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You searched for: Journal name Journal of microbiological methods Remove constraint Journal name: Journal of microbiological methods Subject humans Remove constraint Subject: humans
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1. Analysis of beta-hemolysis in human blood agars by Streptococcus pyogenes

Author:
Kamiar Zomorodian; Mohammad Javad Rahimi; Akbar Safaei; Abdollah Bazargani; Marjan Motamadi; Mahboobeh Kharazi; Setareh Mostaghni; Keyvan Pakshir; Hamid Ghaedi; Mohammad Hossein Afsarian
Source:
Journal of microbiological methods 2011 v.85 no.3 pp. 233-234
ISSN:
0167-7012
Subject:
Streptococcus pyogenes; agar; blood; blood groups; hemolysis; humans
Abstract:
... The aim of the study was to assess the reliability of human blood agar media (HuBA) in identifying Streptococcus pyogenes by hemolysis analysis. We analyze several factors that might affect the accuracy of HuBA media for microbial analysis, including incubation time, blood group, Rh factor and presence of antistreptolysin-o. ...
DOI:
10.1016/j.mimet.2011.03.009

2. Development and validation of ELISA for detection of antibodies to Legionella pneumophila serogroup 1, 3 and 6 in human sera

Author:
Pernille L. Elverdal; Christina W. Svarrer; Charlotte S. Jørgensen; Ian C. Skovsted; Søren A. Uldum
Source:
Journal of microbiological methods 2011 v.86 no.3 pp. 298-303
ISSN:
0167-7012
Subject:
Legionella pneumophila; antibodies; antigens; blood serum; early diagnosis; enzyme-linked immunosorbent assay; fluorescent antibody technique; humans; immunoglobulin G; immunoglobulin M; patients; polymerase chain reaction; serotypes
Abstract:
... The aim of this study was to determine whether separate measurement of immunoglobulin (Ig) M and G antibodies to Legionella (L.) pneumophila serogroups (sg) 1, 3 and 6 as single antigens can facilitate an early diagnosis of Legionnaires' disease. The developed ELISA was evaluated and compared with an in-house indirect Legionella immunofluorescence antibody test (IFAT) measuring Total Ig. A total o ...
DOI:
10.1016/j.mimet.2011.05.022

3. Development and validation of a microbial source tracking marker for the detection of fecal pollution by muskrats

Author:
Romain Marti; Yun Zhang; David R. Lapen; Edward Topp
Source:
Journal of microbiological methods 2011 v.87 no.1 pp. 82-88
ISSN:
0167-7012
Subject:
DNA; Ondatra zibethicus; birds; feces; genes; humans; livestock; pollution; ribosomal RNA; septic systems; sewage; surface water; swine production; water quality; watersheds; waterways; wildlife; Ontario
Abstract:
... Surface waters in mixed-activity watersheds can be compromised by fecal pollution from livestock production, sewage outflows or leaking septic systems, or avian or mammalian wildlife. While undertaking water quality research in Eastern Ontario Canada, we observed an abundance of muskrats (Ondatra zibethicus) in some waterways, and sought to determine their significance with respect to fecal pollut ...
DOI:
10.1016/j.mimet.2011.07.013

4. Development of a Pulsed-Field Gel Electrophoresis (PFGE) method for molecular typing of clinical isolates of Arcanobacterium haemolyticum

Author:
Aurea E. Flores; Michelle J. Diedrick; Patricia Ferrieri
Source:
Journal of microbiological methods 2011 v.86 no.3 pp. 387-389
ISSN:
0167-7012
Subject:
Arcanobacterium haemolyticum; epidemiological studies; humans; pathogens; pulsed-field gel electrophoresis
Abstract:
... We developed a two-block PFGE method to study molecular variation among clinical isolates of Arcanobacterium haemolyticum, an often overlooked human pathogen. Three main macrorestriction profiles were defined among 15 isolates. PFGE was an objective method for characterizing A. haemolyticum and may be useful in molecular epidemiological studies of this organism. ...
DOI:
10.1016/j.mimet.2011.06.002

5. Diagnosis of Helicobacter pylori bacterial infections using a voltammetric biosensor

Author:
Suw Young Ly; Hai-Soo Yoo; Sung Hoon Choa
Source:
Journal of microbiological methods 2011 v.87 no.1 pp. 44-48
ISSN:
0167-7012
Subject:
DNA; Helicobacter pylori; bacterial infections; biosensors; carbon nanotubes; detection limit; electrodes; electrophoresis; humans; patients; polymerase chain reaction; tissues
Abstract:
... The voltammetric assay of Helicobacter pylori DNA was investigated using a bismuth-immobilized carbon nanotube electrode (BCNE). The analytical cyclic voltammetry (CV) peak potential was obtained at a 0.4V reduction scan, where the diagnostic optimum square-wave (SW) stripping working range was achieved at 0.72–7.92μg/mL H. pylori DNA (11 points). A relative standard deviation of 1.68% (RSD, n=5) ...
DOI:
10.1016/j.mimet.2011.07.002

6. Efficiency of PCR-based methods in discriminating Bifidobacterium longum ssp. longum and Bifidobacterium longum ssp. infantis strains of human origin

Author:
Dagmar Šrůtková; Alena Španova; Miroslav Špano; Vladimír Dráb; Martin Schwarzer; Hana Kozaková; Bohuslav Rittich
Source:
Journal of microbiological methods 2011 v.87 no.1 pp. 10-16
ISSN:
0167-7012
Subject:
Bifidobacterium longum subsp. infantis; Bifidobacterium longum subsp. longum; adults; breast feeding; feces; fermentation; gastrointestinal system; humans; infants; melezitose; probiotics; random amplified polymorphic DNA technique; restriction endonucleases; ribosomal DNA
Abstract:
... Bifidobacterium longum is considered to play an important role in health maintenance of the human gastrointestinal tract. Probiotic properties of bifidobacterial isolates are strictly strain-dependent and reliable methods for the identification and discrimination of this species at both subspecies and strain levels are thus required. Differentiation between B. longum ssp. longum and B. longum ssp. ...
DOI:
10.1016/j.mimet.2011.06.014

7. Efficient insertional mutagenesis system for the dimorphic pathogenic fungus Sporothrix schenckii using Agrobacterium tumefaciens

Author:
Yanhua Zhang; Guangquan Li; Dan He; Baodong Yu; Koji Yokoyama; Li Wang
Source:
Journal of microbiological methods 2011 v.84 no.3 pp. 418-422
ISSN:
0167-7012
Subject:
Agrobacterium radiobacter; Sporothrix schenckii; conidia; fungi; humans; insertional mutagenesis; mutants; phenotype; polymerase chain reaction; transfer DNA
Abstract:
... Sporothrix schenckii is a dimorphic pathogenic fungus that causes human and animal sporotrichosis globally. Here we developed and optimized an Agrobacterium tumefaciens-mediated transformation (ATMT) system of S. schenckii for insertional mutagenesis. The transformation efficiency reached more than 600 transformants per 10⁶ conidia. Using this protocol enabled us to obtain a large number of T-DNA ...
DOI:
10.1016/j.mimet.2011.01.017

8. Enumeration of Vibrio parahaemolyticus in the viable but nonculturable state using direct plate counts and recognition of individual gene fluorescence in situ hybridization

Author:
Kimberly J. Griffitt; Nicholas F. Noriea III; Crystal N. Johnson; D. Jay Grimes
Source:
Journal of microbiological methods 2011 v.85 no.2 pp. 114-118
ISSN:
0167-7012
Subject:
DNA; Vibrio alginolyticus; Vibrio fischeri; Vibrio harveyi; Vibrio parahaemolyticus; Vibrio vulnificus; bacteria; fluorescence; fluorescence in situ hybridization; genes; hemolysins; human health; humans; plate count; population density; risk; waterborne diseases
Abstract:
... Vibrio parahaemolyticus is a gram-negative, halophilic bacterium indigenous to marine and estuarine environments and it is capable of causing food and water-borne illness in humans. It can also cause disease in marine animals, including cultured species. Currently, culture-based techniques are used for quantification of V. parahaemolyticus in environmental samples; however, these can be misleading ...
DOI:
10.1016/j.mimet.2011.02.006

9. Establishment of a human CEACAM1 transgenic mouse model for the study of gonococcal infections

Author:
Guocai Li; Hongmei Jiao; Hua Yan; Jinsong Wang; Xiaohong Wang; Mingchun Ji
Source:
Journal of microbiological methods 2011 v.87 no.3 pp. 350-354
ISSN:
0167-7012
Subject:
Neisseria gonorrhoeae; Western blotting; animal models; cell membranes; flow cytometry; humans; inflammation; mice; polymerase chain reaction; sequence analysis; sexually transmitted diseases; tissues; transgenes; transgenic animals; zygote
Abstract:
... Neisseria gonorrhoeae is the causative microorganism for the sexually transmitted disease (STD) gonorrhea and humans are its only natural host. An animal model would be a useful tool for gonorrhea research, therefore we developed the hCEACAM1 transgenic mice, using an eukaryotic expression vector, pCDPCAM1-GI. This construct was microinjected into the zygotes of C57BL/6 mice and 22 F0 generation t ...
DOI:
10.1016/j.mimet.2011.09.012

10. Establishment of a semi-automated pathogen DNA isolation from whole blood and comparison with commercially available kits

Author:
Herbert Wiesinger-Mayr; Elena Jordana-Lluch; Elisa Martró; Silvia Schoenthaler; Christa Noehammer
Source:
Journal of microbiological methods 2011 v.85 no.3 pp. 206-213
ISSN:
0167-7012
Subject:
DNA; bacteria; blood; centrifugation; detection limit; genes; humans; isolation techniques; microarray technology; nucleic acid hybridization; pathogen identification; pathogens; polymerase chain reaction; ribosomal RNA
Abstract:
... Molecular methods for bacterial pathogen identification are gaining increased importance in routine clinical diagnostic laboratories. Achieving reliable results using DNA based technologies is strongly dependent on pre-analytical processes including isolation of target cells and their DNA of high quality and purity. In this study a fast and semi-automated method was established for bacterial DNA i ...
DOI:
10.1016/j.mimet.2011.03.003

11. How accurately can we detect Mycobacterium avium subsp. paratuberculosis infection?

Author:
Verlaine J. Timms; Michelle M. Gehringer; Hazel M. Mitchell; George Daskalopoulos; Brett A. Neilan
Source:
Journal of microbiological methods 2011 v.85 no.1 pp. 1-8
ISSN:
0167-7012
Subject:
Crohn disease; DNA; Mycobacterium avium complex; Mycobacterium avium subsp. paratuberculosis; RNA; food chain; genetic relationships; human diseases; humans; livestock; livestock and meat industry; molecular biology; paratuberculosis; polymerase chain reaction; rapid methods; scientists; serology
Abstract:
... Mycobacteria have thwarted detection by scientists for centuries. Mycobacterium paratuberculosis is one of the most fastidious of the Mycobacteriaceae, and has been implicated in both animal and human diseases. In domestic livestock, M. paratuberculosis has been associated with Johne's disease, which given its increasing incidence, is currently a cause for concern, due to the potential for M. para ...
DOI:
10.1016/j.mimet.2011.01.026

12. Molecular pathogen detection in biosolids with a focus on quantitative PCR using propidium monoazide for viable cell enumeration

Author:
Jessica K. van Frankenhuyzen; Jack T. Trevors; Hung Lee; Cecily A. Flemming; Marc B. Habash
Source:
Journal of microbiological methods 2011 v.87 no.3 pp. 263-272
ISSN:
0167-7012
Subject:
DNA; Escherichia coli; biosolids; cell viability; compliance; exposure duration; heavy metals; humans; indicator species; land application; laws and regulations; microbial detection; microorganisms; organic matter; pathogens; propidium; quantitative polymerase chain reaction; sewage sludge; turbidity; wastewater; wastewater treatment
Abstract:
... Sewage sludge is the solid, organic material remaining after wastewater is treated and discharged from a wastewater treatment plant. Sludge is treated to stabilize the organic matter and reduce the amount of human pathogens. Once government regulations are met, including material quality standards (e.g., E. coli levels and heavy metal content) sludge is termed “biosolids”, which may be disposed of ...
DOI:
10.1016/j.mimet.2011.09.007

13. Optimizing the growth of stressed Helicobacter pylori

Author:
Crystal L. Richards; Brittany J. Buchholz; Timothy E. Ford; Susan C. Broadaway; Barry H. Pyle; Anne K. Camper
Source:
Journal of microbiological methods 2011 v.84 no.2 pp. 174-182
ISSN:
0167-7012
Subject:
Gram-negative bacteria; Helicobacter pylori; RNA; agar; blood serum; cell division; cell viability; culture media; erythrocytes; genes; humans; oxygen; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; stomach; stomach ulcers; trace elements
Abstract:
... Helicobacter pylori is a Gram-negative bacterium that colonizes the human stomach and is responsible for causing gastric ulcers. H. pylori is known to become stressed and nonculturable after exposure to unfavorable conditions. In this study, we enhanced previously published resuscitation procedures, characterized conditions under which stressed H. pylori can be recovered, and formulated a selectiv ...
DOI:
10.1016/j.mimet.2010.11.015
PubMed:
21129415
PubMed Central:
PMC3034813

14. Orientation and expression of methicillin-resistant Staphylococcus aureus small RNAs by direct multiplexed measurements using the nCounter of NanoString technology

Author:
Marie Beaume; David Hernandez; Mylène Docquier; Céline Delucinge-Vivier; Patrick Descombes; Patrice François
Source:
Journal of microbiological methods 2011 v.84 no.2 pp. 327-334
ISSN:
0167-7012
Subject:
RNA; Staphylococcus aureus; algorithms; antibiotic resistance; bacteria; enzymatic reactions; gene expression; host-pathogen relationships; humans; methicillin; pathogenicity islands; pathogens; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; tissues; virulence
Abstract:
... Staphylococcus aureus is a versatile bacterial opportunist responsible for a wide spectrum of infections. Several genomes of this major human pathogen have been publicly available for almost 10years, but comprehensive links between virulence or epidemicity and genome content of the bacterium are still missing. This project aims at characterizing a set of small transcribed molecules currently ignor ...
DOI:
10.1016/j.mimet.2010.12.025

15. Quantification of specific E. coli in gut mucosa from Crohn's disease patients

Author:
Stina Rikke Jensen; Lisbeth Nielsen Fink; Carsten Struve; Claus Sternberg; Jens Bo Andersen; Jørn Brynskov; Ole Haagen Nielsen; Susanne Brix
Source:
Journal of microbiological methods 2011 v.86 no.1 pp. 111-114
ISSN:
0167-7012
Subject:
Crohn disease; Escherichia coli; digestive tract mucosa; humans; intestines; patients; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction
Abstract:
... We here present a method based on qRT-PCR to quantify E. coli LF82 in intestinal human samples. Two different primer-probe sets were designed to detect LF82, and a third to target total E. coli. The assay showed high robustness and specificity for detection of LF82 in the presence of intestinal tissue. ...
DOI:
10.1016/j.mimet.2011.04.002

16. Serodiagnosis of environmental mycobacterial infections

Author:
Henriette Stavri; Irina Ulea; Dorel L. Radu; Manuela Gheorghiu Branaru; Olga Moldovan; Miron A. Bogdan; Cornelia Tudose; Marinela Raileanu; Dan Duiculescu; Luminita Ene; Viorel Olar; Catalin Ionita; Gabriela Loredana Popa; Mircea I. Popa; Patrick J. Brennan
Source:
Journal of microbiological methods 2011 v.86 no.3 pp. 283-290
ISSN:
0167-7012
Subject:
Human immunodeficiency virus 1; Mycobacterium xenopi; antigens; antibodies; humans; immunomagnetic separation; Mycobacterium kansasii; Mycobacterium scrofulaceum; immunosuppression; respiratory tract diseases; enzyme-linked immunosorbent assay; serodiagnosis; tuberculosis; Mycobacterium avium complex; patients; early diagnosis; Mycobacterium gordonae; Mycobacterium tuberculosis
Abstract:
... To demonstrate the usefulness of enzyme-linked immunosorbent assay for serodiagnosis of mycobacterioses due to environmental mycobacteria we utilized a panel of glycolipid antigens selective for Mycobacterium avium–intracellulare, Mycobacterium kansasii, Mycobacterium xenopi, Mycobacterium scrofulaceum and Mycobacterium gordonae. The levels of circulating antibodies were determined against the env ...
DOI:
10.1016/j.mimet.2011.05.010

17. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach

Author:
Lisa M. Durso; Gregory P. Harhay; James L. Bono; Timothy P.L. Smith
Source:
Journal of microbiological methods 2011 v.84 no.2 pp. 278-282
ISSN:
0167-7012
Subject:
rumen; agricultural soils; beef cattle; animal health; genes; cows; anthropogenic activities; bacterial toxins; lakes; DNA; cecum; feces; virulence; microbial communities; humans; community structure; Proteobacteria; metagenomics; species diversity; soil sampling; toxicity; food safety; chickens; biosynthesis; antibiotic resistance; nucleotide sequences; habitats; bacteria; Sargasso Sea; Antarctic region
Abstract:
... The bovine fecal microbiota impacts human food safety as well as animal health. Although the bacteria of cattle feces have been well characterized using culture-based and culture-independent methods, techniques have been lacking to correlate total community composition with community function. We used high throughput sequencing of total DNA extracted from fecal material to characterize general com ...
Handle:
10113/48149
DOI:
10.1016/j.mimet.2010.12.008

18. The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition

Author:
Lilliana I. Moreno; DeEtta Mills; Jill Fetscher; Krista John-Williams; Lee Meadows-Jantz; Bruce McCord
Source:
Journal of microbiological methods 2011 v.84 no.3 pp. 388-393
ISSN:
0167-7012
Subject:
DNA; environmental exposure; genes; humans; indicator species; intestines; microbial communities; monitoring; mouth; nitrogen-fixing bacteria; nitrogenase; polymerase chain reaction; soil; soil bacteria
Abstract:
... The placement of cadavers in shallow, clandestine graves may alter the microbial and geochemical composition of the underlying and adjacent soils. Using amplicon length heterogeneity-PCR (LH-PCR) the microbial community changes in these soils can be assessed. In this investigation, nine different grave sites were examined over a period of 16weeks. The results indicated that measurable changes occu ...
DOI:
10.1016/j.mimet.2010.11.023

19. A human single-chain variable fragment targeting to Vibrio vulnificus RtxA toxin

Author:
Fang-Yu Hsu; Li-Fang Chou; Lien-I Hor; Hwan-You Chang
Source:
Journal of microbiological methods 2011 v.84 no.1 pp. 94-100
ISSN:
0167-7012
Subject:
DNA libraries; Vibrio vulnificus; antigens; bacteria; bacteriophages; calcium; cytotoxins; diagnostic techniques; enzyme-linked immunosorbent assay; host-pathogen relationships; hosts; human cell lines; humans; immunization; pathogenesis; screening; secretion
Abstract:
... Vibrio vulnificus secretes a multifunctional cytotoxin RtxA (VvRtxA), which plays a major role in the bacterial pathogenesis. The lack of an efficient VvRtxA detection tool has hampered the progress of V. vulnificus pathogenesis research. This study aims to isolate VvRtxA specific single-chain variable fragments (scFv) to serve as a detection agent. The VvRtxA C-terminal Gly-Asp (GD) repeat-contai ...
DOI:
10.1016/j.mimet.2010.11.006

20. A new high resolution screening method for study of phenotype stress responses of Saccharomyces cerevisae mutants

Author:
Håvard Sletta; Geir Klinkenberg; Asgeir Winnberg; Hans Fredrik Nyvold Kvitvang; Marianne Bakke Nilsen; Hans Einar Krokan; Marit Otterlei; Per Bruheim
Source:
Journal of microbiological methods 2011 v.87 no.3 pp. 363-367
ISSN:
0167-7012
Subject:
DNA; DNA damage; Saccharomyces cerevisiae; absorbance; cisplatin; computer software; diploidy; fluorouracil; genes; growth retardation; humans; knockout mutants; phenotype; screening; stress response; yeasts
Abstract:
... A high resolution high throughput screening method has been developed for stress response phenotyping of the global Saccharomyces cerevisiae knock out mutant collection. Stress causing agent is added at three concentrations to individual mutant cultures growing in early exponentially phase in 384-well microplates, and the dynamic effect of stress agent exposure is measured by following subsequent ...
DOI:
10.1016/j.mimet.2011.10.003

21. An optimized method for suicide vector-based allelic exchange in Klebsiella pneumoniae

Author:
Jon Jurriaan van Aartsen; Kumar Rajakumar
Source:
Journal of microbiological methods 2011 v.86 no.3 pp. 313-319
ISSN:
0167-7012
Subject:
Klebsiella pneumoniae; bacteria; genes; genetic variation; gentamicin; human diseases; humans; loci; multiple drug resistance; phenotype; plasmid vectors; plasmids; temperature
Abstract:
... Klebsiella pneumoniae is an important and versatile bacterium that can be found in diverse environments and is also a frequent cause of human infections. Limited data exists on the mechanisms of interaction between K. pneumoniae and the human host and of adaptations to other environments. Coupled with the high genetic diversity of this species, these factors highlight the necessity for substantial ...
DOI:
10.1016/j.mimet.2011.06.006

22. A rapid detection method using flow cytometry to monitor the risk of Legionella in bath water

Author:
Toshitsugu Taguri; Yasunori Oda; Kanji Sugiyama; Toru Nishikawa; Takuro Endo; Shinji Izumiyama; Masayuki Yamazaki; Fumiaki Kura
Source:
Journal of microbiological methods 2011 v.86 no.1 pp. 25-32
ISSN:
0167-7012
Subject:
Legionella; ammonium compounds; bacteria; biofilm; chlorination; chlorine; disinfection; flow cytometry; fluorescence; hot springs; humans; iron; manganese; models; rapid methods; risk; Japan
Abstract:
... Legionella species are the causative agents of human legionellosis, and bathing facilities have been identified as the sources of infection in several outbreaks in Japan. Researchers in Japan have recently reported evidence of significant associations between bacterial counts and the occurrence of Legionella in bathing facilities and in a hot tub model. A convenient and quantitative bacterial enum ...
DOI:
10.1016/j.mimet.2011.03.012

23. Comparison of in vitro and in vivo systems to study ica-independent Staphylococcus aureus biofilms

Author:
Fabienne Antunes Ferreira; Raquel Rodrigues Souza; Raquel Regina Bonelli; Marco Antônio Américo; Sérgio Eduardo Longo Fracalanzza; Agnes Marie Sá Figueiredo
Source:
Journal of microbiological methods 2012 v.88 no.3 pp. 393-398
ISSN:
0167-7012
Subject:
Staphylococcus aureus; animal models; antibiotic resistance; bacteremia; biofilm; blood serum; fibronectins; humans; methicillin; mutants; pathogenesis; polystyrenes; polyurethanes; prostheses; washing
Abstract:
... The ability of Staphylococcus aureus to form biofilms is considered an important factor in the pathogenesis of central venous catheter-related bacteremia and infections associated with the use of medical prostheses. Different methods have been described for assessing staphylococcal biofilms, but few comparative studies have been attempted to evaluate these techniques; especially related to ica-ind ...
DOI:
10.1016/j.mimet.2012.01.007

24. Comparison of nucleic acid extraction platforms for detection of select biothreat agents for use in clinical resource limited settings

Author:
Michelle A. Shipley; Jeffrey W. Koehler; David A. Kulesh; Timothy D. Minogue
Source:
Journal of microbiological methods 2012 v.91 no.1 pp. 179-183
ISSN:
0167-7012
Subject:
Bacillus anthracis; DNA; RNA; Vaccinia virus; Venezuelan equine encephalitis virus; Yersinia pestis; biomedical research; blood; centrifugation; diagnostic techniques; gamma radiation; humans; infectious diseases; laboratory equipment; microbial detection; quantitative polymerase chain reaction; spores; viability; United States
Abstract:
... High-quality nucleic acids are critical for optimal PCR-based diagnostics and pathogen detection. Rapid sample processing time is important for the earliest administration of therapeutic and containment measures, especially in the case of biothreat agents. In this context, we compared the Fujifilm QuickGene-Mini80 to Qiagen's QIAamp Mini Purification kits for extraction of DNA and RNA for potentia ...
DOI:
10.1016/j.mimet.2012.06.008

25. Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis

Author:
Jorunn Pauline Cavanagh; Claus Klingenberg; Anne-Merethe Hanssen; Elizabeth Aarag Fredheim; Patrice Francois; Jacques Schrenzel; Trond Flægstad; Johanna Ericson Sollid
Source:
Journal of microbiological methods 2012 v.89 no.3 pp. 159-166
ISSN:
0167-7012
Subject:
Staphylococcus haemolyticus; clones; essential genes; humans; loci; minisatellite repeats; pathogens; patients; phylogeny; population structure; pulsed-field gel electrophoresis
Abstract:
... The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for ...
DOI:
10.1016/j.mimet.2012.03.014

26. DNA binding site analysis of Burkholderia thailandensis response regulators

Author:
Kristy L. Nowak-Lovato; Alexana J. Hickmott; Tuhin S. Maity; Martha L. Bulyk; John Dunbar; Elizabeth Hong-Geller
Source:
Journal of microbiological methods 2012 v.90 no.1 pp. 46-52
ISSN:
0167-7012
Subject:
Burkholderia pseudomallei; Burkholderia thailandensis; DNA; DNA-binding domains; binding sites; gels; gene expression regulation; humans; loci; microarray technology; pathogens; prediction; protein binding; regulator genes; signal transduction; transcription (genetics); transcription factors
Abstract:
... Bacterial response regulators (RR) that function as transcription factors in two component signaling pathways are crucial for ensuring tight regulation and coordinated expression of the genome. Currently, consensus DNA binding sites in the promoter for very few bacterial RRs have been identified. A systematic method to characterize these DNA binding sites for RRs would enable prediction of specifi ...
DOI:
10.1016/j.mimet.2012.03.019

27. Developing an integrated proteo-genomic approach for the characterisation of biomarkers for the identification of Bacillus anthracis

Author:
Raju V. Misra; Nadia Z. Ahmod; Robert Parker; Min Fang; Haroun Shah; Saheer Gharbia
Source:
Journal of microbiological methods 2012 v.88 no.2 pp. 237-247
ISSN:
0167-7012
Subject:
Bacillus anthracis; Bacillus cereus; anthrax; bacteria; bioinformatics; biomarkers; chromatography; energy; humans; mass spectrometry; models; nucleotide sequences; peptides; proteins; proteome; proteomics; sequence analysis
Abstract:
... Bacillus anthracis is the causative agent of anthrax, an acute and often fatal disease in humans. Due to the high genomic relatedness within the Bacillus cereus group of species it is a challenge to identify B. anthracis consistently. Alternative strategies such as proteomics coupled with mass spectrometry (MS) provide a powerful approach for biomarker discovery. However, validating and evaluating ...
DOI:
10.1016/j.mimet.2011.12.001

28. Establishment of loop-mediated isothermal amplification (LAMP) for rapid detection of Brucella spp. and application to milk and blood samples

Author:
Liuyan Song; Juntao Li; Shuiping Hou; Xunde Li; Shouyi Chen
Source:
Journal of microbiological methods 2012 v.90 no.3 pp. 292-297
ISSN:
0167-7012
Subject:
Brucella; DNA; bacteria; blood; detection limit; genes; humans; loop-mediated isothermal amplification; magnesium; rapid methods; raw milk; sheep; temperature
Abstract:
... Brucella spp. are facultative intracellular bacteria that infect humans and animals. In this study, the loop-mediated isothermal amplification (LAMP) was used to detect the Brucella-specific gene omp25. Reaction conditions were optimized as temperature 65°C, reaction time 60min, Mg²⁺ concentration 8.0mmol/L, polymerase content Bst DNA, 0.5μL, deoxyribonucleotide concentration 1.6mmol/L, and inner/ ...
DOI:
10.1016/j.mimet.2012.05.024

29. Evaluation of two quantitative PCR assays using Bacteroidales and mitochondrial DNA markers for tracking dog fecal contamination in waterbodies

Author:
Dinah D. Tambalo; Tyler Boa; Karen Liljebjelke; Christopher K. Yost
Source:
Journal of microbiological methods 2012 v.91 no.3 pp. 459-467
ISSN:
0167-7012
Subject:
Alces alces; Oreamnos americanus; Rangifer tarandus; bison; deer; dogs; freshwater; genetic markers; horses; humans; mitochondrial DNA; nontarget organisms; parks; quantitative polymerase chain reaction; ribosomal RNA; sewage; surface water; swine; Alberta; Saskatchewan
Abstract:
... This study describes a comparative performance evaluation of two qPCR assays targeting a dog-associated Bacteroidales 16S rRNA genetic marker (CanBac-UCD) and a dog mitochondrial DNA (mtDNA) marker. The same fecal and environmental samples were assayed for the two markers thereby allowing direct comparison. A wide range of non-target species including, human, pig, horse, deer, mountain goat, bison ...
DOI:
10.1016/j.mimet.2012.09.029

30. Gene transfection of Toxoplasma gondii using PEI/DNA polyplexes

Author:
Nasrin Salehi; Ching-An Peng
Source:
Journal of microbiological methods 2012 v.91 no.1 pp. 133-137
ISSN:
0167-7012
Subject:
Toxoplasma gondii; bradyzoites; drugs; fibroblasts; genes; green fluorescent protein; humans; light scattering; parasites; pathogenicity; plasmids; screening; tachyzoites; transfection; zeta potential
Abstract:
... The purpose of this study was to explore the potential of using cationic polyethylenimine (PEI) to deliver green fluorescent protein (GFP) to protozoan parasite Toxoplasma gondii. PEI/DNA polyplexes were formed using branched PEI and pEGFP-N1 plasmid with various N/P ratios that ranged from 5 to 50. With the increment of N/P ratio, the average size of formed PEI/DNA polyplexes determined by dynami ...
DOI:
10.1016/j.mimet.2012.08.001

31. Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing

Author:
Hein Min Tun; Manreetpal Singh Brar; Nina Khin; Li Jun; Raymond Kin-Hi Hui; Scot E. Dowd; Frederick Chi-Ching Leung
Source:
Journal of microbiological methods 2012 v.88 no.3 pp. 369-376
ISSN:
0167-7012
Subject:
Archaea; Bacteroides; Firmicutes; Proteobacteria; antibiotic resistance; cats; chickens; descriptive studies; dogs; feces; fungi; gastrointestinal system; genes; hosts; human health; humans; intestinal microorganisms; metagenomics; mice; microbiome; nutritional intervention; pathogens; phylogeny; sequence analysis; titanium; viruses
Abstract:
... The feline gastrointestinal microbiota have direct influence on feline health and also human health as a reservoir for potential zoonotic pathogens and antibiotic resistant bacterial strains. In order to describe the feline gastrointestinal microbial diversity, fecal samples from cats have been characterized using both culture-dependent and culture-independent methods. However, data correlating to ...
DOI:
10.1016/j.mimet.2012.01.001
PubMed:
22265636
PubMed Central:
PMC7114314

32. Genetic Manipulation of Pathogenicity Loci in Non-Typhimurium Salmonella

Author:
Kristen Butela; Jeffrey G. Lawrence
Source:
Journal of microbiological methods 2012 v.91 no.3 pp. 477-482
ISSN:
0167-7012
Subject:
Salmonella Typhimurium; bacteriophages; foodborne illness; genetic engineering; hosts; humans; intestinal microorganisms; livestock; loci; mutants; pathogenicity; pathogenicity islands; serotypes
Abstract:
... The traditional genetic tools used in Salmonella enterica serovar Typhimurium rely heavily on a high-transducing mutant of bacteriophage P22. P22 recognizes its hosts by the structure of their O-antigens, which vary among serovars of Salmonella; therefore, it cannot be used in most non-Typhimurium Salmonella, including the majority of those causing food-borne illnesses in both humans and livestock ...
DOI:
10.1016/j.mimet.2012.09.013
PubMed:
23041268
PubMed Central:
PMC3658464

33. Identification of Staphylococcus saprophyticus isolated from patients with urinary tract infection using a simple set of biochemical tests correlating with 16S–23S interspace region molecular weight patterns

Author:
Adriano Martison Ferreira; Mariana Fávero Bonesso; Alessandro Lia Mondelli; Maria de Lourdes Ribeiro de Souza da Cunha
Source:
Journal of microbiological methods 2012 v.91 no.3 pp. 406-411
ISSN:
0167-7012
Subject:
Staphylococcus saprophyticus; antibiotic resistance; humans; molecular weight; novobiocin; pathogens; patients; polymerase chain reaction; rapid methods; urinary tract diseases; urine
Abstract:
... The emergence of Staphylococcus spp. not only as human pathogens, but also as reservoirs of antibiotic resistance determinants, requires the development of methods for their rapid and reliable identification in medically important samples. The aim of this study was to compare three phenotypic methods for the identification of Staphylococcus spp. isolated from patients with urinary tract infection ...
DOI:
10.1016/j.mimet.2012.09.024

34. Novel TaqMan® PCR for detection of Leptospira species in urine and blood: Pit-falls of in silico validation

Author:
Steen Villumsen; Rebecca Pedersen; Martin Binderup Borre; Peter Ahrens; Jørgen Skov Jensen; Karen Angeliki Krogfelt
Source:
Journal of microbiological methods 2012 v.91 no.1 pp. 184-190
ISSN:
0167-7012
Subject:
Leptospira; bacteria; blood; detection limit; genes; humans; leptospirosis; patients; quantitative polymerase chain reaction; ribosomal RNA; urine
Abstract:
... In the acute phase of leptospirosis, the diagnosis can be established with high sensitivity by testing blood and urine samples with polymerase chain reaction (PCR). However, only few real-time PCR assays have been validated for diagnostic use. The diagnostic accuracy of a novel TaqMan® PCR (LipL32 real-time PCR) targeting the lipl32 gene (or hap-1) and a previously described TaqMan® PCR (16S real- ...
DOI:
10.1016/j.mimet.2012.06.009

35. Plasmid integration method: a new tool for analysis of the essentiality and function of genes in S. aureus

Author:
Shinichiro Yamachika; Yoshikuni Onodera; Keiichi Hiramatsu; Hiroyuki Takase
Source:
Journal of microbiological methods 2012 v.90 no.3 pp. 250-255
ISSN:
0167-7012
Subject:
NAD (coenzyme); Staphylococcus aureus; essential genes; genetic vectors; humans; plasmids
Abstract:
... Staphylococcus aureus is a Gram-positive coccus and one of the major causes of community‐acquired and hospital-acquired infections. We established the convenient and reliable experimental system for analyzing the essentiality and function of genes, the plasmid integration (PI) method. This method is based on plasmid integration into the genome by single cross-over recombination using a temperature ...
DOI:
10.1016/j.mimet.2012.05.017

36. Rapid identification of oral isolates of Aggregatibacter actinomycetemcomitans obtained from humans and primates by an ultrafast super convection based polymerase chain reaction

Author:
M. Karched; D. Furgang; N. Sawalha; D.H. Fine
Source:
Journal of microbiological methods 2012 v.89 no.1 pp. 71-75
ISSN:
0167-7012
Subject:
Actinobacillus actinomycetemcomitans; Callitrichidae; DNA; Macaca mulatta; Pan troglodytes; Papio; adolescents; agarose; bacteria; gels; humans; periodontitis; polymerase chain reaction; rapid methods; Wisconsin
Abstract:
... Aggregatibacter actinomycetemcomitans is a Gram negative oral bacterium associated with localized aggressive periodontitis (LAP). Detection of A. actinomycetemcomitans in clinical samples is routinely done by PCR. Our aim was to develop a rapid and reliable PCR method that can be used as a chair-side tool to detect A. actinomycetemcomitans in clinical samples. Sensitivity and specificity assessmen ...
DOI:
10.1016/j.mimet.2012.01.016
PubMed:
22326236
PubMed Central:
PMC5568535

37. Rapid quantification of pathogenic fungi by Cellometer image-based cytometry

Author:
Charlotte A. Berkes; Leo Li-Ying Chan; Alisha Wilkinson; Benjamin Paradis
Source:
Journal of microbiological methods 2012 v.91 no.3 pp. 468-476
ISSN:
0167-7012
Subject:
Candida albicans; Histoplasma capsulatum; acridine orange; amphotericin B; biosafety; cytotoxicity; dose response; flow cytometry; humans; itraconazole; macrophages; pathogens; phagosomes; propidium; rapid methods; yeasts
Abstract:
... The objective of this study was to develop an image-based cytometric methodology for the quantification of viable pathogenic yeasts, which can offer increased sensitivity and efficiency when compared to the traditional colony forming unit (CFU) assay. Live/dead yeast quantification by flow cytometry has been previously demonstrated, however, adoption of flow cytometric detection of pathogenic yeas ...
DOI:
10.1016/j.mimet.2012.09.008

38. Real-time PCR and pyrosequencing for differentiation of medically relevant Bartonella species

Author:
Sarah N. Buss; Linda L. Gebhardt; Kimberlee A. Musser
Source:
Journal of microbiological methods 2012 v.91 no.2 pp. 252-256
ISSN:
0167-7012
Subject:
Bartonella; algorithms; humans; quantitative polymerase chain reaction; sequence analysis
Abstract:
... Multiple Bartonella species cause disease in humans. Although fast and accurate species differentiation could inform effective treatment interventions, species-level diagnosis of Bartonella infections is not typical. Here we describe a real-time PCR and pyrosequencing based algorithm for rapid differentiation of at least 11 medically relevant Bartonella spp. ...
DOI:
10.1016/j.mimet.2012.08.014

39. Synthesis of O-serogroup specific positive controls and real-time PCR standards for nine clinically relevant non-O157 STECs

Author:
Cheyenne C. Conrad; Brandon H. Gilroyed; Tim A. McAllister; Tim Reuter
Source:
Journal of microbiological methods 2012 v.91 no.1 pp. 52-56
ISSN:
0167-7012
Subject:
Shiga toxin; Shiga toxin-producing Escherichia coli; antigens; bacteria; biosafety; cell culture; human diseases; humans; pathogens; plasmid vectors; plasmids; quantitative polymerase chain reaction; screening; sequence analysis; serotypes
Abstract:
... Non-O157 Shiga toxin producing Escherichia coli (STEC) are gaining recognition as human pathogens, but no standardized method exists to identify them. Sequence analysis revealed that STEC can be classified on the base of variable O antigen regions into different O serotypes. Polymerase chain reaction is a powerful technique for thorough screening and complex diagnosis for these pathogens, but requ ...
DOI:
10.1016/j.mimet.2012.07.007

40. Use of RapidChek® SELECT™ Salmonella to detect shedding of live attenuated Salmonella enterica serovar Typhi vaccine strains

Author:
Karen E. Brenneman; Caitlin McDonald; Sandra M. Kelly-Aehle; Kenneth L. Roland; Roy Curtiss III
Source:
Journal of microbiological methods 2012 v.89 no.2 pp. 137-147
ISSN:
0167-7012
Subject:
lipopolysaccharides; humans; antibodies; vaccines; mutation; bacteriophages; feces; clinical trials; Salmonella Typhi
Abstract:
... Identification of individuals shedding Salmonella enterica serovar Typhi in stool is imperative during clinical trial safety evaluations. Recovery of live attenuated S. Typhi vaccine strains can be difficult because the mutations necessary for safety in humans often compromise survival in stringent selective enrichment media. RapidChek® SELECT™ Salmonella is a highly sensitive detection method for ...
DOI:
10.1016/j.mimet.2012.03.001

41. A comparison of two approaches to extracting Cryptosporidium DNA from human stools as measured by a real-time PCR assay

Author:
K. Elwin; G. Robinson; S.J. Hadfield; H.V. Fairclough; M. Iturriza-Gómara; R.M. Chalmers
Source:
Journal of microbiological methods 2012 v.89 no.1 pp. 38-40
ISSN:
0167-7012
Subject:
Cryptosporidium; DNA; automation; guanidines; humans; oocysts; quantitative polymerase chain reaction; silica
Abstract:
... Direct extraction of Cryptosporidium DNA from 46 stools by bead-beating, guanidine thiocyanate and silica purification provided slightly lower PCR positivity (93.5% vs. 100%) and higher threshold cycle values (mean 34.93 vs. 28.03; P=0.00) than spin-column extraction from boiled, semi-purified oocyst suspensions. However, direct extraction is cheaper, and amenable to automation. ...
DOI:
10.1016/j.mimet.2012.02.006

42. An improved medium for growing Staphylococcus aureus biofilm

Author:
Ping Chen; Johnathan J. Abercrombie; Nicole R. Jeffrey; Kai P. Leung
Source:
Journal of microbiological methods 2012 v.90 no.2 pp. 115-118
ISSN:
0167-7012
Subject:
Staphylococcus aureus; biofilm; growing media; humans; viability
Abstract:
... A medium (Brain Heart Infusion plus 10% human plasma) was developed, tested, and validated for growing Staphylococcus aureus biofilm in vitro. With this medium, S. aureus forms reproducible and robust biofilms in flow chambers under controlled shear flow and with increased viability recovery in static well plates. ...
DOI:
10.1016/j.mimet.2012.04.009

43. A novel high-resolution melting analysis-based method for Yersinia pseudotuberculosis genotyping

Author:
Roberto A. Souza; Juliana P. Falcão
Source:
Journal of microbiological methods 2012 v.91 no.3 pp. 329-335
ISSN:
0167-7012
Subject:
epidemiological studies; ribosomal RNA; humans; serotypes; genetic variation; melting; nucleotides; multilocus sequence typing; phylogeny; genetic databases; genotype; cost effectiveness; Yersinia pseudotuberculosis; pathogens; single nucleotide polymorphism
Abstract:
... Yersinia pseudotuberculosis is an enteric pathogen that is environmentally widespread and is known to cause human and animal infections. The development of a fast and inexpensive typing system is necessary to facilitate epidemiological studies of Y. pseudotuberculosis infections. In this study, we aimed to develop a method of Y. pseudotuberculosis genotyping based on determining differences in sin ...
DOI:
10.1016/j.mimet.2012.09.006

44. Antimicrobial resistance in Campylobacter: Susceptibility testing methods and resistance trends

Author:
Beilei Ge; Fei Wang; Maria Sjölund-Karlsson; Patrick F. McDermott
Source:
Journal of microbiological methods 2013 v.95 no.1 pp. 57-67
ISSN:
0167-7012
Subject:
Campylobacter jejuni; antibiotic resistance; campylobacteriosis; ciprofloxacin; erythromycin; gentamicin; humans; minimum inhibitory concentration; monitoring; polymerase chain reaction; public health; sequence analysis; tetracycline; therapeutics
Abstract:
... Most Campylobacter infections are self-limiting but antimicrobial treatment (e.g., macrolides, fluoroquinolones) is necessary in severe or prolonged cases. Susceptibility testing continues to play a critical role in guiding therapy and epidemiological monitoring of resistance. The methods of choice for Campylobacter recommended by the Clinical and Laboratory Standards Institute (CLSI) are agar dil ...
DOI:
10.1016/j.mimet.2013.06.021

45. Assessment of a new Bacteroidales marker targeting North American beaver (Castor canadensis) fecal pollution by real-time PCR

Author:
Romain Marti; Yun Zhang; Yuan-Ching Tien; David R. Lapen; Edward Topp
Source:
Journal of microbiological methods 2013 v.95 no.2 pp. 201-206
ISSN:
0167-7012
Subject:
Castor canadensis; Cryptosporidium; Giardia; feces; genes; humans; pathogens; pollution; quantitative polymerase chain reaction; ribosomal RNA; rodents; surface water; watersheds; wildlife
Abstract:
... In many settings wildlife can be a significant source of fecal pathogen input into surface water. The North American beaver (Castor canadensis) is a zoonotic reservoir for several human pathogens including Cryptosporidium spp. and Giardia spp. In order to specifically detect fecal pollution by beavers, we have developed and validated a beaver-specific Bacteroidales marker, designated Beapol01, bas ...
DOI:
10.1016/j.mimet.2013.08.016

46. Campylobacter spp. detection in the 21st century: A review of the recent achievements in biosensor development

Author:
Xiaoyun Yang; Jeffrey Kirsch; Aleksandr Simonian
Source:
Journal of microbiological methods 2013 v.95 no.1 pp. 48-56
ISSN:
0167-7012
Subject:
Campylobacter; biosensors; detection limit; food matrix; humans; infectious diseases; monitoring
Abstract:
... Campylobacter spp. are an important cause of acute bacterial diseases in humans worldwide. Many bacterial species in the Campylobacter genus are considered harmful and may cause several infectious diseases. Currently, there are no commercial biosensors available to detect Campylobacter spp. in food matrices, and little to no testing has been done in research laboratories with actual food matrices. ...
DOI:
10.1016/j.mimet.2013.06.023

47. Comparison of the Caco-2, HT-29 and the mucus-secreting HT29-MTX intestinal cell models to investigate Salmonella adhesion and invasion

Author:
Mélanie Gagnon; Annina Zihler Berner; Noémie Chervet; Christophe Chassard; Christophe Lacroix
Source:
Journal of microbiological methods 2013 v.94 no.3 pp. 274-279
ISSN:
0167-7012
Subject:
Salmonella; adhesion; epithelial cells; epithelium; humans; intestines; models; mucins; mucus; pathogenicity; pathogens; tight junctions
Abstract:
... Human intestinal cell models are widely used to study host-enteric pathogen interactions, with different cell lines exhibiting specific characteristics and functions in the gut epithelium. In particular, the presence of mucus may play an important role in adhesion and invasion of pathogens. The aim of this study was to evaluate the suitability of the mucus-secreting HT29-MTX intestinal epithelial ...
DOI:
10.1016/j.mimet.2013.06.027

48. Detection and identification of opportunistic Exophiala species using the rolling circle amplification of ribosomal internal transcribed spacers

Author:
M.J. Najafzadeh; S. Dolatabadi; M. Saradeghi Keisari; A. Naseri; P. Feng; G.S. de Hoog
Source:
Journal of microbiological methods 2013 v.94 no.3 pp. 338-342
ISSN:
0167-7012
Subject:
Exophiala; agarose; cross reaction; diagnostic techniques; disease course; fungi; gels; humans; internal transcribed spacers; melanization; patients; polymerase chain reaction; rapid methods; ribosomal DNA; single nucleotide polymorphism
Abstract:
... Deep infections by melanized fungi deserve special attention because of a potentially fatal, cerebral or disseminated course of disease in otherwise healthy patients. Timely diagnostics are a major problem with these infections. Rolling circle amplification (RCA) is a sensitive, specific and reproducible isothermal DNA amplification technique for rapid molecular identification of microorganisms. R ...
DOI:
10.1016/j.mimet.2013.06.026

49. Development and evaluation of a method for the quantification of airborne Thermoactinomyces vulgaris by real-time PCR

Author:
Laetitia Betelli; Philippe Duquenne; Frédéric Grenouillet; Xavier Simon; Emeline Scherer; Evelyne Géhin; Alain Hartmann
Source:
Journal of microbiological methods 2013 v.92 no.1 pp. 25-32
ISSN:
0167-7012
Subject:
Actinomycetales; DNA; Thermoactinomyces vulgaris; air; bioaerosols; composting; fluorescence microscopy; genes; humans; hydrolysis; microbial communities; quantitative polymerase chain reaction; risk assessment; selective media
Abstract:
... Actinomycetes are ubiquitous and some can be potentially pathogenic for humans when present in the air of some working areas. It's notably the case for Thermoactinomyces vulgaris in composting facilities where aerial concentrations can reach high values of more than 10⁷CFU·m⁻³. Workers exposure to these inhalable bioaerosols can be the source of various diseases. The literature reveals a lack of k ...
DOI:
10.1016/j.mimet.2012.10.009

50. Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

Author:
Julie A.K. McDonald; Kathleen Schroeter; Susana Fuentes; Ineke Heikamp-deJong; Cezar M. Khursigara; Willem M. de Vos; Emma Allen-Vercoe
Source:
Journal of microbiological methods 2013 v.95 no.2 pp. 167-174
ISSN:
0167-7012
Subject:
Firmicutes; adults; community development; denaturing gradient gel electrophoresis; ecosystems; feces; gels; humans; in vitro studies; inoculum; intestinal microorganisms; intestines; microarray technology; microbial communities; models; phylogeny
Abstract:
... In vitro gut models provide several advantages over in vivo models for the study of the human gut microbiota. However, because communities developed in these models are inevitably simplified simulations of the in vivo environment, it is necessary to broadly define the differences between in vitro consortia and the communities from which they are derived. In this study we characterized microbial co ...
DOI:
10.1016/j.mimet.2013.08.008