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- Author:
- Yamada, Akiteru; Umeki, Kazumi; Saeki, Yuji; Hashikura, Yuuki; Nomura, Hajime; Yamamoto, Ikuo; Umekita, Kunihiko; Takajo, Ichiro; Koshimoto, Chihiro; Okayama, Akihiko
- 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://dx.doi.org/10.1016/j.mimet.2018.11.005
- Author:
- Li, Huiying; Du, Yuhui; Qian, Chengqian; Li, Lingyu; Jiang, Lingyan; Jiang, Xiaolong; Cao, Hengchun; Guo, Xi; Liu, Bin
- 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://dx.doi.org/10.1016/j.mimet.2018.11.006
- Author:
- Das, Durga Prasad; Malik, Satya Veer Singh; Sahu, Radhakrishna; Yadav, Jay Prakash; Rawool, Deepak B.; Barbuddhe, Sukhadeo B.
- 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://dx.doi.org/10.1016/j.mimet.2018.11.011
- Author:
- Bilal, Tanveer; Malik, Bisma; Hakeem, Khalid Rehman
- Source:
- Journal of microbiological methods 2018 v.155 pp. 65-69
- ISSN:
- 0167-7012
- Subject:
- DNA; bioengineering; biofuels; energy; enzymes; ethanol production; metagenomics; microorganisms; nucleotide sequences
- Abstract:
- ... Although second generation biofuel technology is a sustainable route for bioethanol production it is not currently a robust technology because of certain hindrances viz., unavailability of potential enzyme resources, low efficiency of enzymes and restricted availability of potent enzymes that work under harsh conditions in industrial processes. Therefore, bioprospecting of extremophilic microorgan ...
- DOI:
- 10.1016/j.mimet.2018.11.014
-
https://dx.doi.org/10.1016/j.mimet.2018.11.014
- Author:
- Murata, Takatoshi; Ishikawa, Masao; Shibuya, Koji; Hanada, Nobuhiro
- Source:
- Journal of microbiological methods 2018 v.155 pp. 49-54
- ISSN:
- 0167-7012
- Subject:
- DNA; Streptococcus mutans; affinity chromatography; antibiotic resistance; gene targeting; genes; genetic markers; phenotype; polymerase chain reaction
- Abstract:
- ... Typical methods for elucidating the function of a particular gene involve comparative phenotypic analysis of the wild-type strain and a strain in which the gene of interest has been disrupted. We previously described a simple method for the generation of a gene-disrupted strain in Streptococcus mutans by replacing the gene of interest with an antibiotic resistance marker gene. It is also crucial t ...
- DOI:
- 10.1016/j.mimet.2018.11.010
-
https://dx.doi.org/10.1016/j.mimet.2018.11.010
- Author:
- Schriefer, Andrew E.; Cliften, Paul F.; Hibberd, Matthew C.; Sawyer, Christopher; Brown-Kennerly, Victoria; Burcea, Lauren; Klotz, Elliott; Crosby, Seth D.; Gordon, Jeffrey I.; Head, Richard D.
- Source:
- Journal of microbiological methods 2018 v.154 pp. 6-13
- ISSN:
- 0167-7012
- Subject:
- DNA; algorithms; bacterial communities; computer software; genes; germ-free animals; habitats; high-throughput nucleotide sequencing; metagenomics; mice; microfluidic technology; phylogeny; polymerase chain reaction; ribosomal RNA
- Abstract:
- ... Metagenomic sequencing of bacterial samples has become the gold standard for profiling microbial populations, but 16S rRNA profiling remains widely used due to advantages in sample throughput, cost, and sensitivity even though the approach is hampered by primer bias and lack of specificity. We hypothesized that a hybrid approach, that combined targeted PCR amplification with high-throughput sequen ...
- DOI:
- 10.1016/j.mimet.2018.09.019
- PubMed:
- 30273610
- PubMed Central:
- PMC6375304
-
https://dx.doi.org/10.1016/j.mimet.2018.09.019
- Author:
- Jang, Jaeyoun; Hendriksen, Niels Bohse; Jakobsen, Hans H.; Gosewinkel, Ulrich
- 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://dx.doi.org/10.1016/j.mimet.2018.10.012
- Author:
- Pieczul, Katarzyna; Perek, Agnieszka; Kubiak, Krzysztof
- 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
-
http://dx.doi.org/10.1016/j.mimet.2018.10.018
- Author:
- Li, Runze; Dhankhar, Dinesh; Chen, Jie; Cesario, Thomas C.; Rentzepis, Peter M.
- 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://dx.doi.org/10.1016/j.mimet.2018.10.010
- Author:
- Staley, Christopher; Sadowsky, Michael J.
- Source:
- Journal of microbiological methods 2018 v.154 pp. 14-18
- ISSN:
- 0167-7012
- Subject:
- DNA; algorithms; biogeography; bioinformatics; ecosystems; genetic markers; habitats; high-throughput nucleotide sequencing; interdisciplinary research; metagenomics; microbial communities; microbiome; microorganisms; research programs; statistical analysis; technology
- Abstract:
- ... Recent advancements in metagenomic-based studies, especially analyses of amplicon-based DNA sequencing targeting taxonomic marker genes, has led to an unprecedented characterization of microbial communities from diverse ecosystems around the world. While originally constrained by a lack of appropriate analytical tools and sequencing depth, new technologies and computational and statistical algorit ...
- DOI:
- 10.1016/j.mimet.2018.09.020
-
https://dx.doi.org/10.1016/j.mimet.2018.09.020
- Author:
- Rusak, Leonardo Alves; de Castro Lisboa Pereira, Rodrigo; Freitag, Isabelle Geoffroy; Hofer, Cristina Barroso; Hofer, Ernesto; Asensi, Marise Dutra; Vallim, Deyse Christina
- Source:
- Journal of microbiological methods 2018 v.154 pp. 107-111
- ISSN:
- 0167-7012
- Subject:
- DNA; Yersinia enterocolitica; biosynthesis; digestive system diseases; feces; hospitals; humans; monitoring; peptide elongation factors; polymerase chain reaction; pregnant women; public health; rapid methods; selective media; serotypes; Europe
- Abstract:
- ... Yersinia enterocolitica, a member of the Enterobacteriaceae family, is a zoonotic agent that causes gastrointestinal diseases and some extraintestinal disorders in humans. Y. enterocolitica ssp. palearctica bioserotype 4/O:3 is the primary pathogenic bioserotype in Europe, where it has a high public health relevance. The isolation and identification of Y. enterocolitica from various sources on sel ...
- DOI:
- 10.1016/j.mimet.2018.10.014
-
https://dx.doi.org/10.1016/j.mimet.2018.10.014
- Author:
- Kim, YoungJoong; Kim, Sanghyo
- Source:
- Journal of microbiological methods 2018 v.153 pp. 99-103
- ISSN:
- 0167-7012
- Subject:
- DNA; Gram-positive bacteria; agar gel electrophoresis; carbon; heat; point-of-care testing; virulent strains
- Abstract:
- ... In the process of developing a point-of-care testing device, we fabricated a plane heating element using carbon paste capable of thermal lysis. The plane heating element can generate heat of 150 °C within 60 s at 0.4 A power supply within 8 W. The developed plane heating element was very effective in the extraction of DNA from both Gram-negative and Gram-positive bacteria which was further confirm ...
- DOI:
- 10.1016/j.mimet.2018.09.012
-
http://dx.doi.org/10.1016/j.mimet.2018.09.012
- Author:
- Podduturi, Raju; Jørgensen, Niels O.G.
- 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
-
http://dx.doi.org/10.1016/j.mimet.2018.09.010
- Author:
- Du, Yuhui; Li, Huiying; Yin, Zhiqiu; Rozalski, Antoni; Torzewska, Agnieszka; Yang, Pan; Qian, Chengqian; Xu, Tingting; Cao, Hengchun; Wu, Pan; Jiang, Lingyan; Guo, Xi; Huang, Di; Liu, Bin
- 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://dx.doi.org/10.1016/j.mimet.2018.08.009
- Author:
- Chan, Maurice Kok Leong; Koo, Seok Hwee; Quek, Qingyao; Pang, Wan Sia; Jiang, Boran; Ng, Lily Siew Yong; Tan, Si Huei; Tan, Thean Yen
- 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://dx.doi.org/10.1016/j.mimet.2018.09.017
- Author:
- Dunbar, John; Gallegos-Graves, La Verne; Gans, Jason; Morse, Stephen A.; Pillai, Segaran; Anderson, Kevin; Hodge, David R.
- 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
-
http://dx.doi.org/10.1016/j.mimet.2018.09.006
- Author:
- Bonk, Fabian; Popp, Denny; Harms, Hauke; Centler, Florian
- Source:
- Journal of microbiological methods 2018 v.153 pp. 139-147
- ISSN:
- 0167-7012
- Subject:
- DNA; cost effectiveness; ecosystems; high-throughput nucleotide sequencing; mathematical models; microbial communities; operon; quantitative polymerase chain reaction; ribosomal RNA; variance
- Abstract:
- ... The quantification of relative and absolute taxa-specific abundances in complex microbial communities is crucial for understanding and modeling natural and engineered ecosystems. Many errors inherent to this quantification are, though well-known, still insufficiently addressed and can potentially lead to a completely different interpretation of experimental results. This review provides a critical ...
- DOI:
- 10.1016/j.mimet.2018.09.015
-
http://dx.doi.org/10.1016/j.mimet.2018.09.015
- Author:
- Wang, Yong-xiang; Zhang, An-yun; Yang, Yong-qiang; Lei, Chang-wei; Cheng, Guang-yang; Zou, Wen-cheng; Zeng, Jin-xin; Chen, Yan-peng; Wang, Hong-ning
- Source:
- Journal of microbiological methods 2018 v.153 pp. 24-30
- ISSN:
- 0167-7012
- Subject:
- DNA; Salmonella Indiana; bacteria; detection limit; food contamination; food pathogens; foods; host range; humans; nucleotide sequences; poultry; quantitative polymerase chain reaction; rapid methods; screening; swine
- Abstract:
- ... Salmonella enterica serovar Indiana (S. Indiana) was the most frequently reported foodborne pathogen, which has a broad host range including poultry, swine, and humans. Traditional methods used for the detection of S. Indiana from contaminated food products are time-consuming and labor-intensive. Therefore, rapid detection methods with high sensitivity and specificity are vitally important to prev ...
- DOI:
- 10.1016/j.mimet.2018.08.003
-
https://dx.doi.org/10.1016/j.mimet.2018.08.003
- Author:
- Kang, Minji; Yang, Jeong Seong; Kim, Yoojeong; Kim, Kyungjong; Choi, Hongjo; Lee, Seung Heon
- 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://dx.doi.org/10.1016/j.mimet.2018.07.019
- Author:
- Lemus-Minor, Carlos German; Ovalle-Marroqui, Diego Fernando; Vazquez-Jimenez, J. Gustavo; Reales-Agüero, Diana Laura; Sepulveda-Alcantara, Perla Michelle; Rodriguez-Sánchez, Jesús René; Diaz-Molina, Raúl; Machado-Contreras, Jesús René
- 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://dx.doi.org/10.1016/j.mimet.2018.07.002
