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Molecular microbiology

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https://www.readbyqxmd.com/read/29147976/evaluation-of-microbial-consortia-and-chemical-changes-in-spontaneous-maize-bran-fermentation
#1
Marilù Decimo, Mattia Quattrini, Giovanni Ricci, Maria Grazia Fortina, Milena Brasca, Tiziana Silvetti, Federica Manini, Daniela Erba, Franca Criscuoli, Maria Cristina Casiraghi
Sustainable exploitation of agro-industrial by-products has attracted great interest in cereal bran valorization. In this research, a polyphasic approach has been carried out to characterize maize bran at microbiological and chemical level during a sourdough like fermentation process, in order to enhance its technological and nutritional properties. Autochthonous microbiota was isolated at different refreshment steps and subjected to identification and molecular characterization. Fermentation was characterized by a rapid increase in lactic acid bacteria and yeasts, with a co-dominance, at the initial stage, of Weissella spp...
November 16, 2017: AMB Express
https://www.readbyqxmd.com/read/29145121/role-of-acid-alkali-treatment-in-primary-sludge-anaerobic-fermentation-insights-into-microbial-community-structure-functional-shifts-and-metabolic-output-by-high-throughput-sequencing
#2
Xiao Huang, Wenyi Dong, Hongjie Wang, Yangyang Feng
This study aimed to investigate the effect of acid- or alkali-treatment on volatile fatty acids (VFAs) production and microbiological mechanism during primary sludge anaerobic fermentation. Seven fermentation experiments were conducted at different pH (3-12). Results showed that the optimal pH was 10 for accumulation of VFAs. High-throughput sequencing results indicated that acid and alkali treatment could inhibit Erysipelotrichaceae_UCG-004 and norank_p_Aminicenantes, instead of promoting Pseudomonas and Tissierella at acidic and alkaline condition, respectively...
November 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29142077/syndromic-panel-based-testing-in-clinical-microbiology
#3
REVIEW
Poornima Ramanan, Alexandra L Bryson, Matthew J Binnicker, Bobbi S Pritt, Robin Patel
The recent development of commercial panel-based molecular diagnostics for the rapid detection of pathogens in positive blood culture bottles, respiratory specimens, stool, and cerebrospinal fluid has resulted in a paradigm shift in clinical microbiology and clinical practice. This review focuses on U.S. Food and Drug Administration (FDA)-approved/cleared multiplex molecular panels with more than five targets designed to assist in the diagnosis of bloodstream, respiratory tract, gastrointestinal, or central nervous system infections...
January 2018: Clinical Microbiology Reviews
https://www.readbyqxmd.com/read/29137109/potential-applications-and-limitations-of-electronic-nose-devices-for-plant-disease-diagnosis
#4
REVIEW
Antonio Cellini, Sonia Blasioli, Enrico Biondi, Assunta Bertaccini, Ilaria Braschi, Francesco Spinelli
Electronic nose technology has recently been applied to the detection of several plant diseases and pests, with promising results. However, in spite of its numerous advantages, including operational simplicity, non-destructivity, and bulk sampling, drawbacks include a low sensitivity and specificity in comparison with microbiological and molecular methods. A critical review of the use of an electronic nose for plant disease diagnosis and pest detection is presented, describing the instrumental and procedural advances of sensorial analysis, for the improvement of discrimination between healthy and infected or infested plants...
November 11, 2017: Sensors
https://www.readbyqxmd.com/read/29135992/internal-quality-assurance-in-diagnostic-microbiology-a-simple-approach-for-insightful-data
#5
Valentin Scherz, Christian Durussel, Gilbert Greub
Given the importance of microbiology results on patient care, high quality standards are expected. Internal quality assurance (IQA) could mitigate the limitations of internal quality control, competency assessment and external quality assurance, adding a longitudinal insight, including pre- and post-analytical steps. Here, we implemented an IQA program in our clinical microbiology facilities with blind resubmission of routine samples during 22 months. One-hundred-and-twenty-one out of 123 (98.4%) serological analyses and 112 out of 122 (91...
2017: PloS One
https://www.readbyqxmd.com/read/29131507/the-disruptive-effect-of-lysozyme-on-the-bacterial-cell-wall-explored-by-an-in-silico-structural-outlook
#6
Emiliano D Primo, Lisandro H Otero, Francisco Ruiz, Sebastián Klinke, Walter Giordano
The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall and disrupt the bacterial life cycle by cleaving the linkage between the NAG and NAM carbohydrates. Lab exercises focused on the effects of lysozyme on the bacterial cell wall are frequently incorporated in biochemistry classes designed for undergraduate students in diverse fields as biology, microbiology, chemistry, agronomy, medicine, and veterinary medicine...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29130748/evaluation-of-two-matrices-for-long-term-ambient-storage-of-bacterial-dna
#7
Karen M Miernyk, Carolynn K DeByle, Karen M Rudolph
BACKGROUND: Culture-independent molecular analyses allow researchers to identify diverse microorganisms. This approach requires microbiological DNA repositories. The standard for DNA storage is liquid nitrogen or ultralow freezers. These use large amounts of space, are costly to operate, and could fail. Room temperature DNA storage is a viable alternative. In this study, we investigated storage of bacterial DNA using two ambient storage matrices, Biomatrica DNAstable(®) Plus and GenTegra(®) DNA...
November 13, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/29126084/a-simple-and-highly-selective-molecular-imprinting-polymer-based-methodology-for-propylparaben-monitoring-in-personal-care-products-and-industrial-waste-waters
#8
Ana Vicario, Leslie Aragón, Chien C Wang, Franco Bertolino, María R Gomez
In this work, a novel molecularly imprinted polymer (MIP) proposed as solid phase extraction sorbent was developed for the determination of propylparaben (PP) in diverse cosmetic samples. The use of parabens (PAs) is authorized by regulatory agencies as microbiological preservative; however, recently several studies claim that large-scale use of these preservatives can be a potential health risk and harmful to the environment. Diverse factors that influence on polymer synthesis were studied, including template, functional monomer, porogen and crosslinker used...
November 4, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29126024/nitrate-attenuation-in-low-permeability-sediments-based-on-isotopic-and-microbial-analyses
#9
Yuexia Wu, Ligang Xu, Sai Wang, Zhenglu Wang, Jianying Shang, Xiqing Li, Chunmiao Zheng
This study investigated nitrate attenuation in low-permeability sediments (LPS) in a multi-layer aquifer by integrating hydrochemical, isotopic and microbiological molecular techniques in a field site. In the meantime, the overlying high-permeability sediment (HPS) was also examined on the nitrate attenuation for the sake of comparison. Additionally, laboratory flow-through experiments were conducted to assess the overall nitrate reduction rate in the two types of sediment. The δ(15)N-NO3(-) and δ(34)S-SO4(2-) values were more enriched by approximately 37‰ and 15‰ in the LPS than the overlying HPS associated with substantial reductions of the NO3(-) and SO4(2-) concentration, indicating the occurrence of strong bio-reductions in nitrate and sulfate...
November 7, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29121443/can-e-coli-fly-the-role-of-flies-as-transmitters-of-escherichia-coli-to-food-in-an-urban-slum-in-bangladesh
#10
Yrja Lisa Lindeberg, Karen Egedal, Zenat Zebin Hossain, Matthew Phelps, Suhella Tulsiani, Israt Farhana, Anowara Begum, Peter Kjaer Mackie Jensen
OBJECTIVE: To investigate the transmission of fecal bacteria by flies to food under natural settings. METHODS: Over a period of two months paired (exposed and non-exposed) containers with cooked rice were placed on the ground in kitchen areas in an urban slum area in Dhaka, Bangladesh, and the numbers of flies landing on the exposed rice were counted. Following exposure, the surface of the rice was microbiologically and molecularly analysed for the presence of E...
November 9, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/29119076/are-there-benefits-in-early-diagnosis-of-prosthetic-joint-infection-with-multiplex-polymerase-chain-reaction
#11
Christian Lausmann, Akos Zahar, Mustafa Citak, Julian Brañes, Stefan Schmidl, Lars Frommelt, Thorsten Gehrke, Matthias Gebauer
Purpose Identification of bacteria and susceptibility are fundamental in periprosthetic joint infection (PJI). Especially in the case of systemic inflammatory response syndrome (SIRS) rapid detection of pathogens is essential for proper therapy. Bacterial cultures are time consuming. The polymerase chain reaction (PCR) is a non-culture molecular method and is able to rapidly identify pathogens and their resistance genes. Multiplex PCR (mPCR) can amplify several different DNA sequences simultaneously. The aim of this study was to show the value of mPCR for early diagnosis of PJI...
2017: Journal of bone and joint infection
https://www.readbyqxmd.com/read/29118166/laboratory-focus-on-improving-the-culture-of-biosafety-statewide-risk-assessment-of-clinical-laboratories-that-process-specimens-for-microbiologic-analysis
#12
Erik Munson, Erin J Bowles, Richard Dern, Eric Beck, Raymond P Podzorski, Allen C Bateman, Timothy K Block, Joshua L Kropp, Tyler Radke, Karen Siebers, Brian Simmons, Mary A Smith, Frances Spray-Larson, David M Warshauer
The Wisconsin State Laboratory of Hygiene challenged Wisconsin laboratories to examine their biosafety practices and improve their culture of biosafety. 103 clinical and public health laboratories completed a questionnaire-based, microbiology-focused biosafety risk assessment. Greater than 96% of respondents performed activities related to specimen processing, direct microscopic examination, and rapid non-molecular testing, while approximately 60% performed culture interpretation. Although important to assessing risk, data specific to patient occupation, symptoms, and travel history were often unavailable to the laboratory and, therefore, less contributory to microbiology biosafety risk assessment than information relative to specimen source and test requisition...
November 8, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29117578/practical-issues-in-implementing-whole-genome-sequencing-in-routine-diagnostic-microbiology
#13
REVIEW
John W A Rossen, Alexander W Friedrich, Jacob Moran-Gilad
BACKGROUND: next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology that is being adopted in microbiology, the integration of NGS into clinical and routine workflows needs to be carefully managed. AIM: to review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories. SOURCES: review of the literature and expert opinion. CONTENT: in this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory...
November 5, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29112122/identification-and-antimicrobial-susceptibility-testing-of-anaerobic-bacteria-rubik-s-cube-of-clinical-microbiology
#14
REVIEW
Márió Gajdács, Gabriella Spengler, Edit Urbán
Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically...
November 7, 2017: Antibiotics
https://www.readbyqxmd.com/read/29108709/update-on-actinomucor-elegans-a-mucormycete-infrequently-detected-in-human-specimens-how-combined-microbiological-tools-contribute-efficiently-to-a-more-accurate-medical-care
#15
J Dorin, M D'Aveni, A Debourgogne, M Cuenin, M Guillaso, A Rivier, P Gallet, G Lecoanet, M Machouart
Actinomucor elegans is a fungus belonging to mucormycetes and is still probably underdiagnosed due to misidentification. Based on a recent first case of Actinomucor elegans sinusitis in Europe, in an immunocompromised patient under voriconazole treatment, this paper aims to summarize knowledge about A. elegans mucormycoses. Even if the diagnosis of mucormycosis was made using traditional mycology techniques, precise identification of the fungus could only be achieved using molecular tools. In this observation, the galactomannan dosage was positive until the introduction of treatment and surgical debridement...
October 26, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29108108/antibacterial-aryl-crowned-polyketide-from-bacillus-subtilis-associated-with-seaweed-anthophycus-longifolius
#16
Kajal Chakraborty, Bini Thilakan, Vinaya Kizhakkepatt Kizhakkekalam
AIMS: Microbiological, biotechnological and chemical characterization of a previously undescribed aryl-crowned polyketide from Bacillus subtilis MTCC 10403 isolated from brown seaweed Anthophycus longifolius with activity against opportunistic Gram-negative food-borne pathogenic bacterial strains. METHODS AND RESULTS: A culture-dependent method was used to isolate heterotrophic B. subtilis associated with A. longifolius, and assessed for its antimicrobial properties...
November 6, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29101081/molecular-characterization-of-multidrug-resistant-bacteroides-isolates-from-hungarian-clinical-samples
#17
Károly Péter Sárvári, József Sóki, Katalin Kristóf, Emese Juhász, Cecilia Miszti, Szilvia Zsóka Melegh, Krisztina Latkóczy, Edit Urbán
INTRODUCTION: Members of the Bacteroides fragilis group are the most important components of the normal human gut microbiota, but these bacteria can cause severe infections as well. Due to the frequent usage of antibiotics, the spreading of the MDR strains is a real threat worldwide. MATERIALS AND METHODS: In a multicentre study 400 Bacteroides isolates from five Hungarian microbiological laboratories were cultured and identified by MALDI TOF-MS. The MIC values of ten antibiotics were determined by the agar dilution method and evaluated by the breakpoints of EUCAST or CLSI...
October 31, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29099868/evaluation-of-a-multiplex-panel-for-the-diagnosis-of-acute-infectious-diarrhea-in-immunocompromised-hematologic-patients
#18
Izaskun Alejo-Cancho, Francesc Fernández Avilés, Alicia Capón, Cristina Rodríguez, Josep Barrachina, Pilar Salvador, Mª Eugenia Valls, Miriam J Álvarez-Martínez, Yuliya Zboromyrska, Jordi Vila, Mª Ángeles Marcos
INTRODUCTION: Diarrhea is a frequent complication in hematologic patients, being an infectious cause frequently suspected. Rapid and accurate detection of gastrointestinal pathogens is vital in immunocompromised hosts. The aim of this study was to compare routine diagnostic methods versus a multiplex polymerase chain reaction (PCR) assay for the diagnosis of infectious diarrhea in immunocompromised hematologic patients. MATERIAL AND METHODS: We conducted a prospective observational study from March 2015 to January 2016 to compare conventional methods for the diagnosis of infectious diarrhea with FIlmArray GI Panel (BioFire-bioMérieux, France)...
2017: PloS One
https://www.readbyqxmd.com/read/29090355/microbiological-comparison-of-blood-culture-and-amplification-of-16s-rdna-methods-in-combination-with-dgge-for-detection-of-neonatal-sepsis-in-blood-samples
#19
Isela García-Gudiño, Eucario Yllescas-Medrano, Rolando Maida-Claros, Diana Soriano-Becerril, Nestor F Díaz, Guadalupe García-López, Anayansí Molina-Hernández, Oscar Flores-Herrera, Francisco J Zavala-Díaz de la Serna, María Del Rosario Peralta-Pérez, Héctor Flores-Herrera
It is estimated that 15% of all newborns admitted to the neonatal intensive care unit (NICU) for suspected sepsis receive multiple broad-spectrum antibiotics without pathogen identification. The gold standard for bacterial sepsis detection is blood culture, but the sensitivity of this method is very low. Recently, amplification and analysis of the 16S ribosomal DNA (rDNA) bacterial gene in combination with denaturing gradient gel electrophoresis (DGGE) has proven to be a useful approach for identifying bacteria that are difficult to isolate by standard culture methods...
October 31, 2017: European Journal of Pediatrics
https://www.readbyqxmd.com/read/29084263/a-plasmid-based-escherichia-coli-gene-expression-system-with-cell-to-cell-variation-below-the-extrinsic-noise-limit
#20
Zach Hensel
Experiments in synthetic biology and microbiology can benefit from protein expression systems with low cell-to-cell variability (noise) and expression levels precisely tunable across a useful dynamic range. Despite advances in understanding the molecular biology of microbial gene regulation, many experiments employ protein-expression systems exhibiting high noise and nearly all-or-none responses to induction. I present an expression system that incorporates elements known to reduce gene expression noise: negative autoregulation and bicistronic transcription...
2017: PloS One
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