Journal: Journal of microbiological methods / Publication Year: 2018

1. Aerobic cultivation of anaerobic rumen protozoa, Entodinium caudatum and Epidinium caudatum

Author:: Tansol Park; Zhongtang Yu
Source:: Journal of microbiological methods 2018 v.152 pp. 186-193
ISSN:: 0167-7012
Subject:: Entodinium caudatum; Epidinium caudatum; Protozoa; aerobic conditions; alpha-ketoglutaric acid; anaerobic conditions; animals; antioxidants; ascorbic acid; cryopreservation; fermentation; glutathione; rumen; rumen protozoa; viability
Abstract:: ... Rumen protozoa, primarily ciliates, are one of the important groups of strictly anaerobic microbes living in the rumen. Despite their ubiquitous occurrence in the rumen and significant contribution to host animals, it is still poorly understood why they live only in the rumen and similar environment. Because rumen protozoa require strict anaerobic conditions to sustain their viability and grow, on ...
DOI:: 10.1016/j.mimet.2018.08.006
CHORUS:: 10.1016/j.mimet.2018.08.006
: https://doi.org/10.1016/j.mimet.2018.08.006

2. Air-drying is sufficient pre-treatment for in situ visualization of microbes on minerals with scanning electron microscopy

Author:: Anu Hynninen; Marian Külaviir; Kalle Kirsimäe
Source:: Journal of microbiological methods 2018 v.146 pp. 77-82
ISSN:: 0167-7012
Subject:: air drying; bacteria; bacterial communities; basalt; biofilm; minerals; scanning electron microscopy
Abstract:: ... Scanning electron microscopy (SEM) is a powerful tool for observing microbe-mineral interactions in situ. Despite its wide usage in geomicrobiology there is no consensus on how the samples should be handled before visualizing in SEM. We compared response of artificial laboratory-grown bacterial community and natural in situ microbes on terrestrial basalt to different sample pre-treatment methods w ...
DOI:: 10.1016/j.mimet.2018.02.007
: https://doi.org/10.1016/j.mimet.2018.02.007

3. Antibacterial activity of lysozyme-binding proteins from chicken egg white

Author:: Youji Shimazaki; Ayumi Takahashi
Source:: Journal of microbiological methods 2018 v.154 pp. 19-24
ISSN:: 0167-7012
Subject:: Bacillus subtilis; Escherichia coli; Gram-negative bacteria; antibacterial properties; cathodes; digital images; egg albumen; isoelectric focusing; lysozyme; ovalbumin; phosphoric acid; sodium hydroxide; two-dimensional gel electrophoresis
Abstract:: ... The purpose of this study was to establish a method for determining the bacteriolytic activity after separation of lysozyme-binding proteins from egg white. Lysozyme-binding proteins such as ovotransferrin and ovalbumin were separated by non-denaturing two-dimensional electrophoresis (2DE) and transferred to a membrane. The lysozyme activity of the separated and immobilized egg white proteins was ...
DOI:: 10.1016/j.mimet.2018.10.001
: https://doi.org/10.1016/j.mimet.2018.10.001

4. Application of Cytosense flow cytometer for the analysis of airborne bacteria collected by a high volume impingement sampler

Author:: Jaeyoun Jang; Niels Bohse Hendriksen; Hans H. Jakobsen; Ulrich Gosewinkel
Source:: Journal of microbiological methods 2018 v.154 pp. 63-72
ISSN:: 0167-7012
Subject:: DNA; air; airborne microorganisms; bacteria; flow cytometry; genes; quantitative polymerase chain reaction; regression analysis; relative humidity; ribosomal RNA; wastewater treatment
Abstract:: ... Characterization of airborne bacterial cells requires efficient collection, concentration, and analysis techniques, particularly to overcome the challenge of their dilute nature in outdoor environments. This study aims to establish a rapid and reliable approach for quantification of bacteria in air samples. To do this, a high volume impingement sampler was applied to collect airborne bacteria from ...
DOI:: 10.1016/j.mimet.2018.10.012
: https://doi.org/10.1016/j.mimet.2018.10.012

5. Application of the biocopolymer preparation system, rapid BACpro® II kit, for mass-spectrometry-based bacterial identification from positive blood culture bottles by the MALDI Biotyper system

Author:: Sachio Tsuchida; Syota Murata; Akiko Miyabe; Mamoru Satoh; Masaki Takiwaki; Kazuho Ashizawa; Takashi Terada; Daisuke Ito; Kazuyuki Matsushita; Fumio Nomura
Source:: Journal of microbiological methods 2018 v.152 pp. 86-91
ISSN:: 0167-7012
Subject:: analytical kits; bacteria; biosafety; blood; bottles; composite polymers; matrix-assisted laser desorption-ionization mass spectrometry; wastewater
Abstract:: ... Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for identification of microorganisms from positive blood cultures. Pretreatments to effectively remove non-bacterial components and selectively collect microorganisms are a prerequisite for successful identification, and a variety of home-brew and commercial protocols have been reported ...
DOI:: 10.1016/j.mimet.2018.07.017
: https://doi.org/10.1016/j.mimet.2018.07.017

6. Applying simple linear combination, multiple logistic and factor analysis methods for candidate fecal bacteria as novel biomarkers for early detection of adenomatous polyps and colon cancer

Author:: Sama Rezasoltani; Maryam Sharafkhah; Hamid Asadzadeh Aghdaei; Ehsan Nazemalhosseini Mojarad; Hossein Dabiri; Abbas Akhavan Sepahi; Mohammad Hossein Modarressi; Mohammad Mehdi Feizabadi; Mohammad Reza Zali
Source:: Journal of microbiological methods 2018 v.155 pp. 82-88
ISSN:: 0167-7012
Subject:: Bacteroides fragilis; Enterococcus; Fusobacterium nucleatum; Porphyromonas; Streptococcus bovis; biomarkers; burden of disease; colonoscopy; colorectal neoplasms; confidence interval; disease diagnosis; factor analysis; fecal bacteria; graphs; hospitals; intestinal microorganisms; logit analysis; models; patients; polyps (pathological conditions); quantitative polymerase chain reaction; risk factors; screening; Iran
Abstract:: ... Colorectal cancer (CRC) is the third leading cause of cancer, and presents a considerable disease burden, worldwide. Recently, the gut microbiota has been proposed as a potential risk factor for CRC, and even adenomatous polyps (AP). Here, the aim of this study was to investigate the role of selected gut bacteria as fecal bacterial biomarkers, in early detection of CRC and AP.Fecal samples (n = 93 ...
DOI:: 10.1016/j.mimet.2018.11.007
: https://doi.org/10.1016/j.mimet.2018.11.007

7. Aptamer-based fluorometric assay for direct identification of methicillin-resistant Staphylococcus aureus from clinical samples

Author:: Jinjuan Qiao; Xiangying Meng; Yufang Sun; Qian Li; Ronglan Zhao; Yun Zhang; Jiaqi Wang; Zhengjun Yi
Source:: Journal of microbiological methods 2018 v.153 pp. 92-98
ISSN:: 0167-7012
Subject:: antibiotic resistance; bacteria; fluorometry; immunomagnetic separation; methicillin; methicillin-resistant Staphylococcus aureus; proteins
Abstract:: ... Accurate and rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is of important clinical significance. In this study, a novel aptamer-based fluorometric assay was developed for detection of MRSA in clinical samples by coupling with immunomagnetic separation. The S. aureus cells in clinical specimens were enriched by magnetic separation. Following lysis by staphylococcal lys ...
DOI:: 10.1016/j.mimet.2018.09.011
: https://doi.org/10.1016/j.mimet.2018.09.011

8. Assessment of flow cytometry for microbial water quality monitoring in cooling tower water and oxidizing biocide treatment efficiency

Author:: Karim Helmi; Fabienne David; Patrick Di Martino; Marie-Pierre Jaffrezic; Valérie Ingrand
Source:: Journal of microbiological methods 2018 v.152 pp. 201-209
ISSN:: 0167-7012
Subject:: Legionella; adenosine triphosphate; bacteria; biocides; cooling towers; disinfection; flow cytometry; metabolism; monitoring; nucleic acids; propidium; water pollution; water quality
Abstract:: ... The control of Legionella proliferation in cooling tower water circuits requires regular monitoring of water contamination and effective disinfection procedures. In this study, flow cytometry was assessed to monitor water contamination and disinfection treatment efficiency on bacterial cells regarding nucleic acid injury (SYBR® Green II), cell integrity (SYBR® Green II and propidium iodide) and me ...
DOI:: 10.1016/j.mimet.2018.06.009
: https://doi.org/10.1016/j.mimet.2018.06.009

9. Autofluorescence of yeast Saccharomyces cerevisiae cells caused by glucose metabolism products and its methodological implications

Author:: Roman Maslanka; Magdalena Kwolek-Mirek; Renata Zadrag-Tecza
Source:: Journal of microbiological methods 2018 v.146 pp. 55-60
ISSN:: 0167-7012
Subject:: Saccharomyces cerevisiae; fluorescence; fluorescent dyes; glucose; metabolism; physiological state; pyridoxine; riboflavin; tryptophan; yeasts
Abstract:: ... Autofluorescence is the natural fluorescence emitted by cellular compounds which have light emission properties. The main examples of these compounds, identified as an endogenous fluorophores, include aromatic amino acids, vitamins, coenzymes and electron acceptors. As many of them play a critical role in cell metabolism, changes in their content may provide important information on the physiologi ...
DOI:: 10.1016/j.mimet.2018.01.017
: https://doi.org/10.1016/j.mimet.2018.01.017

10. Automated counting of bacterial colonies on agar plates based on images captured at near-infrared light

Author:: Guozhen Zhu; Bin Yan; Mengting Xing; Chunna Tian
Source:: Journal of microbiological methods 2018 v.153 pp. 66-73
ISSN:: 0167-7012
Subject:: algorithms; automation; cameras; cost effectiveness; lighting; microbiological criteria; user interface
Abstract:: ... Counting colonies is usually used in microbiological analysis to assess if samples meet microbiological criteria. Although manual counting remains gold standard, the process is subjective, tedious, and time-consuming. Some developed automatic counting methods could save labors and time, but their results are easily affected by uneven illumination and reflection of visible light. To offer a method ...
DOI:: 10.1016/j.mimet.2018.09.004
: https://doi.org/10.1016/j.mimet.2018.09.004

11. Bio oil production from microalgae via hydrothermal liquefaction technology under subcritical water conditions

Author:: P. Kiran Kumar; S. Vijaya Krishna; Kavita Verma; K. Pooja; D. Bhagawan; K. Srilatha; V. Himabindu
Source:: Journal of microbiological methods 2018 v.153 pp. 108-117
ISSN:: 0167-7012
Subject:: Botryococcus braunii; Chlorella vulgaris; Fourier transform infrared spectroscopy; Scenedesmus quadricauda; biofuels; biomass; drying; energy; fossil fuels; furans; gas chromatography; gases; global warming; hydrothermal liquefaction; liquids; microalgae; moieties; oils; phenol; pollution; polymerization; temperature
Abstract:: ... The upsurge in the concerning issues like global warming, environmental pollution and depletion of fossil fuel resources led to the thrust on third generation biofuels. Algal research has gained a lot of importance in the recent years. Effective utilization of algal biomass in a single step is necessary as it can produce Bio-oil (BO), gases and in addition to a variety of valuable products, along ...
DOI:: 10.1016/j.mimet.2018.09.014
: https://doi.org/10.1016/j.mimet.2018.09.014

12. Chlamydia trachomatis antibody detection in home-collected blood samples for use in epidemiological studies

Author:: B.M. Hoenderboom; E.F. van Ess; I.V.F. van den Broek; I.H.M. van Loo; C.J.P.A. Hoebe; S. Ouburg; S.A. Morré
Source:: Journal of microbiological methods 2018 v.144 pp. 164-167
ISSN:: 0167-7012
Subject:: Chlamydia trachomatis; ambient temperature; antibody detection; blood sampling; blood serum; centrifugation; epidemiological studies; immunoglobulin G
Abstract:: ... Capillary blood collected in serum tubes was subjected to centrifugation delay while stored at room temperature. Chlamydia trachomatis (CT) IgG concentrations in aliquoted serum of these blood samples remained stable for seven days after collection. CT IgG concentrations can reliably be measured in mailed blood samples in epidemiological studies. ...
DOI:: 10.1016/j.mimet.2017.11.022
: https://doi.org/10.1016/j.mimet.2017.11.022

13. Colorimetric assay for active biomass quantification of Fusarium fujikuroi

Author:: Yu-Ke Cen; Jian-Guang Lin; Jun-You Wang; Zhi-Qiang Liu; Yu-Guo Zheng
Source:: Journal of microbiological methods 2018 v.155 pp. 37-41
ISSN:: 0167-7012
Subject:: Fusarium fujikuroi; biomass; biosynthesis; carbon; cell growth; colorimetry; fermentation; gibberellins; menadione; quantitative analysis; tetrazolium
Abstract:: ... A colorimetric assay has been developed for quantitative analysis of active biomass of Fusarium fujikuroi, based on the reduction of the tetrazolium salt 2,3-Bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) when menadione was present as an electron coupling agent. The optimum assay-conditions were set as 200 μg/ml XTT, 5 μM menadione and one-hour reaction time. Under thes ...
DOI:: 10.1016/j.mimet.2018.11.009
: https://doi.org/10.1016/j.mimet.2018.11.009

14. Combination of MALDI-TOF MS and PBP2′ latex agglutination assay for rapid MRSA detection

Author:: Marianna Ábrók; Andrea Lázár; Mária Szécsényi; Judit Deák; Edit Urbán
Source:: Journal of microbiological methods 2018 v.144 pp. 122-124
ISSN:: 0167-7012
Subject:: agglutination; culture media; latex; matrix-assisted laser desorption-ionization mass spectrometry; methicillin-resistant Staphylococcus aureus; screening
Abstract:: ... Sample preparation was optimized for MALDI-TOF MS directly from the selective enrichment broth to detect Staphylococcus aureus. A combination of MALDI-TOF MS and the PBP2′ latex agglutination assay was applied for MRSA screening and evaluated on 255 clinical samples. MRSA colonisation can be reported already 18–24h after sample collection. ...
DOI:: 10.1016/j.mimet.2017.11.021
: https://doi.org/10.1016/j.mimet.2017.11.021

15. Combining diagnostic methods for antimicrobial susceptibility testing – A comparative approach

Author:: Sylvia Natalie Kłodzińska; Petra Alexandra Priemel; Thomas Rades; Hanne Mørck Nielsen
Source:: Journal of microbiological methods 2018 v.144 pp. 177-185
ISSN:: 0167-7012
Subject:: antibacterial properties; antibiotic resistance; antibiotics; aspartate transaminase; bacteria; calorimetry; diagnostic techniques; drugs; fluorescent dyes; microbial growth; minimum inhibitory concentration; patients; propidium; regrowth; screening; staining
Abstract:: ... The minimum inhibitory concentration (MIC) is a measure of antimicrobial susceptibility testing (AST) of a given antibiotic but provides insufficient information when bacterial killing is crucial, e.g., when treating immunocompromised patients. In these cases, the minimum bactericidal concentration (MBC) is a more reliable measure of antibiotic activity. Here, we aim to demonstrate and recommend c ...
DOI:: 10.1016/j.mimet.2017.11.010
: https://doi.org/10.1016/j.mimet.2017.11.010

16. Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens

Author:: T.L. Masters; C.A. Hilker; P.R. Jeraldo; A.V. Bhagwate; K.E. Greenwood-Quaintance; B.W. Eckloff; N. Chia; A.D. Hanssen; M.P. Abdel; J.Z. Yao; J. Jen; R. Patel
Source:: Journal of microbiological methods 2018 v.154 pp. 55-62
ISSN:: 0167-7012
Subject:: RNA; bacteria; cDNA libraries; complementary DNA; diagnostic techniques; hosts; infectious diseases; pathogens; sequence analysis; transcriptomics
Abstract:: ... With the emergence of RNA sequencing technologies, metatranscriptomic studies are rapidly gaining attention as they simultaneously provide insight into gene expression profiles and therefore disease association pathways of microbial pathogens and their hosts. This approach, therefore, holds promise for applicability in infectious disease diagnostics. A challenge of this approach in the clinical se ...
DOI:: 10.1016/j.mimet.2018.10.008
PubMed:: 30332617
PubMed Central:: PMC6242773
: https://doi.org/10.1016/j.mimet.2018.10.008

17. Comparison of DNA extraction methods for drug susceptibility testing by allele-specific primer extension on a microsphere-based platform: Chelex-100 (in-house and commercialized) and MagPurix TB DNA Extraction Kit

Author:: Minji Kang; Jeong Seong Yang; Yoojeong Kim; Kyungjong Kim; Hongjo Choi; Seung Heon Lee
Source:: Journal of microbiological methods 2018 v.152 pp. 105-108
ISSN:: 0167-7012
Subject:: Bacilli; DNA; Mycobacterium tuberculosis; automation; death; drug resistance; drugs; magnetism; mutation; polymerase chain reaction; sodium hydroxide; species identification; tuberculosis
Abstract:: ... Tuberculosis (TB), caused by infections of the Mycobacterium tuberculosis (MTB) complex, is the ninth leading cause of death worldwide, and several molecular approaches for MTB species identification and the detection of mutations associated with drug resistance have been developed to date. We previously developed a diagnostic assay for drug susceptibility testing that can detect mutations conferr ...
DOI:: 10.1016/j.mimet.2018.07.019
: https://doi.org/10.1016/j.mimet.2018.07.019

18. Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile

Author:: Zhirong Li; Xiaolei Liu; Jianhong Zhao; Kaiyue Xu; Tiantian Tian; Jing Yang; Cuixin Qiang; Dongyan Shi; Honglian Wei; Suju Sun; Qingqing Cui; Ruxin Li; Yanan Niu; Bixing Huang
Source:: Journal of microbiological methods 2018 v.147 pp. 50-55
ISSN:: 0167-7012
Subject:: Clostridium difficile; clones; cost effectiveness; cross infection; diarrhea; epidemiological studies; health services; multilocus sequence typing; outbreak investigation; pathogens; ribotypes; virulence
Abstract:: ... Clostridium difficile is the causative pathogen for antibiotic-related nosocomial diarrhea. For epidemiological study and identification of virulent clones, a new binary typing method was developed for C. difficile in this study. The usefulness of this newly developed optimized 10-loci binary typing method was compared with two widely used methods ribotyping and multilocus sequence typing (MLST) i ...
DOI:: 10.1016/j.mimet.2018.02.012
: https://doi.org/10.1016/j.mimet.2018.02.012

19. Comparison of biofilm cell quantification methods for drinking water distribution systems

Author:: Sharon A. Waller; Aaron I. Packman; Martina Hausner
Source:: Journal of microbiological methods 2018 v.144 pp. 8-21
ISSN:: 0167-7012
Subject:: biofilm; cast iron; cement; confocal laser scanning microscopy; disinfectants; drinking water; flow cytometry; health promotion; odors; pathogens; pipes; plate count; poly(vinyl chloride); samplers; staining; water distribution; water quality; water treatment
Abstract:: ... 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 dr ...
DOI:: 10.1016/j.mimet.2017.10.013
: https://doi.org/10.1016/j.mimet.2017.10.013

20. Comparison of the Purelyse® – IS6110 nested PCR with the Xpert® MTB/RIF test in clinical samples with suspected tuberculosis

Author:: Carlos German Lemus-Minor; Diego Fernando Ovalle-Marroqui; J. Gustavo Vazquez-Jimenez; Diana Laura Reales-Agüero; Perla Michelle Sepulveda-Alcantara; Jesús René Rodriguez-Sánchez; Raúl Diaz-Molina; Jesús René Machado-Contreras
Source:: Journal of microbiological methods 2018 v.152 pp. 48-51
ISSN:: 0167-7012
Subject:: DNA; Mycobacterium tuberculosis complex; diagnostic techniques; mortality; patients; polymerase chain reaction; rifampicin; tuberculosis
Abstract:: ... Tuberculosis (TB) has a high incidence, prevalence and mortality in the world. Due to its high level of transmission and long-term pharmacological treatment, it is important to have sensitive and specific diagnostic tests. Recently, the PureLyse® system, which is a novel DNA extraction method, was proposed to be an important tool for molecular diagnosis of TB. Here, we compare the PureLyse® system ...
DOI:: 10.1016/j.mimet.2018.07.002
: https://doi.org/10.1016/j.mimet.2018.07.002

21. Comparison of three DNA extraction methods for molecular confirmation of Mycobacterium avium subspecies paratuberculosis from the VersaTrek™ liquid cultures of bovine fecal samples

Author:: Nagaraja R. Thirumalapura; Willard Feria; Deepanker Tewari
Source:: Journal of microbiological methods 2018 v.152 pp. 27-30
ISSN:: 0167-7012
Subject:: DNA; Mycobacterium avium subsp. paratuberculosis; cattle; feces; liquids; polyethylene glycol
Abstract:: ... We evaluated three DNA extraction methods for confirmation of Mycobacterium avium subspecies paratuberculosis from liquid cultures of bovine feces. Use of DNA Extract All Reagents Kit™ resulted in efficient extraction of amplifiable DNA from higher proportion (96.29%) of known positive samples compared to Chelex-100 resin (25.92%) and polyethylene glycol (0%). ...
DOI:: 10.1016/j.mimet.2018.07.012
: https://doi.org/10.1016/j.mimet.2018.07.012

22. Comparison of various RNA extraction methods, cDNA preparation and isolation of calmodulin gene from a highly melanized isolate of apple leaf blotch fungus Marssonina coronaria

Author:: Arjun Chauhan; J.N. Sharma; Manju Modgil; Sundaresha Siddappa
Source:: Journal of microbiological methods 2018 v.151 pp. 7-15
ISSN:: 0167-7012
Subject:: Diplocarpon mali; RNA; analytical kits; apples; calmodulin; color; complementary DNA; defoliation; fungal diseases of plants; fungi; genes; leaf blotch; leaves; melanin; melanization; microbial culture; molecular biology; nucleotide sequences; pellets; reverse transcriptase polymerase chain reaction
Abstract:: ... Marssonina coronaria causes apple blotch disease resulting in severe premature defoliation, and is distributed in many leading apple-growing areas in the world. Effective, reliable and high-quality RNA extraction is an indispensable procedure in any molecular biology study. No method currently exists for RNA extraction from M. coronaria that produces a high quantity of melanin-free RNA. Therefore, ...
DOI:: 10.1016/j.mimet.2018.05.023
: https://doi.org/10.1016/j.mimet.2018.05.023

23. Concentration of Listeria monocytogenes in skim milk and soft cheese through microplate immunocapture

Author:: Steven A. Rogers; Melissa Calicchia; Rosalee S. Hellberg
Source:: Journal of microbiological methods 2018 v.153 pp. 54-59
ISSN:: 0167-7012
Subject:: Listeria monocytogenes; bacteria; food pathogens; quantitative polymerase chain reaction; skim milk; soft cheeses; yeast extract
Abstract:: ... Microplate immunocapture is an inexpensive method for the concentration of foodborne pathogens using an antibody-coated microplate. The objective of this study was to determine the efficacy of microplate immunocapture as an alternative to traditional enrichment for concentrating Listeria monocytogenes to levels detectable with selective plating or real-time PCR. L. monocytogenes isolates serologic ...
DOI:: 10.1016/j.mimet.2018.09.005
: https://doi.org/10.1016/j.mimet.2018.09.005

24. Conidia-based fluorescence quantification of Streptomyces

Author:: Raju Podduturi; Niels O.G. Jørgensen
Source:: Journal of microbiological methods 2018 v.153 pp. 104-107
ISSN:: 0167-7012
Subject:: DNA; Gram-positive bacteria; Streptomyces; conidia; fluorescence; liquids; quantitative polymerase chain reaction; staining
Abstract:: ... Determination of cell numbers in filamentous bacteria, such as Streptomyces, is challenging due to the tangled and twisted structure of the filaments and formation of cell clumps in liquid cultures. Here, we developed a conidia-based approach, in which fluorescence of conidia, after staining with the DNA-binding stain SYBR Green 1, was related to SYBR Green 1 fluorescence of DNA in Streptomyces. W ...
DOI:: 10.1016/j.mimet.2018.09.010
: https://doi.org/10.1016/j.mimet.2018.09.010

25. Creation of a drug-sensitive reporter strain of Pseudomonas aeruginosa as a tool for the rapid screening of antimicrobial products

Author:: Raelene Engelberg; Ashley Danielson; Shirley Wang; Manu Singh; Alvan Wai; John Sorensen; Kangmin Duan; Georg Hausner; Ayush Kumar
Source:: Journal of microbiological methods 2018 v.152 pp. 1-6
ISSN:: 0167-7012
Subject:: Pseudomonas aeruginosa; antibiotic resistance; antibiotics; bacteria; drying; human health; rapid methods; screening; soil fungi
Abstract:: ... Antibiotic resistance of bacteria is a considerable challenge to human health in the 21st century. With our discovery pipeline for new and effective antibiotics rapidly drying out, innovative approaches are needed to find new antimicrobials. Soil fungi are known to produce a variety of antimicrobials but rapid screening of fungi that produce such compounds remains a challenge. In this work, we use ...
DOI:: 10.1016/j.mimet.2018.07.001
: https://doi.org/10.1016/j.mimet.2018.07.001

26. Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings

Author:: Laura Pereckaite; Vacis Tatarunas; Agne Giedraitiene
Source:: Journal of microbiological methods 2018 v.152 pp. 154-164
ISSN:: 0167-7012
Subject:: Enterobacteriaceae; antibiotic resistance; antibiotics; bacterial infections; beta-lactamase; diagnostic techniques; phenotype
Abstract:: ... The worldwide prevalence of beta-lactamase-producing Enterobacteriaceae (BL-E) is increasing. Bacterial infections involving ESBLs can be more difficult to treat because of antibiotic resistance, as there are fewer effective antibiotics left to be used. Moreover, treatment failure is often observed. Thus, quick and accurate identification of β-lactamases is imperative to minimize it.This review ar ...
DOI:: 10.1016/j.mimet.2018.07.014
: https://doi.org/10.1016/j.mimet.2018.07.014

27. Deletion of pyruvate decarboxylase gene in Zymomonas mobilis by recombineering through bacteriophage lambda red genes

Author:: Rohit Khandelwal; Sonal Agrawal; Divya Singhi; Preeti Srivastava; Virendra Swarup Bisaria
Source:: Journal of microbiological methods 2018 v.151 pp. 111-117
ISSN:: 0167-7012
Subject:: Zymomonas mobilis; bacteria; bacteriophages; biobased products; ethanol; genes; genetic engineering; metabolic engineering; metabolites; mutants; plasmids; polymerase chain reaction; pyruvate decarboxylase
Abstract:: ... Zymomonas mobilis ZM4 is a gram negative ethanologenic bacterium used in several biotechnological applications. Metabolic engineering in this bacterium is limited because of the available genome engineering tools. In the present study, we report genome engineering in this bacterium using bacteriophage lambda Red genes. Stability of plasmid replicons RK2 (pSIM9) and pBBR1 (pSIM7) containing the lam ...
DOI:: 10.1016/j.mimet.2018.06.008
: https://doi.org/10.1016/j.mimet.2018.06.008

28. Detecting pathogens with Zinc-Finger, TALE and CRISPR- based programmable nucleic acid binding proteins

Author:: Angelo C. Batista; Luis G.C. Pacheco
Source:: Journal of microbiological methods 2018 v.152 pp. 98-104
ISSN:: 0167-7012
Subject:: DNA; Papillomaviridae; RNA-binding proteins; Zika virus; enzymes; gene editing; genotyping; pathogens; point-of-care systems; technology; transcription (genetics)
Abstract:: ... The recent availability of highly adaptable engineered nucleic acid binding proteins has brought about a revolution in the genome-editing field. Now, several studies have harnessed these Zinc-Finger-based, Transcription Activator-like Effector (TALE)-based, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based programmable DNA and RNA-binding proteins to develop very specifi ...
DOI:: 10.1016/j.mimet.2018.07.024
: https://doi.org/10.1016/j.mimet.2018.07.024

29. Detection of Tilletia caries, Tilletia laevis and Tilletia controversa wheat grain contamination using loop-mediated isothermal DNA amplification (LAMP)

Author:: Katarzyna Pieczul; Agnieszka Perek; Krzysztof Kubiak
Source:: Journal of microbiological methods 2018 v.154 pp. 141-146
ISSN:: 0167-7012
Subject:: Alternaria; Cladosporium; DNA; Fusarium; Helminthosporium; Penicillium; Tilletia controversa; Tilletia laevis; Tilletia tritici; detection limit; fungi; protocols; rapid methods; smut diseases; teliospores; wheat
Abstract:: ... The study describes a novel diagnostic protocol based on a loop-mediated isothermal DNA amplification (LAMP) for identification of wheat grains infection by Tilletia laevis, Tilletia caries (common bunt) and Tilletia controversa (draft bunt). The presented data showed that the LAMP analysis is a simple, specific and rapid method that could be used for detection of Tilletia spp. in contaminated gra ...
DOI:: 10.1016/j.mimet.2018.10.018
: https://doi.org/10.1016/j.mimet.2018.10.018

30. Detection of carbapenem-resistant Enterobacteriaceae by chromogenic screening media

Author:: Naser Alizadeh; Mohammad Ahangarzadeh Rezaee; Hossein Samadi Kafil; Mohammad Hossein Soroush Barhaghi; Mohammad Yousef Memar; Morteza Milani; Alka Hasani; Reza Ghotaslou
Source:: Journal of microbiological methods 2018 pp. -
ISSN:: 0167-7012
Subject:: Enterobacteriaceae; beta-lactamase; carbapenems; humans; intestinal microorganisms; monitoring; multiple drug resistance; patients; public health; rapid methods; screening
Abstract:: ... Enterobacteriaceae are a part of the human intestinal flora easily spread by hand carriage, water and food. Treatment of infections due to Enterobacteriaceae is difficult mainly in countries with a low socioeconomic state. Carbapenems are considered as a last-resort antibiotic for the treatment of infections due to multidrug-resistant Enterobacteriaceae. Carbapenem-resistant Enterobacteriaceae (CR ...
DOI:: 10.1016/j.mimet.2018.09.001
: https://doi.org/10.1016/j.mimet.2018.09.001

31. Detection of carbapenemases with a newly developed commercial assay using Matrix Assisted Laser Desorption Ionization-Time of Flight

Author:: Ellionor Rapp; Ørjan Samuelsen; Martin Sundqvist
Source:: Journal of microbiological methods 2018 v.146 pp. 37-39
ISSN:: 0167-7012
Subject:: Acinetobacter; Enterobacteriaceae; Pseudomonas aeruginosa; beta-lactamase; desorption
Abstract:: ... This study evaluated the performance of the MBT STAR-Carba kit (Bruker Daltonics), to detect carbapenemase producing Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter spp. in comparison with the RAPIDEC® CARBA NP test (BioMerieux). MBT STAR-Carba allowed the detection of carbapenemases in Enterobacteriaceae and P. aeruginosa. ...
DOI:: 10.1016/j.mimet.2018.01.008
: https://doi.org/10.1016/j.mimet.2018.01.008

32. Detection of carbapenemases, AmpC and ESBL genes in Acinetobacter isolates from ICUs by DNA microarray

Author:: Fakhur Uddin; Timothy D. McHugh; Kerry Roulston; Gareth Platt; Taseer Ahmed Khan; Muhammad Sohail
Source:: Journal of microbiological methods 2018 v.155 pp. 19-23
ISSN:: 0167-7012
Subject:: Acinetobacter baumannii; DNA microarrays; beta-lactamase; developing countries; genes; health services; imipenem; meropenem; monitoring; phenotype; polymerase chain reaction; resistance mechanisms; Pakistan
Abstract:: ... The accumulation of multiple inherent and acquired resistance mechanisms in Acinetobacter spp. results in emergence of “pandrug resistant” strains which is one of the major concerns in healthcare sectors worldwide. Surveillance of the carbapenemase/ extended-spectrum β-lactamases (ESBLs) genes in A. baumannii by phenotypic methods is challenging especially in developing countries, like Pakistan. I ...
DOI:: 10.1016/j.mimet.2018.11.004
: https://doi.org/10.1016/j.mimet.2018.11.004

33. Detection of different classes of carbapenemases: Adaptation and assessment of a phenotypic method applied to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii, and proposal of a new algorithm

Author:: Guillaume Gautier; Thomas Guillard; Bianca Podac; Béatrice Bercot; Véronique Vernet-Garnier; Christophe de Champs
Source:: Journal of microbiological methods 2018 v.147 pp. 26-35
ISSN:: 0167-7012
Subject:: Acinetobacter baumannii; Klebsiella pneumoniae; Pseudomonas aeruginosa; algorithms; beta-lactamase; immunoaffinity chromatography; molecular biology; phenotype
Abstract:: ... A new phenotypic method for detecting carbapenemases has been adapted (assembling of two MAST® kits, including one that contains faropenem to which a temocillin disk has been added) then assessed using 101 bacterial strains (Enterobacteriaceae with assays on Pseudomonas aeruginosa and Acinetobacter baumannii) including 62 which produce genetically identified carbapenemases. Concerning Carbapenemas ...
DOI:: 10.1016/j.mimet.2018.02.013
: https://doi.org/10.1016/j.mimet.2018.02.013

34. Detection of microbial genes in a single leukocyte by polymerase chain reaction following laser capture microdissection

Author:: Akiteru Yamada; Kazumi Umeki; Yuji Saeki; Yuuki Hashikura; Hajime Nomura; Ikuo Yamamoto; Kunihiko Umekita; Ichiro Takajo; Chihiro Koshimoto; Akihiko Okayama
Source:: Journal of microbiological methods 2018 v.155 pp. 42-48
ISSN:: 0167-7012
Subject:: DNA; Escherichia coli; Staphylococcus aureus; animal models; bacteria; bacterial culture; bacterial infections; genes; mice; neutrophils; nucleotide sequences; peritonitis; phagocytosis; polymerase chain reaction; ribosomal RNA; specific pathogen-free animals; staining
Abstract:: ... Although isolation and identification of bacteria in a clinical specimen constitute essential steps for the diagnosis of bacterial infection, positive results of the bacterial culture are not always attained, despite observing the bacteria by Gram staining. As bacteria phagocytosed by the leukocytes are considered as the causative agents of infectious diseases, this study aims to introduce a new a ...
DOI:: 10.1016/j.mimet.2018.11.005
: https://doi.org/10.1016/j.mimet.2018.11.005

35. Detection of resistance to fluoroquinolones and injectable drugs among antituberculosis drugs by allele-specific primer extension on a microsphere-based platform

Author:: Kyungjong Kim; Jeong Seong Yang; Hee Baeg Choi; Seung Heon Lee
Source:: Journal of microbiological methods 2018 v.144 pp. 111-116
ISSN:: 0167-7012
Subject:: DNA; Mycobacterium tuberculosis; confidence interval; drugs; fluoroquinolones; genes; microparticles; multiple drug resistance; mutation; phenotype; polymerase chain reaction; tuberculosis
Abstract:: ... 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, wh ...
DOI:: 10.1016/j.mimet.2017.11.007
: https://doi.org/10.1016/j.mimet.2017.11.007

36. Detection of root-infecting fungi on cool-season turfgrasses using loop-mediated isothermal amplification and recombinase polymerase amplification

Author:: Brijesh B. Karakkat; Kurt Hockemeyer; Margot Franchett; Megan Olson; Cortney Mullenberg; Paul L. Koch
Source:: Journal of microbiological methods 2018 v.151 pp. 90-98
ISSN:: 0167-7012
Subject:: Gaeumannomyces; Ophiosphaerella korrae; cold season; economic investment; equipment; fungi; lawns and turf; loop-mediated isothermal amplification; pathogens; polymerase chain reaction; temperate zones; turf grasses
Abstract:: ... Root-infecting fungal pathogens such as Gaeumannomyces avenae, Ophiosphaerella korrae, and Magnaporthiopsis poae cause extensive damage to amenity turfgrasses in temperate climates. The diseases they cause are difficult to diagnose by visual symptoms or microscopic inspection, and traditional polymerase chain reaction-based assays require large financial investments in equipment such as thermal cy ...
DOI:: 10.1016/j.mimet.2018.06.011
: https://doi.org/10.1016/j.mimet.2018.06.011

37. Determination of intracellular pH in phytoplankton using the fluorescent probe, SNARF, with detection by fluorescence spectroscopy

Author:: Rachel L. Golda-VanEeckhoutte; Lauren T. Roof; Joseph A. Needoba; Tawnya D. Peterson
Source:: Journal of microbiological methods 2018 v.152 pp. 109-118
ISSN:: 0167-7012
Subject:: carbon; energy balance; enzyme activity; equipment; esterases; fluorescein diacetate; fluorescence; fluorescence emission spectroscopy; homeostasis; isotope labeling; metabolism; microscopy; ocean acidification; pH; photobleaching; phytoplankton; radionuclides; wavelengths
Abstract:: ... The maintenance of pH homeostasis is critical for a variety of cellular metabolic processes. Although ocean acidification is likely to influence cellular metabolism and energy balance, the degree to which intracellular pH in phytoplankton differs from the external environment under varying environmental pH levels is not well characterized. While there are numerous existing methods for the determin ...
DOI:: 10.1016/j.mimet.2018.07.023
: https://doi.org/10.1016/j.mimet.2018.07.023

38. Determination of live:dead bacteria as a function of antibiotic treatment

Author:: Runze Li; Dinesh Dhankhar; Jie Chen; Thomas C. Cesario; Peter M. Rentzepis
Source:: Journal of microbiological methods 2018 v.154 pp. 73-78
ISSN:: 0167-7012
Subject:: DNA; antibiotic resistance; antibiotics; bacteria; drugs; fluorescence emission spectroscopy; patients; principal component analysis; tryptophan; tyrosine
Abstract:: ... Antibiotics are drugs that react against, kill, or inhibit the growth of bacteria. The method most often employed to evaluate the effectiveness of an antibiotic to kill bacteria requires at least 16 to 24 h for bacterial incubation. The requirement of long periods of time for the determination of the number of bacteria still alive after antibiotic treatment, may, in many cases, be detrimental to t ...
DOI:: 10.1016/j.mimet.2018.10.010
: https://doi.org/10.1016/j.mimet.2018.10.010

39. Development and characterization of a 3D oral mucosa model as a tool for host-pathogen interactions

Author:: Kássia de Carvalho Dias; Denise Lins de Sousa; Paula Aboud Barbugli; Paulo Sérgio Cerri; Vehid Max Salih; Carlos Eduardo Vergani
Source:: Journal of microbiological methods 2018 v.152 pp. 52-60
ISSN:: 0167-7012
Subject:: coculture; collagen; eosin; fibroblasts; gels; gingiva; histology; host-pathogen relationships; humans; immunocytochemistry; keratinocytes; lactate dehydrogenase; models; mucosa; transmission electron microscopy
Abstract:: ... The aim of this study was to (i) design, develop and validate a practical and physiologically relevant reconstituted in vitro oral mucosa tissue model and (ii) to assess its applicability in in vitro host-pathogen interactions with C. albicans and S. aureus. Co-culture organotypic constructions were created by incorporating specific numbers of keratinocytes (NOK-si) onto cellularised, collagen gel ...
DOI:: 10.1016/j.mimet.2018.07.004
: https://doi.org/10.1016/j.mimet.2018.07.004

40. Development and evaluation of two multi-antigen serological assays for the diagnosis of bovine tuberculosis in cattle

Author:: Stefania Fontana; Maria Pacciarini; Mery Boifava; Roberta Pellesi; Barbara Casto; Michele Gastaldelli; Heike Koehler; Nicola Pozzato; Francesco Casalinuovo; M. Beatrice Boniotti
Source:: Journal of microbiological methods 2018 v.153 pp. 118-126
ISSN:: 0167-7012
Subject:: blood serum; bovine tuberculosis; cattle; herds; interferon-gamma; necropsy; tuberculin
Abstract:: ... There is currently an increased interest in the use of serological approaches in combination with traditional cell-mediated immunity-based techniques to improve the detection of tuberculosis (TB)-infected animals. In the present study, we developed and validated two different serological TB-detection assays using four antigens, MPB70, MPB83, ESAT6 and CFP10, and the tuberculin PPDb. A conventional ...
DOI:: 10.1016/j.mimet.2018.09.013
: https://doi.org/10.1016/j.mimet.2018.09.013

41. Development and testing of an 18S rRNA phylogenetic microarray for marine sediments

Author:: Katrine Lekang; Kenan Hadziavdic; Katrine Sandnes Skaar; Inge Jonassen; Eric M. Thompson; Christofer Troedsson
Source:: Journal of microbiological methods 2018 v.154 pp. 95-106
ISSN:: 0167-7012
Subject:: DNA barcoding; anthropogenic activities; automation; biodiversity; ecosystems; eukaryotic cells; filtration; genetic markers; marine sediments; microarray technology; monitoring; nucleic acid hybridization; phylogeny; remote sensing; ribosomal DNA; ribosomal RNA; sequence homology
Abstract:: ... There is increasing interest in finding new, more efficient methods for routine monitoring of anthropogenic effects on benthic biodiversity and ecosystems. A range of molecular methods have been developed for assessing biodiversity the last decades. Particularly interesting are microarrays targeting phylogenetic marker genes, such as the small subunit of ribosomal RNA in eukaryotes (18S rRNA). Thi ...
DOI:: 10.1016/j.mimet.2018.10.007
: https://doi.org/10.1016/j.mimet.2018.10.007

42. Development of a high throughput optical density assay to determine fungicide sensitivity of oomycetes

Author:: Shannon Hunter; Rebecca McDougal; Mike J. Clearwater; Nari Williams; Peter Scott
Source:: Journal of microbiological methods 2018 v.154 pp. 33-39
ISSN:: 0167-7012
Subject:: Phytophthora cinnamomi; absorbance; biological resistance; fungicides; growth retardation; inventories; median effective concentration; mycelium
Abstract:: ... A high-throughput assay was developed to screen Phytophthora species for fungicide sensitivity using optical density measurements for unbiased, automated measurement of mycelial growth. The efficacy of the optical density assay (OD) to measure phosphite sensitivity in Phytophthora species was compared to two widely used methods, radial growth (RG) and dry weight (DW) assays. Three isolates of each ...
DOI:: 10.1016/j.mimet.2018.10.006
: https://doi.org/10.1016/j.mimet.2018.10.006

43. Development of a molecular serotyping scheme and a multiplexed luminex-based array for Providencia

Author:: Yuhui Du; Huiying Li; Zhiqiu Yin; Antoni Rozalski; Agnieszka Torzewska; Pan Yang; Chengqian Qian; Tingting Xu; Hengchun Cao; Pan Wu; Lingyan Jiang; Xi Guo; Di Huang; Bin Liu
Source:: Journal of microbiological methods 2018 v.153 pp. 14-23
ISSN:: 0167-7012
Subject:: DNA; Gram-negative bacteria; Morganella; O-antigens; Proteus; Providencia; animal pathogens; biosynthesis; detection limit; monitoring; multigene family; ozone; serotypes; urine; uropathogenic Escherichia coli
Abstract:: ... Providencia is an opportunistic human pathogen that belongs to the Enterobacteriaceae family. The bacterial cell surface O-antigen is one of the most structurally variable cell constituents and serves as a basis for serotyping gram-negative bacteria. In this work, the genomes of 12 Providencia strains were sequenced, and genes driving O-antigen biosynthesis were analyzed. The O-antigen-synthesizin ...
DOI:: 10.1016/j.mimet.2018.08.009
: https://doi.org/10.1016/j.mimet.2018.08.009

44. Development of a rapid PCR-Nucleic Acid Lateral Flow Immunoassay (PCR-NALFIA) based on rDNA IGS sequence analysis for the detection of Macrophomina phaseolina in soil

Author:: Susanna Pecchia; Daniele Da Lio
Source:: Journal of microbiological methods 2018 v.151 pp. 118-128
ISSN:: 0167-7012
Subject:: Macrophomina phaseolina; biotin; color; densitometry; electrophoresis; immunoassays; intergenic DNA; mycelium; pathogens; polymerase chain reaction; ribosomal DNA; sclerotia; sequence analysis; silica; soil
Abstract:: ... The ‘Nucleic Acid Lateral Flow Immunoassay’ (NALFIA) using a generic ‘Lateral Flow Device’ (LFD), combined with PCR employing labelled primers (PCR-NALFIA), enables to circumvent the use of electrophoresis, making the diagnostic procedure more rapid and easier. If the specific amplicon is present in the sample, a coloured band, with an intensity proportional to the amplicon concentration, will dev ...
DOI:: 10.1016/j.mimet.2018.06.010
: https://doi.org/10.1016/j.mimet.2018.06.010

45. Development of a real-time assay to determine the frequency of qac genes in methicillin resistant Staphylococcus aureus

Author:: Maurice Kok Leong Chan; Seok Hwee Koo; Qingyao Quek; Wan Sia Pang; Boran Jiang; Lily Siew Yong Ng; Si Huei Tan; Thean Yen Tan
Source:: Journal of microbiological methods 2018 v.153 pp. 133-138
ISSN:: 0167-7012
Subject:: DNA; agar gel electrophoresis; antibiotic resistance; antiseptics; bacitracin; chlorhexidine; genes; genetic variation; methicillin; methicillin-resistant Staphylococcus aureus; neomycin; quantitative polymerase chain reaction; quaternary ammonium compounds; transporters
Abstract:: ... The emergence of antiseptic resistance and/or antiseptic-resistance genes in methicillin-resistant Staphylococcus aureus (MRSA) may result in failure of decolonization treatments. Plasmid-encoded efflux pump genes qacA/B and qacC (smr) confer tolerance to chlorhexidine and quaternary ammonium compounds. The objective of this study was to develop and validate a multiplex real time-PCR assay for det ...
DOI:: 10.1016/j.mimet.2018.09.017
: https://doi.org/10.1016/j.mimet.2018.09.017

46. Development of a simple and practical method of discrimination between Vibrio furnissii and V. fluvialis based on single-nucleotide polymorphisms of 16S rRNA genes observed in V. furnissii but not in V. fluvialis

Author:: 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
Source:: Journal of microbiological methods 2018 v.144 pp. 22-28
ISSN:: 0167-7012
Subject:: DNA primers; Vibrio furnissii; bacteria; equipment; genes; mass spectrometry; polymerase chain reaction; restriction endonucleases; restriction fragment length polymorphism; ribosomal RNA; single nucleotide polymorphism
Abstract:: ... 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 ...
DOI:: 10.1016/j.mimet.2017.10.014
: https://doi.org/10.1016/j.mimet.2017.10.014

47. Development of a tick-borne pathogen QPCR panel for detection of Anaplasma, Ehrlichia, Rickettsia, and Lyme disease Borrelia in animals

Author:: Zhenyu Shen; Michael Z. Zhang; Roger W. Stich; William J. Mitchell; Shuping Zhang
Source:: Journal of microbiological methods 2018 v.151 pp. 83-89
ISSN:: 0167-7012
Subject:: Anaplasma; Borrelia; DNA; Ehrlichia; Lyme disease; Rickettsia; blood; cross reaction; dogs; horses; humans; melting point; pathogens; rapid methods; screening
Abstract:: ... Anaplasma spp., Ehrlichia spp., Rickettsia spp., and Lyme disease associated Borrelia spp. are the most common tick-borne pathogens reported to infect human beings worldwide and other animals, such as dogs and horses. In the present study, we developed a broad-coverage SYBR Green QPCR panel consisting of four individual assays for the detection and partial differentiation of the aforementioned pat ...
DOI:: 10.1016/j.mimet.2018.05.019
: https://doi.org/10.1016/j.mimet.2018.05.019

48. Development of an Sce-I mutagenesis system for Burkholderia cepacia complex strains

Author:: Ashraf Abdu; Gerardo Juarez-Lara; Jonathan J. Dennis
Source:: Journal of microbiological methods 2018 v.146 pp. 16-21
ISSN:: 0167-7012
Subject:: Burkholderia cenocepacia; Gram-negative bacteria; antibiotic resistance; biodegradation; biosynthesis; clones; fungi; genes; humans; mutagenesis; plant growth; plants (botany); pollutants; restriction endonucleases
Abstract:: ... The Burkholderia cepacia complex (Bcc) consists of at least 20 phenotypically similar but genotypically distinct Gram-negative bacteria that are ubiquitous in nature, are capable of promoting plant growth and biodegradation of pollutants, but that also are highly antibiotic resistant and produce damaging effects towards plants, fungi, and humans. To study these genetically recalcitrant bacteria in ...
DOI:: 10.1016/j.mimet.2018.01.011
: https://doi.org/10.1016/j.mimet.2018.01.011

49. Development of an efficient conjugal DNA transfer system between Escherichia coli and a non-sporulating Streptomyces strain

Author:: Diana Rocha; Beatriz Ruiz-Villafán; Monserrat Manzo; Romina Rodríguez-Sanoja; Sergio Sánchez
Source:: Journal of microbiological methods 2018 v.144 pp. 60-66
ISSN:: 0167-7012
Subject:: Escherichia coli; Streptomyces peucetius; bacteria; doxorubicin; genetic conjugation; genetic engineering; mutants; mycelium; spores
Abstract:: ... 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 m ...
DOI:: 10.1016/j.mimet.2017.11.006
: https://doi.org/10.1016/j.mimet.2017.11.006

50. Development of an efficient genetic system in a gene cluster-rich endophytic fungus Calcarisporium arbuscula NRRL 3705

Author:: Fei Cao; Jin-Tao Cheng; Xin-Ai Chen; Yong-Quan Li; Xu-Ming Mao
Source:: Journal of microbiological methods 2018 v.151 pp. 1-6
ISSN:: 0167-7012
Subject:: Agrobacterium radiobacter; DNA; bioactive properties; biosynthesis; endophytes; enzymology; fluorescence; fungi; gene expression regulation; gene overexpression; gene targeting; genetic engineering; models; multigene family; mutants; mycotoxins; product development; promoter regions
Abstract:: ... Filamentous fungi are emerging as attractive producers of natural products with novel structures, diverse bioactivities and unprecedented enzymology. But their genetic systems are poorly developed, especially in some non-model endogenic fungi, which have hampered our genetic manipulation of their natural product development. Calcarisporium arbuscula NRRL 3705 is an endophytic filamentous fungus ri ...
DOI:: 10.1016/j.mimet.2018.05.026
: https://doi.org/10.1016/j.mimet.2018.05.026

51. Development of duplex PCR-ELISA for simultaneous detection of Salmonella spp. and Escherichia coli O157: H7 in food

Author:: Jinqiang Hu; Runna Huang; Yi Wang; Xiangke Wei; Zhangcun Wang; Yao Geng; Jianzhou Jing; Hui Gao; Xincheng Sun; Caiwen Dong; Chunpeng Jiang
Source:: Journal of microbiological methods 2018 v.154 pp. 127-133
ISSN:: 0167-7012
Subject:: Escherichia coli O157; Salmonella; antibodies; bacteria; beef; biotin; cabbage; chickens; color; detection limit; digoxin; enzyme-linked immunosorbent assay; food sanitation; foodborne illness; genes; juices; microbial detection; milk; monitoring; nucleic acid hybridization; polymerase chain reaction; pork; shrimp; streptomycin
Abstract:: ... In the current study, a duplex PCR-ELISA method was developed targeting the specific genes, invA of Salmonella spp. and rfbE of Escherichia coli O157: H7, to detect one or both bacteria in food. In brief, PCR product amplified by PCR primer labeled with digoxin at the 5′-end and a probe labeled with biotin at the 3′-end can form dimer by nucleic acid hybridization which can be captured by binding ...
DOI:: 10.1016/j.mimet.2018.10.017
: https://doi.org/10.1016/j.mimet.2018.10.017

52. Development of new versatile plasmid-based systems for λRed-mediated Escherichia coli genome engineering

Author:: Dmitrii M. Bubnov; Tigran V. Yuzbashev; Tatiana V. Vybornaya; Alexander I. Netrusov; Sergey P. Sineoky
Source:: Journal of microbiological methods 2018 v.151 pp. 48-56
ISSN:: 0167-7012
Subject:: DNA repair; Escherichia coli; alleles; base pair mismatch; gene editing; plasmids; replication origin; rhamnose; temperature
Abstract:: ... Plasmid-based systems are the most appropriate for multistep lambda Red (λRed)-mediated recombineering, such as the assembly of strains for biotechnological applications. Currently, the widely used λRed-expressing plasmids use a temperature-sensitive origin of replication or temperature shift control of λRed expression. In this work, we have constructed a new, conditionally replicating vector that ...
DOI:: 10.1016/j.mimet.2018.06.001
: https://doi.org/10.1016/j.mimet.2018.06.001

53. Direct detection of carbapenemase-associated proteins of Acinetobacter baumannii using nanodiamonds coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Author:: Kai-Chih Chang; Chin-Yi Chung; Chen-Hsing Yeh; Kuo-Hsiu Hsu; Ya-Ching Chin; Sin-Siang Huang; Bo-Rong Liu; Hsi-An Chen; Anren Hu; Po-Chi Soo; Wen-Ping Peng
Source:: Journal of microbiological methods 2018 v.147 pp. 36-42
ISSN:: 0167-7012
Subject:: Acinetobacter baumannii; DNA; bacteria; beta-lactamase; biomarkers; desorption; genes; imipenem; matrix-assisted laser desorption-ionization mass spectrometry; nanodiamonds; polymerase chain reaction; proteins
Abstract:: ... The appearance and spread of carbapenem-resistant Acinetobacter baumannii (CRAB) pose a challenge for optimization of antibiotic therapies and outbreak preventions. The carbapenemase production can be detected through culture-based methods (e.g. Modified Hodge Test-MHT) and DNA based methods (e.g. Polymerase Chain Reaction-PCR). The culture-based methods are time-consuming, whereas those of PCR as ...
DOI:: 10.1016/j.mimet.2018.02.014
: https://doi.org/10.1016/j.mimet.2018.02.014

54. Direct diagnosis of Brucella species through multiplex PCR formed by a new method

Author:: Ahmet Murat Saytekin; Seyyal Ak
Source:: Journal of microbiological methods 2018 v.154 pp. 86-94
ISSN:: 0167-7012
Subject:: Brucella; brucellosis; fetus; liver; lungs; polymerase chain reaction; ruminants; stomach
Abstract:: ... This study aimed to develop direct PCR methods, which enable the diagnosis of brucellosis agents from ruminant aborted fetus samples at species and genus levels, and determine the applicability of the newly developed methods. For this purpose, 137 lung, 137 liver, and 52 fetal stomach fluid samples belonging to 166 ruminant aborted fetuses (326 samples in total) were examined. Firstly, agent isola ...
DOI:: 10.1016/j.mimet.2018.10.011
: https://doi.org/10.1016/j.mimet.2018.10.011

55. Directed freeze-fracturing of Bacillus subtilis biofilms for conventional scanning electron microscopy

Author:: Felix M. Fuchs; Gudrun Holland; Ralf Moeller; Michael Laue
Source:: Journal of microbiological methods 2018 v.152 pp. 165-172
ISSN:: 0167-7012
Subject:: Bacillus subtilis; biofilm; models; scanning electron microscopy
Abstract:: ... Biofilms have been intensively investigated over the past decades. Bacillus subtilis is able to form highly structured colony biofilms, and as one of the most studied Gram-positive model organisms, has helped to decipher the complex genetic regulation of biofilms. Several methods have been developed to analyze the architecture of biofilms. In this paper, we describe a method which allows the analy ...
DOI:: 10.1016/j.mimet.2018.08.005
: https://doi.org/10.1016/j.mimet.2018.08.005

56. Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds?

Author:: Vaibhav Diwan; Hans-Jørgen Albrechtsen; Barth F. Smets; Arnaud Dechesne
Source:: Journal of microbiological methods 2018 v.151 pp. 28-34
ISSN:: 0167-7012
Subject:: DNA primers; bacteria; genes; microbial communities; nucleotide sequences; prokaryotic cells; ribosomal RNA
Abstract:: ... Universal (i.e., targeting most bacteria/prokaryotes) 16S rRNA gene based amplicon sequencing is widely used for assessing microbial communities due to its low cost, time efficiency, and ability to provide a full overview of the community. However, it is currently unclear if it can yield reliable information on specific microbial guilds, as obtained by using primer sets targeting functional genes ...
DOI:: 10.1016/j.mimet.2018.05.025
: https://doi.org/10.1016/j.mimet.2018.05.025

57. The EDTA-based disk-combination tests are unreliable for the detection of MCR-mediated colistin-resistance in Enterobacteriaceae

Author:: Mathieu Clément; Thomas Büdel; Odette J. Bernasconi; Luigi Principe; Vincent Perreten; Francesco Luzzaro; Andrea Endimiani
Source:: Journal of microbiological methods 2018 pp. -
ISSN:: 0167-7012
Subject:: EDTA (chelating agent); Enterobacteriaceae; agar; chelating agents; colistin
Abstract:: ... We evaluated several EDTA-based combined-disk tests to detect 25 mcr producers among 48 Enterobacteriaceae. Colistin disks plus EDTA (292/584 μg) on MH and CAMH agar were used. Results were positive if with chelator there was an inhibition zone increase ≥3 mm compared to colistin alone. All tests resulted unreliable (sensitivity ≤68%). ...
DOI:: 10.1016/j.mimet.2018.08.008
: https://doi.org/10.1016/j.mimet.2018.08.008

58. Efficient construction of xenogeneic genomic libraries by circumventing restriction-modification systems that restrict methylated DNA

Author:: Satoshi Hasegawa; Toru Jojima; Masayuki Inui
Source:: Journal of microbiological methods 2018 v.146 pp. 13-15
ISSN:: 0167-7012
Subject:: Corynebacterium glutamicum; DNA-directed DNA polymerase; Escherichia coli; genomic libraries; plasmids
Abstract:: ... An efficient method to construct xenogeneic genomic libraries with low errors and bias by circumventing restriction-modification systems that restrict methylated DNA was developed. Un-methylated genomic DNA of Escherichia coli prepared by ϕ29 DNA polymerase was introduced to Corynebacterium glutamicum R after ligation with un-methylated vector plasmids. ...
DOI:: 10.1016/j.mimet.2018.01.005
: https://doi.org/10.1016/j.mimet.2018.01.005

59. Efficient transformation of Pleurotus eryngii with a safe selective marker mutated from the Pesdi1 gene

Author:: Junjun Shang; Yan Li; Ruiheng Yang; Ying Wang; Wenjun Mao; Lihua Tang; Yingying Wu; Takehito Nakazawa; Yoichi Honda; Dapeng Bao
Source:: Journal of microbiological methods 2018 v.152 pp. 7-9
ISSN:: 0167-7012
Subject:: Pleurotus eryngii; carboxin; genes; mutants; mutation; polyethylene; protoplasts
Abstract:: ... We introduced a site-directed mutation in the sdi1 gene and used it as a selective marker for the polyethylene glycol-mediated transformation of Pleurotus eryngii monokaryon protoplasts. The transformants displayed obvious and stable resistance to the fungicide carboxin indicating that the mutant Pesdi1 gene is an efficient selective marker. ...
DOI:: 10.1016/j.mimet.2018.07.006
: https://doi.org/10.1016/j.mimet.2018.07.006

60. Enhanced sensitivity and fast turnaround time in laboratory diagnosis for bovine paratuberculosis in faecal samples

Author:: A.K. Schwalm; A. Obiegala; M. Pfeffer; R. Sting
Source:: Journal of microbiological methods 2018 v.152 pp. 39-47
ISSN:: 0167-7012
Subject:: DNA; Mycobacterium avium subsp. paratuberculosis; cattle; droplets; feces; freezing; laboratory diagnosis; liquids; magnetism; microbial growth; paratuberculosis; pathogens; quantitative polymerase chain reaction; thawing
Abstract:: ... Bovine paratuberculosis (Johne's disease in cattle) is caused by the pathogen Mycobacterium avium subsp. paratuberculosis (MAP) and is a widespread chronic bacterial infectious disease in cattle. Due to the peculiarities of the pathogen, detection of MAP in faeces remains difficult.DNA extraction and real-time PCR for detection of MAP in bovine faeces (direct PCR) have been refined and feasible pr ...
DOI:: 10.1016/j.mimet.2018.07.010
: https://doi.org/10.1016/j.mimet.2018.07.010

61. Enrichment of low-density symbiont DNA from minute insects

Author:: Corinne M. Stouthamer; Suzanne Kelly; Martha S. Hunter
Source:: Journal of microbiological methods 2018 v.151 pp. 16-19
ISSN:: 0167-7012
Subject:: DNA; arthropods; bacteria; genomics; high-throughput nucleotide sequencing; hosts; insects; learning; phenotype; rearing; symbionts
Abstract:: ... Symbioses between bacteria and insects are often associated with changes in important biological traits that can significantly affect host fitness. To a large extent, studies of these interactions have been based on physiological changes or induced phenotypes in the host, and the genetic mechanisms by which symbionts interact with their hosts have only recently become better understood. Learning a ...
DOI:: 10.1016/j.mimet.2018.05.013
: https://doi.org/10.1016/j.mimet.2018.05.013

62. Enrichment of semen culture in the diagnosis of bacterial prostatitis

Author:: Maria Rosaria Iovene; Francesca Martora; Enza Mallardo; Marco De Sio; Davide Arcaniolo; Chiara Del Vecchio; Chiara Pagliuca; Giuseppe Signoriello; Mariateresa Vitiello
Source:: Journal of microbiological methods 2018 v.154 pp. 124-126
ISSN:: 0167-7012
Subject:: bacterial infections; prostatitis; protocols; semen
Abstract:: ... The objective was to investigate the diagnostic accuracy of our microbiological protocol to simplify the evaluation of bacterial prostatitis in the clinical practice.Our findings show the possibility to apply our alternative enrichment semen culture method to detect prostatic bacterial infection with higher sensitivity than the gold standard M&S technique. ...
DOI:: 10.1016/j.mimet.2018.10.016
: https://doi.org/10.1016/j.mimet.2018.10.016

63. Enzymatic Kraft lignin demethylation and fungal O-demethylases like vanillate-O-demethylase and syringate O-demethylase catalyzed catechol-Fe3+ complexation method

Author:: Balaji Venkatesagowda
Source:: Journal of microbiological methods 2018 v.152 pp. 126-134
ISSN:: 0167-7012
Subject:: Aspergillus; Galerina; absorbance; ammonium sulfate; caffeic acid; catechol; chemical bonding; culture filtrates; demethylation; deprotonation; enzyme activity; enzymes; fungi; gallic acid; glycols; hydrogen peroxide; iron; lignin; models; moieties; nitrous acid; pH; pyrocatechol; titanium; vanillin
Abstract:: ... The ability of enzymatic Kraft Lignin (KL) demethylation was determined using catechol and ferric ion coordination (catechol-Fe³⁺ complexes) by reduction of Fe³⁺ to Fe²⁺ and formation of mono, bis- and/or tris-catechol-Fe³⁺ complexes has been investigated to identify enzyme that can strip-off O-methyl groups from lignin such as O-demethylase. To detect fungal demethylation and release of catechol- ...
DOI:: 10.1016/j.mimet.2018.07.021
: https://doi.org/10.1016/j.mimet.2018.07.021

64. Establishment of a suspension array for Pseudomonas aeruginosa O-antigen serotyping

Author:: Huiying Li; Yuhui Du; Chengqian Qian; Lingyu Li; Lingyan Jiang; Xiaolong Jiang; Hengchun Cao; Xi Guo; Bin Liu
Source:: Journal of microbiological methods 2018 v.155 pp. 59-64
ISSN:: 0167-7012
Subject:: DNA; Gram-negative bacteria; O-antigens; Pseudomonas aeruginosa; diagnostic techniques; hospitals; multigene family; patients; serotypes; transferases
Abstract:: ... Pseudomonas aeruginosa (P. aeruginosa) is widespread in the environment. It readily infects hospital and immunocompromised patients. Traditional biochemical and immunological diagnoses of P. aeruginosa infection cannot meet clinical demands. The variability of O-antigens is the primary basis for the serotyping schemes of many gram-negative bacteria, which is the most widely used method for pathoge ...
DOI:: 10.1016/j.mimet.2018.11.006
: https://doi.org/10.1016/j.mimet.2018.11.006

65. Evaluation of ATR-FTIR for analysis of bacterial cellulose impurities

Author:: Mark E. Fuller; Christina Andaya; Kevin McClay
Source:: Journal of microbiological methods 2018 v.144 pp. 145-151
ISSN:: 0167-7012
Subject:: Fourier transform infrared spectroscopy; bacteria; cellulose; lipids; models; nucleic acids; spectral analysis
Abstract:: ... 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 aci ...
DOI:: 10.1016/j.mimet.2017.10.017
: https://doi.org/10.1016/j.mimet.2017.10.017

66. Evaluation of DNA extraction methods to detect bacterial targets in aerosol samples

Author:: John Dunbar; La Verne Gallegos-Graves; Jason Gans; Stephen A. Morse; Segaran Pillai; Kevin Anderson; David R. Hodge
Source:: Journal of microbiological methods 2018 v.153 pp. 48-53
ISSN:: 0167-7012
Subject:: Bacillus anthracis; Burkholderia pseudomallei; DNA; Francisella tularensis; Yersinia pestis; aerosols; air; filters; filtration; genome; monitoring; particulates; pathogens; spores
Abstract:: ... DNA-based monitoring of pathogens in aerosol samples requires extraction methods that provide high recovery of DNA. To identify a suitable method, we evaluated six DNA extraction methods for recovery of target-specific DNA from samples with four bacterial agents at low abundance (<10,000 genome copies per detection assay). These methods differed in rigor of cell disruption, approach for DNA captur ...
DOI:: 10.1016/j.mimet.2018.09.006
: https://doi.org/10.1016/j.mimet.2018.09.006

67. Evaluation of a novel optical assay for rapid detection of methicillin-resistant Staphylococcus aureus in liquid culture

Author:: Dennis Knaack; Evgeny A. Idelevich; Barbara Körber-Irrgang; Michael Kresken; Karsten Becker
Source:: Journal of microbiological methods 2018 v.146 pp. 68-70
ISSN:: 0167-7012
Subject:: agar; antibiotic resistance; coagulase negative staphylococci; light scattering; liquids; methicillin; methicillin-resistant Staphylococcus aureus; rapid methods; screening; Germany
Abstract:: ... Valid detection of methicillin-resistant Staphylococcus aureus (MRSA) is a precondition for MRSA prevention measures. Most of the available MRSA screening tests are based either on the identification of colony material grown on solid agar media or on direct molecular approaches. The HB&L MRSA KIT (Alifax, Polverara, Italy) is designed to screen for MRSA in liquid cultures applying the light scatte ...
DOI:: 10.1016/j.mimet.2018.01.016
: https://doi.org/10.1016/j.mimet.2018.01.016

68. Evaluation of modified saponin preparation method for the direct identification and antimicrobial susceptibility testing from positive blood culture

Author:: Ji Eun Lee; Sung Jin Jo; Kang Gyun Park; Hyun Soo Suk; Sung Il Ha; Jeong Seob Shin; Yeon-Joon Park
Source:: Journal of microbiological methods 2018 v.154 pp. 118-123
ISSN:: 0167-7012
Subject:: Campylobacter; Streptococcus pneumoniae; anaerobes; antibiotic resistance; bacteria; blood; bottles; diagnostic techniques; matrix-assisted laser desorption-ionization mass spectrometry; pellets; saponins; yeasts
Abstract:: ... We evaluated the two in-house sample preparation methods (saponin method (SAP) and [saponin + Sputazyme] method (SSPZ)) for direct identification of microorganisms using MALDI-TOF MS from positive blood culture bottles. Also, we evaluated the [saponin + Sputazyme] method for direct antimicrobial susceptibility testing (AST) using Vitek 2 system.For direct identification, 163 prospective, monomicro ...
DOI:: 10.1016/j.mimet.2018.10.004
: https://doi.org/10.1016/j.mimet.2018.10.004

69. Evaluation of sampling and storage procedures on preserving the community structure of stool microbiota: A simple at-home toilet-paper collection method

Author:: Kait F. Al; Jordan E. Bisanz; Gregory B. Gloor; Gregor Reid; Jeremy P. Burton
Source:: Journal of microbiological methods 2018 v.144 pp. 117-121
ISSN:: 0167-7012
Subject:: feces; humans; intestinal microorganisms; paper; patients; ribosomal RNA; sampling; sequence analysis; storage conditions; temperature
Abstract:: ... The increasing interest on the impact of the gut microbiota on health and disease has resulted in multiple human microbiome-related studies emerging. However, multiple sampling methods are being used, making cross-comparison of results difficult. To avoid additional clinic visits and increase patient recruitment to these studies, there is the potential to utilize at-home stool sampling. The aim of ...
DOI:: 10.1016/j.mimet.2017.11.014
: https://doi.org/10.1016/j.mimet.2017.11.014

70. Evaluation of the multiplex PCR Allplex-GI assay in the detection of bacterial pathogens in diarrheic stool samples

Author:: Ariadna Martín; Ana Pérez-Ayala; Fernando Chaves; David Lora; M. Ángeles Orellana
Source:: Journal of microbiological methods 2018 v.144 pp. 33-36
ISSN:: 0167-7012
Subject:: Aeromonas; Campylobacter; Salmonella; Shigella; bacteria; diagnostic techniques; disease control; enteroinvasive Escherichia coli; feces; gastroenteritis; gastrointestinal system; mass spectrometry; pathogens; polymerase chain reaction; therapeutics
Abstract:: ... 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 ...
DOI:: 10.1016/j.mimet.2017.10.016
: https://doi.org/10.1016/j.mimet.2017.10.016

71. Evaluation of the rapid biochemical β-CARBA™ test for detection of carbapenemase-producing Gram-negative bacteria

Author:: Vladimira Hinić; Josiane Reist; Adrian Egli
Source:: Journal of microbiological methods 2018 v.144 pp. 44-46
ISSN:: 0167-7012
Subject:: Acinetobacter; Gram-negative bacteria; beta-lactamase; phenotype; screening
Abstract:: ... 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. ...
DOI:: 10.1016/j.mimet.2017.10.008
: https://doi.org/10.1016/j.mimet.2017.10.008

72. Evaluation of the reproducibility of a serological test for antibodies to Chlamydia trachomatis pgp3: A potential surveillance tool for trachoma programs

Author:: Hemjot Kaur; Laura Dize; Beatriz Munoz; Charlotte Gaydos; Sheila K. West
Source:: Journal of microbiological methods 2018 v.147 pp. 56-58
ISSN:: 0167-7012
Subject:: Chlamydia trachomatis; antibodies; blood; children; correlation; fluorescence; immunologic techniques; monitoring; seroprevalence
Abstract:: ... Serological testing for antibodies to Chlamydia trachomatis pgp3 is being evaluated as a tool to use for trachoma surveillance. There are limited data on the reproducibility of the test results using a multiplex platform.We tested the reproducibility of a serologic test for C. trachomatis pgp3 in 6 dried blood spots collected from a random sample of 45 children from a trachoma endemic area. The sp ...
DOI:: 10.1016/j.mimet.2018.02.017
: https://doi.org/10.1016/j.mimet.2018.02.017

73. Evaluation of two real time PCR assays for the detection of bacterial DNA in amniotic fluid

Author:: Patricia Girón de Velasco-Sada; Iker Falces-Romero; Inmaculada Quiles-Melero; Adela García-Perea; Jesús Mingorance
Source:: Journal of microbiological methods 2018 v.144 pp. 107-110
ISSN:: 0167-7012
Subject:: DNA; Mycoplasma; Ureaplasma urealyticum; amniotic fluid; hospitals; microorganisms; quantitative polymerase chain reaction; sequence analysis
Abstract:: ... The aim of this study was to evaluate two non-commercial Real-Time PCR assays for the detection of microorganisms in amniotic fluid followed by identification by pyrosequencing.We collected 126 amniotic fluids from 2010 to 2015 for the evaluation of two Real-Time PCR assays for detection of bacterial DNA in amniotic fluid (16S Universal PCR and Ureaplasma spp. specific PCR). The method was develop ...
DOI:: 10.1016/j.mimet.2017.11.013
: https://doi.org/10.1016/j.mimet.2017.11.013

74. Extensive evaluation of fastidious anaerobic bacteria recovery from the Copan eSwab® transport system

Author:: Thomas Demuyser; Deborah De Geyter; Daisy Van Dorpe; Kristof Vandoorslaer; Ingrid Wybo
Source:: Journal of microbiological methods 2018 v.144 pp. 73-78
ISSN:: 0167-7012
Subject:: Clostridium clostridioforme; anaerobes; antibiotic resistance; bacteria; containers; liquids; pathogens; temperature; transportation; viability
Abstract:: ... 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 thes ...
DOI:: 10.1016/j.mimet.2017.11.009
: https://doi.org/10.1016/j.mimet.2017.11.009

75. Extraction of high-quality RNA from Bacillus subtilis with a lysozyme pre-treatment followed by the Trizol method

Author:: Eber Villa-Rodríguez; Cuauhtemoc Ibarra-Gámez; Sergio de los Santos-Villalobos
Source:: Journal of microbiological methods 2018 v.147 pp. 14-16
ISSN:: 0167-7012
Subject:: Bacillus subtilis; RNA; developmental stages; lysozyme; microbial growth
Abstract:: ... A suitable technique (lysozyme combined with Trizol reagent) was developed to improve the RNA yield, purity and integrity from Bacillus subtilis, under different bacterial growth stages. The obtained RNA was intact, having the required characteristics for downstream applications. ...
DOI:: 10.1016/j.mimet.2018.02.011
: https://doi.org/10.1016/j.mimet.2018.02.011

76. Filling the gaps in clinical proteomics: a do-it-yourself guide for the identification of the emerging pathogen Arcobacter by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Author:: Anne-Marie Van den Abeele; Dirk Vogelaers; Peter Vandamme; Elke Vanlaere; Kurt Houf
Source:: Journal of microbiological methods 2018 v.152 pp. 92-97
ISSN:: 0167-7012
Subject:: Arcobacter; Campylobacter fetus; bacteria; databases; formic acid; gastrointestinal system; humans; matrix-assisted laser desorption-ionization mass spectrometry; pathogens; proteomics; public health; species identification; therapeutics
Abstract:: ... Arcobacters are considered emerging gastrointestinal pathogens. Rapid, reliable and species-specific identification of these bacteria is important. Biochemical tests commonly yield negative or variable results. Molecular methods prove more reliable but are time consuming and lack specificity. Matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a fast, che ...
DOI:: 10.1016/j.mimet.2018.07.007
: https://doi.org/10.1016/j.mimet.2018.07.007

77. Flow cytometry as a new complementary tool to study Coxiella burnetii in cell cultures

Author:: Annica Rebbig; Svea Matthiesen; Anja Lührmann; Michael R. Knittler
Source:: Journal of microbiological methods 2018 v.151 pp. 39-43
ISSN:: 0167-7012
Subject:: Coxiella burnetii; cell culture; dose response; flow cytometry; fluorescent dyes
Abstract:: ... Flow cytometry enables the analysis of cells by labeling them with fluorescent probes. We describe a novel flow cytometric approach permitting reliable analysis of Coxiella (C.) burnetii-infected cells. The method quantifies infection-forming units (IFUs) in a dose-dependent manner and allows for the specific detection of infection/replication-competent coxiella in cell cultures. ...
DOI:: 10.1016/j.mimet.2018.05.022
: https://doi.org/10.1016/j.mimet.2018.05.022

78. Furukawa Agar – A novel bacteriological agar designed to inhibit fungal contamination when sampling organic compost

Author:: Maika Furukawa; Jonathan Stirling; Naoaki Misawa; John E. Moore
Source:: Journal of microbiological methods 2018 v.144 pp. 88-90
ISSN:: 0167-7012
Subject:: agar; bacteria; composts; fungi; microbial contamination
Abstract:: ... 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. ...
DOI:: 10.1016/j.mimet.2017.10.012
: https://doi.org/10.1016/j.mimet.2017.10.012

79. Gibson Assembly facilitates bacterial allelic exchange mutagenesis

Author:: Oleksandra Silayeva; Andrew C. Barnes
Source:: Journal of microbiological methods 2018 v.144 pp. 157-163
ISSN:: 0167-7012
Subject:: DNA; DNA assembly; Streptococcus iniae; alleles; clones; homologous recombination; mutagenesis; mutagens; mutants; polymerase chain reaction; screening
Abstract:: ... Allelic exchange mutagenesis that relies on RecA-mediated homologous recombination up- and downstream from the targeted gene is a generalizable method of site-specific bacterial gene knock-out and knock-in. However, generation of a mutagenic DNA construct (alternative allele flanked by regions surrounding the gene target) and subsequent mutant selection are laborious procedures. Here we demonstrat ...
DOI:: 10.1016/j.mimet.2017.11.023
: https://doi.org/10.1016/j.mimet.2017.11.023

80. Have you tried spermine? A rapid and cost-effective method to eliminate dextran sodium sulfate inhibition of PCR and RT-PCR

Author:: Łukasz Krych; Witold Kot; Katja M.B. Bendtsen; Axel K. Hansen; Finn K. Vogensen; Dennis S. Nielsen
Source:: Journal of microbiological methods 2018 v.144 pp. 1-7
ISSN:: 0167-7012
Subject:: DNA libraries; RNA; animal models; colitis; complementary DNA; cost effectiveness; dextran sulfate; fluorometry; humans; molecular biology; quantitative analysis; quantitative polymerase chain reaction; quantitative traits; reverse transcriptase polymerase chain reaction; reverse transcription; spermine
Abstract:: ... 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 ex ...
DOI:: 10.1016/j.mimet.2017.10.015
: https://doi.org/10.1016/j.mimet.2017.10.015

81. High-throughput method for the evaluation of esterase activity in soils

Author:: Shun Tsuboi; Takumi Tanaka; Kimiko Yamamoto-Tamura; Hiroko Kitamoto
Source:: Journal of microbiological methods 2018 v.146 pp. 22-24
ISSN:: 0167-7012
Subject:: color; enzyme activity; esterases; soil
Abstract:: ... We describe a method to quickly evaluate soil esterase activity using p‑nitrophenyl valerate as the substrate. Unwanted coloration of the control samples was suppressed by cooling. Esterase activity can be evaluated using arbitrary amounts of soil. Sample dispensation was simplified and the number of examinations per soil sample reduced. ...
DOI:: 10.1016/j.mimet.2018.01.009
: https://doi.org/10.1016/j.mimet.2018.01.009

82. Highly conserved exposed immunogenic peptides of Omp34 against Acinetobacter baumannii: An innovative approach

Author:: Abolfazl Jahangiri; Iraj Rasooli; Parviz Owlia; Abbas Ali Imani Fooladi; Jafar Salimian
Source:: Journal of microbiological methods 2018 v.144 pp. 79-85
ISSN:: 0167-7012
Subject:: Acinetobacter baumannii; B-lymphocytes; analytical kits; antibodies; epithelial cells; epitopes; humans; immune response; immunotherapy; in vivo studies; peptides; vaccines; virulence
Abstract:: ... 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 invo ...
DOI:: 10.1016/j.mimet.2017.11.008
: https://doi.org/10.1016/j.mimet.2017.11.008

83. Highly efficient transformation of a (hemi-)cellulases-producing fungus Eupenicillium parvum 4–14 by Agrobacterium tumefaciens

Author:: Liangkun Long; Qunying Lin; Yuexin Shi; Jing Wang; Shaojun Ding
Source:: Journal of microbiological methods 2018 v.146 pp. 40-45
ISSN:: 0167-7012
Subject:: Agrobacterium radiobacter; Eupenicillium; acetosyringone; ascospores; coculture; fungi; genes; genetic engineering; glyceraldehyde-3-phosphate dehydrogenase; green fluorescent protein; heat tolerance; hygromycin B; plasmids; temperature
Abstract:: ... The mesophilic fungus Eupenicillium parvum 4–14 is an important producer of thermotolerant hemicellulolytic and cellulolytic enzymes. The aim of this study was to establish a method for genetic manipulation of the fungus by Agrobacterium tumefaciens. The promotor PgpdA of a glyceraldehyde-3-phosphate dehydrogenase gene was isolated from E. parvum 4–14. To transform the fungus, an expression plasmi ...
DOI:: 10.1016/j.mimet.2018.01.013
: https://doi.org/10.1016/j.mimet.2018.01.013

84. Identification of Campylobacter fetus by fluorescence in situ hybridization (FISH)

Author:: Matti Karg; Hagen Frickmann; Helmut Hotzel; Raimond Lugert; Uwe Groß; Ralf M. Hagen; Herbert Tomaso; Sven Poppert; Andreas E. Zautner
Source:: Journal of microbiological methods 2018 v.151 pp. 44-47
ISSN:: 0167-7012
Subject:: Campylobacter fetus; DNA; fetus; fluorescence in situ hybridization
Abstract:: ... Two new DNA FISH-probes for Campylobacter fetus were designed, in silico checked for cross-reactions and successfully evaluated in a multi-centric approach with 41 Campylobacter fetus isolates including isolates of all three know subspecies: Campylobacter fetus ssp. fetus, Campylobacter fetus ssp. venerealis, and Campylobacter fetus ssp. testudinum and 40 strains of five non-target Campylobacter s ...
DOI:: 10.1016/j.mimet.2018.05.020
: https://doi.org/10.1016/j.mimet.2018.05.020

85. Identification of Escherichia coli strains for the heterologous overexpression of soluble Clostridium difficile exosporium proteins

Author:: Christian Brito-Silva; Jaime Pizarro-Cerda; Fernando Gil; Daniel Paredes-Sabja
Source:: Journal of microbiological methods 2018 v.154 pp. 46-51
ISSN:: 0167-7012
Subject:: Clostridium difficile; Escherichia coli; exine; molecular biology; morphs; recombinant proteins; spores
Abstract:: ... Clostridium difficile infections are one of the leading causes of hospital-acquired infections. C. difficile spores are considered the morphotype of transmission and recurrent infection due to its natural spore resistance properties. The outermost spore layer, the exosporium, provides the first contact with the environment and the host. However, molecular biology studies on exosporium proteins are ...
DOI:: 10.1016/j.mimet.2018.10.002
: https://doi.org/10.1016/j.mimet.2018.10.002

86. Improved biovolume estimation of Microcystis aeruginosa colonies: A statistical approach

Author:: I. Alcántara; C. Piccini; A.M. Segura; S. Deus; C. González; G. Martínez de la Escalera; C. Kruk
Source:: Journal of microbiological methods 2018 v.151 pp. 20-27
ISSN:: 0167-7012
Subject:: Microcystis aeruginosa; biomass; data collection; estuaries; freshwater; geometry; light microscopy; linear models; monitoring; prediction; seawater; statistical analysis
Abstract:: ... The Microcystis aeruginosa complex (MAC) clusters many of the most common freshwater and brackish bloom-forming cyanobacteria. In monitoring protocols, biovolume estimation is a common approach to determine MAC colonies biomass and useful for prediction purposes. Biovolume (μm3 mL−1) is calculated multiplying organism abundance (orgL−1) by colonial volume (μm3org−1). Colonial volume is estimated b ...
DOI:: 10.1016/j.mimet.2018.05.021
: https://doi.org/10.1016/j.mimet.2018.05.021

87. Improved intracellular PHA determinations with novel spectrophotometric quantification methodologies based on Sudan black dye

Author:: Mauricio A. Porras; Marcelo A. Villar; María A. Cubitto
Source:: Journal of microbiological methods 2018 v.148 pp. 1-11
ISSN:: 0167-7012
Subject:: Sudan dyes; absorbance; experimental design; granules; laboratory equipment; monitoring; polyhydroxyalkanoates; prediction; regression analysis; response surface methodology
Abstract:: ... The presence of intracellular polyhydroxyalkanoates (PHAs) is usually studied using Sudan black dye solution (SB). In a previous work it was shown that the PHA could be directly quantified using the absorbance of SB fixed by PHA granules in wet cell samples. In the present paper, the optimum SB amount and the optimum conditions to be used for SB assays were determined following an experimental des ...
DOI:: 10.1016/j.mimet.2018.03.008
: https://doi.org/10.1016/j.mimet.2018.03.008

88. Improved pH-ratiometry for the three-dimensional mapping of pH microenvironments in biofilms under flow conditions

Author:: Sebastian Schlafer; Vibeke Baelum; Irene Dige
Source:: Journal of microbiological methods 2018 v.152 pp. 194-200
ISSN:: 0167-7012
Subject:: biofilm; fluorescent dyes; glucose; monitoring; pH
Abstract:: ... Confocal microscopy-based monitoring of pH in biofilms is gaining increasing interest, as it allows for a quick assessment of horizontal pH gradients without mechanically perturbing the biofilm. Ratiometric monitoring of pH with the fluorescent dye C-SNARF-4 has been used to reliably map extracellular pH in the basal layers of biofilms, but only under static conditions. Here, we expand this method ...
DOI:: 10.1016/j.mimet.2018.08.007
: https://doi.org/10.1016/j.mimet.2018.08.007

89. Improvement of a rapid direct blood culture microbial identification protocol using MALDI-TOF MS and performance comparison with SepsiTyper kit

Author:: Francesca Di Gaudio; Serena Indelicato; Sergio Indelicato; Maria Rita Tricoli; Giuseppe Stampone; David Bongiorno
Source:: Journal of microbiological methods 2018 v.155 pp. 1-7
ISSN:: 0167-7012
Subject:: bacterial culture; blood; matrix-assisted laser desorption-ionization mass spectrometry; pathogens; prices; processing time; protocols; therapeutics
Abstract:: ... Fast diagnosis of pathogens is critical to guarantee the most adequate therapy for infections; bacterial culture methods, which constitute the actual gold standard, are precise and sensitive but rather slow. Today, new methods have been made available to enable faster diagnosis, with the Matrix-Assisted Laser Desorption Ionization–Time Of Flight Mass Spectrometry (MALDI-TOF MS) technique being the ...
DOI:: 10.1016/j.mimet.2018.10.015
: https://doi.org/10.1016/j.mimet.2018.10.015

90. Improving the selection efficiency of the counter-selection marker pheS* for the genetic engineering of Bacillus amyloliquefaciens

Author:: Maria S. Kharchenko; Petr N. Teslya; Maria N. Babaeva; Natalia P. Zakataeva
Source:: Journal of microbiological methods 2018 v.148 pp. 18-21
ISSN:: 0167-7012
Subject:: Bacillus amyloliquefaciens; Bacillus subtilis; genetic engineering
Abstract:: ... Bacillus subtilis pheS was genetically modified to obtain a counter-selection marker with high selection efficiency in Bacillus amyloliquefaciens. The application of the new replication-thermosensitive integrative vector pNZTM1, containing this marker, pheSBsT255S/A309G, with a two-step replacement recombination procedure provides an effective tool for the genetic engineering of industrially impor ...
DOI:: 10.1016/j.mimet.2018.03.011
: https://doi.org/10.1016/j.mimet.2018.03.011

91. In vitro approaches for generation of Mycobacterium tuberculosis mutants resistant to bedaquiline, clofazimine or linezolid and identification of associated genetic variants

Author:: N. Ismail; S.V. Omar; N.A. Ismail; R.P.H. Peters
Source:: Journal of microbiological methods 2018 v.153 pp. 1-9
ISSN:: 0167-7012
Subject:: Mycobacterium tuberculosis; drug resistance; drugs; genes; genetic variation; linezolid; minimum inhibitory concentration; mutants; phenotype; tuberculosis
Abstract:: ... Bedaquiline, clofazimine and linezolid are pertinent drugs for drug-resistant tuberculosis. Drug-resistant mutants provide insight into important resistance acquisition mechanisms. Methods for in vitro Mycobacterium tuberculosis mutant generation are poorly described.Induction (serial passaging) and spontaneous (adapted Luria-Delbrück assay) approaches using M. tuberculosis ATCC reference strains ...
DOI:: 10.1016/j.mimet.2018.08.011
: https://doi.org/10.1016/j.mimet.2018.08.011

92. Isolation of multi-metal tolerant ubiquitin fusion protein from metal polluted soil by metatranscriptomic approach

Author:: Bharti Thakur; Rajiv Yadav; Laurence Fraissinet-Tachet; Roland Marmeisse; M. Sudhakara Reddy
Source:: Journal of microbiological methods 2018 v.152 pp. 119-125
ISSN:: 0167-7012
Subject:: biomarkers; cDNA libraries; cadmium; cobalt; complementary DNA; copper; edaphic factors; food chain; genes; heavy metals; messenger RNA; polluted soils; public health; sequence analysis; soil microorganisms; toxicity; transcriptomics; ubiquitin; yeasts; zinc; zinc finger motif
Abstract:: ... Release of heavy metals into the soil pose a significant threat to the environment and public health because of their toxicity accumulation in the food chain and persistence in nature. The potential of soil microbial diversity of cadmium (Cd) contaminated site was exploited through functional metatranscriptomics by construction of cDNA libraries A (0.1–0.5 kb), B (0.5–1.0 kb), and C (1-4 kb) of va ...
DOI:: 10.1016/j.mimet.2018.08.001
: https://doi.org/10.1016/j.mimet.2018.08.001

93. Label-free Raman characterization of bacteria calls for standardized procedures

Author:: Cristina García-Timermans; Peter Rubbens; Frederiek-Maarten Kerckhof; Benjamin Buysschaert; Dmitry Khalenkow; Willem Waegeman; Andre G. Skirtach; Nico Boon
Source:: Journal of microbiological methods 2018 v.151 pp. 69-75
ISSN:: 0167-7012
Subject:: Raman spectroscopy; bacteria; environmental factors; microbial communities
Abstract:: ... Raman spectroscopy has gained relevance in single-cell microbiology for its ability to detect bacterial (sub)populations in a non-destructive and label-free way. However, the Raman spectrum of a bacterium can be heavily affected by abiotic factors, which may influence the interpretation of experimental results. Additionally, there is no publicly available standard for the annotation of metadata de ...
DOI:: 10.1016/j.mimet.2018.05.027
: https://doi.org/10.1016/j.mimet.2018.05.027

94. Laboratory diagnosis of urinary tract infections: Towards a BILULU consensus guideline

Author:: Matthijs Oyaert; Britt Van Meensel; Reinoud Cartuyvels; Johan Frans; Wim Laffut; Patricia Vandecandelaere; Hans De Beenhouwer
Source:: Journal of microbiological methods 2018 v.146 pp. 92-99
ISSN:: 0167-7012
Subject:: guidelines; laboratory diagnosis; microbiology; technicians; urinary tract diseases; urine
Abstract:: ... Urinary tract infections (UTI) are very common throughout life and account for the majority of the workload in the clinical microbiology laboratory. Clear instructions for the interpretation of urine cultures by the laboratory technicians are indispensable to obtain standardized, reliable, and clinically useful results. In literature, there is often a lack of evidence-based practice in processing ...
DOI:: 10.1016/j.mimet.2018.02.006
: https://doi.org/10.1016/j.mimet.2018.02.006

95. Large-scale evaluation of a rapid diagnostic test for diarrhea caused by enterotoxigenic Escherichia coli targeting the heat-labile toxin

Author:: Camila Henrique; Bruna A. Caetano; Thais Mitsunari; Luís Fernando dos Santos; Roxane M.F. Piazza; Letícia B. Rocha
Source:: Journal of microbiological methods 2018 v.144 pp. 125-127
ISSN:: 0167-7012
Subject:: antibodies; cutting; diarrhea; enterotoxigenic Escherichia coli; immunoaffinity chromatography
Abstract:: ... We standardized an immunochromatographic test (IC) for heat-labile toxin I (LT-I) detection using LT-I antibodies and a specific platform containing the apparatus for application, assembly and cutting. IC detected as little as 62.5ng/mL of purified LT-I toxin and presented 91% sensitivity, 99.5% specificity and 96.0% accuracy, thereby proving to be an excellent point-of-care test for the diagnosis ...
DOI:: 10.1016/j.mimet.2017.11.020
: https://doi.org/10.1016/j.mimet.2017.11.020

96. Limitations of routine MALDI-TOF mass spectrometric identification of Acinetobacter species and remedial actions

Author:: Ondrej Šedo; Lenka Radolfová-Křížová; Alexandr Nemec; Zbyněk Zdráhal
Source:: Journal of microbiological methods 2018 v.154 pp. 79-85
ISSN:: 0167-7012
Subject:: Acinetobacter haemolyticus; Acinetobacter junii; Acinetobacter venetianus; databases; ferulic acid; matrix-assisted laser desorption-ionization mass spectrometry; phylogeny
Abstract:: ... A set of 204 taxonomically well-defined strains belonging to 17 Acinetobacter spp., including 11 recently described species (A. albensis, A. bohemicus, A. colistiniresistens, A. courvalinii. A. dispersus, A. gandensis, A. modestus, A. proteolyticus, A. seifertii, A. variabilis, and A. vivianii) and six species of the so-called haemolytic clade (A. beijerinckii, A. gyllenbergii, A. haemolyticus, A. ...
DOI:: 10.1016/j.mimet.2018.10.009
: https://doi.org/10.1016/j.mimet.2018.10.009

97. Loop-mediated isothermal amplification assay for detection of Coxiella burnetii targeting the com1 gene

Author:: Durga Prasad Das; Satya Veer Singh Malik; Radhakrishna Sahu; Jay Prakash Yadav; Deepak B. Rawool; Sukhadeo B. Barbuddhe
Source:: Journal of microbiological methods 2018 v.155 pp. 55-58
ISSN:: 0167-7012
Subject:: Coxiella burnetii; DNA; blood serum; genes; humans; loop-mediated isothermal amplification; screening
Abstract:: ... We developed the com1 gene based loop-mediated isothermal amplification (LAMP) assay for the detection of Coxiella burnetii and validated it by screening DNA isolated from serum samples collected from animals and humans. The detection of Coxiella by LAMP assay was comparable with the com1 based-PCR. ...
DOI:: 10.1016/j.mimet.2018.11.011
: https://doi.org/10.1016/j.mimet.2018.11.011

98. MALDI-Biotyper as a tool to identify polymer producer bacteria

Author:: Bruno Karolski; Letícia O.B. Cardoso; Louise H. Gracioso; Cláudio A.O. Nascimento; Elen A. Perpetuo
Source:: Journal of microbiological methods 2018 v.153 pp. 127-132
ISSN:: 0167-7012
Subject:: bacteria; carbon; desorption; ionization; methane; methanol; plastics; polyhydroxybutyrate; polypropylenes; prices
Abstract:: ... The methylotrophs bacteria can use methane and methanol as carbon sources to produce biopolymers including the polyhydroxybutyrate (PHB) a very promised substitute for the environment contaminant oil-derived polypropylene. This kind of bacteria can be very effective to help to decrease PHB price production and promote its use in substitution of several environment contaminant plastics. The search ...
DOI:: 10.1016/j.mimet.2018.09.016
: https://doi.org/10.1016/j.mimet.2018.09.016

99. MALDI-TOF mass spectrometry-based identification of Listeria species in surveillance: A prospective study

Author:: Pierre Thouvenot; Guillaume Vales; Hélène Bracq-Dieye; Nathalie Tessaud-Rita; Mylène M. Maury; Alexandra Moura; Marc Lecuit; Alexandre Leclercq
Source:: Journal of microbiological methods 2018 v.144 pp. 29-32
ISSN:: 0167-7012
Subject:: Listeria; matrix-assisted laser desorption-ionization mass spectrometry; monitoring; prospective studies
Abstract:: ... 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. ...
DOI:: 10.1016/j.mimet.2017.10.009
: https://doi.org/10.1016/j.mimet.2017.10.009

100. Mapping bacteria on filter membranes, an innovative SERS approach

Author:: Siyue Gao; Brooke Pearson; Lili He
Source:: Journal of microbiological methods 2018 v.147 pp. 69-75
ISSN:: 0167-7012
Subject:: Escherichia coli; Listeria monocytogenes; Raman spectroscopy; Salmonella enterica; bacteria; drinking water; enzyme-linked immunosorbent assay; humans; plate count; polymerase chain reaction; porosity; rapid methods
Abstract:: ... The existence of pathogenic bacteria in drinking water has been a threat to the safety of human well-being. Traditional methods to detect bacteria are standard plate counts or rapid methods such as ELISA and PCR. However, those methods can be time-consuming or require pre-enrichment when detecting low concentrations of bacteria. Filter membrane has been used for bacteria collection and culturing w ...
DOI:: 10.1016/j.mimet.2018.03.005
: https://doi.org/10.1016/j.mimet.2018.03.005

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1. Aerobic cultivation of anaerobic rumen protozoa, Entodinium caudatum and Epidinium caudatum

2. Air-drying is sufficient pre-treatment for in situ visualization of microbes on minerals with scanning electron microscopy

3. Antibacterial activity of lysozyme-binding proteins from chicken egg white

4. Application of Cytosense flow cytometer for the analysis of airborne bacteria collected by a high volume impingement sampler

5. Application of the biocopolymer preparation system, rapid BACpro® II kit, for mass-spectrometry-based bacterial identification from positive blood culture bottles by the MALDI Biotyper system

6. Applying simple linear combination, multiple logistic and factor analysis methods for candidate fecal bacteria as novel biomarkers for early detection of adenomatous polyps and colon cancer

7. Aptamer-based fluorometric assay for direct identification of methicillin-resistant Staphylococcus aureus from clinical samples

8. Assessment of flow cytometry for microbial water quality monitoring in cooling tower water and oxidizing biocide treatment efficiency

9. Autofluorescence of yeast Saccharomyces cerevisiae cells caused by glucose metabolism products and its methodological implications

10. Automated counting of bacterial colonies on agar plates based on images captured at near-infrared light

11. Bio oil production from microalgae via hydrothermal liquefaction technology under subcritical water conditions

12. Chlamydia trachomatis antibody detection in home-collected blood samples for use in epidemiological studies

13. Colorimetric assay for active biomass quantification of Fusarium fujikuroi

14. Combination of MALDI-TOF MS and PBP2′ latex agglutination assay for rapid MRSA detection

15. Combining diagnostic methods for antimicrobial susceptibility testing – A comparative approach

16. Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens

17. Comparison of DNA extraction methods for drug susceptibility testing by allele-specific primer extension on a microsphere-based platform: Chelex-100 (in-house and commercialized) and MagPurix TB DNA Extraction Kit

18. Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile

19. Comparison of biofilm cell quantification methods for drinking water distribution systems

20. Comparison of the Purelyse® – IS6110 nested PCR with the Xpert® MTB/RIF test in clinical samples with suspected tuberculosis

21. Comparison of three DNA extraction methods for molecular confirmation of Mycobacterium avium subspecies paratuberculosis from the VersaTrek™ liquid cultures of bovine fecal samples

22. Comparison of various RNA extraction methods, cDNA preparation and isolation of calmodulin gene from a highly melanized isolate of apple leaf blotch fungus Marssonina coronaria

23. Concentration of Listeria monocytogenes in skim milk and soft cheese through microplate immunocapture

24. Conidia-based fluorescence quantification of Streptomyces

25. Creation of a drug-sensitive reporter strain of Pseudomonas aeruginosa as a tool for the rapid screening of antimicrobial products

26. Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings

27. Deletion of pyruvate decarboxylase gene in Zymomonas mobilis by recombineering through bacteriophage lambda red genes

28. Detecting pathogens with Zinc-Finger, TALE and CRISPR- based programmable nucleic acid binding proteins

29. Detection of Tilletia caries, Tilletia laevis and Tilletia controversa wheat grain contamination using loop-mediated isothermal DNA amplification (LAMP)

30. Detection of carbapenem-resistant Enterobacteriaceae by chromogenic screening media

31. Detection of carbapenemases with a newly developed commercial assay using Matrix Assisted Laser Desorption Ionization-Time of Flight

32. Detection of carbapenemases, AmpC and ESBL genes in Acinetobacter isolates from ICUs by DNA microarray

33. Detection of different classes of carbapenemases: Adaptation and assessment of a phenotypic method applied to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii, and proposal of a new algorithm

34. Detection of microbial genes in a single leukocyte by polymerase chain reaction following laser capture microdissection

35. Detection of resistance to fluoroquinolones and injectable drugs among antituberculosis drugs by allele-specific primer extension on a microsphere-based platform

36. Detection of root-infecting fungi on cool-season turfgrasses using loop-mediated isothermal amplification and recombinase polymerase amplification

37. Determination of intracellular pH in phytoplankton using the fluorescent probe, SNARF, with detection by fluorescence spectroscopy

38. Determination of live:dead bacteria as a function of antibiotic treatment

39. Development and characterization of a 3D oral mucosa model as a tool for host-pathogen interactions

40. Development and evaluation of two multi-antigen serological assays for the diagnosis of bovine tuberculosis in cattle

41. Development and testing of an 18S rRNA phylogenetic microarray for marine sediments

42. Development of a high throughput optical density assay to determine fungicide sensitivity of oomycetes

43. Development of a molecular serotyping scheme and a multiplexed luminex-based array for Providencia

44. Development of a rapid PCR-Nucleic Acid Lateral Flow Immunoassay (PCR-NALFIA) based on rDNA IGS sequence analysis for the detection of Macrophomina phaseolina in soil

45. Development of a real-time assay to determine the frequency of qac genes in methicillin resistant Staphylococcus aureus

46. Development of a simple and practical method of discrimination between Vibrio furnissii and V. fluvialis based on single-nucleotide polymorphisms of 16S rRNA genes observed in V. furnissii but not in V. fluvialis

47. Development of a tick-borne pathogen QPCR panel for detection of Anaplasma, Ehrlichia, Rickettsia, and Lyme disease Borrelia in animals

48. Development of an Sce-I mutagenesis system for Burkholderia cepacia complex strains

49. Development of an efficient conjugal DNA transfer system between Escherichia coli and a non-sporulating Streptomyces strain

50. Development of an efficient genetic system in a gene cluster-rich endophytic fungus Calcarisporium arbuscula NRRL 3705

51. Development of duplex PCR-ELISA for simultaneous detection of Salmonella spp. and Escherichia coli O157: H7 in food

52. Development of new versatile plasmid-based systems for λRed-mediated Escherichia coli genome engineering

53. Direct detection of carbapenemase-associated proteins of Acinetobacter baumannii using nanodiamonds coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

54. Direct diagnosis of Brucella species through multiplex PCR formed by a new method

55. Directed freeze-fracturing of Bacillus subtilis biofilms for conventional scanning electron microscopy

56. Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds?

57. The EDTA-based disk-combination tests are unreliable for the detection of MCR-mediated colistin-resistance in Enterobacteriaceae

58. Efficient construction of xenogeneic genomic libraries by circumventing restriction-modification systems that restrict methylated DNA

59. Efficient transformation of Pleurotus eryngii with a safe selective marker mutated from the Pesdi1 gene

60. Enhanced sensitivity and fast turnaround time in laboratory diagnosis for bovine paratuberculosis in faecal samples

61. Enrichment of low-density symbiont DNA from minute insects

62. Enrichment of semen culture in the diagnosis of bacterial prostatitis

63. Enzymatic Kraft lignin demethylation and fungal O-demethylases like vanillate-O-demethylase and syringate O-demethylase catalyzed catechol-Fe3+ complexation method

64. Establishment of a suspension array for Pseudomonas aeruginosa O-antigen serotyping

65. Evaluation of ATR-FTIR for analysis of bacterial cellulose impurities

66. Evaluation of DNA extraction methods to detect bacterial targets in aerosol samples

67. Evaluation of a novel optical assay for rapid detection of methicillin-resistant Staphylococcus aureus in liquid culture

68. Evaluation of modified saponin preparation method for the direct identification and antimicrobial susceptibility testing from positive blood culture

69. Evaluation of sampling and storage procedures on preserving the community structure of stool microbiota: A simple at-home toilet-paper collection method

70. Evaluation of the multiplex PCR Allplex-GI assay in the detection of bacterial pathogens in diarrheic stool samples