SEARCH · Search PubMed

Results for “pathogen identification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 541 records · Page 30Linked to original sources

PubMed1982

Application of flow cytometry to studies of pathogenic free-living amoebae.

Species of small, free-living amoebae of the genera Naegleria and Acanthamoeba can cause fatal amoebic meningoencephalitis. Previous investigations have shown that pathogenic amoebae are associated with thermally altered water. Flow cytometric techniques for identifying species of pathogenic and nonpathogenic amoebae from such water have been developed, using immunofluorescence and fluorescein-bound concanavalin A. Flow cytometry is accomplished with a cytofluorograph, in which cells are dispersed in a suspended carrier liquid and passed in front of a focused argon ion laser beam. Cells are then distinguished by the degree of scattered light (size) or fluorescence. Flow cytometry techniques have proven efficient for environmental samples, as indicated by the identification of pathogenic Naegleria fowleri and nonpathogenic Naegleri gruberi and Acanthamoeba castellanii isolated from the Savannah River Plant in South Carolina. Cytofluorographic analysis of environmental samples has several advantages over the current methods of isolation and classification of free-living amoebae. With this system, it is possible to rapidly identify species and quantitate mixtures of pathogenic amoebae in environmental samples. Cytofluorographic analysis of amoebic isolates reduces the time presently required to screen environmental sites for pathogenic amoebae. The cytofluorograph permits detection and species identification of nonthermophilic Naegleria spp. and Acanthamoeba spp. that could not easily be isolated for species identification by conventional methods. Other advantages of flow cytometry over fluorescent microscopy include a high degree of statistical precision due to the large numbers measured, high immunofluorescent titers, and elimination of subjectivity and fluorescence fading.

Agglutination Tests↗

PubMed2006

Proteomic survey of the pathogenic Mycoplasma hyopneumoniae strain 7448 and identification of novel post-translationally modified and antigenic proteins.

Mycoplasma hyopneumoniae is an important pathogen for pigs, being the causative agent of enzootic pneumonia. Recently, the genome sequences of three strains, J, 7448 and 232 have been reported. Here, we describe the results of a proteomic analysis, based on two-dimensional gel electrophoresis of soluble protein extracts, immunoblot and mass spectrometry, which was carried out aiming the identification of gene products and antigenic proteins from the M. hyopneumoniae pathogenic strain 7448. A preliminary M. hyopneumoniae proteome map in two pH ranges (3-10 and 4-7) was produced. A total of 31 different coding DNA sequences (CDSs), including three hypothetical ones, were experimentally verified with the identification of the corresponding protein products by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. According to the Clusters of Orthologous Groups (COG) functional classification, the identified proteins were assigned to the groups of metabolism (13), cellular processes (5) and information and storage processing (4). Nine of the identified proteins were not classifiable by COG, including some related to cytoadherence and possibly involved in pathogenicity. Moreover, at least five highly antigenic proteins of M. hyopneumoniae were identified by immunoblots, including four novel ones (a heat shock protein 70, an elongation factor Tu, a pyruvate dehydrogenase E1-beta subunit and the P76 membrane protein). The now available proteome map is expected to serve as a reference for comparative analyses between M. hyopneumoniae pathogenic and non-pathogenic strains, and for methabolic studies based on cells cultured under modified conditions.

Animals↗

PubMed2000

Raman spectroscopic method for identification of clinically relevant microorganisms growing on solid culture medium.

Routine clinical microbiological identification of pathogenic microorganisms is largely based on nutritional and biochemical tests. In the case of severely ill patients, the unavoidable time delay associated with such identification procedures can be fatal. We present a novel identification method based on confocal Raman microspectroscopy. With this approach it is possible to obtain Raman spectra directly from microbial microcolonies on the solid culture medium, which have developed after only 6 h of culturing for the most commonly encountered organisms. Due to the limited thickness of microcolonies, some of the underlying culture medium is sampled together with the bacteria. Spectra measured at different depths in a microcolony contain different amounts of the medium signal. A mathematical routine, involving vector algebra, is described for the nonsubjective correction of spectra for variable signal contributions of the medium. To illustrate the possibilities of our approach for the identification of microorganisms, Raman spectra were collected from 6-h microcolonies of five bacterial strains on solid culture medium. The classification results show that confocal Raman microspectroscopy has great potential as a powerful new tool in clinical diagnostic microbiology.

Bacteriological Techniques↗

PubMed2005

Taxonomy and pathogenesis of the Burkholderia cepacia complex.

Patients with cystic fibrosis (CF) are susceptible to chronic respiratory infection with a number of bacterial pathogens. The Burkholderia cepacia complex bacteria are problematic CF pathogens because (i) they are very resistant to antibiotics, making respiratory infection difficult to treat and eradicate; (ii) infection with these bacteria is associated with high mortality in CF; (iii) they may spread from one CF patient to another, leading to considerable problems for both patients and carers; and (iv) B. cepacia complex bacteria are difficult to identify and nine new species have now been found to constitute isolates originally identified as 'B. cepacia' based on their phenotypic properties. Here we review the changes that have occurred in the taxonomy of the B. cepacia complex and the pathogenic factors these bacteria possess. While the taxonomy of the B. cepacia complex has advanced considerably with the development of accurate methods for their identification, the pathogenic mechanisms employed by these CF pathogens are only just beginning to be explored at the molecular level. Several virulence factors have been defined for B. cenocepacia (the dominant CF pathogen within the complex); however, knowledge of the disease mechanisms employed by other B. cepacia complex species is limited. The recent determination of the complete genome sequences for several of the B. cepacia complex species should greatly enhance our ability to study these problematic CF pathogens.

Burkholderia Infections↗

PubMed2003

Molecular approaches to the identification and treatment monitoring of periodontal pathogens.

Two different PCR-based molecular approaches, a commercial kit for detection of A. actinomycetemcomitans, P. gingivalis, P. intermedia, B. forsythus and T. denticola (Amplimedical "Paradonthosis") and a home-made multiplex PCR for A. actinomycetemcomitans, P. gingivalis and B. forsythus were compared for monitoring the efficacy of different dental treatments on localized persistent periodontal pockets. 44 sites were randomized in two treatment groups: mechanical treatment (22 control sites) and in conjunction with the application of tetracycline fibres (22 experimental sites). 40/44 sites were found positive with both tests for A. actinomycetemcomitans, P. gingivalis and B. forsythus pretheraphy. P. intermedia was detected alone in only three sites during the follow-up, while T. denticola. was always associated with the other pathogens. 20 sites were positive in conventional cultures for one to three of the pathogens. PCR-based approaches provided a sensitive and reliable method for identification and monitoring treatment of periodontal pathogens.

Actinobacillus Infections↗

PubMed2001

Identification of a novel pathogen-responsive element in the promoter of the tobacco gene HSR203J, a molecular marker of the hypersensitive response.

The tobacco gene, HSR203J, which is specifically activated during the early steps of incompatible plant/pathogen interactions has been shown to be a molecular marker of the hypersensitive response (HR). It constitutes an ideal model for the identification of HR-responsive cis-regulatory elements. As a first step in the promoter dissection, deletion mutants of the 5' flanking sequence of HSR203J fused to the GUS reporter gene were analyzed. Then, the construction and study of chimeric constructs containing HSR203J promoter fragments fused to a minimal promoter enabled us to identify a 28-bp regulatory element located between -106 and -79 upstream of the transcription initiation site. This element has been shown to be necessary and sufficient for transcriptional activation in response to pathogen. It contains a 10-bp palindrome followed by its imperfect repeat. The mutagenesis of these two sequence elements led to the identification of a 12-bp motif termed HSRE (HSR203 responsive element) responsible for the marked induction of the HSR203J gene during the HR. Since this DNA region did not show any homology with known regulatory sequences, this 12 bp motif corresponds to a novel cis-regulatory element.

Base Sequence↗

PubMed2006

Viral meningitis.

Viruses probably account for most cases of acute meningitis. Viral meningitis is often assumed to be a largely benign disease. For the commonest pathogens causing meningitis, enteroviruses, this is usually the case; however, for many of the other pathogens causing viral meningitis, and for common pathogens in the immunocompromised or infants, viral meningitis is frequently associated with substantial neurological complications and a significant mortality. Diagnostic methods for rapid and accurate identification of pathogens have improved over recent years, permitting more precise and earlier diagnoses. There have been fewer developments in therapies for viral meningitis, and there remain no effective therapies for most pathogens, emphasising the importance of prevention and early diagnosis. This review focuses on the presentation, diagnosis and management of viral meningitis and also covers the prevention of meningitis for pathogens where effective vaccines are available.

Antiviral Agents↗

PubMed1999

Molecular detection of pathogen DNA in ticks (Acari: Ixodidae): a review.

Ticks play an important role in human and veterinary medicine, in particular due to their ability to transmit a wide spectrum of pathogenic micro-organisms of protozoal, rickettsial, bacterial and viral origin. Pathogens in ticks can be identified by conventional methods such as indirect immunofluorescence, isolation in cell culture or by using histological staining techniques. However, the advent of the polymerase chain reaction (PCR) has resulted in tremendous improvements in the specific and sensitive detection of pathogen DNA in ticks. In this paper, literature on DNA extraction methods, PCR protocols, primers and probes, which are in use for the successful detection and identification of pathogens in ticks, are critically reviewed. Some recommendations are also given towards the end of this review.

Anaplasma↗

PubMed2006

The pathogen-host interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity.

Fungal and oomycete pathogens of plants and animals are a major global problem. In the last 15 years, many genes required for pathogenesis have been determined for over 50 different species. Other studies have characterized effector genes (previously termed avirulence genes) required to activate host responses. By studying these types of pathogen genes, novel targets for control can be revealed. In this report, we describe the Pathogen-Host Interactions database (PHI-base), which systematically compiles such pathogenicity genes involved in pathogen-host interactions. Here, we focus on the biology that underlies this computational resource: the nature of pathogen-host interactions, the experimental methods that exist for the characterization of such pathogen-host interactions as well as the available computational resources. Based on the data, we review and analyze the specific functions of pathogenicity genes, the host-specific nature of pathogenicity and virulence genes, and the generic mechanisms of effectors that trigger plant responses. We further discuss the utilization of PHI-base for the computational identification of pathogenicity genes through comparative genomics. In this context, the importance of standardizing pathogenicity assays as well as integrating databases to aid comparative genomics is discussed.

Computational Biology↗

PubMedDate not supplied

[Joint effort to improve quality in a Brazilian pediatric public hospital through cross-infection control]

OBJECTIVES: To examine the role of the laboratory in nosocomial infection control from January 1993 to December 1996 in Centro Geral de Pediatria of Hospital Foundation of Minas Gerais state. METHODS: Follow -up of 101,139 patient-days (11,147 discharges + deaths + transfers) in the wards and intensive care unit by using the National Nosocomial Infection Surveillance (NNIS) system proposed by the Centers for Disease Control and Prevention (CDC- Atlanta). Prospective surveillance of nosocomial infections at all sites was performed according to the hospital - wide (since 1992) and intensive care unit (since 1996) NNIS components. The CDC definitions since 1988 and Brazilian Ministry of Health regulation number 930 since 1992 were used to diagnose the nosocomial infections. RESULTS: The five most frequent nosocomial pathogens (from a total of 139 isolates) were Klebsiella sp = 24.5%; S. aureus = 18%; P. aeruginosa = 13.7%; E. coli = 12.9%; S. epidermidis = 12.2%. The percentage of identification of pathogens isolated from nosocomial infection sites has increased from 6.2% in 1993 to 13.3% in 1995 and 28.2% in 1996 (p< 0.001) and so has the attempt to isolate the pathogens: 7.5% in 1993, 16.1% in 1995, 33.8% in 1996 (p< 0.001). The time interval taken for lab results (from specimen collected to microbiology result) has decreased from the average of ten days in 1993 to six days in 1996 (p = 0.001). CONCLUSIONS: The continuing education and improved communication among infection control personnel, pediatricians, surgeons and members of the laboratory have proven to play a key role in the epidemiology of nosocomial infections by defining their etiologies in the Centro Geral de Pediatria. A task force to determine the microbiology has been achieved by the understanding of all clinicians that it is important to treat their patients specifically. The NNIS method applied to Brazilian hospitals has shown its impact on the microbiology lab role in nosocomial infection control as well.

Journal Article↗

PubMed2004

Use of DNA microarrays for rapid genotyping of TEM beta-lactamases that confer resistance.

Standard clinical procedures for pathogen resistance identification are laborious and usually require 2 days of cultivation before the resistance can be determined unequivocally. In contrast, clinicians and patients face increasing threats from antibiotic-resistant pathogenic bacteria in terms of their frequencies and levels of resistance. A major class of microbial resistance stems from the occurrence of beta-lactamases, which, if mutated, can cause the severe extended-spectrum beta-lactamase (ESBL) or inhibitor-resistant TEM (IRT) phenotype, which cause resistance to extended-spectrum cephalosporins, monobactams, and beta-lactamase inhibitors. We describe an oligonucleotide microarray for identification of the single nucleotide polymorphisms (SNPs) of 96% of the TEM beta-lactamase variants described to date which are related to the ESBL and/or IRT phenotype. The target DNA, originating from Escherichia coli, Enterobacter cloacae, and Klebsiella pneumoniae cells isolated from clinical samples, was amplified and fluorescently labeled by PCR with consensus primers in the presence of cyanine 5-labeled nucleotides. The total assay, including PCR, hybridization, and image analysis, could be performed in 3.5 h. The microarray results were validated by standard clinical procedures. The microarray outperformed the standard procedures in terms of assay time and the depth of information provided. In conclusion, this array offers an attractive option for the identification and epidemiologic monitoring of TEM beta-lactamases in the routine clinical diagnostic laboratory.

Base Sequence↗

PubMedDate not supplied

Rapid ribosequencing--an effective diagnostic tool for detecting microbial infection.

BACKGROUND: Rapid and reliable identification of microorganisms is a prerequisite for the diagnosis and subsequent treatment of infectious diseases. The identification of pathogenic bacteria is traditionally based on their isolation from clinical samples and propagation on culture medium in the routine laboratory. However, despite clinical signs of infection, culture of the pathogenic agent often fails. This may be due to a low number of microorganisms, prior antibiotic treatment, nonculturable microorganisms or specific culture requirements for presently unknown pathogens. Amplification and sequencing of the entire prokaryotic 16S-rRNA is time consuming, labor intensive and expensive. MATERIALS AND METHODS: We describe here a procedure for the identification of a wide range of known and unknown clinically relevant microorganisms by sequencing a small, but highly informative region of the prokaryotic 16S-rRNA gene. This rapid ribosequencing method was evaluated with various reference strains and with clinical samples including eye anterior chamber fluid, cerebrospinal fluid (CSF) and blood cultures. RESULTS: All sequences obtained from the reference strains corresponded to the sequences in databases. We correlated severe eye infection with the isolation of Pseudomonas putida, neurological disorder with Tropheryma whippelii and disseminated visceral abscesses in a child with Blastobacter denitrificans. CONCLUSION: We consider the rapid ribosequencing method as a promising new tool for the analysis of infectious agents in primarily sterile body fluids where conventional culturing of microorganisms fails.

Bacteria↗

PubMed2026

Long-read sequencing reveals a hidden Alu-mediated splice defect in CPLANE1, causing orofaciodigital syndrome type VI.

Orofaciodigital syndrome type VI (OFD VI) is a recessive ciliopathy characterized by excessive polydactyly, molar tooth sign, cleft lip, and developmental delay, caused by pathogenic variants in CPLANE1. Here, we present a patient with OFD VI that remained genetically unexplained after routine genetic testing, including short-read whole genome sequencing (WGS). Using long-read sequencing, we found two biallelic splice-site variants in CPLANE1, c.8633-4_8633-3del, and an Alu element insertion close to an exon-intron boundary. Transcript analysis showed that each variant independently resulted in exon skipping, and quantitative expression studies revealed reduced total CPLANE1 mRNA levels in patient-derived fibroblasts. Based on these findings, we were able to re-classify the c.8633-4_8633-3del variant from a variant of uncertain significance (VUS) to likely pathogenic. The identification of an Alu element insertion missed by short-read WGS highlights the added diagnostic value of long-read sequencing in uncovering cryptic, transposable element-associated pathogenic variants.

Journal Article↗

PubMed1996

Nail infections.

The increasing prevalence of onychomycoses, along with the wider range of organisms now recognized as potential pathogens, necessitates the accurate laboratory identification of the specific fungus involved. Although the majority of infections still are caused by dermatophyte and Candida species, many other nondermatophyte molds, such as Scytalidium dimidiatum, have been shown to be common agents of disease in certain geographic areas. It is well recognized that infections by nondermatophytes such as Scopulariopsis, Acremonium, and Aspergillus species occur worldwide. The availability of a range of new antifungal agents with various spectra of activity means that the exact identification of the pathogen is necessary to select the optimum treatment.

Fungi↗

PubMed2007

Whole-genome analysis to identify type III-secreted effectors.

Many Gram-negative plant and animal pathogens share a common virulence strategy that relies on the specialized type III secretion system. This apparatus is used to secrete virulence factors, called effectors, into the extracellular host environment and directly into the cytoplasm of host cells. Effectors interfere with host signaling and host metabolism to create an optimal environment for pathogen replication. The identification of effectors in plant pathogens was limited for many years to those effectors that elicit strong plant defenses on some hosts. The members of this subset, called avirulence proteins, can be readily identified because they dominantly confer strong defense-inducing properties to a heterologous virulent strain. This chapter describes two methods to identify type III-secreted effectors in plant pathogens independently of their phenotype. The first method consists of an in vivo molecular genetic screen that uses the activity of an avirulence protein to identify effectors without avirulence activity. It should be possible to apply this method to most Gram-negative plant pathogens. The second method consists of a bioinformatic approach applicable to those pathogens for which at least a draft genome sequence is available.

Arabidopsis↗

PubMed1983

[Communicable disease problems of sewage with special reference to human pathogenic viruses].

Summarizing, it can be said that the epidemiological hygienic risk originating from community waste water can be controlled. This risk appears to be considerably lower when directly handling waste water than indirectly by contact with water contaminated by waste water. The sewage treatment technologies presently in use reduce the contents of viruses, bacteria, protozoa and worm eggs to a varying extent. Owing to the fluctuating concentrations in the inflow to the sewage treatment plant, a proportion of these microbes or proliferation stages of parasitic worms must always be expected not to be eliminated. The pathogens held back in the treatment plant burden primarily the sewage sludge. The various processes of sludge stabilisation influence their number and degree of infectiousness to a varying extent (2, 3, 6). The most important risks of infection which waste water entails, originate from contaminations of raw water and above all of treated drinking water. Statistics from the United States indicate that the above-mentioned bacteria, protozoa and part of the viruses have caused drinking water epidemics (23, 24). Attention has to be paid to bacteria and viruses because some of them prove harmful already in very low doses. Moreover, the occurrence of protozoa should be investigated more intensely. Apart from changes in pathogenicity and low infectious doses, also the fact should be duly considered that these microorganisms are likely to increasingly invade our waste waters, as millions of people yearly head for southern climates. There they fall easily prey to infections which overwhelmingly remain inapparent clinically, and discharge pathogens frequently for a very long period without revealing any symptoms. Also in connection with methods of virus analysis, improved meanwhile the constant efforts for improved indicator systems in the identification of pathogenic organisms must be continued so that epidemiological hygienic problems can be better evaluated and solved.

Bacteria↗

PubMed1995

Characterization of native pathogenic antigens of Onchocerca volvulus: identification of high molecular mass protein antigens eliciting interstitial keratitis in a guinea pig model.

Sclerosing keratitis is the predominant cause of blindness due to onchocerciasis which is a major human parasitic disease caused by the filarial parasite Onchocerca volvulus. In the present investigation, native pathogenic antigens of O. volvulus which are particularly potent in causing interstitial keratitis were characterized utilizing a guinea pig model. Following demonstration of the protein nature of these antigens using pronase digestion, the crude O. volvulus antigen extract was subjected to stepwise procedures of protein purification. At each stage of purification, pooled antigen fractions were injected into one cornea of presensitized guinea pigs followed by clinical evaluation of stromal inflammation and vascularization at different intervals of time after intrastromal challenge. Initial purification of the pathogenic antigens was carried out in the following order: molecular sieve chromatography on Bio-gel A-5m. anion exchange chromatography on Mono Q followed by DEAE-Sepharose CL-6B and cation exchange chromatography on Mono S. Two out of six different pools from the Mono S column (pool a eluted unbound at 10 mM-NaCl and pool e eluted between 130 mM and 475 mM-NaCl) were found to be most pathogenic. Further purification of Mono S pool a and pool e separately by gel filtration chromatography using Superose 12 demonstrated that the fractions which were most potent in inducing interstitial keratitis contained proteins with approximate molecular masses between 100 and 200 kDa. These results show that minor subfractions of total crude antigens of O. volvulus are largely responsible for induction of experimental interstitial keratitis. We have demonstrated the presence of these antigens in O. volvulus microfilariae by their cross-reactivities with anti-microfilarial antibodies, and hence the relevance of the purified antigens to ocular onchocerciasis in man since sclerosing keratitis is associated with invasion of the cornea by O. volvulus microfilariae. Isolation of these two pathogenic antigen pools represents the practical limits of purification and subsequent animal experiments possible with the available amounts of native parasite material obtained from infected human individuals in the absence of a suitable non-human host or of an in vitro culture system for O. volvulus.

Animals↗

PubMedDate not supplied

Molecular methods for identification and detection of bacterial food pathogens.

The polymerase chain reaction (PCR) shortens conventional microbiological methods for the detection of food pathogens either by replacing the conventional biochemical and serological identification or by its direct use on pre-enrichment media or food products. PCR allows fast and highly reliable identification of bacterial taxa, particularly phenotypically atypical bacterial strains. For reliablity, PCR primers and reaction conditions must be thoroughly optimized and evaluated, appropriate sample preparations must be developed, and a stringent laboratory protocol must be followed. Positive control systems are used to monitor possible inhibition of the reaction and negative controls are needed to monitor for contamination. The most recent developments involve messenger RNA-based (mRNA-based) detection of viable bacterial pathogens and real-time PCR quantitation of pathogens.

Bacteria↗