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Journal of Microbiological Methods

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https://www.readbyqxmd.com/read/28803790/utility-of-the-cytochrome-c-oxidase-subunit-i-gene-for-the-diagnosis-of-toxoplasmosis-using-pcr
#1
Xue Feng, Kazumi Norose, Kexin Li, Kenji Hikosaka
Toxoplasmosis is caused by the protozoan parasite Toxoplasma gondii, which belongs to the phylum Apicomplexa. Since this parasite causes severe clinical symptoms in immunocompromised patients, early diagnosis of toxoplasmosis is essential. PCR is currently used for early diagnosis, but there is no consensus regarding the most effective method for amplifying Toxoplasma DNA. In this study, we considered the utility of the cytochrome c subunit I (cox1) gene, which is encoded in the mitochondrial DNA of this parasite, as a novel target of PCR for the diagnosis of toxoplasmosis...
August 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28803789/the-anti-bacterial-effect-of-an-electrochemical-anti-fouling-method-intended-for-the-protection-of-miniaturised-oceanographic-sensors
#2
Jonathan S McQuillan, Andrew K Morris, Martin Arundell, Robin Pascal, Matthew C Mowlem
An electrochemical anti-fouling method, based upon the generation of chlorine from seawater, was applied to a proprietary design of Lab on a Chip conductivity, temperature and dissolved oxygen sensor. The method was evaluated using PCR after a six-week field trial in which it significantly reduced the burden of bacterial biofouling.
August 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28802722/quantification-of-biofilm-biomass-by-staining-non-toxic-safranin-can-replace-the-popular-crystal-violet
#3
Pernille Ommen, Natalia Zobek, Rikke Louise Meyer
Crystal violet staining is commonly used for quantification of biofilm formation, although it is highly toxic. Here we test safranin as a non-toxic replacement. Safranin staining provided similar results as crystal violet, but with higher reproducibility. We therefore recommend safranin staining for biofilm biomass quantification.
August 9, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28802721/comparison-of-commercially-available-preservatives-for-maintaining-the-integrity-of-bacterial-dna-in-human-milk
#4
Kimberly A Lackey, Janet E Williams, William J Price, Janae M Carrothers, Sarah L Brooker, Bahman Shafii, Mark A McGuire, Michelle K McGuire
BACKGROUND: Inhibiting changes to bacteria in human milk between sample collection and analysis is necessary for unbiased characterization of the milk microbiome. Although cold storage is considered optimal, alternative preservation is sometimes necessary. RESEARCH AIM/QUESTION: The objective of this study was to compare the effectiveness of several commercially-available preservatives with regard to maintaining bacterial DNA in human milk for delayed microbiome analysis...
August 9, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28802720/application-of-green-fluorescent-protein-to-measure-antimicrobial-efficacy-and-the-kinetics-of-cell-death-against-escherichia-coli
#5
Richard Greenhalgh, Malcolm Greenhalgh, Fadwa Alshareef, Geoffrey D Robson
Industrial antimicrobials have been extensively used to control unwanted microbial growth by incorporation into a variety of products such as plastics and paints, reducing biodeterioration and biofouling and extending the lifespan of the product. Industrial antimicrobials generally have broad sites of action affecting core cellular functions such as central metabolism, enzyme function, cell wall or DNA synthesis and can either be biocidal or biostatic. In addition, susceptibility can be affected by the metabolic state of the microbe, with metabolically inactive cells generally more resistant than metabolically active cells...
August 9, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28802531/corrigendum-to-characterization-of-the-efficiency-and-uncertainty-of-skimmed-milk-flocculation-for-the-simultaneous-concentration-and-quantification-of-water-borne-viruses-bacteria-and-protozoa-j-microbiol-methods-134-2017-46-53
#6
Eloy Gonzales-Gustavson, Yexenia Cárdenas-Youngs, Miquel Calvo, Marcelle Figueira Marques da Silva, Ayalkibet Hundesa, Inmaculada Amorós, Yolanda Moreno, Laura Moreno-Mesonero, Rosa Rosell, Llilianne Ganges, Rosa Araujo, Rosina Girones
No abstract text is available yet for this article.
August 9, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28780272/current-challenges-in-the-accurate-identification-of-streptococcus-pneumoniae-and-its-serogroups-serotypes-in-the-vaccine-era
#7
REVIEW
Rosemol Varghese, Ranjith Jayaraman, Balaji Veeraraghavan
Streptococcus pneumoniae is a major cause of pneumonia, meningitis and other invasive diseases resulting in high mortality and morbidity among children under the age of five. Inaccurate identification of S. pneumoniae masks the exact estimation of disease burden and could delay treatment options. This is the common problem most frequently faced in developing countries due to several reasons that include poor infrastructure, insensitive operational procedures and lack of expertise. Inconsistent methods for phenotypic detection often delay the early identification and confirmation of S...
August 2, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28760586/inactivation-of-microbicidal-active-halogen-compounds-by-sodium-thiosulphate-and-histidine-methionine-for-time-kill-assays
#8
Barbara Böttcher, Bettina Sarg, Herbert H Lindner, Markus Nagl
Rapid inactivation of antimicrobial test agents after exact incubation times with microorganisms is required in time-kill assays. Sodium thiosulphate and a combination of methionine and histidine were compared for neutralisation of active halogen compounds. Test oxidants were mixed with surplus sodium thiosulphate (3%-6%) or histidine/methionine (1% each) in phosphate-buffered saline and incubated for different times, followed by addition of Staphylococcus aureus, Escherichia coli, or Pseudomonas aeruginosa at 1000CFU/ml...
July 29, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28756184/development-and-validation-of-a-new-loop-mediated-isothermal-amplification-for-detection-of-pathogenic-leptospira-species-in-clinical-materials
#9
Yun-Hsiu Hsu, Shih-Jen Chou, Chih-Cheng Chang, Ming-Jeng Pan, Wei-Cheng Yang, Chuen-Fu Lin, Kun-Wei Chan
Leptospirosis, a global zoonotic disease, is often neglected but has a significant impact on human health. Here we reported a new loop mediated isothermal amplification (LAMP) assay targeting lipL32 gene of pathogenic Leptospira spp. Polymerase chain reaction (PCR), nested-PCR and real-time PCR assays were included in this study for the comparison of analytic and diagnostic sensitivity and specificity. LipL32 LAMP we designed enables detection of 10 copies of L. interrogans and has a higher diagnostic sensitivity (91...
July 26, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28754448/evaluation-of-omnigene%C3%A2-%C3%A2-sputum-for-tuberculosis-sample-processing-and-liquid-culture-at-a-hospital-laboratory-in-india
#10
Remya Nambiar, Kaitlyn Shaw, Patricia S Curry
This preliminary evaluation examined the reagent OMNIgene®•SPUTUM (OM-S) as a tool to eliminate NaOH/NALC processing prior to Middlebrook liquid culture for Mycobacterium tuberculosis (MTb). Twenty-seven manually split samples (OM-S-treated vs. NaOH/NALC) showed 100% agreement: 81.5% MTb-positive and 18.5% MTb-negative. On average, OM-S-treated specimens required 1.2 additional days to culture positivity.
July 25, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28754447/maldi-tof-ms-identification-and-antimicrobial-susceptibility-testing-directly-from-positive-enrichment-broth
#11
Tré-Hardy Marie, Lambert Barbara, Despas Noémie, Bressant Florian, Laurenzano Clémentine, Rodriguez-Villalobos Hector, Verroken Alexia
A rapid preparation procedure was validated for MALDI-TOF MS identification followed by an antimicrobial susceptibility testing directly from a non-selective enrichment broth of sterile fluid samples associated with negative classical cultures. This method can be easily integrated in the laboratory routine allowing precious time gain for microbe identification and subsequent adequate treatment initiation.
July 25, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28754446/selection-of-reliable-reference-genes-for-gene-expression-studies-in-trichoderma-afroharzianum-ltr-2-under-oxalic-acid-stress
#12
Yuping Lyu, Xiaoqing Wu, He Ren, Fangyuan Zhou, Hongzi Zhou, Xinjian Zhang, Hetong Yang
An appropriate reference gene is required to get reliable results from gene expression analysis by quantitative real-time reverse transcription PCR (qRT-PCR). In order to identify stable and reliable reference genes in Trichoderma afroharzianum under oxalic acid (OA) stress, six commonly used housekeeping genes, i.e., elongation factor 1, ubiquitin, ubiquitin-conjugating enzyme, glyceraldehyde-3-phosphate dehydrogenase, α-tubulin, actin, from the effective biocontrol isolate T. afroharzianum strain LTR-2 were tested for their expression during growth in liquid culture amended with OA...
July 25, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28732695/optimization-of-genotypic-and-biochemical-methods-to-profile-p-acnes-isolates-from-a-patient-population
#13
Rubén Cebrián, Sergio Arévalo, Salvador Arias-Santiago, Cristina Riazzo, M Dolores Rojo, Pilar Bermúdez, Eva Valdivia, Manuel Martínez-Bueno, Mercedes Maqueda
Propionibacterium acnes is a key factor in the pathogenesis of acne vulgaris, although currently it is also being associated with medical-device infections. The aim of this work was to validate a safe and quick identification and typing of 24 clinical isolates of Propionibacterium acnes, applying a range of biochemical as well as genetic methods, and investigating the pathogenic potential to associate the different types with human health. RAPD-PCRs revealed the existence of two discernible clusters in correspondence with the phylogroups I and II, according to the PAtig gene polymorphism, leading them to be assigned as P...
July 18, 2017: Journal of Microbiological Methods
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
#14
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
#15
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
#16
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/28716657/evaluation-of-sofia-fluorescent-immunoassay-analyzer-for-pneumococcal-urinary-antigen-detection-in-hospitalized-patients-with-community-acquired-pneumonia
#17
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 15, 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
#18
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/28711528/comparison-of-five-methods-for-isolation-of-dna-from-mycoplasma-cynos
#19
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
#20
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
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