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Molecular microbiology

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https://www.readbyqxmd.com/read/29776630/diagnostic-molecular-microbiology-a-2018-snapshot
#1
REVIEW
Marilynn Ransom Fairfax, Martin H Bluth, Hossein Salimnia
Molecular biological techniques have evolved expeditiously and in turn have been applied to the detection of infectious disease. Maturation of these technologies and their coupling with related technological advancement in fluorescence, electronics, digitization, nanodynamics, and sensors among others have afforded clinical medicine additional tools toward expedient identification of infectious organisms at concentrations and sensitivities previously unattainable. These advancements have been adapted in select settings toward addressing clinical demands for more timely and effective patient management...
June 2018: Clinics in Laboratory Medicine
https://www.readbyqxmd.com/read/29774547/petunia-as-model-for-elucidating-adventitious-root-formation-and-mycorrhizal-symbiosis-at-the-nexus-of-physiology-genetics-microbiology-and-horticulture
#2
Uwe Druege, Philipp Franken
Adventitious root formation in cuttings and establishment of arbuscular mycorrhizal symbiosis reflect the enormous plasticity of plants and are key factors in the efficient and sustainable clonal propagation and production of ornamental crops. Based on the high importance of Petunia hybrida for the European and US annual bedding plant markets and its suitability as a model for basic plant sciences, petunia has been established as an experimental system for elucidating the molecular and physiological processes underlying adventitious root formation and mycorrhizal symbiosis...
May 17, 2018: Physiologia Plantarum
https://www.readbyqxmd.com/read/29773905/establishing-anaerobic-hydrocarbon-degrading-enrichment-cultures-of-microorganisms-under-strictly-anoxic-conditions
#3
Rafael Laso-Pérez, Viola Krukenberg, Florin Musat, Gunter Wegener
Traditionally, the description of microorganisms starts with their isolation from an environmental sample. Many environmentally relevant anaerobic microorganisms grow very slowly, and often they rely on syntrophic interactions with other microorganisms. This impedes their isolation and characterization by classic microbiological techniques. We developed and applied an approach for the successive enrichment of syntrophic hydrocarbon-degrading microorganisms from environmental samples. We collected samples from microbial mat-covered hydrothermally heated hydrocarbon-rich sediments of the Guaymas Basin and mixed them with synthetic mineral medium to obtain sediment slurries...
June 2018: Nature Protocols
https://www.readbyqxmd.com/read/29769498/quantitative-analysis-of-nucleic-acid-extraction-methods-for-vibrio-cholerae-using-real-time-pcr-and-conventional-pcr
#4
Z Z Hossain, J Ferdous, S M Tulsiani, P M Jensen, A Begum
The devastating diarrheal disease cholera is caused by the bacterium Vibrio cholerae. Nucleic acid extraction is the primary step for several molecular detection approaches. In order to identify the sources of cholera illness, an efficient, fast and easy DNA extraction method for toxigenic Vibrio cholerae is desired which can be applied on diverse type of samples. This methodology developmental setup study was performed in the Environmental Microbiology Lab, Department of Microbiology, University of Dhaka, Bangladesh from March 2015 to May 2015 attempted to compare three DNA extraction methods for efficient detection and quantification of Vibrio cholerae...
April 2018: Mymensingh Medical Journal: MMJ
https://www.readbyqxmd.com/read/29765239/the-clinical-significance-of-silent-mutations-with-respect-to-ciprofloxacin-resistance-in-mrsa
#5
Chih-Cheng Lai, Chi-Chung Chen, Ying-Chen Lu, Yin-Ching Chuang, Hung-Jen Tang
Background: The aim of this study was to investigate the genotypic differences between different sequence type MRSA isolates, especially focusing on silent rpoB 474 mutations and the relationship between such mutations and ciprofloxacin resistance. Methods: Seventy-nine MRSA isolates were obtained for antibiotic susceptibility tests and molecular study. Results: Among these isolates, we found that the MIC50 , MIC90 , and minimum inhibitory concentration (MIC) range of ciprofloxacin were much higher for the isolates without the rpoB 474 mutation than for isolates with the rpoB 474 mutation...
2018: Infection and Drug Resistance
https://www.readbyqxmd.com/read/29764190/delafloxacin-an-improved-fluoroquinolone-developed-through-advanced-molecular-engineering
#6
Matteo Bassetti, Elda Righi, Davide Pecori, Glenn Tillotson
The emergence of antimicrobial resistance threatens current clinical practice across a range of infection types. Delafloxacin, a non-zwitterionic fluoroquinolone recently approved by the US FDA for the treatment of acute bacterial skin and skin structure infections, has been developed to address some of these challenges. Uniquely delafloxacin has increased intracellular penetration and enhanced antibacterial activity under acidic conditions, an environment seen in many infection sites including abscesses. Delafloxacin is active against a wide range of Gram-positive and -negative species including methicillin-resistant Staphylococcus aureus and many fluoroquinolone-resistant strains...
May 16, 2018: Future Microbiology
https://www.readbyqxmd.com/read/29763469/rapid-diagnosis-of-bloodstream-infections-in-the-critically-ill-evaluation-of-the-broad-range-pcr-esi-ms-technology
#7
Martina Tassinari, Silvia Zannoli, Patrizia Farabegoli, Maria Federica Pedna, Anna Pierro, Antonio Mastroianni, Riccardo Fontan, Luciano Luongo, Giuseppe Sarnataro, Elisa Menegatti, Assunta Caruso, Vittorio Sambri
Bloodstream infection (BSI) and associated sepsis represent a major source of mortality in industrialized countries. Prompt treatment with targeted antibiotics affects both the financial impact and the clinical outcome of BSI: every hour gained in initiating the correct antimicrobial therapy significantly increases the probability of patient survival. However, the current standard-of-care, which depends on blood culture-based diagnosis, are often unable to provide such a fast response. Fast and sensitive molecular techniques for the detection of sepsis-related pathogens from primary blood samples are strongly needed...
2018: PloS One
https://www.readbyqxmd.com/read/29757343/dietary-fiber-intervention-on-gut-microbiota-composition-in-healthy-adults-a-systematic-review-and-meta-analysis
#8
Daniel So, Kevin Whelan, Megan Rossi, Mark Morrison, Gerald Holtmann, Jaimon T Kelly, Erin R Shanahan, Heidi M Staudacher, Katrina L Campbell
Background: Dysfunction of the gut microbiota is frequently reported as a manifestation of chronic diseases, and therefore presents as a modifiable risk factor in their development. Diet is a major regulator of the gut microbiota and certain types of dietary fiber may modify bacterial numbers and metabolism, including short-chain fatty acid (SCFA) generation. Objective: A systematic review and meta-analysis were undertaken to assess the effect of dietary fiber interventions on gut microbiota composition in healthy adults...
May 11, 2018: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/29756430/-evaluation-of-a-pcr-multiplex-technique-for-the-rapid-diagnosis-of-bacteriemia
#9
M F López-Fabal, J L Gómez-Garcés, M López Lomba, M Ruiz Bastián
OBJECTIVE: Rapid and safe diagnosis of bacteremia is a continuous challenge in clinical microbiology. In this work, we evaluated a multiple PCR system that identifies 23 common pathogens as well as the production of 3 resistance mechanisms potentially present in them. METHODS: During a period of 2 months the positive blood cultures were processed in the usual way for identification and determination of their antimicrobial sensitivity. At the same time were incorporated into FilmArray panels...
May 11, 2018: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/29754026/precipitation-influences-pathogenic-bacteria-and-antibiotic-resistance-gene-abundance-in-storm-drain-outfalls-in-coastal-sub-tropical-waters
#10
Warish Ahmed, Qian Zhang, Aldo Lobos, Jacob Senkbeil, Michael J Sadowsky, Valerie J Harwood, Nazanin Saeidi, Oswald Marinoni, Satoshi Ishii
Stormwater contamination can threaten the health of aquatic ecosystems and human exposed to runoff via nutrient and pathogen influxes. In this study, the concentrations of 11 bacterial pathogens and 47 antibiotic resistance genes (ARGs) were determined by using high-throughput microfluidic qPCR (MFQPCR) in several storm drain outfalls (SDOs) during dry and wet weather in Tampa Bay, Florida, USA. Data generated in this study were also compared with the levels of fecal indicator bacteria (FIB) and sewage-associated molecular markers (i...
May 10, 2018: Environment International
https://www.readbyqxmd.com/read/29752756/soluble-urokinase-type-plasminogen-activator-receptor-is-associated-with-signs-of-periodontitis-in-adolescents
#11
Peter D Skottrup, Gunnar Dahlén, Vibeke Baelum, Rodrigo Lopez
Owing to its molecular stability in body fluids, soluble urokinase-type plasminogen activator receptor (suPAR) is used as a biomarker for the level of systemic inflammation. This study compares the suPAR levels in serum with those in the saliva of adolescents and evaluates their association with the periodontal conditions. Adolescents identified as screen positive (n = 87) or screen negative (n = 73) for periodontitis had saliva and serum samples taken, along with subgingival plaque samples. The concentrations of suPAR were determined in saliva and serum, and 18 microbial species and the immunoglobulin response to them was evaluated...
May 11, 2018: European Journal of Oral Sciences
https://www.readbyqxmd.com/read/29752627/maldi-tof-ms-supplementary-database-for-species-identification-employing-the-yeast-diversity-encountered-on-southern-brazil-grapes
#12
Bruna Carla Agustini, Gildo Almeida da Silva, Tania Maria Bordin Bonfim
The study of grape microflora is of interest when autochthonous yeasts, which are related to typical wine characteristics, are intended to be used in winemaking. The election of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) as the first method for yeast identification was based on its accuracy and rapidity compared to alternative laboratory protocols for identification. The aims of this study are to consolidate the MALDI-TOF MS Supplementary database for environmental yeasts already constructed, to expand it through the addition of standard spectra of not included yeast species, and to discuss the grape microflora encountered in Southern Brazil...
May 11, 2018: Folia Microbiologica
https://www.readbyqxmd.com/read/29752561/searching-whole-genome-sequences-for-biochemical-identification-features-of-emerging-and-reemerging-pathogenic-corynebacterium-species
#13
André S Santos, Rommel T Ramos, Artur Silva, Raphael Hirata, Ana L Mattos-Guaraldi, Roberto Meyer, Vasco Azevedo, Liza Felicori, Luis G C Pacheco
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis...
May 11, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29746375/prevalence-and-molecular-characterization-of-s-aureus-and-mrsa-on-children-s-playgrounds
#14
Dipendra Thapaliya, Jhalka Kadariya, Mike Capuano, Haleigh Rush, Clair Yee, Mark Oet, Sapana Lohani, Tara C Smith
BACKGROUND: Staphylococcus aureus is a major public health concern due to the emergence of virulent and drug resistant strains such as methicillin-resistant Staphylococcus aureus (MRSA). Although numerous studies have been conducted to assess the environmental contamination of S. aureus in health-care and household settings, little is known about the prevalence and epidemiology of S. aureus, including MRSA, on environmental surfaces of children's playgrounds. This study investigated the prevalence and molecular epidemiology of S...
May 9, 2018: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/29744693/microbial-community-composition-and-trophic-role-along-a-marked-salinity-gradient-in-laguna-puilar-salar-de-atacama-chile
#15
Cristina Dorador, Patrick Fink, Martha Hengst, Gonzalo Icaza, Alvaro S Villalobos, Drina Vejar, Daniela Meneses, Vinko Zadjelovic, Lisa Burmann, Jana Moelzner, Chris Harrod
The geological, hydrological and microbiological features of the Salar de Atacama, the most extensive evaporitic sedimentary basin in the Atacama Desert of northern Chile, have been extensively studied. In contrast, relatively little attention has been paid to the composition and roles of microbial communities in hypersaline lakes which are a unique feature in the Salar. In the present study biochemical, chemical and molecular biological tools were used to determine the composition and roles of microbial communities in water, microbial mats and sediments along a marked salinity gradient in Laguna Puilar which is located in the "Los Flamencos" National Reserve...
May 9, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29744211/molecular-analyses-of-two-bacterial-sampling-methods-in-ligature-induced-periodontitis-in-rats
#16
Carla Raquel Fontana, Clovis Grecco, Vanderlei Salvador Bagnato, Laura Marise de Freitas, Constantinos I Boussios, Nikolaos S Soukos
The prevalence profile of periodontal pathogens in dental plaque can vary as a function of the detection method; however, the sampling technique may also play a role in determining dental plaque microbial profiles. We sought to determine the bacterial composition comparing two sampling methods, one well stablished and a new one proposed here. In this study, a ligature-induced periodontitis model was used in 30 rats. Twenty-seven days later, ligatures were removed and microbiological samples were obtained directly from the ligatures as well as from the periodontal pockets using absorbent paper points...
February 2018: Clinical and Experimental Dental Research
https://www.readbyqxmd.com/read/29740520/the-%C3%AE-bt1-large-serine-recombinase-catalyzes-dna-integration-at-pseudo-attb-sites-in-the-genus-nocardia
#17
Marion Herisse, Jessica L Porter, Romain Guerillot, Takehiro Tomita, Anders Goncalves Da Silva, Torsten Seemann, Benjamin P Howden, Timothy P Stinear, Sacha J Pidot
Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems for genetic manipulation are limited. Site specific integrases catalyze recombination between phage and bacterial attachment sites ( attP and attB , respectively) and the best studied integrases in the actinomycetes are the serine integrases from the Streptomyces bacteriophages ΦC31 and ΦBT1. As this reaction is unidirectional and highly stable, vectors containing phage integrase systems have been used in a number of genetic engineering applications...
2018: PeerJ
https://www.readbyqxmd.com/read/29735822/molecular-characterisation-of-staphylococcus-aureus-using-spa-typing-as-a-diagnostic-tool-in-haryana-india
#18
Gurjeet Singh, Shobha Broor, Priti Agarwal
Background: Staphylococcus aureus is one of the top six most common etiologic agents of nosocomial, community and livestock acquired bacterial infections. These infections although initially were described as a major problem in hospitals have now also become a serious threat in community not only in India but also worldwide. Its prevalence varies depending on the health-care setting, country or a particular region. Thus to better understand the epidemiology of methicillin-resistant S...
January 2018: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29731643/ugly-bugs-in-healthy-guts-carriage-of-multidrug-resistant-and-esbl-producing-commensal-enterobacteriaceae-in-the-intestine-of-healthy-nepalese-adults
#19
Anjila Maharjan, Anjeela Bhetwal, Shreena Shakya, Deepa Satyal, Shashikala Shah, Govardhan Joshi, Puspa Raj Khanal, Narayan Prasad Parajuli
Background: Fecal carriage of multidrug-resistant and extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is one of the important risk factors for infection with antibiotic-resistant bacteria. In this report, we examined the prevalence of multidrug-resistant and ESBL-producing common enterobacterial strains colonizing the intestinal tract of apparently healthy adults in Kathmandu, Nepal. Methods: During a 6-month period (February-July 2016), a total of 510 stool specimens were obtained from apparently healthy students of Manmohan Memorial Institute of Health Sciences, Kathmandu, Nepal...
2018: Infection and Drug Resistance
https://www.readbyqxmd.com/read/29729621/the-characteristics-and-performance-of-sustainable-releasing-compound-carbon-source-material-applied-on-groundwater-nitrate-in-situ-remediation
#20
Wen Zhang, Xiaohong Ruan, Ying Bai, Lin Yin
Recently, reductant and carbon source were frequently used in groundwater nitrate remediation worldwide. Agricultural waste as a promising organic carbon source, has been paid much attention but the problem of sustainability, bioavailability and secondary pollution remained unsolved. This study was conducted to depict the characteristic and performance of developed sustainable-releasing compound carbon source material (SCCM) applied on the in-situ remediation of nitrate in shallow groundwater. Results showed the SCCM based on agricultural waste and zero valent-iron (ZVI) has a stable carbon releasing rate, which is suitable for stimulating the low microbial active environment in groundwater continuously, and capable of avoiding rapid TOC releasing in the early stage...
April 25, 2018: Chemosphere
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