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 901 records · Page 50Linked to original sources

PubMed2005

Ribosomal DNA sequencing: experiences from use in the Danish National Reference Laboratory for Identification of Bacteria.

Diagnostic tools for identification of bacteria have developed dramatically in the last decade. Sequencing of genes coding for rRNA has led to revolutionary insights into the phylogeny and taxonomy of bacteria, and to new demands on the service provided by national reference laboratories for identification of bacteria. At the Danish Reference Laboratory for Identification of Bacteria, partial 16S rDNA sequencing has been used since 2001 to identify "difficult" strains submitted for taxonomic elucidation. Experiences relating to phenotypic as well as 16S rDNA sequencing of the first 175 strains examined are presented. Approximately 2/3 of the strains were Gram-positive and 1/3 Gram-negative. One fifth of the strains were anaerobic, while 4/5 were either facultatively anaerobic or aerobic. Methodological agreement was seen for most strains at species and/or genus level. Methodological disagreement was relatively rare. In 1/6 of the strains valuable information was obtained from sequencing results, while for some strains identification was based primarily on the phenotypic results. Only a few strains could not be clearly identified by either method. A very large number of strains representing taxons ranging from facultatively anaerobic to aerobic and anaerobic species and genera, Gram-positive as well as Gram-negative, were successfully examined. Of the submitted strains many have only rarely been encountered as human pathogens. Thus, genotypic identification may result in recognition of hitherto seldom recognized or unrecognized bacteria as human pathogens, which will lead to a better understanding of the nature of human infections. It is self evident that we should focus on slowly growing, fastidious or 'difficult' organisms when using sequencing for national reference purposes. Short sequences (450-650 base pairs) seem sufficient for most identifications. Molecular bacterial identification is a powerful tool for national reference laboratories, enhancing both the speed and validity of examinations performed.

Bacteria↗

PubMed1988

Intestinal infections in patients with the acquired immunodeficiency syndrome (AIDS). Etiology and response to therapy.

STUDY OBJECTIVE: To determine the frequency of pathogenic gastrointestinal microorganisms in patients with the acquired immunodeficiency syndrome (AIDS) and diarrhea, and to determine if treatment for identifiable microorganisms improves symptoms. DESIGN: Prospective, consecutive sample study. SETTING: Referral-based clinic and wards, National Institutes of Health. PATIENTS: Twenty of twenty-two consecutive homosexual males with AIDS and diarrhea, and 10 homosexual males with AIDS without diarrhea. INTERVENTIONS: All patients had a complete physical examination; serial stool examinations for viral, bacterial, fungal, and protozoan pathogens; and esophagogastroduodenoscopy and colonoscopy to obtain duodenal fluid and mucosal tissue to analyze for enteric pathogens or histopathology. Patients with diarrhea had a malabsorption evaluation. Patients with treatable pathogenic microorganisms received standard antimicrobial therapy. MEASUREMENTS AND MAIN RESULTS: The 20 patients with AIDS and diarrhea had greater weight loss, lower mean numbers of helper-inducer (OKT4) lymphocytes, and a higher incidence of extraintestinal opportunistic infections than the 10 patients without diarrhea. One or more enteric pathogen was identified in 17 of 20 patients (85%; 95% confidence interval [CI], 65% to 96%) with diarrhea. Only 1 patient without diarrhea was infected with an enteric pathogen. Nineteen of twenty patients with diarrhea and all 10 patients without diarrhea had chronic inflammatory changes in their intestinal biopsy specimens. Sixteen patients with identifiable enteric pathogens and diarrhea were treated; 11 (69%; 95% CI, 43% to 87%) showed microbiologic, histologic, or clinical improvement. CONCLUSIONS: Thorough diagnostic evaluation can lead to the identification of enteric pathogens in a high percentage of patients with AIDS and diarrhea. Specific therapy can lead to symptomatic improvement.

Acquired Immunodeficiency Syndrome↗

PubMed1994

Identification of bacterial cell-surface virulence determinants with TnphoA.

Insertion mutagenesis using TnphoA has proved to be a potent device for the creation of easily screened knockout mutations in genes encoding virulence determinants in a variety of pathogenic bacteria. Initial identification of genes with TnphoA directly initiates more sophisticated genetic and biochemical studies on these factors essential to our understanding of bacterial pathogenesis.

Alkaline Phosphatase↗

PubMed1994

Efficacy of microbial identification system for epidemiologic typing of coagulase-negative staphylococci.

The lack of an adequate typing system hampers our understanding of the epidemiology of infections caused by coagulase-negative staphylococci (CoNS). CoNS have become recognized as important nosocomial pathogens and the principal cause of infections associated with invasive devices. Sensitive, specific, and convenient methods are needed to evaluate whether implementing infection control guidelines reduces the risk of nosocomial infections from CoNS and other pathogens. The Microbial Identification System (MIDI) (Microbial ID Inc., Newark, Del.), a semiautomated system for fatty acid methyl ester analysis, shows considerable promise for clinical and epidemiologic applications. Its predictive accuracy and reliability were tested by using epidemiologically related and replicated CoNS isolates as well as CoNS from epidemiologically unrelated clinical infections, which were obtained from five established hospital culture collections in diverse geographic locations. Two hundred isolates were fully characterized in 5 days by one person using MIDI, and the results were similar to those produced by more expensive and time-consuming conventional typing methods. MIDI appears to be a useful screening tool that could be used before more expensive and labor-intensive molecular methods. It offers important advantages to hospital epidemiologists and clinical microbiologists who must identify and type CoNS isolates.

Bacterial Typing Techniques↗

PubMed2004

Evaluation of a rapid polymerase chain reaction based identification technique for Vibrio cholerae isolates.

Rapid and accurate identification of waterborne pathogens, such as Vibrio cholerae, in drinking-water sources is important to enable effective resource management and public health protection. Phenotypic systems currently being used for the identification of Vibrio cholerae isolates are time-consuming and the need exists for the development of suitable molecular techniques that can offer both fast and reliable identification. During this study, isolates identified as Vibrio cholerae by means of two different biochemical test systems (API 20E and VITEK 32) were analysed with the polymerase chain reaction (PCR) to compare the reliability of the various identification systems. The selected PCR technique amplified a sequence within the outer membrane protein of Vibrio cholerae, a gene specific for V. cholerae. It was found that out of 243 isolates biochemically identified as V. cholerae with either the API or VITEK system, 21 isolates did not give a positive result with the PCR detection method. Sequencing the 16S rDNA of more than half of these isolates and comparison of the sequences with Internet databases indicated that most of the isolates belonged to the genus Aeromonas. The results indicated that the rapid PCR procedure was more accurate than the API or VITEK systems currently being used for the phenotypic identification of Vibrio cholerae isolates.

Environmental Monitoring↗

PubMed2000

Improved detection of microorganisms by polymerase chain reaction in delayed endophthalmitis after cataract surgery.

OBJECTIVE: To evaluate whether the use of polymerase chain reaction (PCR) improves the identification of the causative pathogen in eyes developing delayed endophthalmitis after cataract surgery. DESIGN: Prospective, noncomparative case series. PARTICIPANTS: Consecutive series of 25 eyes with the clinical diagnosis of delayed endophthalmitis after cataract. MAIN OUTCOME MEASURE: Presence of bacterial or fungal DNA in aqueous humor and vitreous samples. RESULTS: In the aqueous humor the causative pathogen was identified in 84% (n = 21) of the eyes by PCR compared with 0% by diagnostic culture and 0% by microscopy. In the vitreous samples the pathogen was identified in 92% (n = 23) of the eyes by PCR compared with 24% by diagnostic culture (n = 6) and 0% by microscopy. CONCLUSIONS: PCR is useful for the identification of the causative pathogen in delayed endophthalmitis and had a higher rate of positive identification of the causative organism than microscopy or diagnostic culture.

Aqueous Humor↗

PubMed1999

Identification of Burkholderia spp. in the clinical microbiology laboratory: comparison of conventional and molecular methods.

Cystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situation is not in the least due to the poorly defined taxonomic status of these bacteria, and further validation of the available diagnostic assays is required. A total of 114 geographically diverse bacterial isolates, previously identified in reference laboratories as Burkholderia cepacia (n = 51), B. gladioli (n = 14), Ralstonia pickettii (n = 6), B. multivorans (n = 2), Stenotrophomonas maltophilia (n = 3), and Pseudomonas aeruginosa (n = 11), were collected from environmental, clinical, and reference sources. In addition, 27 clinical isolates putatively identified as Burkholderia spp. were recovered from the sputum of Dutch CF patients. All isolates were used to evaluate the accuracy of two selective growth media, four systems for biochemical identification (API 20NE, Vitek GNI, Vitek NFC, and MicroScan), and three different PCR-based assays. The PCR assays amplify different parts of the ribosomal DNA operon, either alone or in combination with cleavage by various restriction enzymes (PCR-restriction fragment length polymorphism [RFLP] analysis). The best system for the biochemical identification of B. cepacia appeared to be the API 20NE test. None of the biochemical assays successfully grouped the B. gladioli strains. The PCR-RFLP method appeared to be the optimal method for accurate nucleic acid-mediated identification of the different Burkholderia spp. With this method, B. gladioli was also reliably classified in a separate group. For the laboratory diagnosis of B. cepacia, we recommend parallel cultures on blood agar medium and selective agar plates. Further identification of colonies with a Burkholderia phenotype should be performed with the API 20NE test. For final confirmation of species identities, PCR amplification of the small-subunit rRNA gene followed by RFLP analysis with various enzymes is recommended.

Bacterial Typing Techniques↗

PubMed2004

Natural atypical Listeria innocua strains with Listeria monocytogenes pathogenicity island 1 genes.

Identification of bona fide Listeria isolates into the six species of the genus normally requires only a few tests. Aberrant isolates do occur, but even then only one or two extra confirmatory tests are generally needed for identification to species level. We have discovered a hemolytic-positive, rhamnose and xylose fermentation-negative Listeria strain with surprising recalcitrance to identification to the species level due to contradictory results in standard confirmatory tests. The issue had to be resolved by using total DNA-DNA hybridization testing and then confirmed by further specific PCR-based tests including a Listeria microarray assay. The results show that this isolate is indeed a novel one. Its discovery provides the first fully documented instance of a hemolytic Listeria innocua strain. This species, by definition, is typically nonhemolytic. The L. innocua isolate contains all the members of the PrfA-regulated virulence gene cluster (Listeria pathogenicity island 1) of L. monocytogenes. It is avirulent in the mouse pathogenicity test. Avirulence is likely at least partly due to the absence of the L. monocytogenes-specific allele of iap, as well as the absence of inlA, inlB, inlC, and daaA. At least two of the virulence cluster genes, hly and plcA, which encode the L. monocytogenes hemolysin (listeriolysin O) and inositol-specific phospholipase C, respectively, are phenotypically expressed in this L. innocua strain. The detection by PCR assays of specific L. innocua genes (lin0198, lin0372, lin0419, lin0558, lin1068, lin1073, lin1074, lin2454, and lin2693) and noncoding intergenic regions (lin0454-lin0455 and nadA-lin2134) in the strain is consistent with its L. innocua DNA-DNA hybridization identity. Additional distinctly different hemolytic L. innocua strains were also studied.

Animals↗

PubMed1983

Rapid and economical identification and antimicrobial susceptibility test methodology for urinary tract pathogens.

To decrease the time and cost of processing urine cultures, we devised a critical pathway to identify and perform antibiotic susceptibility tests on commonly isolated microbial pathogens within 6 h of growth detection. The strategy was based on eliminating expensive kits and automated procedures when not required. A pathway utilizing a statistical matrix and three rapid biochemical tests required to identify the most common pathogen, Escherichia coli, was developed. This species, which represented 82% of urinary isolates, was identified in 1 h for less than 10% the cost of a commercial kit. The specificity of the 1-h E. coli identification battery was greater than or equal to 99.9% with a sensitivity of 93%. In addition, this critical pathway, adapting published methods, permitted the identification of other enteric pathogens, the group D streptococci, and Pseudomonas aeruginosa within 4 to 6 h. Furthermore, it accounted for other microbes that required longer periods of incubation. The pathway also included a rapid disk diffusion sensitivity test. Utilizing the critical pathway strategy, 76% (E. coli frequency of 0.82 X E. coli sensitivity of 0.93) of all urinary pathogens were identified within 1 h, and 98% were identified within 4 h with an antibiotic sensitivity test available within 6 h after the observation of growth. Costs were reduced from 2.5 to 5.0 times. This methodology is applicable to other specimen types.

Anti-Bacterial Agents↗

PubMed1993

Evaluation of an outbreak of foodborne illness initiated in the emergency department.

STUDY OBJECTIVES: For many foodborne outbreaks, the pathogen and food vehicle never are identified. Delayed collection of epidemiologic and microbiologic information may contribute to this. We postulated that collection of this information from ill persons as they presented to the emergency department during a recent outbreak might contribute to earlier identification of the pathogen and vehicle. DESIGN: At least 690 of 1,900 conventioneers developed gastrointestinal symptoms after attending a banquet. A questionnaire was developed to collect information on specific food histories, incubation periods, symptoms, physical findings, and demographics. These results were compared with results of investigations by the city and state departments of public health. SETTING: The ED of Rush-Presbyterian-St Luke's Medical Center, a tertiary care university hospital in Chicago, Illinois. TYPE OF PARTICIPANTS: Adults (24 men and nine women) presenting to the ED with gastrointestinal symptoms after eating a common meal. MEASUREMENTS AND MAIN RESULTS: The clinical syndrome suggested an invasive pathogen. Based on this, clinical microbiology laboratory procedures were modified (isolation plates were reviewed during the evening shift). This led to early identification of the first isolates (Salmonella enteritidis) from the outbreak. The questionnaire also narrowed the vehicle to one of two foods served. Investigations by the departments of public health subsequently identified one of these, bread pudding with a raw egg based-sauce, as the vehicle. CONCLUSION: Outbreak evaluations can begin in the ED or any other patient care facility. This evaluation need not always add significantly to the expenditure of time, manpower, or laboratory studies. The evaluation of even a small percentage of ill persons from a large outbreak may provide useful epidemiologic information and be particularly important in settings with limited public health resources.

Adult↗

PubMed1996

Emerging fungal infections in cancer patients.

The increasing number of reports in cancer patients that describe unusual or new fungal pathogens in severe systemic infections may be due, in part, to new treatment regimens but also to increased recognition of clinical disease by physicians and unusual organisms by microbiologists. Identification of these pathogens requires specialized expertise but the diagnosis may often be too late to permit effective therapeutic intervention. An unfortunate limitation of current antifungal agents is their limited efficacy in the heavily immunosuppressed, even when the drugs show good activity in vitro. Infections with Candida spp., and non-Candida yeasts and moulds are often disseminated and are frequently fatal in patients with severe immunosuppression. Therapeutic outcomes could be improved with more precise and rapid diagnostic procedures, standardized treatments for each pathogen and improved therapeutic agents. Liposomal amphotericin B formulations, new azole antifungals, more aggressive surgery and haemopoietic growth factors may improve the poor outcome that currently occurs with many of those infections.

Cross Infection↗

PubMed2004

Direct detection of bacterial pathogens in brain abscesses by polymerase chain reaction amplification and sequencing of partial 16S ribosomal deoxyribonucleic acid fragments.

OBJECTIVE: To evaluate the feasibility of detecting bacterial pathogens directly from the clinical brain abscess specimens by polymerase chain reaction (PCR) amplification and sequencing of bacterial 16S ribosomal deoxyribonucleic acid (rDNA). METHODS: A total of 14 specimens were tested by both culture and PCR amplification, targeting the full-length or a partial region of 16S rDNA. 16S rDNA is known to be conserved in bacteria. Sequencing of partial-length and full-length 16S rDNA was performed. The sequence data were compared with known sequences of 16S rDNA in the National Center for Biotechnology Information GenBank by using the Basic Local Alignment Search Tool (BLAST) algorithm. The species with the best match of similarity were regarded as the pathogenic species in the samples. We also developed a Streptococcus-specific multiplex PCR analysis for identifying members of the Streptococcus species, the most common pathogen of brain abscesses. RESULTS: The 10 culture-positive specimens were all PCR-positive for partial 16S rDNA, but only seven were positive for full-length 16S rDNA amplification. Bacterial DNA was not detected in the remaining four specimens with a negative culture. Species identification by phenotypes from culture was in agreement with that by sequencing results of partial-length (or full-length) 16S rDNA. The Streptococcus-specific PCR analysis could detect Streptococcus species correctly in one step. CONCLUSION: Bacterial 16S rDNA sequences provide reliable clues to the identification of unknown pathogens. PCR analysis of 16S rDNA and sequencing may identify pathogens to the species level directly from brain abscesses. This approach is rapid and is useful especially in the identification of slow-growing and fastidious organisms.

Adolescent↗

PubMed2006

Identification of genomic islands in six plant pathogens.

Genomic islands (GIs) play important roles in microbial evolution, which are acquired by horizontal gene transfer. In this paper, the GIs of six completely sequenced plant pathogens are identified using a windowless method based on Z curve representation of DNA sequences. Consequently, four, eight, four, one, two and four GIs are recognized with the length greater than 20-Kb in plant pathogens Agrobacterium tumefaciens str. C58, Rolstonia solanacearum GMI1000, Xanthomonas axonopodis pv. citri str. 306 (Xac), Xanthomonas campestris pv. campestris str. ATCC33913 (Xcc), Xylella fastidiosa 9a5c and Pseudomonas syringae pv. tomato str. DC3000, respectively. Most of these regions share a set of conserved features of GIs, including an abrupt change in GC content compared with that of the rest of the genome, the existence of integrase genes at the junction, the use of tRNA as the integration sites, the presence of genetic mobility genes, the difference of codon usage, codon preference and amino acid usage, etc. The identification of these GIs will benefit the research for the six important phytopathogens.

Agrobacterium tumefaciens↗

PubMed2006

Rapid detection of Staphylococcus aureus by a combination of monoclonal antibody-coated latex and capillary electrophoresis.

The rapid detection of pathogenic bacteria is extremely important in biotechnology and clinical diagnosis. CE has been utilized in the field of bacterial analysis for many years, but to some extent, simultaneous separation and identification of certain microbes from complex samples by CE coupled with UV detector is still a challenge. In this paper, we propose a new strategy for rapid separation and identification of Staphylococcus aureus (S. aureus) in bacterial mixtures by means of specific mAb-coated latex coupled with CZE. An appropriate set of conditions that selectively isolated S. aureus from the microorganisms Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were established. S. aureus could be differentiated from the others by unique peaks in the electropherograms. The validity was also confirmed by LIF with antibodies specific to both the latex and the microbial cells. The LOD is as low as 9.0 x 10(5) colony forming unit/mL. We have also utilized this technology to identify S. aureus in a stool sample coming from a healthy volunteer spiked successfully with S. aureus. This CZE-UV technique can be applied to rapid diagnosis of enteritis caused by S. aureus or other bacterial control-related fields needing rapid identification of target pathogens from microbial mixtures. In theory, this method is suitable for the detection of any bacterium as long as corresponding bacterium-specific antibody-coated latex is available.

Antibodies, Bacterial↗

PubMedDate not supplied

[Vibrios pathogenic to humans and laboratory diagnosis of diseases caused by them].

Present-day taxonomic status of vibrios pathogenic for humans is discussed, as are the phenotypical characteristics of some species, factors of virulence, and clinical manifestations of diseases caused by these agents. A scheme of isolation and identification of vibrios pathogenic for humans is offered.

Bacteriological Techniques↗

PubMed1990

Acute respiratory infections during the first three months of life: clinical, radiologic and physiologic predictors of etiology.

The usefulness of clinical, radiologic, and physiologic characteristics to identify pathogens was assessed in 90 infants aged two through 12 weeks, presenting to an outpatient clinic with an acute respiratory infection. Eighty-four cases had cultures or rapid diagnostic tests for RSV, of which 25 were positive. Eighty-two infants had cultures or rapid diagnostic tests for Chlamydia, of which 16 were positive. Additional respiratory pathogens identified included parainfluenza (6 cases), rhinovirus (3 cases), pertussis (2 cases), and CMV (1 case). Multiple pathogens were identified in four cases: Chlamydia and RSV (2 cases), Chlamydia and parainfluenza (1 case), and Chlamydia and CMV (1 case). Clinical characteristics other than the need for hospitalization were not useful predictors of specific pathogens. X-rays were obtained in 20 (80%) of the RSV infections, 13 (81%) of the Chlamydia infections, six of the parainfluenza infections, two pertussis infections, and 25 cases without identification of the pathogen. X-ray findings could not distinguish between patients with or without a pathogen or between the pathogens. Severe findings were present in 28% (11/40) of cases with a pathogen identified, compared to 12% (3/26) of cases without a pathogen identified (NS). Moderate findings were present in 58% (23/40) of cases with a pathogen identified compared to 62% (16/26) of cases without a pathogen identified. Slight/negative findings were present in 15% (6/40) of cases with a pathogen identified, compared to 27% (7/26) of cases without a pathogen identified. Pulse oximetry was done in 30 cases, 22 of which had a pathogen identified (RSV 14, Chlamydia 7, pertussis 1).(ABSTRACT TRUNCATED AT 250 WORDS)

Diagnosis, Differential↗

PubMed2002

Autoimmune thyroid disease: new models of cell death in autoimmunity.

Autoimmunity to thyroid antigens leads to two distinct pathogenic processes with opposing clinical outcomes: hypothyroidism in Hashimoto's thyroiditis and hyperthyroidism in Graves' disease. The high frequency of these diseases and easy accessibility of the thyroid gland has allowed the identification of key pathogenic mechanisms in organ-specific autoimmune diseases. In early investigations, antibody- and T-cell-mediated death mechanisms were proposed as being responsible for autoimmune thyrocyte depletion. Later, studies on apoptosis have provided new insights into autoimmune target destruction, indicating the involvement of death receptors and cytokine-regulated apoptotic pathways in the pathogenesis of thyroid autoimmunity.

Apoptosis↗

PubMed1994

Endocarditis with pericardial bioprostheses: clinico-pathologic characteristics, immediate and long term prognosis.

Between 1977 and 1992, 30 consecutive episodes of infective endocarditis in 28 patients involving pericardial bioprostheses were diagnosed and treated in our hospital. Eleven (37%) were early pericardial valve endocarditis occurring in the first 60 days following valve surgery, and 19 (63%) were late endocarditis. In both the early and late groups, more aortic that mitral valves were affected (19/30). The most frequent pathogen in the early cases was staphylococcus, (S. epidermidis in five cases, S. aureus in one). The most frequent pathogen among late cases was streptococcus: (St. viridans in four, St. faecalis in two, St. bovis in one). In four cases (13%) no pathogen was isolated. Twelve patients received antibiotic treatment alone, six specific for the pathogen and other six only arbitrarily chosen regimen. All patients were cured in the former and all patients died in the latter group (four with negative blood cultures and two in whom identification of the pathogen was delayed-Proteus mirabillis in one case and Brucella mellitensis in the other). Valve replacement during the infective endocarditis episode was necessary in 18 cases, either because of failure of the antibiotic treatment or because of heart failure secondary to prosthetic malfunction. Peri-annular abscess was present in five cases. Surgical mortality was 22.2% (4/18). In all, 11 patients (39%) died during the active stage of infective endocarditis. The most frequent cause of death was heart failure (45.5%). All four patients with negative blood cultures died. The most advisable strategy for treating bacterial endocarditis of pericardial bioprostheses is a combination of antibiotic therapy and early surgery, especially in cases of staphylococcus endocarditis.(ABSTRACT TRUNCATED AT 250 WORDS)

Anti-Bacterial Agents↗