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At least 289 records · Page 16Linked to original sources
PubMed1995

[Epidemiologic studies on three episodes of acute bacillary dysentery outbreak].

Three episodes of illness outbreak, with major symptoms of acute abdominal pain and diarrhea, occurred in 1990 to 1991 in the army forces stationed in Beijing. Bacillary dysentery outbreak caused by Shigella dysentariae were confirmed with epidemiological investigations and pathogen identification. Drug sensitivity tests with Kirby-Bauer method for the strain isolated showed it had obvious resistance to 13 of 14 kinds of antibiotics tested. Detection of plasmid with Birnboim method showed most of the strains had R-plasmid of 120-140 Md and few had small plasmid. It suggested inherent connection between drug-resistance of the strains and plasmid.

China↗
PubMed1976

[Identification of conditionally pathogenic enterobacteria in laboratory practice in the diagnosis of acute intestinal diseases].

Identification of 361 cultures isolated from patients suffering from various acute intestinal diseasesand from persons who had sustained them, as well as from contacts and persons examined prophylactically with the use of various biochemical tests showed that ty their taxonomic properties the cultures were referred to conditionally-pathogenic representatives of Enterobacteriaceae of the corresponding genera:Citrobacter, Hafnia, Klebsiella, Proteus, Providencia. Serological typing of the strains of bacteria of the Citrobacter pointed to the most frequent circulation of the strains of the serological groups 04, 01, 03, 013, 05, 022, 08; among these groups 04, encountered among all the categories under study, prevailed. At the current stage of identification of conditionally pathogenic enterobacteria in practical laboratories it is of expedience to use in the diagnosis of intestinal diseases the serological typing along with a complex from several additional biochemical tests.

Citrobacter↗
PubMed2004

Can throat swab after physiotherapy replace sputum for identification of microbial pathogens in children with cystic fibrosis?

OBJECTIVE: To compare cultures throat swab after physiotherapy with results of sputum culture in identification of lower airway pathogens in children with cystic fibrosis. METHODS: 387 samples of sputum cough swabs, throat swab and throat swab after physiotherapy were collected from 48 patients of cystic fibrosis and cultured for aerobic bacteria. The results of cultures of cough swabs, throat swab and throat swab after physiotherapy were compared with results of sputum culture. RESULTS: There was good concordance between culture results of sputum and other methods. Over all concordance was 70%, 81% and 92% with cough swab, throat swab and throat swab after physiotherapy. Sensitivity for isolation of Pseudomonas aeruginosa by throat swab, cough swab and throat swab after physiotherapy was 40%, 42% and 82% respectively. Specificity for isolation of Pseudomonas by throat swab, cough swab and throat swab after physiotherapy was 99%, 100% and 99% respectively. Sensitivity for isolation of Staphylococcus aureus by throat swab, cough swab and throat swab after physiotherapy was 57%, 50% and 100% respectively. Specificity for isolation of Staphylococcus by throat swab, cough swab and throat swab after physiotherapy was 99% for all these methods. CONCLUSION: It is concluded that throat swab after physiotherapy in a child with CF can be used reliably for identification of lower airway pathogens.

Child↗
PubMed2002

Detection and identification of bacterial pathogens of fish in kidney tissue using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes.

We report the application of a nucleic acid-based assay that enables direct detection and identification of bacterial pathogens in fish kidney tissue without the need for bacterial culture. The technique, known as terminal restriction fragment length polymorphism (T-RFLP), employs the polymerase chain reaction (PCR) using a primer pair that targets 2 highly conserved regions of the gene that encodes for the 16S small subunit of the bacterial ribosome. Each primer is 5' labeled with a different fluorescent dye, which results in each terminus of the resulting amplicon having a distinguishable fluorescent tag. The amplicon is then digested with a series of 6 restriction endonucleases, followed by size determination of the 2 labeled terminal fragments by capillary electrophoresis with laser-induced fluorescence detection. Comparison of the lengths of the full set of 12 terminal fragments with those predicted based on analyses of GenBank submissions of 16S sequences leads to presumptive identification of the pathogen to at least the genus, but more typically the species level. Results of T-RFLP analyses of genomic DNA from multiple strains of a number of fish bacterial pathogens are presented. The assay is further demonstrated on fish kidney tissue spiked with a known number of cells of Flavobacterium psychrophilum where a detection limit of ca. 30 CFU mg(-1) of tissue was estimated. A similar detection limit was observed for several other gram-negative pathogens. This procedure was also used to detect Aeromonas salmonicida and Renibacterium salmoninarum in the kidney tissue of 2 naturally infected salmonids.

Aeromonas↗
PubMed2005

Rapid identification of emerging pathogens: coronavirus.

We describe a new approach for infectious disease surveillance that facilitates rapid identification of known and emerging pathogens. The process uses broad-range polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry for accurate mass measurements of PCR products, and base composition signature analysis to identify organisms in a sample. We demonstrate this principle by using 14 isolates of 9 diverse Coronavirus spp., including the severe acute respiratory syndrome-associated coronavirus (SARS-CoV). We show that this method could identify and distinguish between SARS and other known CoV, including the human CoV 229E and OC43, individually and in a mixture of all 3 human viruses. The sensitivity of detection, measured by using titered SARS-CoV spiked into human serum, was approximate, equals1 PFU/mL. This approach, applicable to the surveillance of bacterial, viral, fungal, or protozoal pathogens, is capable of automated analysis of >900 PCR reactions per day.

Animals↗
PubMed1997

Detection and identification of fungal pathogens in blood by using molecular probes.

A PCR assay was developed for the detection and identification of Candida and Aspergillus species. The design of the oligonucleotide primer pair as well as the species-specific probes used for species identification was derived from a comparison of the sequences of the 18S rRNA genes of various fungal pathogens. The primers targeted a consensus sequence for a variety of fungal pathogens. The assay was tested for sensitivity and specificity with 134 fungal and 85 nonfungal isolates. To assess clinical applicability, 601 blood samples from four defined groups were tested: group A (n = 35), controls; groups B to D (n = 86), patients with febrile neutropenia, without fungal colonization (group B; n = 29) and with fungal colonization (group C; n = 36); and patients with documented invasive fungal infection (IFI) (group D; n = 21). The assay detected and, by species-specific hybridization, identified most of the clinically relevant Candida and Aspergillus species at 1 CFU/ml of blood. Amplification was 100% sensitive for all molds and yeasts tested, with Histoplasma capsulatum being the only non-Aspergillus species hybridizing with the Aspergillus spp. probe. None of 35 group A patients and only 3 of 65 group B and C patients were PCR positive. The sensitivity of the assay for specimens from patients with IFI (21 patients in group D) was 100% if two specimens were tested. For specificity, 3 of 189 specimens from patients at risk but with negative cultures were positive by the assay, for a specificity of 98%. PCR preceded radiological signs by a median of 4 days (range, 4 to 7 days) for 12 of 17 patients with hepatosplenic candidiasis or pulmonary aspergillosis. For the 10 patients with IFI responding to antifungal therapy, PCR assays became persistently negative after 14 days of treatment, in contrast to the case for 11 patients, who remained PCR positive while not responding to antifungal therapy. Thus, the described PCR assay allows for the highly sensitive and specific detection and identification of fungal pathogens in vitro and in vivo. Preliminary data from the screening of a selected group of patients revealed some value in the early diagnosis and monitoring of antifungal therapy.

Amphotericin B↗
PubMed2004

[Detection and identification of the pathogenic cause of a brain abscess by molecular genetic methods].

Brain abscesses are life-threatening and detection and identification of the causative pathogens are crucial for substantiating the diagnosis and for selecting the optimal antibiotic regimen. In approximately 20% of the patients microbiological cultures of abscess material remain sterile. The polymerase chain reaction (PCR) provides a methodological alternative, but data about the use of broad spectrum PCR assays to detect the causative pathogens in brain abscesses are rare. We report on the case of a 65-years-old patient with a brain abscess caused by Fusobacterium spp., which was only diagnosed by broad spectrum PCR. To our knowledge this is the second report about a brain abscess, where Fusobacterium spp. was identified only by broad spectrum PCR and subsequent DNA sequencing.

Aged↗
PubMed1984

Evaluation of Gonochek-II as a rapid identification system for pathogenic Neisseria species.

The Gonochek-II test kit (E-Y Laboratories, San Mateo, Calif.) may be used to rapidly identify (within 30 min) Neisseria gonorrhoeae, Neisseria meningitidis, Neisseria lactamica, and Branhamella catarrhalis. The kit consists of oxidase swabs, chromogenic substrates, and EY-20 reagent (diazonium salt derivative). A beta-lactamase tube is also included. Fifty-two clinical isolates were tested from cervical (22 isolates), urethral (13), throat (11), rectal (5), and urine (1) sources. All strains were oxidase-positive, gram-negative diplococci isolated on Thayer-Mayer plates incubated at 35 degrees C in 5% CO2 for 18 to 24 h. Each strain was tested by Gonochek-II, RapID NH (Innovative Diagnostics, Decatur, Ga.), and conventional rapid carbohydrate utilization. Forty-four isolates of N. gonorrhoeae and six N. meningitidis were identified. Only two isolates tested (4%) were identified as species other than these two. Gonochek-II outperformed all other methods for identification of N. gonorrhoeae from cervical and urethral areas. N. meningitidis strains were correctly identified in all cases. Ease and rapidity of the procedure, coupled with a small inoculum requirement and reliable results, led us to favor Gonochek-II for routine identification of pathogenic Neisseria species.

Aminopeptidases↗
PubMed1994

Lipooligosaccharide biosynthesis in pathogenic Neisseria. Cloning, identification, and characterization of the phosphoglucomutase gene.

The lipooligosaccharide (LOS) of pathogenic Neisseria is an important factor in disease pathogenesis. Little is known about the genes involved in neisserial LOS biosynthesis. To elucidate specific LOS biosynthetic genes, we screened a Tn916 library that was constructed in Neisseria meningitidis strain NMB. This strain expresses a single LOS that has an molecular mass of 4.5 kDa and binds monoclonal antibody (mAb) 3F11. This library was screened using a mAb panel that recognizes structural differences in neisserial LOS oligosaccharides. A stable LOS mutant of strain NMB was identified which we designated NMB-R6. This mutant expressed an LOS with an molecular mass of approximately 3.1-3.2 kDa and did not bind mAb 3F11. Genomic DNA from this mutant transformed N. meningitidis strain NMB to the tetracycline resistant NMB-R6 phenotype greater than 10(-4)/recipient/micrograms of DNA. In addition, we transformed Neisseria gonorrhoeae strain 1291 (LOS phenotype molecular mass 4.5 kDa, mAb 3F11+) to the NMB-R6 LOS phenotype with N. meningitidis NMB-R6 genomic DNA. Analysis of N. gonorrhoeae strain 1291-R6 LOS by mass spectroscopy showed that the LOS oligosaccharide structure is GlcNAc-->Hep2phosphoethanolamine-->2-keto-3-deoxymannooctuloson ic acid (where Hep is heptose). Sequence analysis showed that the transposon is inserted into the 3' end of a gene that has homology to the human phosphoglucomutase (PGM) gene. Sequence comparison indicated that the putative PGM gene in N. gonorrhoeae 1291 and N. meningitidis NMB had 92% identity at the DNA level. PGM and glucokinase activity was present in cell free extracts of N. meningitidis NMB and N. gonorrhoeae strain 1291. N. meningitidis NMB-R6 and N. gonorrhoeae strain 1291-R6 had no detectable PGM activity, whereas glucokinase activity was similar to the wild type strains. PGM activity can be reconstituted in N. meningitidis strain NMB-R6 by transformation with the cloned PGM gene. SDS-polyacrylamide gel electrophoresis demonstrated that NMB-R6 transformed with the PGM gene expressed the 3F11+, 4.5-kDa LOS of the parent NMB strain. The inability of N. meningitidis NMB-R6 and N. gonorrhoeae strain 1291-R6 to convert glucose 6-phosphate to glucose 1-phosphate results in the truncated LOS phenotype expressed by these mutants.

Amino Acid Sequence↗
PubMed2005

New approaches to identification of bacterial pathogens by surface enhanced laser desorption/ionization time of flight mass spectrometry in concert with artificial neural networks, with special reference to Neisseria gonorrhoeae.

Surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) has been applied in large numbers of oncological studies but the microbiological field has not been extensively explored to date. This paper describes the application of SELDI-TOF MS in concert with a multi-layer perceptron artificial neural network (ANN) with a back propagation algorithm for the identification of Neisseria gonorrhoeae. N. gonorrhoeae, the aetiological agent of gonorrhoea, is the second most common sexually transmitted disease in the UK and USA. Analysis of over 350 strains of N. gonorrhoeae and closely related species by SELDI-TOF MS facilitated the design of an ANN model and revealed 20 ion peak descriptors of positive, negative and secondary nature that were paramount for the identification of the pathogen. The model performed with over 96 % efficiency when based on these 20 ion peak descriptors and exhibited a sensitivity of 95.7 % and a specificity of 97.1 %, with an area under the curve value of 0.996. The technology has the potential to link several ANN models for a comprehensive rapid identification platform for clinically important pathogens.

Bacteria↗
PubMed2006

Molecular-genetic approaches to identification and typing of pathogenic Candida yeasts.

Currently, invasive candidal infections represent an increasing cause of morbidity and mortality in seriously ill hospitalised patients. Because the accurate diagnosis of candidiasis remains difficult, a fast and reliable assay for characterization of fungal pathogens is critical for the early initiation of adequate antifungal therapy and/or for introduction of preventive measures. As novel molecular genetic techniques are continuously introduced, their role in the management of infectious diseases has also been growing. Today, molecular strategies complement conventional methods and provide more accurate and detailed insight. It can be expected that future technical development will improve their potential furthermore. In this article, we provide a critical review on the value and limitations of molecular tools in pathogenic Candida species identification and strain typing regarding their sensitivity, discriminatory power, reproducibility, cost and ease of performance.

Candida↗
PubMed2003

PCR-RFLP detection and species identification of fungal pathogens in patients with febrile neutropenia.

OBJECTIVE: To assess the usefulness of polymerase chain reaction (PCR) assays in the diagnosis of fungal infections in immunocompromised patients. METHODS: A rapid and sensitive PCR-based assay for the detection and identification of fungal pathogens was designed and applicability of this method was investigated in a group of children with cancer and febrile neutropenia (FN). RESULTS: The ITS2 sequences and adjacent regions of 40 fungal pathogens were analyzed and primers for detection of all analyzed fungal species were designed. Amplification product length polymorphism (APLP) and restriction fragment length polymorphism (RFLP) generated genus- or species-specific patterns. The sensitivity of the method was approximately three cells of Candida albicans per 1 mL of blood. The results were available within 8 h after sample collection. The method was tested on 53 blood samples and one lung biopsy sample from 24 children with cancer and febrile neutropenia (FN). The PCR assay detected fungal DNA in 25 clinical samples from ten patients. Blood cultures were positive in only five samples, while another two blood-culture negative patients had positive cultures from throat swabs. The remaining 14 patients were both culture- and PCR-negative. Culture-isolated strains matched completely those obtained by PCR-APLP-RFLP identification. The identity of fungal species was confirmed by direct sequencing of amplified products. CONCLUSION: Our results suggest that PCR-APLP-RFLP assays can be useful in the diagnosis of fungal infections in immunocompromised patients.

Adolescent↗
PubMed2005

Nucleic acid amplification-based techniques for pathogen detection and identification.

Nucleic acid amplification techniques have revolutionised diagnostic and research industries. Current technologies that allow the detection of amplification in real-time are fast becoming industry standards, particularly in a diagnostic context. In this review, we describe and explore the application of numerous real-time detection chemistries and amplification techniques for pathogen detection and identification, including the polymerase chain reaction, nucleic acid sequence-based amplification, strand displacement amplification and the ligase chain reaction. The emergence of newer technologies, such as lab-on-a-chip devices and photo-cleavable linkers, is also discussed.

DNA, Bacterial↗
PubMed2002

Development of a multilocus sequence typing scheme for the pig pathogen Streptococcus suis: identification of virulent clones and potential capsular serotype exchange.

Streptococcus suis is an important pathogen of pigs and occasionally causes serious human disease. However, little is known about the S. suis population structure, the clonal relationships between strains, the potential of particular clones to cause disease, and the relevance of serotype as a marker for epidemiology. Here we describe a multilocus sequence typing (MLST) scheme for S. suis developed in order to begin to address these issues. Seven housekeeping gene fragments from each of 294 S. suis isolates obtained from various S. suis diseases and from asymptomatic carriage representing 28 serotypes and nine distinct countries of origin were sequenced. Between 32 and 46 alleles per locus were identified, giving the ability to distinguish >1.6 x 10(11) sequence types (STs). However only 92 STs were identified in this study. Of the 92 STs 18 contained multiple isolates, the most common of which, ST1, was identified on 141 occasions from six countries. Assignment of the STs to lineages resulted in 37 being identified as unique and unrelated STs while the remaining 55 were assigned to 10 complexes. ST complexes ST1, ST27, and ST87 dominate the population; while the ST1 complex was strongly associated with isolates from septicemia, meningitis, and arthritis, the ST87 and ST27 complexes were found to contain significantly higher numbers of lung isolates. In agreement with the observed distribution of disease-causing isolates of S. suis, most isolates previously characterized as of high virulence in porcine infection models belong to ST1, while isolates belonging to other STs appear to be less virulent in general. Finally nine STs were found to contain isolates of multiple serotypes, and many isolates belonging to the same serotypes were found to have very disparate genetic backgrounds. As well as highlighting that the serotype can often be a poor indicator of genetic relatedness between S. suis isolates, these findings suggest that capsular genes may be moving horizontally through the S. suis population.

Animals↗
PubMed2006

Rapid molecular identification of fungal pathogens in corneal samples from suspected keratomycosis cases.

An increase in the incidence of fungal infections has highlighted the need for rapid and precise detection and identification methods in clinical mycology. This report describes the data obtained on corneal samples from 24 patients with suspected keratomycosis using a conventional cultural approach in parallel with PCR amplification and sequencing of the internal transcribed spacers (ITSs) of the rDNA regions. Using the cultural approach, seven samples (58.3 % of the 12 samples positive for an infectious pathogen) tested positive for a fungal aetiology, with final identification taking a mean time of more than 5 days. In two cases, diagnosis required 10 days. Using the ITS-based molecular approach, a direct diagnosis was obtained in only five of the seven fungus-positive cases (71.4 %) starting from the clinical samples, but identification was still possible in all seven cases within 24 h (by using 16 h cultures for the two remaining cases). Despite the less-than-optimal sensitivity when working directly on clinical samples, the obtained data indicate that the molecular strategy used in this study is a useful complement to the conventional diagnostic approaches used for keratomycosis and, in particular, allows precise and fast fungal identification, in response to the clinical requirements. Similar studies on larger panels of patients and on different clinical samples are required for further investigation of the clinical potential of ITS-based approaches in the diagnosis of mycotic infections.

Base Sequence↗
PubMed1994

[Genetic identification of bacterial pathogens].

Conventional biochemical characterization system of pathogenic bacteria spent too much time to identify pathogens. However, the introduction of new genetic technique has pushed these classical methods aside and rapid determination of pathogenic bacteria in infectious disease become possible. Quantitative DNA/DNA hybridization, Specific DNA probe, and PCR techniques are developed for the identification and detection of almost all medically important pathogens. This development was mainly brought by the accumulation of 16S rRNA sequences of bacteria. From conserved area of 16S rRNA and 18S rRNA sequence, universal PCR primers are designed and universal bacterial and fungal detection system are applied for the rapid diagnosis of causative agent of sepsis and meningitis.

Bacteria↗
PubMed1995

Identification of urinary pathogens by the RAPIDEC ur system.

A commercial method (RAPIDEC ur; bioMérieux UK Ltd, Basingstoke) and an in-house scheme based on conventional tests were compared for the identification of 179 commonly encountered gram-negative urinary pathogens. The methods identified correctly to genus level 97% and 84% of organisms, respectively. RAPIDEC ur was superior at identifying Escherichia coli, due to the detection of beta-glucuronidase activity, but less cost-effective than the in-house scheme.

Gram-Negative Bacteria↗
PubMed1989

[A latex agglutination test for the rapid identification of periodontally pathogenic microorganisms in subgingival plaque. The preliminary results].

Latex agglutination tests (LA) have been evaluated for identifying periodontal pathogens. This preliminary study compared LA tests with indirect immunofluorescence (IF) for the rapid identification of A. actinomycetemcomitans, B. gingivalis, and B. intermedius in clinical subgingival plaque samples. A total of 58 sites from 12 patients suffering from advanced periodontitis, exhibiting recent attachment loss were examined before and after initial periodontal treatment. The results of the two examinations were pooled and a total of 116 sites were statistically evaluated. The overall agreement between LA and IF was 75.8% for black pigmented Bacteroides (BPB) and 74.1% for Aa. These results demonstrate the feasibility of LA as a rapid, inexpensive, and reliable tool for monitoring periodontal disease offered to the general practitioner.

Actinobacillus↗