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Journal of Microbiological Methods

Thomas Demuyser, Deborah De Geyter, Daisy Van Dorpe, Kristof Vandoorslaer, Ingrid Wybo
Anaerobic infections are difficult to diagnose and treat, because of the often slow in vitro growth, the polymicrobial nature and the increasing antimicrobial resistance. Furthermore because of their fastidiousness, anaerobic bacteria often stay unrecognized in clinical practice. Clinical specimens potentially harboring these species require special handling to permit satisfactory recovery of these potential important pathogens. In a clinical setting, temporary storage and transportation to the laboratory are unavoidable before these specimens can be cultured...
November 13, 2017: Journal of Microbiological Methods
Jun Sakai, Takuya Maeda, Norihito Tarumoto, Kazuhisa Misawa, Shinsuke Tamura, Kazuo Imai, Toshiyuki Yamaguchi, Satoshi Iwata, Takashi Murakami, Shigefumi Maesaki
No abstract text is available yet for this article.
November 11, 2017: Journal of Microbiological Methods
Abolfazl Jahangiri, Iraj Rasooli, Parviz Owlia, Abbas Ali Imani Fooladi, Jafar Salimian
Omp34, also known as Omp34kDa or Omp33-36 is a virulence factor associated with A. baumannii metabolic fitness or its adherence and invasion to human epithelial cells. This protein is also introduced as a specific antigen which could induce strong antibody responses. In the present in silico study, recent vaccine design strategies such as 'antigen minimization' and 'high epitope density' were invoked to design a soluble immunogen with higher antigenicity. As an advantage, the tools employed in the current study are easily available...
November 10, 2017: Journal of Microbiological Methods
Kyungjong Kim, Jeong Seong Yang, Hee Baeg Choi, Seung Heon Lee
Molecular drug susceptibility testing (DST) for antituberculosis drugs is important for improving the efficacy of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) treatment. In this study, we developed a molecular high-throughput assay system based on allele-specific primer extension (ASPE) and MagPlex-TAG microspheres, referred to here as TAG-ASPE, which can detect mutations related to resistance to injectable second-line drugs and fluoroquinolones. Target genes were amplified by multiplex PCR using DNA from H37Rv and 190 clinical Mycobacterium tuberculosis strains and extended by ASPE using 22 ASPE primers...
November 9, 2017: Journal of Microbiological Methods
Hongchao Gou, Juan Li, Rujian Cai, Shuai Song, Miao Li, Dongxia Yang, Zhiyong Jiang, Yan Li, Pinpin Chu, Chunling Li
Haemophilus parasuis infection is of considerable economic importance in the swine industry due to high morbidity and mortality in naive swine populations. Accurate detection and identification of the causative agent are difficult, yet necessary, for disease control. In this study, a simple and rapid method of cross-priming amplification (CPA) with a vertical flow (VF) visualization strip was established to detect H. parasuis. The reaction can specifically identify 15 serovar reference strains and 57 clinically isolated strains of H...
November 9, 2017: Journal of Microbiological Methods
Ramadevi Prathapam, Tsuyoshi Uehara
Tools to enable genome editing are essential for understanding physiology. Here we report a gene replacement method in Pseudomonas aeruginosa using a temperature-sensitive replicon plasmid that does not require mating or isolation of a merodiploid intermediate. This approach was validated by replacing the non-essential ampD gene with a gentamicin resistance cassette. In addition lpxA and lpxD, both located in a complex gene cluster including multiple downstream essential genes, were inactivated when complemented by each target gene in trans...
November 9, 2017: Journal of Microbiological Methods
Diana Rocha, Beatriz Ruiz-Villafán, Monserrat Manzo, Romina Rodríguez-Sanoja, Sergio Sánchez
Bacterial conjugation is a powerful tool used for DNA transfer from Escherichia coli into various bacteria including streptomycetes. In this methodology, spores are usually employed as recipient cells of the genetic information. However, some industrially important Streptomyces do not produce spores making difficult their genetic manipulation. In these strains, the use of mechanically fragmented mycelia allows DNA transfer with low efficiency. Streptomyces peucetius var. caesius is a non-sporulating bacteria which produces the antitumor compound doxorubicin...
November 7, 2017: Journal of Microbiological Methods
Badal C Saha, Gregory J Kennedy
Itaconic acid (IA) is a building block platform chemical that is currently produced industrially from glucose by fermentation with Aspergillus terreus. However, lignocellulosic biomass has the potential to serve as low cost source of sugars for production of IA. Previously, 100 A. terreus strains were evaluated for production of IA from pentose sugars in shake-flasks. Six selected strains were then investigated for IA production in shake-flasks. But none of the strains grew and produced IA using biomass hydrolyzates...
November 3, 2017: Journal of Microbiological Methods
Dongxin Liu, Bing Zhao, Xichao Ou, Huiwen Zheng, Aijing Ma, Wencong He, Shengfen Wang, Yang Zhou, Hui Xia, Yang Zheng, Ping Hou, Guangxue He, Yanlin Zhao
Mycobacterium tuberculosis (MTB) is the causative agent of pulmonary tuberculosis. Rapid and accurate diagnosis is crucial to tuberculosis control and prevention. A series of diagnostic methods has been available for MTB detection; however, new rapid, simple and affordable methods are needed. In this study, a multiple cross displacement amplification (MCDA)-based assay was developed to detect the IS6110 gene of the M. tuberculosis complex. Hydroxy naphthol blue (HNB), a colorimetric indicator, was used to detect amplification products...
November 3, 2017: Journal of Microbiological Methods
Mark E Fuller, Christina Andaya, Kevin McClay
This research evaluated the utility of using the large amount of spectral data obtained during attenuated total reflection Fourier-transform infrared spectrophotometry (ATR-FTIR) analysis of dried biocellulose (BC) to estimate the type and concentration of potential bacterial cells impurities present in the BC. Pre-cleaned BC was contaminated with known concentrations of representative nucleic acid, lipid, and protein impurities, as well as whole bacterial cells. These impurity standards were then subjected to ATR-FTIR analysis, and the resulting spectral data were used to develop models to estimate the concentrations of impurities in differentially processed BC...
November 2, 2017: Journal of Microbiological Methods
Ariadna Martín, Ana Pérez-Ayala, Fernando Chaves, David Lora, M Ángeles Orellana
Rapid and accurate detection of the pathogens that cause gastrointestinal infection is important for appropriate therapy and proper infection control. This study assesses the performance of a new molecular assay for simultaneous detection of 13 different gastrointestinal bacteria in stool specimens. Using the Allplex GI-Bacteria (AGI-BI/AGI-BII) assay, a total of 394 stool samples were tested and the results were compared with culturing on selective differential followed by identification by mass spectroscopy...
October 31, 2017: Journal of Microbiological Methods
Łukasz Krych, Witold Kot, Katja M B Bendtsen, Axel K Hansen, Finn K Vogensen, Dennis S Nielsen
The Dextran Sulfate Sodium (DSS) induced colitis mouse model is commonly used to investigate human inflammatory bowel disease (IBD). Nucleic acid extracts originating from these animals are often contaminated with DSS, which is a strong inhibitor of many enzymatic based molecular biology reactions including PCR and reverse-transcription (RT). Methods for removing DSS from nucleic acids extracts exist for RNA, but no effective protocol for DNA or cDNA is currently available. However, spermine has previously been shown to be an effective agent for counteracting DSS inhibition of polynucleotide kinase, which led to the hypothesis, that spermine could be used to counteract DSS inhibition of PCR and RT...
October 28, 2017: Journal of Microbiological Methods
Sharon A Waller, Aaron I Packman, Martina Hausner
Drinking water quality typically degrades after treatment during conveyance through the distribution system. Potential causes include biofilm growth in distribution pipes which may result in pathogen retention, inhibited disinfectant diffusion, and proliferation of bad tastes and odors. However, there is no standard method for direct measurement of biofilms or quantification of biofilm cells in drinking water distribution systems. Three methods are compared here for quantification of biofilm cells grown in pipe loops samplers: biofilm heterotrophic plate count (HPC), biofilm biovolume by confocal laser scanning microscopy (CLSM) and biofilm total cell count by flow cytometry (FCM) paired with Syto 9...
October 27, 2017: Journal of Microbiological Methods
Ichiro Takajo, Akiteru Yamada, Kazumi Umeki, Yuji Saeki, Yuuki Hashikura, Ikuo Yamamoto, Kunihiko Umekita, Midori Urayama-Kawano, Shogo Yamasaki, Takako Taniguchi, Naoaki Misawa, Akihiko Okayama
Vibrio furnissii and V. fluvialis are closely related, the discrimination of which by conventional biochemical assay remains a challenge. Investigation of the sequence of the 16S rRNA genes in a clinical isolate of V. furnissii by visual inspection of a sequencing electropherogram revealed two sites of single-nucleotide polymorphisms (SNPs; positions 460 A/G and 1261 A/G) in these genes. A test of 12 strains each of V. fluvialis and V. furnissii revealed these SNPs to be common in V. furnissii but not in V...
October 27, 2017: Journal of Microbiological Methods
Maika Furukawa, Jonathan Stirling, Naoaki Misawa, John E Moore
A novel bacteriological agar, named Furukawa Agar, has been specifically designed to inhibit the growth of filamentous fungi during microbiological examination of bacteria from organic compost, thereby allowing complete analysis of the resulting bacterial organisms, without the overgrowth with filamentous fungi.
October 26, 2017: Journal of Microbiological Methods
Fedor N Dultsev, Nina N Kurus
Rupture Event Scanning (REVS) was used to study oligonucleotide unwinding under mechanical load. Oligonucleotide melting temperature was successfully estimated using this method. To estimate the enthalpy of reaction, we represented denaturation process as a unimolecular reaction. This gave us the possibility to recover the force profile from the experimental data obtained in force measurements at different scanning time (reaction time) for different temperatures.
October 26, 2017: Journal of Microbiological Methods
Weijia Liu, Bing Li, Haiqing Chu, Zhemin Zhang, Liulin Luo, Wei Ma, Shiyi Yang, Qi Guo
Clarithromycin resistance is increasing dramatically among Mycobacterium abscessus complex. The main resistance mechanisms are mutations in the erm(41) and rrl genes. Here we report PCR-based denaturing gradient gel electrophoresis (DGGE) as an alternative method for rapidly detection of mutations in erm(41) and rrl among M. abscessus isolates. Four primer sets targeting the full-length erm(41) gene and a 354bp fragment of the rrl gene were designed. A combination of 16 different DGGE patterns were observed for erm(41) gene, including 16 in M...
October 24, 2017: Journal of Microbiological Methods
Pierre Thouvenot, Guillaume Vales, Hélène Bracq-Dieye, Nathalie Tessaud-Rita, Mylène M Maury, Alexandra Moura, Marc Lecuit, Alexandre Leclercq
This study aimed to evaluate MALDI-TOF MS for species discrimination of Listeria in the context of routine surveillance. MALDI-TOF MS yielded 100% accuracy for the identification of L. monocytogenes, L. innocua, L. ivanovii, L. fleischmannii, L. grayi, L. seeligeri, L. weihenstephanensis and L. welshimeri, as confirmed by whole genome sequence analyses.
October 21, 2017: Journal of Microbiological Methods
Ramona Kuhn, Jörg Böllmann, Kathrin Krahl, Isaac Mbir Bryant, Marion Martienssen
DNA extraction for molecular biological applications usually requires target optimized extraction procedures depending on the origin of the samples. For environmental samples, a range of different procedures has been developed. We compared the applicability and efficiency of ten selected DNA extraction methods published in recent literature using four different environmental samples namely: activated sludge from a domestic wastewater treatment plant, river sediment, anaerobic digestion sludge and nitrifying enrichment culture...
October 19, 2017: Journal of Microbiological Methods
Vladimira Hinić, Josiane Reist, Adrian Egli
We evaluated a rapid biochemical screening test β-CARBA™ for detection of Gram-negative carbapenemase producers. The sensitivity of the test after 30min incubation was 98.2%, but increased to 100% after 1h. β-CARBA™ proved reliable for carbapenemase screening in Acinetobacter spp. for which currently no commercial phenotypic assays are available.
October 19, 2017: Journal of Microbiological Methods
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