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Journal of Microbiological Methods

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https://www.readbyqxmd.com/read/28732694/development-and-evaluation-of-latex-agglutination-tests-for-the-detection-of-human-antibodies-to-the-lipopolysaccharides-of-verocytotoxin-producing-escherichia-coli-vtec-serogroups-o157-and-non-o157
#1
Waldemar Rastawicki, Anna Chróst, Kornelia Gielarowiec
Latex agglutination tests (LAT) were developed and evaluated for the rapid detection of LPS antibodies against E. coli serogroup O157, O26, O104, O111 and O145. The latex tests have been proved to be sensitive, fast, easy-to-perform and cost-efficient tools for the screening serodiagnosis of VTEC infections causing haemolytic-uraemic syndrome.
July 18, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28728910/rapid-differentiation-of-bacterial-communities-using-high-resolution-melting-analysis
#2
Steven Everman, Shiao Y Wang
Analysis of microbial communities is of broad interest in biology and high throughput sequencing is now the preferred method. However, some studies may not need the level of detail high throughput sequencing provides and its cost may limit the number of samples that can be sequenced. High resolution melting analysis (HRM) of 16S rRNA gene variable regions has been proposed as an efficient and low cost method to prioritize samples for sequencing but more specific primers are needed and its efficacy needs to be confirmed...
July 17, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28728909/assessing-impacts-of-dna-extraction-methods-on-next-generation-sequencing-of-water-and-wastewater-samples
#3
Connie Walden, Franck Carbonero, Wen Zhang
Next Generation Sequencing (NGS) is increasingly affordable and easier to perform. However, standard protocols prior to the sequencing step are only available for few selected sample types. Here we investigated the impact of DNA extraction methods on the consistency of NGS results. Four commercial DNA extraction kits (QIAamp DNA Mini Kit, QIAamp DNA Stool Mini Kit, MO BIO Power Water Kit, and MO BIO Power Soil DNA Isolation Kit) were used on sample sources including lake water and wastewater, and sample types including planktonic and biofilm bacteria communities...
July 17, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28716658/stool-antigen-immunodetection-for-diagnosis-of-giardia-duodenalis-infection-in-human-subjects-with-hiv-and-cancer
#4
Maryam Nooshadokht, Behjat Kalantari-Khandani, Iraj Sharifi, Hossein Kamyabi, Namal P M Liyanage, Laurel A Lagenaur, Martin F Kagnoff, Steven M Singer, Zahra Babaei, Shahram Solaymani-Mohammadi
Human infection with the protozoan parasite Giardia duodenalis is one the most common parasitic diseases worldwide. Higher incidence rates of giardiasis have been reported from human subjects with multiple debilitating chronic conditions, including hypogammaglobulinemia and common variable immunodeficiency (CVID). In the current study, stool specimens were collected from 199 individuals diagnosed with HIV or cancer and immunocompetent subjects. The sensitivity of microscopy-based detection on fresh stool preparations, trichrome staining and stool antigen immunodetection for the diagnosis of G...
July 14, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28716657/evaluation-of-sofia-fluorescent-immunoassay-analyzer-for-pneumococcal-urinary-antigen-detection-in-hospitalized-patients-with-community-acquired-pneumonia
#5
Diego Vicente, Maddi López-Olaizola, Idoia de la Caba, Gustavo Cilla
The Sofia Streptococcus pneumoniae FIA® test was prospectively evaluated in non-concentrated urine samples of 106 hospitalized patients with community-acquired pneumonia. The test detected pneumococcal urinary antigen in 24/31 (77.4%) confirmed pneumococcal community-acquired pneumonia episodes. The specificity of the test was 86.7% (92% after urine heating).
July 14, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28711528/comparison-of-five-methods-for-isolation-of-dna-from-mycoplasma-cynos
#6
Aslı Sakmanoglu, Zafer Sayin, Uckun Sait Ucan, Yasemin Pinarkara, Ali Uslu, Osman Erganis
Extraction of DNA from Mycoplasma cultured on agar medium is difficult because the plasticity of these microorganisms enables agar penetration. This eventually causes cell loss during harvesting of colonies from the agar surface. Here, we used the GenElute™ gel extraction kit, which is usually used to purify polymerase chain reaction products, for extracting DNA from Mycoplasma. We compared the DNA extraction efficiency of the GenElute™ gel extraction kit from Mycoplasma cynos cultured in agar medium with four other DNA extraction methods...
July 12, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28709898/development-of-a-duplex-taqman-real-time-pcr-assay-for-rapid-identification-of-vibrio-splendidus-related-and-v-aestuarianus-strains-from-bacterial-cultures
#7
Denis Saulnier, Sophie De Decker, Delphine Tourbiez, Marie Agnès Travers
To enable the rapid and accurate identification of Vibrio splendidus-related and V. aestuarianus strains associated with Pacific cupped oyster Crassostrea gigas mortality, we developed a duplex Taqman real-time PCR assay and evaluated its efficacy. This technique proved to be rapid, sensitive, and specific and will be particularly valuable for epidemiologic studies.
July 12, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28694139/systematic-review-and-meta-analysis-of-the-nitrate-reductase-assay-for-drug-susceptibility-testing-of-mycobacterium-tuberculosis-and-the-detection-limits-in-liquid-medium
#8
Miri Kwak, Won-Kyu Lee, Young Ju Lim, Seung Heon Lee, Sungweon Ryoo
Recently, the need for rapid, reliable, and low-cost drug susceptibility testing (DST) methods has increased due to the emergence of multidrug-resistant Mycobacterium tuberculosis. Colorimetric methods of DST provide results more quickly than standard culture methods and are inexpensive than molecular methods. Thus, colorimetric methods, such as the nitrate reductase assay (NRA), are being recommended. We searched Medline PubMed for reports on the NRA for DST of M. tuberculosis written in English and published within the last five years...
July 8, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28679111/understanding-the-fundamental-mechanisms-of-biofilms-development-and-dispersal-biam-biofilm-intensity-and-architecture-measurement-a-new-tool-for-studying-biofilms-as-a-function-of-their-architecture-and-fluorescence-intensity
#9
Marine Baudin, Bertrand Cinquin, Bianca Sclavi, Dominique Pareau, Filipa Lopes
Confocal laser scanning microscopy (CLSM) is one of the most relevant technologies for studying biofilms in situ. Several tools have been developed to investigate and quantify the architecture of biofilms. However, an approach to quantify correctly the evolution of intensity of a fluorescent signal as a function of the structural parameters of a biofilm is still lacking. Here we present a tool developed in the ImageJ open source software that can be used to extract both structural and fluorescence intensity from CLSM data: BIAM (Biofilm Intensity and Architecture Measurement)...
July 2, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28669800/sensitivity-and-specificity-of-matrix-associated-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms-in-discrimination-at-species-level-for-acinetobacter-bacteremia
#10
Meng-San Wu, Sophie Collier, Po-Yu Liu, Yi-Tzu Lee, Shu-Chen Kuo, Ya-Sung Yang, Te-Li Chen, Zi-Yuan Shi, Chin-Fu Lin
We aimed to establish the role of MALDI-TOF MS on species discrimination of phenotypically indistinguishable A. baumannii, A. pittii and A. nosocomialis. Compared to multiplex PCR, the gold standard, MALDI-TOF MS yielded a high sensitivity for A. baumannii (97.9%) and specificity for A. pittii (98.9%) and A. nosocomialis (100%).
June 29, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28669799/comparison-of-dna-extraction-methods-used-to-detect-bacterial-and-yeast-dna-from-spiked-whole-blood-by-real-time-pcr
#11
Libera M Dalla-Costa, Luis G Morello, Danieli Conte, Luciane A Pereira, Jussara K Palmeiro, Altair Ambrosio, Dayane Cardozo, Marco A Krieger, Sonia M Raboni
Sepsis is the leading cause of death in intensive care units (ICUs) worldwide and its diagnosis remains a challenge. Blood culturing is the gold standard technique for blood stream infection (BSI) identification. Molecular tests to detect pathogens in whole blood enable early use of antimicrobials and affect clinical outcomes. Here, using real-time PCR, we evaluated DNA extraction using seven manual and three automated commercially available systems with whole blood samples artificially contaminated with Escherichia coli, Staphylococcus aureus, and Candida albicans, microorganisms commonly associated with BSI...
June 29, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28655557/rapid-identification-of-st131-escherichia-coli-by-a-novel-multiplex-real-time-allelic-discrimination-assay
#12
Patrice François, Eve-Julie Bonetti, Carolina Fankhauser, Damien Baud, Abdessalam Cherkaoui, Jacques Schrenzel, Stephan Harbarth
Escherichia coli sequence type 131 is increasingly described in severe hospital infections. We developed a rapid real-time allelic discrimination assay for the rapid identification of E. coli ST131 isolates. This rapid assay represents an affordable alternative to sequence-based strategies before completing characterization of potentially highly virulent isolates of E. coli.
June 26, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28655556/comparison-of-two-bioinformatics-tools-used-to-characterize-the-microbial-diversity-and-predictive-functional-attributes-of-microbial-mats-from-lake-obersee-antarctica
#13
Hyunmin Koo, Joseph A Hakim, Casey D Morrow, Peter G Eipers, Alfonso Davila, Dale T Andersen, Asim K Bej
In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae...
June 24, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28647582/comparison-of-sequencing-the-d2-region-of-the-large-subunit-ribosomal-rna-gene-microseq%C3%A2-versus-the-internal-transcribed-spacer-its-regions-using-two-public-databases-for-identification-of-common-and-uncommon-clinically-relevant-fungal-species
#14
S Arbefeville, A Harris, P Ferrieri
CONTEXT: Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. OBJECTIVE: The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data...
June 21, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28645480/comparative-performance-of-aspergillus-galactomannan-elisa-and-pcr-in-sputum-from-patients-with-abpa-and-cpa
#15
Samuel Fayemiwo, Caroline B Moore, Philip Foden, David W Denning, Malcolm D Richardson
OBJECTIVES: Galactomannan (GM) and Aspergillus DNA detection are useful tools for the diagnosis of invasive pulmonary aspergillosis (IPA), primarily in blood and bronchoscopy samples. This study aimed to evaluate the utility of both markers for detection of Aspergillus in sputum from patients with allergic bronchopulmonary aspergillosis (ABPA) and chronic pulmonary aspergillosis (CPA). METHODS: ABPA or CPA demographic patient data were retrieved. This retrospective observational audit included 159 patients with at least one sputum pair...
June 21, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28625706/utility-of-acridine-orange-staining-for-detection-of-bacteria-from-positive-blood-cultures
#16
M Neeraja, V Lakshmi, C Padmasri, K Padmaja
The diagnostic performance of AO stain was evaluated for the detection of bacteria and or fungi from positive blood cultures. The sensitivity of Gram stain (GS) was 98.26% while Acridine Orange (AO) stain proved to be more sensitive (100%) with a Positive and Negative Predictive Value of 100% each. The specificity of both the stains was 100%. Overall agreement between the two stains was 98.23% (688/700). The organisms that were missed by GS and positive by AO were Candida species (Sutton, 2006) and Gram negative bacilli (GNB) (Sutton, 2006)...
June 15, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28625705/the-feasibility-of-improved-live-dead-distinction-in-qpcr-based-microbial-source-tracking
#17
Laura Seidel, Martin Strathmann, Andreas Nocker
PCR-based microbial source tracking (MST) has become a useful tool to identify dominant sources of fecal pollution in water. The method has previously been successfully combined with viability PCR (using propidium monoazide) allowing the preferential detection of membrane-intact bacteria. This study aimed at further improving the selectivity for intact cells when targeting host-specific markers in Bacteroidales bacteria. One approach was to increase amplicon sizes that had been shown to be useful for other applications of viability PCR...
June 15, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28627416/a-combined-application-of-tunable-diode-laser-absorption-spectroscopy-and-isothermal-micro-calorimetry-for-calorespirometric-analysis
#18
David Brueckner, Anna Solokhina, Stephan Krähenbühl, Olivier Braissant
Calorespirometry is the simultaneous analysis of the rate of heat emission (Rq), O2 consumption (RO2) and CO2 production (RCO2) by living systems such as tissues or organism cultures. The analysis provides useful knowledge about thermodynamic parameters relevant for e.g. biotechnology where parameter based yield maximization (fermentation) is relevant. The determination of metabolism related heat emission is easy and normally done by a calorimeter. However, measuring the amount of consumed O2 and produced CO2 can be more challenging, as additional preparation or instrumentation might be needed...
June 13, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28610973/a-two-plasmid-inducible-crispr-cas9-genome-editing-tool-for-clostridium-acetobutylicum
#19
François Wasels, Jennifer Jean-Marie, Florent Collas, Ana M López-Contreras, Nicolas Lopes Ferreira
CRISPR/Cas-based genetic engineering has revolutionised molecular biology in both eukaryotes and prokaryotes. Several tools dedicated to the genomic transformation of the Clostridium genus of Gram-positive bacteria have been described in the literature; however, the integration of large DNA fragments still remains relatively limited. In this study, a CRISPR/Cas9 genome editing tool using a two-plasmid strategy was developed for the solventogenic strain Clostridium acetobutylicum ATCC 824. Codon-optimised cas9 from Streptococcus pyogenes was placed under the control of an anhydrotetracycline-inducible promoter on one plasmid, while the gRNA expression cassettes and editing templates were located on a second plasmid...
June 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28606792/improved-method-for-rapid-and-accurate-isolation-and-identification-of-streptococcus-mutans-and-streptococcus-sobrinus-from-human-plaque-samples
#20
Alissa L Villhauer, David J Lynch, David R Drake
Mutans streptococci (MS), specifically Streptococcus mutans (SM) and Streptococcus sobrinus (SS), are bacterial species frequently targeted for investigation due to their role in the etiology of dental caries. Differentiation of S. mutans and S. sobrinus is an essential part of exploring the role of these organisms in disease progression and the impact of the presence of either/both on a subject's caries experience. Of vital importance to the study of these organisms is an identification protocol that allows us to distinguish between the two species in an easy, accurate, and timely manner...
June 9, 2017: Journal of Microbiological Methods
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