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Journal of Microbiological Methods

Chandrashekhar Patil, Rahul Suryawanshi, Sunil Koli, Satish Patil
Aminocyclopropane-1-carboxylate deaminase (ACCD) producing microorganisms support plant growth under a variety of biotic and abiotic stress conditions such as drought, soil salinity, flooding, heavy metal pollution and phyto-pathogen attack. Available screening methods for ACCD give idea only about its primary microbial ACCD activity than the actual potential. In the present investigation, we have simply improved screening method by incorporating pH indicator dyes (phenol red and bromothymol blue) in ACC containing medium...
October 18, 2016: Journal of Microbiological Methods
Manjula Ramya Vutukuru, Divya Khandige Sharma, M S Ragavendar, Susanne Schmolke, Yiwei Huang, Walter Gumbrecht, Nivedita Mitra
Molecular diagnostics is a promising alternative to culture based methods for the detection of bloodstream infections, notably due to its overall lower turnaround time when starting directly from patient samples. Whole blood is usually the starting diagnostic sample in suspected bloodstream infections. The detection of low concentrations of pathogens in blood using a molecular assay necessitates a fairly high starting volume of blood sample in the range of 5-10mL. This large volume of blood sample has a substantial accompanying human genomic content that interferes with pathogen detection...
October 17, 2016: Journal of Microbiological Methods
Xinfeng Liu, Yuyao Guan, Shiliang Cheng, Yidan Huang, Qin Yan, Jun Zhang, Guanjun Huang, Jian Zheng, Tianqiang Liu
Vibrio parahaemolyticus is widely present in brackish water all over the world, causing infections in certain aquatic animals. It is also a foodborne pathogen that causes diarrhea in humans. The aim of this study is to develop an immunochromatographic lateral flow assay (LFA) for rapid detection of V. parahaemolyticus in both aquatic products and human feces of diarrheal patients. Two monoclonal antibody (MAb) pairs, GA1a-IC9 and IC9-KB4c, were developed and proven to be highly specific and sensitive to V. parahaemolyticus...
October 15, 2016: Journal of Microbiological Methods
Didrik Hjertaker Grevskott, Cecilie Smith Svanevik, Astrid Louise Wester, Bjørn Tore Lunestad
Continuous European Union programmes with specified methods for enumeration of Escherichia coli in bivalves for human consumption are currently running. The objective of this research was to examine the species accuracy of the five times three tube Most Probable Number (MPN) EU reference method used for detection of E. coli in marine bivalves. Among 549 samples of bivalves harvested from Norwegian localities during 2014 and 2015, a total number of 200 bacterial isolates were prepared from randomly selected culture-positive bivalves...
October 13, 2016: Journal of Microbiological Methods
Charlotte A Huber, Hanna E Sidjabat, Hosam M Zowawi, David Kvaskoff, Sarah Reed, John F McNamara, Kate L McCarthy, Patrick Harris, Benjamin Toh, Alexander M Wailan, David L Paterson
It has been described that the sensitivity of the Carba NP test may be low in the case of OXA-48-like carbapenamases and mass spectrometry based methods as well as a colorimetry based method have been described as alternatives. We evaluated 84 Enterobacteriaceae isolates including 31 OXA-48-like producing isolates and 13 isolates that produced either an imipenemase (IMP; n=8), New Delhi metallo-β-lactamase (NDM; n=3), or Klebsiella pneumoniae carbapenemase (KPC; n=2), as well as 40 carbapenemase negative Enterobacteriaceae isolates...
October 11, 2016: Journal of Microbiological Methods
Bin-Yan Wu, Jian-Ren Ye, Lin Huang, Ling-Min He, De-Wei Li
Burkholderia pyrrocinia strain JK-SH007 isolated from poplar stems plays a highly significant role in the growth promotion and the biocontrol of poplar canker during colonization in poplar. In this research, the ideal reference gene was filtered and determined for the transcript normalization. Additionally, the expression of pyrG under all four conditions was relatively stable in B. pyrrocinia JK-SH007.
October 7, 2016: Journal of Microbiological Methods
Stephanie Karmann, Stéphanie Follonier, Monica Bassas-Galia, Sven Panke, Manfred Zinn
Poly(3-hydroxyalkanoates) (PHAs) are bio-based and biodegradable polyesters which have been considered as a promising alternative to petrol-based plastics. Its bacterial production is a dynamic process in which intracellular polymerization and depolymerization are closely linked and depend on the availability of carbon substrates and other nutrients. These dynamics require a fast and quantitative method to determine the optimal harvest-time of PHA containing cells or to adjust carbon supply. In principle, flow cytometry (FCM) is an ideal tool that suits these requirements and, in addition, provides data on the PHA content of different cell populations...
October 6, 2016: Journal of Microbiological Methods
Robert D Stedtfeld, Tiffany M Stedtfeld, Farag Samhan, Yogendra H Kanitkar, Paul B Hatzinger, Alison M Cupples, Syed A Hashsham
Nucleic acid amplification of biomarkers is increasingly used to monitor microbial activity and assess remedial performance in contaminated aquifers. Previous studies described the use of filtration, elution, and direct isothermal amplification (i.e. no DNA extraction and purification) as a field-able means to quantify Dehalococcoides spp. in groundwater. This study expands previous work with direct loop mediated isothermal amplification (LAMP) for the detection and quantification of Dehalobacter spp. in groundwater...
October 5, 2016: Journal of Microbiological Methods
M Colby Hunter, Alex E Pozhitkov, Peter A Noble
Conceptual models suggest that certain microorganisms (e.g., the "red" complex) are indicative of a specific disease state (e.g., periodontitis); however, recent studies have questioned the validity of these models.Here, the abundances of 500+ microbial species were determined in 16 patients with clinical signs of one of the following oral conditions: periodontitis, established caries, edentulism, and oral health.Our goal was to determine if the abundances of certain microorganisms reflect dysbiosis or a specific clinical condition that could be used as a 'signature' for dental research...
October 4, 2016: Journal of Microbiological Methods
Rômulo Pessoa-E-Silva, Lays Adrianne Mendonça Trajano-Silva, Maria Almerice Lopes da Silva, Suênia da Cunha Gonçalves-de-Albuquerque, Tayná Correia de Goes, Rayana Carla Silva de Morais, Fábio Lopes de Melo, Milena de Paiva-Cavalcanti
The availability of some sorts of biological samples which require noninvasive collection methods has led to an even greater interest in applying molecular biology on visceral leishmaniasis (VL) diagnosis, since these samples increase the safety and comfort of both patients and health professionals. In this context, this work aimed to evaluate the suitability of the urine as a specimen for Leishmania infantum kinetoplast DNA detection by real-time quantitative PCR (qPCR). Subsequent to the reproducibility analysis, the detection limit of the qPCR assay was set at 5fg (~0...
October 3, 2016: Journal of Microbiological Methods
Fernanda Tomiotto-Pellissier, Allan Henrique Depieri Cataneo, Tatiane Marcuso Orsini, Ana Paula Fortes Dos Santos Thomazelli, Gabriela Alcântara Dalevedo, Admilton Gonçalves de Oliveira, Luciano Aparecido Panagio, Idessania Nazareth Costa, Ivete Conchon-Costa, Wander Rogério Pavanelli, Ricardo Sergio Almeida
Galleria mellonella is an excellent invertebrate model for the study of diseases that involve interactions with cells from the innate immune system, since they have an innate immune system capable of recognizing the pathogens. Here we present for the first time, an alternative model for an in vitro phagocytic assay using hemocytes of G. mellonella larvae to study infection by Leishmania (Viannia) braziliensis. We showed that the insect phagocytic cells were able to engulf promastigotes. Furthermore, this infective form differentiated into the amastigote form inside those cells...
October 3, 2016: Journal of Microbiological Methods
Andrée F Maheux, Adnane Sellam, Yves Piché, Maurice Boissinot, René Pelletier, Dominique K Boudreau, François J Picard, Hélène Trépanier, Marie-Josée Boily, Marc Ouellette, Paul H Roy, Michel G Bergeron
Successful treatment of a Candida infection relies on 1) an accurate identification of the pathogenic fungus and 2) on its susceptibility to antifungal drugs. In the present study we investigated the level of correlation between phylogenetical evolution and susceptibility of pathogenic Candida spp. to antifungal drugs. For this, we compared a phylogenetic tree, assembled with the concatenated sequences (2475-bp) of the ATP2, TEF1, and TUF1 genes from 20 representative Candida species, with published minimal inhibitory concentrations (MIC) of the four principal antifungal drug classes commonly used in the treatment of candidiasis: polyenes, triazoles, nucleoside analogues, and echinocandins...
October 3, 2016: Journal of Microbiological Methods
Alejandro Caicedo-Ramirez, Alison L Ling, Mark Hernandez
A new generation of laminates and cementitious materials incorporate antimicrobial metals into domestic infrastructure. Conventional culturing approaches are unsuitable for assessing the inhibitory properties of these materials. Modifications to the radial Kirby-Bauer antibiotic assay, which incorporate metal impregnated activated carbon in linear formats, reveal relative metal sensitivities of destructive acidophiles.
October 1, 2016: Journal of Microbiological Methods
Linnea K Honeker, Robert A Root, Jon Chorover, Raina M Maier
Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME μXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings...
September 29, 2016: Journal of Microbiological Methods
Janine McGowan, Alvaro De la Mora, Paul H Goodwin, Marc Habash, Mollah Md Hamiduzzaman, Paul G Kelly, Ernesto Guzman-Novoa
The microsporidium fungus Nosema ceranae is an intracellular parasite that infects the midgut of the honey bee, Apis mellifera. A major limitation of research on N. ceranae is that the fungus is non-culturable and thus studying it depends on the seasonal availability of Nosema spores. Also, spore viability and infectivity can vary considerably, and thus there is a need for reliable methods for determining those traits. This study examined different conditions for N. ceranae spore cryopreservation at -70°C, assessing spore viability and infectivity...
September 29, 2016: Journal of Microbiological Methods
Maaike J C van den Beld, Alexander W Friedrich, Evert van Zanten, Frans A G Reubsaet, Mirjam A M D Kooistra-Smid, John W A Rossen
An inter-laboratory collaborative trial for the evaluation of diagnostics for detection and identification of Shigella species and Entero-invasive Escherichia coli (EIEC) was performed. Sixteen Medical Microbiological Laboratories (MMLs) participated. MMLs were interviewed about their diagnostic methods and a sample panel, consisting of DNA-extracts and spiked stool samples with different concentrations of Shigella flexneri, was provided to each MML. The results of the trial showed an enormous variety in culture-dependent and molecular diagnostic techniques currently used among MMLs...
September 28, 2016: Journal of Microbiological Methods
Cecile Levasseur-Garcia, Hugo Malaurie, Nathalie Mailhac
In most vineyards worldwide, agents of grapevine trunk diseases represent a real threat for viticulture and are responsible for significant economic loss to the wine industry. The conventional microbiological isolation technique used to diagnose this disease is tedious and frequently leads to false negatives. Thus, a dire need exists for an alternative method to detect this disease. One possible way involves infrared spectroscopy, which is a rapid, nondestructive analytical tool that is commonly used for quality control of feed stuffs...
September 28, 2016: Journal of Microbiological Methods
Jeremy E Ellis, Dara S Missan, Matthew Shabilla, Delyn Martinez, Stephen E Fry
Currently, there is a critical need to rapidly identify infectious organisms in clinical samples. Next-Generation Sequencing (NGS) could surmount the deficiencies of culture-based methods; however, there are no standardized, automated programs to process NGS data. To address this deficiency, we developed the Rapid Infectious Disease Identification (RIDI™) system. The system requires minimal guidance, which reduces operator errors. The system is compatible with the three major NGS platforms. It automatically interfaces with the sequencing system, detects their data format, configures the analysis type, applies appropriate quality control, and analyzes the results...
September 19, 2016: Journal of Microbiological Methods
Amy L Yang, Thomas E Schmidt, Scott Stibitz, Steven C Derrick, Sheldon L Morris, Marcela Parra
We describe a simplified Mycobacterial Growth Inhibition Assay (MGIA) for pre-clinical assessment of vaccine-mediated protection in mice. The assay is accomplished by directly infecting splenocytes from vaccinated mice with Mycobacterium tuberculosis and quantifying mycobacteria using Mycobacterial Growth Indicator Tubes (MGIT). Vaccine-mediated immunogenicity detected by this assay correlated with protection.
September 17, 2016: Journal of Microbiological Methods
Silvia Angeletti
The microbiological management of patients with suspected bacterial infection includes the identification of the pathogen and the determination of the antibiotic susceptibility. These traditional approaches, based on the pure culture of the microorganism, require at least 36-48 hours. A new method, Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS), has been recently developed to profile bacterial proteins from whole cell extracts and obtain a bacterial fingerprint able to discriminate microorganisms from different genera and species...
September 6, 2016: Journal of Microbiological Methods
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