nuclear antigen in the human malarial pathogen Plasmodium falciparum.

Proliferating cell nuclear antigen seems to exist as a single form in higher eukaryotic cells and plays multiple roles in nucleic acid metabolism. We have identified a second additional proliferating cell nuclear antigen (PfPCNA2) in Plasmodium falciparum on the basis of several lines of evidence. (1) PfPCNA2, consisting of 264 amino acid residues with a predicted molecular mass of 30.2kDa, shares only 29% identity and 53% similarity with PfPCNA1 at the amino acid level. (2) Southern blot analyses revealed that the hybridisation pattern of the Pfpcna2 gene is completely different from that of the Pfpcna1 gene. (3) Chromosomal localisation studies showed that Pfpcna2 is located on chromosome 12 while Pfpcna1 is located on chromosome 13. Northern blot analyses revealed two different transcripts of Pfpcna2, one expressed in both asexual and sexual erythrocytic stages, while the other existed only in the sexual stage, implying that PfPCNA2 may play multiple roles in DNA metabolism in different stages of the parasite. Recombinant protein of PfPCNA2, overexpressed in Escherichia coli, has been purified to near homogeneity and shown to form an oligomer, probably a trimer, as revealed by a size-exclusion chromatography and a native gel electrophoresis, suggesting that PfPCNA2, like its higher eukaryotic counterparts, may serve as a sliding platform which is capable of interaction with diverse proteins and regulation of their activities.

Animals↗
PubMed2003

Identification of the beta cell antigen targeted by a prevalent population of pathogenic CD8+ T cells in autoimmune diabetes.

Type 1 diabetes is an autoimmune disease in which autoreactive T cells attack and destroy the insulin-producing pancreatic beta cells. CD8+ T cells are essential for this beta cell destruction, yet their specific antigenic targets are largely unknown. Here, we reveal that the autoantigen targeted by a prevalent population of pathogenic CD8+ T cells in nonobese diabetic mice is islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP). Through tetramer technology, IGRP-reactive T cells are readily detected in islets and peripheral blood directly ex vivo. The human IGRP gene maps to a diabetes susceptibility locus, suggesting that IGRP also may be an antigen for pathogenic T cells in human type 1 diabetes and, thus, a new, potential target for diagnostic and therapeutic approaches.

Animals↗
PubMedDate not supplied

Identification of a lysA-like gene required for tabtoxin biosynthesis and pathogenicity in Pseudomonas syringae pv. tabaci strain PTBR2.024.

Pseudomonas syringae pv. tabaci strain PTBR2.024 produces tabtoxin and causes wildfire disease on tobacco and green bean. PTBR7.000, a Tn5 mutant of PTBR2.024, does not produce tabtoxin, is nonpathogenic on tobacco, and is prototrophic. A 3-kb fragment from a genomic library of the parent strain PTBR2.024 complemented both mutant phenotypes. This 3-kb fragment contains two open reading frames (ORFs), ORF1 and ORF2, and two truncated ORFs, ORF3 and ORF4. The Tn5 insert in PTBR7.000 was mapped to ORF2, and complementation studies showed that an intact ORF2 was sufficient to restore tabtoxin production and pathogenicity. The deduced amino acid sequences of ORF2 and truncated ORF3 contain significant homology to bacterial lysine biosynthetic enzymes, diaminopimelate decarboxylase, and delta 1-piperidine-2,6-dicarboxylate succinyl transferase, respectively. ORF2, however, is not required for lysine biosynthesis. We designated the sequence corresponding to ORF2 as gene tabA and propose that the product of tabA is an enzyme in the tabtoxin biosynthetic pathway that recognizes a substrate analogue of a compound in the lysine biosynthetic pathway.

Acyltransferases↗
PubMed2002

In vivo identification of the mitogen-activated protein kinase cascade as a central pathogenic pathway in experimental mesangioproliferative glomerulonephritis.

Evidence was recently provided for the activation of extracellular signal-regulated kinase (ERK), the best characterized mitogen-activated protein kinase, as an intracellular convergence point for mitogenic stimuli in animal models of glomerulonephritis (GN). In this study, in vivo ERK activity was blocked, with a pharmacologic inhibitor (U0126) of the ERK-activating kinase, in rats with mesangioproliferative GN. After injection of the monoclonal anti-Thy1.1 antibody (OX-7), the rats were treated (days 3 to 6) with low (10 mg/kg body wt) or high (100 mg/kg body wt) doses of U0126 administered intraperitoneally twice daily. On day 6 after induction of the disease, whole cortical tissue and isolated glomeruli were examined by using kinase activity assays, Western blot analyses, and immunohistochemical assays. Treatment with U0126 significantly reduced glomerular stimulation of ERK in anti-Thy1 GN. In the high dose-treated group, this downregulation was accompanied by a reduction in the number of glomerular mitotic figures, back to healthy control levels, and significant decreases in the numbers of total (P < 0.05) and 5-bromo-2'-deoxyuridine-positive (P < 0.05) glomerular cells. Immunohistochemical double-staining of renal sections demonstrated that mesangial cells were the major glomerular targets of U0126 in anti-Thy1 GN. These observations point to ERK as a putative intracellular mediator of the proliferative response in GN and suggest that pharmacologic treatments that interfere with the activation of ERK may be of potential therapeutic interest.

Animals↗
PubMed1995

Identification of a mutation in the pst-phoU operon that reduces pathogenicity of an Escherichia coli strain causing septicemia in pigs.

We used transposon (TnphoA) mutagenesis to study the role of virulence factors of pathogenic Escherichia coli strains associated with septicemia in calves and piglets. We have produced an avirulent and serum-sensitive mutant of wild-type pathogenic strain 5131 O115:K"V165":F165 and have localized and identified the TnphoA insertion in the pstC gene of the pst-phoU operon. This operon encodes the PstSCAB transporter and PhoU protein that negatively regulate the phosphate (Pho) regulon. This mutation is pleiotropic and could have an effect on pathogenicity and on the production of the surface polysaccharides of strain 5131. The mutant demonstrated restored repressibility of alkaline phosphatase and regained the capacity to resist serum and to survive systemically for at least 5 days in experimentally inoculated pigs when complemented with plasmid pAN92, bearing the pst-phoU operon.

Animals↗
PubMed2002

Identification of a quorum-sensing signal molecule in the facultative intracellular pathogen Brucella melitensis.

Brucella melitensis is a gram-negative alpha2-proteobacterium responsible for abortion in goats and for Malta fever in humans. This facultative intracellular pathogen invades and survives within both professional and nonprofessional phagocytes. A dichloromethane extract of spent culture supernatant from B. melitensis induces bioluminescence in an Escherichia coli acyl-homoserine lactone (acyl-HSL) biosensor strain based upon the activity of the LasR protein of Pseudomonas aeruginosa. HPLC fractionation of the extract, followed by mass spectrometry, identified the major active molecule as N-dodecanoylhomoserine lactone (C12-HSL). This is the first report of the production of an acyl-HSL by an intracellular pathogen. The addition of synthetic C12-HSL to an early log phase culture of either B. melitensis or Brucella suis 1330 reduces the transcription of the virB operon, which contains virulence genes known to be required for intracellular survival. This mimics events seen during the stationary phase of growth and suggests that quorum sensing may play a role in the control of virulence in Brucella.

4-Butyrolactone↗