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Journal of Microbiological Methods

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
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 20, 2017: Journal of Microbiological Methods
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
Seidel Laura, Strathmann Martin, Nocker Andreas
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
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
Xiaoping Zhang, Lichuan Guo, Ranran Ma, Lijuan Cong, Zhonghua Wu, Ying Wei, Shijie Xue, Wei Zheng, Saijun Tang
Rapid Salmonella detection using Recombinase Aided Amplification was established. The reaction completes in 20 min at 39°C and can be performed with a portable device. Once further improved, this method should be a great choice for monitoring contamination, such as foodborne Salmonella or for similar purposes.
June 12, 2017: Journal of Microbiological Methods
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
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
Jiajia Ni, Xiaojing Li, Zhili He, Meiying Xu
Although high-throughput sequencing is an efficient approach to study the structure of microbial communities in detail, it is still impossible to enumerate all individuals using this method. Therefore, it is a common strategy to generate sampling datasets that are representative of the assemblages. However, the representativeness of these sampling datasets has never been assessed. In this study, we developed a method to determine the minimum number sequences that are required to be analyzed to obtain a reliable description of microbial community structure...
June 9, 2017: Journal of Microbiological Methods
Christos-Moritz Loukas, Jonathan S McQuillan, Florian Laouenan, Maria-Nefeli Tsaloglou, Jesus M Ruano-Lopez, Matthew C Mowlem
Now and again, the rapid proliferation of certain species of phytoplankton can give rise to Harmful Algal Blooms, which pose a serious threat to marine life and human health. Current methods of monitoring phytoplankton are limited by poor specificity or by the requirement to return samples to a highly resourced, centralised lab. The Lab Card is a small, microfluidic cassette which, when used in tandem with a portable Lab Card Reader can be used to sensitively and specifically quantify harmful algae in the field, from nucleic acid extracts using RNA amplification; a sensitive and specific method for the enumeration of potentially any species based on their unique genetic signatures...
June 8, 2017: Journal of Microbiological Methods
Juliana Failde Gallo, Juliana Maira Watanabe Pinhata, Claudia Patara Saraceni, Rosangela Siqueira de Oliveira
Drug resistance in tuberculosis is a major threat to public health and control of the disease worldwide. Given the need of a rapid and accurate detection of Mycobacterium tuberculosis resistance to second-line drugs, this study evaluated the performance of the BACTEC MGIT 960 for second-line, drug susceptibility testing in comparison with the resazurin microtiter assay (REMA), in order to implement the automated methodology in the diagnostic routine of a reference laboratory. Drug susceptibility testing (DST) for second-line drugs of 151 MDR M...
June 7, 2017: Journal of Microbiological Methods
Rebecca L Lindsey, L Garcia-Toledo, D Fasulo, L M Gladney, N Strockbine
Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer™ (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E...
June 6, 2017: Journal of Microbiological Methods
Beatriz Alonso, Raquel Cruces, Adrián Pérez, Carlos Sánchez-Carrillo, María Guembe
We assessed whether resazurin was as efficient as XTT in the measurement of the metabolic activity of 209 clinical Staphylococcus aureus biofilm using an vitro model comparing the percentage of formazan and resorufin. The overall categorical agreement was 61.2% (r=0.024), which means that resazurin can not substitute XTT.
June 3, 2017: Journal of Microbiological Methods
Bieke Vanhoutte, Davie Cappoen, Bidart de Macedo Maira, Freya Cools, Eveline Torfs, Tom Coenye, Wim Martinet, Guy Caljon, Louis Maes, Peter Delputte, Paul Cos
Several B. cenocepacia mouse models are available to study the pulmonary infection by this Burkholderia cepacia complex (BCC) species. However, a characterized B. cenocepacia mouse model to evaluate the efficacy of potential new antibacterial therapies is not yet described. Therefore, we optimized and validated the course of infection (i.e. bacterial proliferation in lung, liver and spleen) and the efficacy of a reference antibiotic, tobramycin (TOB), in a mouse lung infection model. Furthermore, the local immune response and histological changes in lung tissue were studied during infection and treatment...
June 3, 2017: Journal of Microbiological Methods
Tomás García-Cayuela, Teresa Requena, M Carmen Martínez-Cuesta, Carmen Peláez
The aim of the study was to evaluate the potential use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for fast and reliable detection of strains producing the lantibiotics nisin, lacticin 481 and lacticin 3147 in a large collection of lactococci. A total of one hundred lactococcal isolates from traditional ewe's and goat's raw milk cheeses were identified to the species level as Lactococcuslactis by MALDI-TOF MS based on comparison with lactococcal entries in the BioTyper database...
June 2, 2017: Journal of Microbiological Methods
Amira Mansour, Salma Tammam, Asma Althani, Hassan M E Azzazy
The global combat against MTB is limited by challenges in accurate affordable detection. In this study, a rapid, affordable, single tube system for detection of unamplified MTB16s rDNA was developed. Utilizing a AuNP based FRET system, this assay achieved a sensitivity and specificity of 98.6% and 90% respectively.
June 2, 2017: Journal of Microbiological Methods
Weili Liu, Chao Li, Zhi-Gang Qiu, Min Jin, Jing-Feng Wang, Dong Yang, Zhong-Hai Xiao, Zhao-Kang Yuan, Jun-Wen Li, Qun-Ying Xu, Zhi-Qiang Shen
Bacteriophages are widely used to the treatment of drug-resistant bacteria and the improvement of food safety through bacterial lysis. However, the limited investigations on bacteriophage restrict their further application. In this study, a novel and highly efficient method was developed for isolating bacteriophage from water based on the electropositive silica gel particles (ESPs) method. To optimize the ESPs method, we evaluated the eluent type, flow rate, pH, temperature, and inoculation concentration of bacteriophage using bacteriophage f2...
May 31, 2017: Journal of Microbiological Methods
Yannick Colin, Marisol Goñi-Urriza, Pierre Caumette, Rémy Guyoneaud
The development of new high-throughput cultivation methods aims to increase the isolation efficiency as compared to standard techniques that often require enrichment procedures to compensate the low microbial recovery. In the current study, estuarine sulfate-reducing bacteria were isolated using an anaerobic isolation procedure in 384-well microplates. Ninety-nine strains were recovered from initial sediments. Isolates were identified according to their partial 16S rRNA sequences and clustered into 13 phylotypes...
May 30, 2017: Journal of Microbiological Methods
Sangeeta Mahableshwar Naik, Arga Chandrashekar Anil
Immediate enumeration of phytoplankton is seldom possible. Therefore, fixation and subsequent storage are required for delayed analysis. This study investigated the influence of glutaraldehyde (GA) concentrations (0.25%, 0.5%, and 1%) and storage temperatures (-80°CLN2, -80°C, -20°C, and 5°C) on Tetraselmis indica for flow cytometric analysis. Cell recovery, granularity, and membrane permeability were independent of GA concentration whereas cell size and chlorophyll autofluorescence were concentration dependent...
May 30, 2017: Journal of Microbiological Methods
Juan Manuel Sánchez-Calvo, José Luís de Francisco, Eva Torres-Martos, Juan Carlos Alados Arboledas, Maria Dolores López Prieto
Outpatient urine samples are among the most commonly processed in a microbiology laboratory, which involves a high economic burden. The aim of this study was compare cost and efficiency to process uropathogens between MicroScan system (2010-2011) versus a chromogenic medium and the disk diffusion method (2013-2014). In the first period, a total 9918 bacterial populations were isolated from urine samples. Annual estimated costs during 2010 and 2011 for processing were EUR 53,818 and EUR 57,306, respectively (EUR 111,124 total)...
May 27, 2017: Journal of Microbiological Methods
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