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PubMed2002

Efficacy of single-dose dexamethasone as adjuvant therapy for acute pharyngitis.

HYPOTHESIS: Pharyngeal inflammatory pain is reduced by a single dose of dexamethasone. STUDY DESIGN: Prospective, randomized, double-blinded, placebo-controlled study. METHODS: From August 1998 to July 2000, a total of 118 patients were enrolled. We compared placebo (n = 37), a 10-mg single dose of intramuscular injection of dexamethasone (n = 39), and a 10-mg single dose of oral dexamethasone (n = 42). All patients were given oral antibiotics and had bacterial throat cultures. RESULTS: Complete telephone follow-up 12 hours after treatment was available in 111 patients, and 24-hour follow-up data were available in 116. The change in pain visual analogue scale scores (pretreatment score minus 12-h follow-up score) reported by patients who were given either intramuscular (median score, 4; mean score +/- SD, 4.2 +/- 2.3) or oral dexamethasone (median score, 3; mean score +/- SD, 3.8 +/- 2.3) was significantly greater than that of the patients who were given placebo (median score, 2; mean score +/- SD, 2.1 +/- 2.0) (P <.001 and P =.002, respectively). This difference in improvement was also evident when the percentage of change was compared in the three treatment arms at 12-hour and 24-hour follow-up. Patients who were given dexamethasone had the onset of pain relief a median of 4 hours earlier than those who were given oral and intramuscular placebo (P =.029). Statistically significant differences among the three treatment arms were confirmed when a bacterial pathogen was identified (n = 47) but not in a subset that did not have a pathogen identified. CONCLUSIONS: Single-dose dexamethasone appears to be a safe, effective, and inexpensive adjunctive treatment for acute pharyngitis in patients 15 years of age and older. Patients treated with intramuscular or oral dexamethasone had significant relief of pain (relative to baseline) compared with patients who were given placebo. Identification of a bacterial pathogen had a significant impact on the response to dexamethasone.

Acute Disease↗
PubMed2003

Pathogenicity islands and phages in Vibrio cholerae evolution.

The identification of accessory genetic elements (plasmids, phages and chromosomal 'pathogenicity islands') encoding virulence-associated genes has facilitated our efforts to understand the origination of pathogenic microorganisms. Toxigenic Vibrio cholerae, the etiologic agent of cholera, represents a paradigm for this process in that this organism evolved from environmental nonpathogenic V. cholerae by acquisition of virulence genes. The major virulence genes in V. cholerae, which are clustered in several chromosomal regions, appear to have been recently acquired from phages or through undefined horizontal gene transfer events. Evidence is accumulating that the interactions of phages with each other can also influence the emergence of pathogenic clones of V. cholerae. Therefore, to track the evolution of pathogens from their nonpathogenic progenitors, it is also crucial to identify and characterize secondary genetic elements that mediate lateral transfer of virulence genes in trans. Understanding the evolutionary events that lead to the emergence of pathogenic clones might provide new approaches to the control of cholera and other infectious diseases.

Biological Evolution↗
PubMed2000

Reduction of endogenous bacteria associated with catfish fillets using the Grovac process.

Fresh catfish (Ictalurus punctatus) fillets are known to be contaminated with a large number of spoilage and pathogenic bacteria. The Grovac method, a new patented (U.S. 5,543,163) process, was evaluated for its efficacy in reducing the number of pathogens and spoilage microorganisms associated with food. This process involves using a processing solution containing ascorbic acid (AA) and sodium chloride (NaCl), vacuum, and tumbling. A total of 51 bacterial isolates were isolated and identified from whole catfish and catfish fillets using both selective and nonselective media, phenotypic tests, and the Vitek identification system. Psychrotrophic foodborne pathogens included: Aeromonas hydrophila, Escherichia coli, Listeria sp., Plesiomonas shigelloides, Proteus sp., Staphylococcus aureus, and Vibrio parahaemolyticus. High aerobic plate counts (2.6 x 10(7) CFU/g) for catfish fillets indicated that fillets were heavily contaminated during processing of catfish. The Grovac process showed that various treatment combinations of AA and NaCl resulted in a 1.2 to 2.3 CFU/g log reduction of microbial counts associated with catfish fillets. The effectiveness of the process may be related to the synergistic effect of tumbling, AA, NaCl, and vacuum. These results suggested that the Grovac process could be used as an alternative processing procedure to reduce microbial populations associated with catfish fillets and may be useful to improve the shelf-life and food safety of the product. Microbiological data from this study will be used for the development of a hazard analysis for the implementation of the hazard analysis critical control point program for processed catfish fillets.

Animals↗
PubMed2003

[A case of inactive Escherichia coli isolated from feces initially suspected to be Shigella boydii subgroup C serotype 14 by conventional biochemical tests in tubes].

A small number of colorless colonies grew from DHL agar of feces culture taken as part of a complete physical for a 42 year-old woman who had lived in Singapore for several years. When cultured for first-stage identification using conventional biochemical tests in tubes for Enterobacteriaceae, such as TSI agar slant and SIM medium, the results for lactose reaction (-), saccharose reaction (-), gas (very weak +) and motility (-) were obtained, and Shigella spp. was suspected. Serological tests (by serotype) for Shigella spp. were then conducted. As a result, clear C14 agglutination was observed. Based on these results, the isolate was strongly suspected to be Shigella boydii serotype 14, but since the woman had no symptoms of abdominal pain, diarrhea or fever, such identification was still questionable. When further identification test was carried out using Walk-Away 96 and VITEK 2, non-Shigella spp. identification results were obtained. In second-stage identification, xylolytic activity, acetate salt utilization and use of carbon sources in CA (citrate-acetate) medium were checked, all results were positive, and the isolate was ultimately identified as Inactive Escherichia coli. While Shigella spp. and E. coli are taxonomically similar, they are quite different from each other in terms of pathogenicity. Accurate and rapid identification of Shigella spp. is therefore important.

Adult↗
PubMed2006

Direct identification of bacteria in clinical respiratory samples using fluorescent amplicon length analysis of 16S-23S rRNA spacer-region.

We describe the development and application of a rapid and universal molecular technique for direct identification of multiple bacteria in clinical samples. Amplification of the 16S-23S rRNA spacer-region using universal primers led to fragment patterns distinct for different bacterial species and that were analyzed with fluorescent amplicon length analysis (FALA). 136 pure cultures of clinical isolates and 20 culture collection strains belonging to 22 different medically important species were used to create a primary database of fragments with sizes between 100 and 1000 bp. Subsequently, 127 respiratory samples were analyzed with culture-based techniques and via FALA of the 16S-23S rRNA spacer-region. Two DNA extraction methods were evaluated: Instagene (FALA-I) and Fastprept (FALA-P). Of the 127 samples, 26 culture-negative samples were also negative with FALA-P. Of 18 samples with growth of commensal oral flora, 10 gave a mixed oral flora pattern with FALA-P and 8 gave a negative result. For 54 samples with growth of a single bacterial species, FALA-P gave an identical result for 46. For 29 samples with growth of more than one bacterial species, identical results were obtained in 19 samples. False-negative results with FALA-P were mostly due to paucity (less than 10(3) CFU/ml) of bacteria (12 out of 18 false-negatives) or difficulties with homogenization of viscous samples (6 out of 18 false-negatives).With regard to identification of all significant pathogens of clinical samples tested, the sensitivity of FALA-P was 77% and its specificity was 100%. With FALA-I, the number of false-negative results was higher than with FALA-P due to less efficient extraction of DNA, particularly with Staphylococcal species. FALA-P allows rapid and direct identification of multiple species directly from clinical samples; pauci-cellular samples may give false-negative results.

Bacteria↗
PubMed2005

A new amplification target for PCR-RFLP detection and identification of Chlamydiaceae species.

The family Chlamydiaceae contains nine species pathogenic to humans and animals, but their routine identification is hampered by inadequate detection methods. In an attempt to find a new region for PCR detection and discrimination of the Chlamydiaceae species, the 3' end of the omp2 gene of Chlamydiaceae has been examined. Since sequence data for this part of the genes of Chlamydophila felis and Chlamydia suis had not been available, the near full length of the omp2 genes of these species were cloned and sequenced. Consensus primers enabling amplification of a previously untargeted region spanning 1,030 bp at the 3' end of the gene were designed. Discrimination of all nine Chlamydiaceae species was achieved via RFLP analysis of the amplicons with RsaI and HinfI or RsaI and TaqI endonucleases or via electrophoretic mobility analysis of the RsaI restriction fragments in agarose gel with bisbenzimide-PEG. Intraspecies uniformity of the RFLP patterns was evaluated by the typing of reference strains, isolates of human and animal origin from culture collections, and clinical specimens, and by computer analysis of GenBank sequences. The 3' end of the omp2 gene was shown to be an appropriate marker region suitable for rapid identification of Chlamydiaceae species and can be used for characterization of collection strains and new isolates in taxonomic, epidemiological, and clinical purposes.

Bacterial Outer Membrane Proteins↗
PubMed2026

ECLIPSE: exploring the dark proteome of ESKAPE pathogens through the sequence similarity network of the Protein Universe Atlas.

MOTIVATION: The accelerating crisis of antimicrobial resistance among the critical so-called ESKAPE pathogens demands the urgent identification of novel molecular targets. However, a substantial fraction of ESKAPE proteomes remains functionally uncharacterized, with many genes annotated as encoding hypothetical proteins. These protein sequences often lack significant similarity to known protein families when conventional homology-based annotation methods are used and thus remain "dark". This limits our ability to explore their roles in pathogenicity, and it is thus crucial to bridge this substantial gap in pathogen biology by developing new strategies to illuminate these "dark" regions of the ESKAPE pan-proteome. RESULTS: We introduce ECLIPSE (ESKAPE Connectome Linkage and Inference for Proteome Sequence Exploration), a network-based computational framework that systematically identifies and prioritizes functionally dark protein families in ESKAPE pan-proteomes. ECLIPSE embeds target ESKAPE pathogen proteomes within the global sequence similarity network of the Protein Universe Atlas. It detects connected components composed entirely of unannotated proteins, called the "dark proteome." As a case study, we applied ECLIPSE to a pan-proteome of 3&#x2006;460&#x2006;657 protein sequences from 635 strains of Pseudomonas aeruginosa (PA). ECLIPSE identified 120&#x2006;985 proteins (4%) residing in completely dark connected components. Furthermore, we have performed a taxonomic diversity analysis using normalized Shannon indices to characterize each dark component by its enrichment in ESKAPE pathogens. The analysis utilized the evenness (E) value (see Methods 2.1), which distinguishes Pseudomonas-specific (target-specific) from ESKAPE-enriched dark components. We then developed the Dark Proteome Prioritization Score (DPPS), a composite multidimensional scoring framework (see Methods 2.5). It ranks these dark components by biological relevance across four orthogonal axes: (i) functional darkness, (ii) P. aeruginosa proportion in the Atlas, (iii) AMR-clade taxonomic restriction, and (iv) conservation across the 635 P. aeruginosa strains. This framework outputs a robust four-tier scoring system; the prioritized Tier I components were validated by weight sensitivity analysis and remained stable across 500 Monte Carlo weight perturbations. Structural characterization of one of the top-ranked ESKAPE-enriched dark components revealed that it belongs to the beta-barrel fold DUF1302 (PF06980) family, for which no experimentally solved three-dimensional structure exists in the PDB. The genomic context analysis indicates that it is co-localized with a LuxR-type transcriptional regulator. Collectively, ECLIPSE identifies evolutionarily conserved, structurally defined, and functionally dark proteins enriched across ESKAPE pathogens; these dark proteins can further be utilized as alternative antimicrobial targets for experimental characterization. AVAILABILITY AND IMPLEMENTATION: The source code and dataset are available for free at: Github: https://github.com/surabhilata/ECLIPSE.git, Zenodo: DOI: 10.5281/zenodo.21064323.

Proteome↗
PubMed1998

Prevalence of viral and bacterial sexually transmitted pathogens in Jamaican pregnant women.

In this study we investigated the prevalence of Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, human immunodeficiency virus type I (HIV-I), human T cell lymphotropic virus type 1 (HTLV-1) and hepatitis B virus (HBV) infections in 200 pregnant women attending antenatal clinics at the University Hospital of the West Indies. 19% of the women had at least one pathogen: C. trachomatis was found in 16%, HTLV-1 in 2%, HIV-1, HBV and N. gonorrhoeae each in 0.5% C. trachomatis infection was more prevalent in women less than 20 years of age (31%) than in those 20 years and older (16%; OR = 0.43; chi 2 = 5.66; p < 0.05). The study demonstrates the need for identification of sexually transmitted pathogens in antenatal women for syndromic management of genital infections as part of the strategy for prevention and control of HIV/AIDS (acquired immunodeficiency syndrome) in Jamaica.

Adolescent↗
PubMed2004

Applications of single-molecule detection to the analysis of pathogenic DNA.

We have devised a new technique based on single fluorescent molecule detection for the analysis of specific sequences of DNA. The method consists of synthesizing a fluorescent reporter molecule using a polymerase extension reaction and labeled nucleotides. The fluorescent reporter products are analyzed in a laser-based single-molecule detection system. We have applied this method to the detection of pUC19 and Bacillus anthracis DNA targets. We expect that this method will have applications in rapid detection and identification of DNA from pathogens as well as other sources, and that it will be used for processing of large number of samples in a short period of time.

Bacillus anthracis↗
PubMed2001

[Nosocomial pneumonia].

Nosocomial pneumonia is a frequent complication, particularly during mechanical ventilation. Microbial patterns differ according to the time of onset: whereas early onset pneumonia (up to the fourth day of hospitalization) is mostly caused by Staphylococcus aureus, Streptococcus pneumoniae and Haemophilus influenzae, leading pathogens of late onset pneumonia (after the fourth day) additionally include gram-negative Enterobacteriaceae and potentially drug resistant microorganisms. These general patterns are modified in the presence of specific individual risk factors. The diagnostic work-up of pneumonia is aimed at the assessment of severity, the confirmation of the presence of pneumonia as well as the identification of the causal pathogens. The results of microbiological investigations must always be interpreted in the clinical context. Antimicrobial treatment must always be initiated empirically based on expected microbial patterns as outlined above. Nosocomial pneumonia in nonventilated and ventilated patients requires different empirical antimicrobial treatment approaches. All patients with antimicrobial treatment failures must be comprehensively reevaluated.

Anti-Bacterial Agents↗
PubMed2001

Experimental allergic encephalomyelitis in the New World monkey Callithrix jacchus.

Models that adequately reflect the complexity of human multiple sclerosis (MS) are needed, especially for preclinical testing of immunomodulatory drugs. Our group has created a unique experimental system in a New World outbred primate, the common marmoset Callithrix jacchus (C. jacchus). Following immunization with myelin, these monkeys develop a chronic, relapsing-remitting form of experimental allergic encephalomyelitis (EAE), which pathologically recapitulates the hallmark features of lesions of human MS. The MS-like lesion in C. jacchus results from a complex immune response against myelin antigens and requires both T cells and pathogenic antibodies. Studies of C. jacchus EAE have permitted the identification of a major target for pathogenic autoantibodies in MS, the myelin/oligodendrocyte glycoprotein. Other advantages of the model include a natural bone-marrow chimerism, which permits T-cell adoptive transfers between siblings, and the possibility of using different antigens to produce either inflammatory or demyelinating phenotypes of EAE. Despite their small size, sequential in vivo imaging and immunological studies are possible in these monkeys, and have been used to monitor efficacy in preclinical trials. Due to close phylogeny and high homology of immune and nervous system genes with humans, this model should fast-track the development of novel therapeutics for MS.

Animals↗
PubMed2005

No correlation between clinical symptoms and Blastocystis hominis in immunocompetent individuals.

UNLABELLED: Abstract Background and Aim: Previous reports regarding the clinical significance and pathogenicity of Blastocystis hominis have been contradictory. The aim of this study was to examine the association between Blastocystis and gastrointestinal symptoms in immunocompetent individuals. METHODS: We monitored over 2800 healthy people for a period of 15 months, and took stool specimens during both asymptomatic periods and during periods of gastrointestinal symptoms. RESULTS: After exclusion of individuals who had simultaneous identification of other fecal pathogens, we compared the proportions of asymptomatic versus symptomatic individuals positive for Blastocystis and found no significant difference (P = 0.5). Symptom status did not correlate with parasite abundance. We found that some individuals were likely to have Blastocystis detected during both asymptomatic and symptomatic periods, possibly suggesting carriage of the organism. CONCLUSION: In conclusion, we found no correlation between clinical symptoms and the presence or absence of Blastocystis among this healthy cohort.

Adolescent↗
PubMed2001

Molecular pathogenesis of pneumococcal pneumonia.

The past two decades have witnessed an explosion of data on the molecular pathogenesis of pneumonia caused by Streptococcus pneumoniae, one of the most important pathogens currently plaguing man. Identification and functional analysis of genes and their proteins, elucidation of mechanisms involved in adherence, colonization, inflammation, and invasion, and an understanding of interactions with the host and with external factors have provided knowledge that can be used to attack this organism with small molecule or vaccine based strategies. Study of the pneumococcus has also led to insights into other pathogens that share a unique spectrum of respiratory disease. In this review we will discuss recent advances in our understanding of the pathogenesis of pneumonia due to S. pneumoniae, highlighting emerging themes common to other organisms such as Haemophilus influenzae and Neisseria meningitidis.

Bacterial Adhesion↗
PubMedDate not supplied

Maximizing the usefulness of food microbiology research.

Funding for food microbiology research often follows disease outbreaks: botulism from vacuum-packed white-fish chubs, listeriosis from soft cheeses, or illness due to Salmonella Enteritidis or Escherichia coli. As a consequence of research, detection, identification, and subtyping methods improve, and more is learned about pathogenicity and virulence. Research also explores the organisms' capacity to multiply or survive in food and to be killed by established or novel processes. However, rarely is there a critical overview of progress or trustworthy statements of generally agreed-on facts. That information is not maintained in a form that can readily be used by regulatory departments and the food industry to ensure a safe food supply. A centralized system is urgently needed that is accessible electronically and carries information in a standardized format on the essential properties of the organisms, including pathogenicity, methods of detection, enumeration and identification, alternative prevention and control methods, and growth and survival characteristics.

Food Microbiology↗
PubMed2003

Prevalence of potentially pathogenic fungi in the bathing sites of the Sulejów Reservoir.

Progressive degradation of water ecosystems may contribute to the propagation of fungi pathogenic to humans and animals. The aim of this study was a quantitative evaluation and identification of species of potentially pathogenic fungi in the littoral zone of the Sulejów Reservoir used as recreation site. We studied samples of surface water and sediments collected from 6 sampling sites of the reservoir in the years 2000 and 2001. In 2000, fungi were isolated from 82.7% of samples, while in 2001 from as many as 95.4%. There were 28 species representing genera: Candida, Cryptococcus, Geotrichum, Kloeckera, Rhodotorula, Saccharomyces, and Trichosporon. The most common species were Rhodotorula glutinis and Candida guilliermondii. The density of the population of identified species depended on the season and sampling site and ranged from 80 to 328000 cells/dm3 (also uncountable growth). The waters of the Sulejów Reservoir may be a covenient place of anamorphic developmental forms, for the 15 cultured species which can also propagate in humans and other mammals.

Bathing Beaches↗
PubMed1989

Phenotypic and genomic studies of "Cytophaga psychrophila" isolated from diseased rainbow trout (Oncorhynchus mykiss) in France.

Five strains of gliding bacteria were isolated in France from farmed diseased rainbow trouts reared at low water temperature. The resemblance of these bacteria to the known fish pathogen "Cytophaga psychrophila" led to their comparative study with reference strain NCMB 1947 and with an American isolate. Morphological, physiological, and biochemical characteristics of the seven strains proved to be similar. Comparison of their DNA by the S1 nuclease DNA-DNA hybridization method showed that the seven strains formed a tight genomic species with DNA relatedness above 90%. This is the first identification of this fish pathogen in a European country. The main phenotypic characteristics differentiating this bacterium from other nonpathogenic gliding bacteria of fish origin include a poor gliding movement, yellow compact or weakly rhizoid colonies on solid media, and the presence of flexirubin-type pigments. The inability to metabolize any carbohydrates, the strong proteolytic activity, the absence of growth in more than 0.5% NaCl, and the tolerance to a maximum temperature of 25 degrees C are also useful characteristics of this group of bacteria.

Animals↗
PubMed2003

Emerging opportunistic fungal infections: where are we heading?

Medical mycology involves the study of pathogenic fungi and their identification in the laboratory. Mycology has developed into a field that demands the attention of all clinicians treating patients in hospitals. Interest in medical mycology has grown in recent years due to a dramatic rise in the rates of fungal infections. An overview of well-known medically significant opportunistic fungi, such as Candida, Cryptococcus, Aspergillus and Zygomycetes, as well as emerging fungal pathogens, are discussed. Antifungal failures in these individuals are high; consequently, mortality rates are also high, despite standard therapy with amphotericin-B, lipid-associated formulation of amphotericin-B and the azoles. This underscores the need for new approaches and therapies to improve outcomes in high-risk individuals.

AIDS-Related Opportunistic Infections↗
PubMed2002

Phylogenetic analysis of Prevotella nigrescens, Prevotella intermedia and Porphyromonas gingivalis clinical strains reveals a clear species clustering.

Prevotella nigrescens, Prevotella intermedia and Porphyromonas gingivalis are oral pathogens from the family Bacteroidaceae, regularly isolated from cases of gingivitis and periodontitis. In this study, the phylogenetic variability of these three bacterial species was investigated by means of 16S rRNA (rrs) gene sequence comparisons of a set of epidemiologically and geographically diverse isolates. For each of the three species, the rrs gene sequences of 11 clinical isolates as well as the corresponding type strains was determined. Comparison of all rrs sequences obtained with those of closely related species revealed a clear clustering of species, with only a little intraspecies variability but a clear difference in the rrs gene with respect to the next related taxon. The results indicate that the three species form stable, homogeneous genetic groups, which favours an rrs-based species identification of these oral pathogens. This is especially useful given the 7% sequence divergence between Prevotella intermedia and Prevotella nigrescens, since phenotypic distinction between the two Prevotella species is inconsistent or involves techniques not applicable in routine identification.

Bacteroidaceae Infections↗