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You searched for: Journal name Journal of microbiological methods Remove constraint Journal name: Journal of microbiological methods Subject term DNA Remove constraint Subject term: DNA
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1. Analysis of DNA extraction methods for detection of Treponema pallidum: A comparison of three methods

Author:
Vera Mileide Trivellato Grassi; Mauro Cunha Ramos; Liliane Trivellato Grassi; Marcia Susana Nunes Silva; Maria Lucia Rosa Rossetti
Source:
Journal of microbiological methods 2022 v.192 pp. 106383
ISSN:
0167-7012
Subject:
DNA; Treponema pallidum; cost benefit analysis; genes; sexually transmitted diseases; sonication; Brazil
Abstract:
... Syphilis is a sexually transmitted disease caused by Treponema pallidum. DNA amplification methods have started to be used to facilitate diagnosis at different stages of the disease. The success of such methodologies depends on obtaining DNA from clinical samples in adequate quantity and quality for molecular reactions. There are many DNA extraction kits, but often the molecular analysis process i ...
DOI:
10.1016/j.mimet.2021.106383

2. Development of real-time PCR methods for the quantification of Methanoculleus, Methanosarcina and Methanobacterium in anaerobic digestion

Author:
Consolación Sánchez-Sánchez; Mercedes Aranda-Medina; Alicia Rodríguez; Alejandro Hernández; María G. Córdoba; Francisco Cuadros-Blázquez; Santiago Ruiz-Moyano
Source:
Journal of microbiological methods 2022 pp. 106529
ISSN:
0167-7012
Subject:
DNA; Methanobacterium; Methanoculleus; Methanosarcina; anaerobic digestion; bioenergy; methanogens; organic wastes; quantitative polymerase chain reaction
Abstract:
... Anaerobic digestion is a growing technology to manage organic waste and produce bioenergy. To promote this technology, it is essential to know, at the molecular level, the dynamics of microbial communities, specifically the methanogenic community. In the present study, three primer pairs were selected from seven primer pairs which were designed and tested with different concentrations and conditio ...
DOI:
10.1016/j.mimet.2022.106529

3. Tracking Mycobacterium tuberculosis sequencing samples using unique spikes of random DNA

Author:
Albert J. de Neeling; Lucia F. Jonckers Nieboer; Arnout Mulder; Rob Mariman; Richard M. Anthony; Dick van Soolingen
Source:
Journal of microbiological methods 2022 v.197 pp. 106482
ISSN:
0167-7012
Subject:
DNA; Mycobacterium tuberculosis; genome; public health; species identification; tuberculosis; Netherlands
Abstract:
... In the Netherlands, local laboratories are involved in the primary diagnosis of tuberculosis. Positive Mycobacterium tuberculosis complex cultures are sent to the National Institute for Public Health and the Environment (RIVM) for species identification, epidemiological typing, and screening for resistance by Whole Genome Sequencing (WGS). Occasional sample-swaps and cross-contaminations are known ...
DOI:
10.1016/j.mimet.2022.106482

4. ccelerated cycling PCR: A novel tool for rapid, sensitive and specific detection of single-nucleotide mutation within 30 min

Author:
Zhixian Luan; Yan Zhao; Yanling Wang; Cuiping Ma; Chao Shi
Source:
Journal of microbiological methods 2022 pp. 106527
ISSN:
0167-7012
Subject:
DNA; Helicobacter pylori; drug resistance; genotype; genotyping; mutation; rapid methods
Abstract:
... Rapid detection of single-nucleotide mutations (SNMs) has played a vital role for point-of-care testing. We herein first introduced accelerated thermal cycling into conventional allele-specific qPCR (AS-qPCR), named accelerated cycling PCR (AC-PCR) to achieve rapid and sensitive detection of SNM. It could simultaneously detect 10 copies of H. pylori DNA and identify its clarithromycin-resistance g ...
DOI:
10.1016/j.mimet.2022.106527

5. Designing and developing of high-resolution melting technique for separating different types of Toxoplasma gondii by analysis of B1 and ROP8 gene regions

Author:
Tahereh Azimpour-Ardakan; Reza Fotouhi-Ardakani; Nasser Hoghooghi-Rad; Nourdehr Rokni; Abbasali Motallebi
Source:
Journal of microbiological methods 2021 v.184 pp. 106188
ISSN:
0167-7012
Subject:
DNA; Toxoplasma gondii; brain; diagnostic techniques; epidemiology; genes; genotyping; livestock; muscle tissues; polymerase chain reaction; rapid methods; toxoplasmosis
Abstract:
... Determination of Toxoplasma gondii genotypes plays an important role in the health management and epidemiology of toxoplasmosis. We developed HRM analysis to differentiate genotypes of T. gondii using the B1 and ROP8 genes, through comparing the sensitivity and specificity of both genes and methods used for the detection of T. gondii.A total of 96 DNA samples of muscle tissue of livestock and poul ...
DOI:
10.1016/j.mimet.2021.106188

6. Development and evaluation of a novel quenching probe PCR (GENECUBE) assay for rapidly detecting and distinguishing between Chlamydia pneumoniae and Chlamydia psittaci

Author:
Kyoko Hisada; Yukio Hida; Naoki Kawabata; Yosuke Kawashima; Yoshihiro Soya; Akihiro Shimada; Masayuki Iwano; Hideki Kimura
Source:
Journal of microbiological methods 2021 v.184 pp. 106212
ISSN:
0167-7012
Subject:
Chlamydophila pneumoniae; Chlamydophila psittaci; DNA; automation; cell culture; genes; pneumonia
Abstract:
... Early detection of the family Chlamydiaceae as pathogens is essential worldwide for the rapid and sufficient management of atypical pneumonia. GENECUBE (TOYOBO) is a novel fully automated gene analyzer capable of amplifying and detecting target DNAs within 50 min. In this study, we developed a new PCR assay with a specific quenching probe (PCR-QC assay) for rapidly distinguishing between Chlamydia ...
DOI:
10.1016/j.mimet.2021.106212

7. Evaluation of a modified rapid viability-polymerase chain reaction method for Bacillus atrophaeus spores in water matrices

Author:
Rebecca N. Bushon; Amie M.G. Brady; Christopher M. Kephart; Vicente Gallardo
Source:
Journal of microbiological methods 2021 v.188 pp. 106293
ISSN:
0167-7012
Subject:
Bacillus atrophaeus; DNA; centrifugation; chlorine; culture media; microfiltration; pathogens; public health; rapid methods; remediation; tap water; ultrafiltration; viability
Abstract:
... A rapid method that provides information on the viability of organisms is needed to protect public health and ensure that remediation efforts following a release of a biological agent are effective. The rapid viability-polymerase chain reaction (RV-PCR) method combines broth culture and molecular methods to provide results on whether viable organisms are present in less than 15 h. In this study, a ...
DOI:
10.1016/j.mimet.2021.106293

8. New approach for the identification of potentially toxigenic Corynebacterium sp. using a multiplex PCR assay

Author:
Sunarno; Khariri; Fauzul Muna; Kambang Sariadji; Yuni Rukminiati; Dwi Febriyana; Tati Febrianti; Ratih Dian Saraswati; Ida Susanti; Nelly Puspandari; Anis Karuniawati; Amarila Malik; Amin Soebandrio
Source:
Journal of microbiological methods 2021 v.184 pp. 106198
ISSN:
0167-7012
Subject:
Corynebacterium; DNA; diphtheria; nucleotide sequences; polymerase chain reaction; prediction; sequence analysis
Abstract:
... In diphtheria laboratory examinations, the PCR test can be applied to isolates and clinical specimens. This study aimed to develop a PCR assay to identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types. Seven reference isolates, four synthetic DNA samples, 36 stored isolates, and 487 clinical samples used for PCR optimization. The PCR resul ...
DOI:
10.1016/j.mimet.2021.106198

9. Production of inactivated gram-positive and gram-negative species with preserved cellular morphology and integrity

Author:
Rahwa Taddese; Clara Belzer; Steven Aalvink; Marien I. de Jonge; Iris D. Nagtegaal; Bas E. Dutilh; Annemarie Boleij
Source:
Journal of microbiological methods 2021 v.184 pp. 106208
ISSN:
0167-7012
Subject:
DNA; cell walls; ethanol; formalin; pasteurization; sodium hydroxide
Abstract:
... There are many approaches available to produce inactive bacteria by termination of growth, each with a different efficacy, impact on cell integrity, and potential for application in standardized inactivation protocols. The aim of this study was to compare these approaches and develop a standardized protocol for generation of inactivated Gram-positive and Gram-negative bacteria, yielding cells that ...
DOI:
10.1016/j.mimet.2021.106208

10. Rapid preparation of 6S RNA-free B. subtilis σA-RNA polymerase and σA

Author:
Sweetha Ganapathy; Jana Christin Wiegard; Roland K. Hartmann
Source:
Journal of microbiological methods 2021 v.190 pp. 106324
ISSN:
0167-7012
Subject:
DNA; DNA-directed RNA polymerase; RNA; genes; journals; methodology; strains
Abstract:
... The regulatory 6S-1 and 6S-2 RNAs of B. subtilis bind to the housekeeping RNA polymerase holoenzyme (σᴬ-RNAP) with submicromolar affinity. We observed copurification of endogenous 6S RNAs from a published B. subtilis strain expressing a His-tagged RNAP. Such 6S RNA contaminations in σᴬ-RNAP preparations reduce the fraction of enzymes that are accessible for binding to DNA promoters. In addition, t ...
DOI:
10.1016/j.mimet.2021.106324

11. Twenty-first century molecular methods for analyzing antimicrobial resistance in surface waters to support One Health assessments

Author:
A.M. Franklin; N.E. Brinkman; M.A. Jahne; S.P. Keely
Source:
Journal of microbiological methods 2021 v.184 pp. 106174
ISSN:
0167-7012
Subject:
DNA; One Health initiative; antibiotic resistance; detection limit; environmental health; humans; metagenomics; monitoring; quantitative polymerase chain reaction; surface water; water quality
Abstract:
... Antimicrobial resistance (AMR) in the environment is a growing global health concern, especially the dissemination of AMR into surface waters due to human and agricultural inputs. Within recent years, research has focused on trying to understand the impact of AMR in surface waters on human, agricultural and ecological health (One Health). While surface water quality assessments and surveillance of ...
DOI:
10.1016/j.mimet.2021.106174

12. A new technique to evaluate Acidithiobacillus thiooxidans growth during a bioleaching process based on DNA quantification

Author:
Andrea M. Rivas-Castillo; Marlenne Gómez-Ramírez; Isaac M. Lucas-Gómez; Yareli Carrillo-Vega; Norma G. Rojas-Avelizapa
Source:
Journal of microbiological methods 2022 v.198 pp. 106494
ISSN:
0167-7012
Subject:
Acidithiobacillus ferrooxidans; Acidithiobacillus thiooxidans; DNA; Thiobacillus; bioleaching; sulfates
Abstract:
... The potential of Acidithiobacillus (Thiobacillus) genus members, namely Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans, for bioleaching purposes is known. Specifically, previous studies have shown the potential of A. thiooxidans strain DSM 26636 used in bioleaching processes to remove metals in high-metal-content matrices. All Acidithiobacillus growth-monitoring techniques availa ...
DOI:
10.1016/j.mimet.2022.106494

13. A novel high-resolution melting analysis-based method for Salmonella genotyping

Author:
Miaomiao Hu; Dong Yang; Xiaoli Wu; Meng Luo; Feng Xu
Source:
Journal of microbiological methods 2020 v.172 pp. 105806
ISSN:
0167-7012
Subject:
DNA; Salmonella; bacteria; butanol; dried milk; food safety; genotyping; melting; salmonellosis; temperature
Abstract:
... To establish a simple and rapid high-resolution melting curve (HRM) method, 5 different strains of Salmonella were identified by adding DNA denaturants at different concentrations into the HRM system to change the characteristics of DNA melting and to obtain different Tm (dissolving temperature) values of DNA from different target bacteria. When the concentration of n-butanol was 7% (v/v), the Tm ...
DOI:
10.1016/j.mimet.2019.105806

14. A simple method for high molecular-weight genomic DNA extraction suitable for long-read sequencing from spores of an obligate biotroph oomycete

Author:
Charlotte Penouilh-Suzette; Sandra Fourré; Guillaume Besnard; Laurence Godiard; Yann Pecrix
Source:
Journal of microbiological methods 2020 v.178 pp. 106054
ISSN:
0167-7012
Subject:
DNA; Helianthus annuus; Plasmopara halstedii; cost effectiveness; downy mildew; gene duplication; genome assembly; genomics; molecular weight; pathogens; temperature
Abstract:
... Long-read sequencing technologies are having a major impact on our approaches to studying non-model organisms and microbial communities. By significantly reducing the cost and facilitating the genome assembly pipelines, any laboratory can now develop its own genomics program regardless of the complexity of the genome studied. The most crucial current challenge is to develop efficient protocols for ...
DOI:
10.1016/j.mimet.2020.106054

15. A single-container procedure for multiple genomic DNA samples preparation for pulsed field gel electrophoresis

Author:
Karen León Arcia; Heidi Quintero Álvarez; Laura María Pantoja-Echevarría; Yainelis Garrido Nicot
Source:
Journal of microbiological methods 2022 v.195 pp. 106453
ISSN:
0167-7012
Subject:
DNA; Escherichia coli; cell growth; cost effectiveness; infectious diseases; pulsed-field gel electrophoresis
Abstract:
... Genomic DNA preparation is a critical step for successful fingerprinting analysis by Pulsed Field Gel Electrophoresis (PFGE). This paper presents a simple and rapid protocol to prepare DNA samples from up to 24 bacterial isolates simultaneously. It involves performing the conventional PFGE sample preparation steps (cell growth and harvest, agarose-immobilization of intact cells, and DNA release an ...
DOI:
10.1016/j.mimet.2022.106453

16. Comparison of DNA/RNA yield and integrity between PMAP36-mediated and other bacterial lysis methods

Author:
Yunjung Lee; Hye-sun Cho; Munjeong Choi; Somasundaram Prathap; Nagasundarapandian Soundrarajan; Youngsok Choi; Hyuk Song; Kwonho Hong; Chankyu Park
Source:
Journal of microbiological methods 2022 v.193 pp. 106396
ISSN:
0167-7012
Subject:
DNA; Gram-positive bacteria; RNA; Staphylococcus aureus
Abstract:
... Currently, several methods are available for the isolation of bacterial DNA and RNA. However, the diversity and complexity of cell envelope structures limit their efficiency depending on the target bacterial species. In this study, we compared the differences in yield and integrity of RNA prepared from four gram-negative and six gram-positive bacterial species using bead-beating, bacteriolytic pro ...
DOI:
10.1016/j.mimet.2021.106396

17. Development and validation of a droplet digital PCR assay for the detection and quantification of Bartonella species within human clinical samples.

Author:
Ricardo G. Maggi; Toni Richardson; Edward B. Breitschwerdt; Jennifer C. Miller
Source:
Journal of microbiological methods 2020 v.176 pp. 106022
ISSN:
0167-7012
Subject:
Borrelia; DNA; bacteremia; blood; diagnostic techniques; droplets; humans; patients; North Carolina
Abstract:
... This report describes the development, optimization, and validation of a ddPCR assay for the detection of Bartonella spp. DNA within several sample matrices, including clinical blood samples from patients with or without documented Bartonella spp. bacteremia. The Bartonella spp. ddPCR assay was developed based upon previously published TaqMan-based qPCR assays that can amplify DNA of over 25 Barto ...
DOI:
10.1016/j.mimet.2020.106022

18. Development of an FTP-LAMP assay based on TaqMan real-time PCR and LAMP for the specific detection of Xylella fastidiosa De Donno and mulberry strains in both plants and insect vectors

Author:
Toufic Elbeaino; Ornella Incerti; Hiba Dakroub; Franco Valentini; Qi Huang
Source:
Journal of microbiological methods 2020 v.175 pp. 105992
ISSN:
0167-7012
Subject:
DNA; Neophilaenus; Philaenus spumarius; Xylella fastidiosa; dyes; fluorescence; genes; loop-mediated isothermal amplification; mulberries; olives; quantitative polymerase chain reaction; France; Germany; Italy; Portugal; Spain
Abstract:
... We developed two real-time detection assays, TaqMan real-time PCR and LAMP, using primers and probe designed based on a sequence annotated to code for a Haemagglutinin-related protein (Hg) of Xylella fastidiosa (Xf), a gene uniquely present in the Italian olive (De Donno of olive) and American mulberry strains, for specific detection of the target Xf strains. These assays were validated with DNA s ...
DOI:
10.1016/j.mimet.2020.105992

19. Development of fluorescence-based nucleic acid blot hybridization method using Cy5.5 labeled DNA probes

Author:
Ying Cheng; Na Wang; Zhenxing Ren; Chenggang Xu
Source:
Journal of microbiological methods 2022 v.197 pp. 106479
ISSN:
0167-7012
Subject:
DNA; Northern blotting; RNA; Southern blotting; bioimaging; cellulolytic bacteria; fluorescence; fluorescent dyes; gene targeting; models; nucleic acid hybridization
Abstract:
... Near-infrared (NIR) fluorophores are widely used as fluorescent probes for bioimaging because of their minimal photodamage to biological samples, deep penetration, and low interference from background autofluorescence. Here, we employed a NIR fluorescent cyanine dye Cy5.5 to label DNA probes for nucleic acid blot hybridization. The specificity and sensitivity of fluorescent DNA probes were proven ...
DOI:
10.1016/j.mimet.2022.106479

20. Evaluation of methods for DNA extraction from Clostridium tyrobutyricum spores and its detection by qPCR

Author:
M. Esteban; P. Marcos; C. Horna; P. Galan-Malo; L. Mata; M.D. Pérez; M. Calvo; L. Sánchez
Source:
Journal of microbiological methods 2020 v.169 pp. 105818
ISSN:
0167-7012
Subject:
Clostridium tyrobutyricum; DNA; DNA packaging; agar; cheese ripening; cheeses; enzymatic treatment; germination; liquids; microwave treatment; milk; proteins; quantitative polymerase chain reaction; raw milk; spores; subtilisin; vegetative cells
Abstract:
... Clostridium tyrobutyricum is the major agent that causes the blowing defect in cheese due to the germination of its dormant spores during the ripening stage. As a result, many of the affected cheeses show cavities and cracks, which cause the product loss in most cases. Nowadays, there is not a fast method capable of detecting milk contaminated with C. tyrobutyricum spores. The aim of this study ha ...
DOI:
10.1016/j.mimet.2019.105818

21. Mining transcriptome data: Utilization of environmentally regulated promoters for protein expression and purification in Clostridium perfringens

Author:
Samantha R. Soncini; Gary J. Camper; Stephen B. Melville
Source:
Journal of microbiological methods 2022 v.199 pp. 106519
ISSN:
0167-7012
Subject:
Clostridium perfringens; DNA; Escherichia coli; Gram-negative bacteria; collagenase; liquids; operon; pathogens; protein synthesis; sequence analysis; toxins; transcriptome
Abstract:
... Clostridium perfringens is a Gram-positive pathogen with low GC content. To identify genes that are transcribed at higher levels when the bacteria grow on a surface, we used RNA-seq in a previous study to measure global transcript levels of cells grown in three types of media on both plates and in liquid culture. We found the arcABDC-argR operon is induced >1000-fold when the cells were grown on p ...
DOI:
10.1016/j.mimet.2022.106519

22. Multi fragment melting analysis system (MFMAS) for one-step identification of lactobacilli

Author:
Zülal Kesmen; Özge Kılıç; Yasin Gormez; Mete Çelik; Burcu Bakir-Gungor
Source:
Journal of microbiological methods 2020 v.177 pp. 106045
ISSN:
0167-7012
Subject:
DNA; Lactobacillus; computer software; fermentation; probiotics
Abstract:
... The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For this reason, in this study, we proposed the Multi Fragment Melting Analysis System (MFMAS)-lactobacilli based on high resolution melting (HRM) analysis of multiple DNA regions that ...
DOI:
10.1016/j.mimet.2020.106045

23. Multiplex droplet digital PCR assay for detection of Flavobacterium psychrophilum and Yersinia ruckeri in Norwegian aquaculture

Author:
Anna S. Lewin; Tone Haugen; Roman Netzer; Anne Tøndervik; Stine W. Dahle; Gunhild Hageskal
Source:
Journal of microbiological methods 2020 v.177 pp. 106044
ISSN:
0167-7012
Subject:
DNA; Flavobacterium psychrophilum; Salmo salar; Yersinia ruckeri; droplets; fish; fish health; monitoring; mortality; pathogens; risk assessment; water quality
Abstract:
... We report the development of ddPCR assays for single and simultaneous detection of the bacterial pathogens Flavobacterium psychrophilum and Yersinia ruckeri in water from land-based recirculation aquaculture systems (RAS), producing Atlantic salmon (Salmo salar) smolt. The method was tested and verified for use in water analyses from RAS production sites, and proved to be specific and with sensiti ...
DOI:
10.1016/j.mimet.2020.106044

24. Primer design to assess bacterial degradation of glyphosate and other phosphonates

Author:
M.E. Morales; M. Allegrini; J. Basualdo; M.B. Villamil; M.C. Zabaloy
Source:
Journal of microbiological methods 2020 v.169 pp. 105814
ISSN:
0167-7012
Subject:
DNA; biochemical pathways; biodegradation; cost effectiveness; glycine (amino acid); glyphosate; metagenomics; operon; phosphonates; phosphorus; quantitative polymerase chain reaction
Abstract:
... Phosphonates are organic phosphorous (P) compounds frequently detected in the environment due to a very stable CP bond that render them relatively recalcitrant. Glyphosate [N-phosphonomethyl glycine] is the most widely used and best-known synthetic phosphonate, and one of the most concerning herbicides in the world today. Microbial degradation of glyphosate and organophosphonates in general, is th ...
DOI:
10.1016/j.mimet.2019.105814

25. Rapid detection of rifampicin-resistant Mycobacterium tuberculosis, based on isothermal DNA amplification and DNA chromatography

Author:
Yutaka Takarada; Takuya Kodera; Kumi Kobayashi; Chie Nakajima; Mitsuo Kawase; Yasuhiko Suzuki
Source:
Journal of microbiological methods 2020 v.177 pp. 106062
ISSN:
0167-7012
Subject:
DNA; Mycobacterium tuberculosis; chromatography; equipment; hybridization; loop-mediated isothermal amplification; mutants; rapid methods; rifampicin; sequence analysis
Abstract:
... Rapid and easy detection of nucleotide point mutations in bacterial pathogens associated with drug resistance is essential for the proper use of antimicrobials. Here, we developed a rapid and simple method for the detection of mutations using Loop-mediated isothermal amplification (LAMP) combined with the single-tag hybridization (STH) chromatographic printed array strips (PAS) method. This proced ...
DOI:
10.1016/j.mimet.2020.106062

26. Rapid sourdough yeast identification using panfungal PCR combined with high resolution melting analysis

Author:
Olga Bazalová; Jaromír Z. Cihlář; Zuzana Dlouhá; Ladislav Bár; Vladimír Dráb; Miloslava Kavková
Source:
Journal of microbiological methods 2022 v.199 pp. 106522
ISSN:
0167-7012
Subject:
DNA; ergot; genes; quantitative polymerase chain reaction; sourdough; sourdough bread; species identification; yeasts
Abstract:
... The microbial composition of the sourdough starter affects the sourdough bread properties. Therefore, it is crucial to find a tool for rapid, time-saving, and economical identification of the sourdough microbiota. We focused on the rapid identification of sourdough yeasts. We designed a panfungal real time-PCR targeting the ITS2 region (ITS-amplicon) and a fragment of D1/D2 region of 26S rRNA gene ...
DOI:
10.1016/j.mimet.2022.106522

27. Syringe filter-based DNA aptamer-enzyme-linked colorimetric assay of Salmonella on lettuce

Author:
John G. Bruno
Source:
Journal of microbiological methods 2022 v.193 pp. 106406
ISSN:
0167-7012
Subject:
DNA; Salmonella Typhimurium; colorimetry; fluorometry; lettuce; nucleotide aptamers; syringes
Abstract:
... A simpler visible colorimetric and less expensive syringe enzymatic filter-based assay (SEFA) utilizing proven anti-Salmonella DNA aptamers is described which is based on a similar previously published fluorometric version of SEFA with larger filter units. The colorimetric SEFA is applied to detection of Salmonella enterica on lettuce with detection limits of less than 1000 cfu per sample. The ass ...
DOI:
10.1016/j.mimet.2022.106406

28. Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood

Author:
Qian Li; Wenhua Huang; Shengwei Zhang; Yuling Zheng; Qingyu Lv; Decong Kong; Lei Zhang; Yan Zhang; Zhihu Zhao; Miaoyu Wang; Hua Jiang; Peng Liu; Yongqiang Jiang
Source:
Journal of microbiological methods 2022 v.192 pp. 106391
ISSN:
0167-7012
Subject:
DNA; antibiotic resistance; blood; blood flow; death; humans; mortality; pathogen identification
Abstract:
... Bloodstream infections are within the top ten causes of death globally, with a mortality rate of up to 70%. Gold standard blood culture testing is time-consuming, resulting in delayed, but accurate, treatment. Molecular methods, such as RT-qPCR, have limited targets in one run. We present a new Ampliseq detection system (ADS) combining target amplification and next-generation sequencing for accura ...
DOI:
10.1016/j.mimet.2021.106391

29. Transformation of Lactiplantibacillus plantarum and Apilactobacillus kunkeei is influenced by recipient cell growth temperature, vector replicon, and DNA methylation

Author:
Dennis L. Welker; Bailey L. Crowley; Justin B. Evans; Martin H. Welker; Jeff R. Broadbent; Robert F. Roberts; David A. Mills
Source:
Journal of microbiological methods 2020 v.175 pp. 105967
ISSN:
0167-7012
Subject:
DNA; DNA methylation; Escherichia coli; cell growth; replicon; temperature
Abstract:
... The effects of recipient cell growth temperature, vector choice, and DNA methylation on transformation efficiency were explored for Lactiplantibacillus plantarum strain B38 and Apilactobacillus kunkeei strains YH15 and 3L. All three parameters significantly affected transformation efficiency. L. plantarum B38 and A. kunkeei YH15 transformed at higher efficiencies with the pTW8 vector than with the ...
DOI:
10.1016/j.mimet.2020.105967

30. A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss)

Author:
Mathis Hildonen; Miyako Kodama; Lara C. Puetz; M. Thomas P. Gilbert; Morten T. Limborg
Source:
Journal of microbiological methods 2019 v.160 pp. 42-48
ISSN:
0167-7012
Subject:
DNA; Oncorhynchus mykiss; digestive system; dry ice; ethanol; fish; freezing; genomic libraries; intestinal microorganisms; labor; mammals; microbiome; new species; research programs; ribosomal RNA; sequence analysis; storage temperature; water content
Abstract:
... Immediate freezing is perhaps the most preferred method used for preserving gut microbial samples, but research on sample preservation has been principally based around samples from mammalian species, and little is known about the advantages or disadvantages relating to different storage methods for fish guts. Fish gut samples may pose additional challenges due to the different chemical and enzyma ...
DOI:
10.1016/j.mimet.2019.03.010

31. A novel bioluminescent approach to the loop-mediated isothermal amplification-based detection of Lactobacillus salivarius in feed samples

Author:
Zhongjie Fei; Rongbin Wei; Dongrui Zhou; Na Li; Pengfeng Xiao
Source:
Journal of microbiological methods 2021 v.187 pp. 106209
ISSN:
0167-7012
Subject:
DNA; Lactobacillus salivarius; bioluminescence; chickens; detection limit; loop-mediated isothermal amplification; pet foods; propidium
Abstract:
... Coupling loop-mediated isothermal amplification (LAMP) with a bioluminescent assay in real-time (LAMP-BART) is a strategy that can be readily leveraged to detect bacteria in particular samples of interest without the need for costly or complicated equipments. However, this approach exhibits poor sensitivity, and it additionally amplifies all target DNA including that derived from non-viable cells. ...
DOI:
10.1016/j.mimet.2021.106209

32. A novel qPCR based-method for detection and quantification of three recurrent species of Penicillium isolated from bioaerosols in mold-damaged homes

Author:
A. Géry; A. Delanoë; N. Heutte; E. Chosson; J. Bonhomme; D. Garon
Source:
Journal of microbiological methods 2021 v.186 pp. 106236
ISSN:
0167-7012
Subject:
DNA; Penicillium brevicompactum; agar; bioaerosols; fungal contamination; fungi; rapid methods; spectroscopy
Abstract:
... Fungal contamination of indoor environments can cause respiratory diseases and induce damages to building materials. Among the fungal species found in mold-damaged homes, Penicillium brevicompactum, P. chrysogenum and P. crustosum can be considered as recurrent strains. In this study, we therefore propose a rapid and novel qPCR-based method in order to allow the monitoring of these three fungal sp ...
DOI:
10.1016/j.mimet.2021.106236

33. A review on application of next-generation sequencing methods for profiling of protozoan parasites in water: Current methodologies, challenges, and perspectives

Author:
N.P. Mthethwa; I.D. Amoah; P. Reddy; F. Bux; S. Kumari
Source:
Journal of microbiological methods 2021 v.187 pp. 106269
ISSN:
0167-7012
Subject:
DNA; Protozoa; data collection; genome; humans; metagenomics; parasites; wastewater
Abstract:
... The advancement in metagenomic techniques has provided novel tools for profiling human parasites in environmental matrices, such as water and wastewater. However, application of metagenomic techniques for the profiling of protozoan parasites in environmental matrices is not commonly reported in the literature. The key factors leading to the less common use of metagenomics are the complexity and la ...
DOI:
10.1016/j.mimet.2021.106269

34. Absolute quantification of priority bacteria in aquaculture using digital PCR

Author:
Roman Netzer; Deni Ribičić; Marianne Aas; Laura Cavé; Trisha Dhawan
Source:
Journal of microbiological methods 2021 v.183 pp. 106171
ISSN:
0167-7012
Subject:
DNA; Desulfovibrio desulfuricans; Flavobacterium psychrophilum; Listeria monocytogenes; Moritella viscosa; Salmonidae; Yersinia ruckeri; animal pathogens; biomass; detection limit; fish health; hydrogen sulfide; mortality; organic matter; probiotics; salmon; toxicity; water quality
Abstract:
... Modern aquaculture systems are designed for intensive rearing of fish or other species. Both land-based and offshore systems typically contain high loads of biomass and the water quality in these systems is of paramount importance for fish health and production. Microorganisms play a crucial role in removal of organic matter and nitrogen-recycling, production of toxic hydrogen sulfide (H₂S), and c ...
DOI:
10.1016/j.mimet.2021.106171

35. Application of ddPCR for detection of Enterococcus spp. in coastal water quality monitoring

Author:
Chad Crain; Keith Kezer; Syreeta Steele; Judith Owiti; Sphoorthy Rao; Maria Victorio; Brett Austin; Alon Volner; William Draper; John Griffith; Joshua Steele; Marva Seifert
Source:
Journal of microbiological methods 2021 v.184 pp. 106206
ISSN:
0167-7012
Subject:
DNA; Enterococcus; coastal water; data collection; droplets; equations; gene dosage; most probable number technique; pollution; water quality; California
Abstract:
... Droplet digital polymerase chain reaction (ddPCR) was evaluated for the detection of fecal indicator bacteria (FIB), Enterococcus spp., in San Diego County beach water samples collected under diverse conditions, from multiple pollution sources, as part of regulatory monitoring activities over 20 months. Two US EPA-approved methods, qPCR (EPA 1609.1) and Enterolert (SM9230D), were used as reference ...
DOI:
10.1016/j.mimet.2021.106206

36. Comparative evaluation of the Bruker Biotyper and Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems for non-albicans Candida and uncommon yeast isolates

Author:
Leyla Teke; Ayşe Barış; Banu Bayraktar
Source:
Journal of microbiological methods 2021 v.185 pp. 106232
ISSN:
0167-7012
Subject:
Candida glabrata; Candida krusei; Candida parapsilosis; Candida tropicalis; Cyberlindnera; DNA; Meyerozyma caribbica; internal transcribed spacers; matrix-assisted laser desorption-ionization mass spectrometry; sequence analysis; yeasts
Abstract:
... Rapid and accurate diagnosis is critically important in invasive and disseminated fungal infections for appropriate antifungal treatment.MALDI-TOF MS systems are effective for fast and accurate identification of Candida species.We aimed to compare two MALDI-TOF MS systems for the rapid identification of non-albicans Candida and rare clinical yeast species.This study included 157 isolates represent ...
DOI:
10.1016/j.mimet.2021.106232

37. Comparative study of IS711 and bcsp31-based polymerase chain reaction (PCR) for the diagnosis of human brucellosis in whole blood and serum samples

Author:
Guilherme Nardi Becker; Felipe Francisco Tuon
Source:
Journal of microbiological methods 2021 v.183 pp. 106182
ISSN:
0167-7012
Subject:
Brucella melitensis biovar Abortus; DNA; blood sampling; blood serum; brucellosis; comparative study; detection limit; humans; quantitative polymerase chain reaction
Abstract:
... Clinical diagnosis of human brucellosis (HB) is often difficult due to non-specific symptoms. Immunological tests have been the most common method used in HB diagnosis, but molecular methods based on quantitative polymerase chain reaction (qPCR) have largely replaced these diagnostic methods. The aim of this study was to validate a HB diagnostic qPCR method; assessing different target Brucella gen ...
DOI:
10.1016/j.mimet.2021.106182

38. Comparison of two DNA extraction methods widely used in aquatic microbial ecology

Author:
Erick Mateus-Barros; Aylan K. Meneghine; Inessa Lacativa Bagatini; Camila C. Fernandes; Luciano T. Kishi; Armando A.H. Vieira; Hugo Sarmento
Source:
Journal of microbiological methods 2019 v.159 pp. 12-17
ISSN:
0167-7012
Subject:
DNA; aquatic environment; biodiversity; community structure; ecological function; lakes; microbial communities
Abstract:
... In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological infere ...
DOI:
10.1016/j.mimet.2019.02.005

39. Development and comparative evaluation of droplet digital PCR and quantitative PCR for the detection and quantification of Chlamydia psittaci

Author:
Radhakrishna Sahu; M.R. Vishnuraj; Ch. Srinivas; Bhargavi Dadimi; G.K. Megha; Niveditha Pollumahanti; Satyaveer S. Malik; S. Vaithiyanathan; Deepak B. Rawool; Sukhadeo B. Barbuddhe
Source:
Journal of microbiological methods 2021 v.190 pp. 106318
ISSN:
0167-7012
Subject:
Chlamydophila psittaci; DNA; cloaca; detection limit; droplets; ducks; humans; lungs; pathogens; pharynx; quantitative polymerase chain reaction
Abstract:
... Chlamydia psittaci is a zoonotic pathogen mainly transmitted by psittacine birds and poultry. The low shedding rate of the pathogen in the apparently healthy birds and human clinical cases may result in false-negative results. In the present study, a droplet digital PCR (ddPCR) assay was developed and compared with optimized quantitative PCR (qPCR) for the detection of C. psittaci from the clinica ...
DOI:
10.1016/j.mimet.2021.106318

40. Development and validation of real-time PCR assays for the detection of Ehrlichia species and E. chaffeensis in clinical specimens

Author:
Ida H. Chung; Amy L. Austin; Cecilia Y. Kato
Source:
Journal of microbiological methods 2021 v.186 pp. 106225
ISSN:
0167-7012
Subject:
DNA; Ehrlichia chaffeensis; cross reaction; detection limit; ehrlichiosis; genomics; human diseases; humans; new species; quantitative polymerase chain reaction; ticks
Abstract:
... Ehrlichiosis, caused by Gram-negative bacteria of the genus Ehrlichia, is considered an emerging infectious disease due to the increasing number of reported cases. Symptoms are non-specific and occur within 1 to 2 weeks following the bite of an infected tick. Confirmatory laboratory diagnostic methods vary in sensitivity and specimen requirements, which can lead to delayed diagnosis. PCR testing s ...
DOI:
10.1016/j.mimet.2021.106225

41. Differentiation among the most important Rodentibacter species by multiplex PCR assays targeting the ITSile+ala sequences of the rRNA operons

Author:
Laurentiu Benga; Eva Engelhardt; W. Peter M. Benten; Werner Nicklas; Martin Sager
Source:
Journal of microbiological methods 2021 v.182 pp. 106150
ISSN:
0167-7012
Subject:
DNA; Pasteurellaceae; geographical distribution; internal transcribed spacers; oligodeoxyribonucleotides; operon; polymerase chain reaction; quality control
Abstract:
... Screening for the Rodentibacter species is part of the microbiologic quality assurance programs of laboratory rodents all over the world. Nevertheless, currently there are no PCR amplification techniques available for the diagnostic of R. ratti, R. heidelbergensis and of a Rodentibacter related β-haemolytic taxon. The aim of this study was to utilize the differences in the sequence of the Internal ...
DOI:
10.1016/j.mimet.2021.106150

42. Establishment and performance evaluation of multiplex PCR-dipstick DNA chromatography assay for simultaneous diagnosis of four sexually transmitted pathogens

Author:
Li Luo; Qianming Chen; Qiang Luo; Sheng Qin; Zhenjie Liu; Qiong Li; Xianzhang Huang; Hui Xiao; Ning Xu
Source:
Journal of microbiological methods 2021 v.186 pp. 106250
ISSN:
0167-7012
Subject:
Chlamydia trachomatis; DNA; Mycoplasma hominis; Neisseria gonorrhoeae; biotin; chromatography; color; detection limit; gold; hybridization; streptavidin
Abstract:
... Rapid, sensitive, and specific diagnostic methods are indispensable for sexually transmitted infections (STIs). In this study, a multiplex PCR-dipstick DNA chromatography assay for diagnosis of four STI pathogens, namely Neisseria gonorrhoeae (N. gonorrhoeae), Mycoplasma hominis (M. hominis), Ureaplasma (U. urealyticum and U. parvum), and Chlamydia trachomatis (C. trachomatis), was established and ...
DOI:
10.1016/j.mimet.2021.106250

43. Excision of selectable markers from the Escherichia coli genome without counterselection using an optimized λRed recombineering procedure

Author:
Dmitrii M. Bubnov; Tigran V. Yuzbashev; Tatiana V. Vybornaya; Alexander I. Netrusov; Sergey P. Sineoky
Source:
Journal of microbiological methods 2019 v.158 pp. 86-92
ISSN:
0167-7012
Subject:
DNA; Escherichia coli; antibiotic resistance; antibiotic resistance genes; chromosomes; electroporation; genetic engineering; mutation
Abstract:
... The introduction of chromosomal mutations into the E. coli genome using λRed-mediated recombineering includes two consecutive steps—the insertion of an antibiotic resistance gene and the subsequent excision of the marker. The second step usually requires a counterselection method, because the efficiency of recombination is not high enough to find recombinants among non-recombinant cells. Most coun ...
DOI:
10.1016/j.mimet.2019.01.022

44. Exogenous contaminating DNA in Taq polymerases: A method to avoid false-positive results when detecting the blaTEM gene

Author:
Yaroslav K. Masalov; Rustam N. Heydarov; Igor A. Shashkov; Igor V. Chebotar; Alexander S. Zasedatelev; Nikolay A. Mayansky; Vladimir M. Mikhailovich
Source:
Journal of microbiological methods 2019 v.160 pp. 36-41
ISSN:
0167-7012
Subject:
DNA; DNA primers; Gram-negative bacteria; antibiotic resistance; enzymes; false positive results; genes; nucleotide sequences; polymerase chain reaction
Abstract:
... In the course of developing an assay to identify genes responsible for antibiotic resistance in gram-negative bacteria, it has been found that standard (not DNA-free) Taq DNA polymerases were contaminated with blaTEM gene fragments that varied in length and quantities. The complete blaTEM gene sequence was either absent or was detected in infinitesimal amounts. We developed an approach to avoid fa ...
DOI:
10.1016/j.mimet.2019.03.018

45. Fast and automated detection of common carbapenemase genes using multiplex real-time PCR on the BD MAX™ system

Author:
Katja Probst; Sébastien Boutin; Michael Bandilla; Klaus Heeg; Alexander H. Dalpke
Source:
Journal of microbiological methods 2021 v.185 pp. 106224
ISSN:
0167-7012
Subject:
DNA; antibiotics; automation; beta-lactamase; genes; hydrolysis; monitoring; quantitative polymerase chain reaction; rapid methods
Abstract:
... Fast detection of carbapenemases in Gram-negative bacilli is necessary for accurate antibiotic treatment, prevention of further spreading and surveillance purposes. We analyzed the current occurrence of gene variants and designed two multiplex PCRs with hydrolysis probes.The assay was developed for the BD MAX™ system that combines DNA extraction and PCR in a fully automated procedure providing res ...
DOI:
10.1016/j.mimet.2021.106224

46. Molecular detection of Phytophthora pluvialis, the causal agent of red needle cast in Pinus radiata

Author:
R.L. McDougal; L. Cunningham; S. Hunter; A. Caird; H. Flint; A. Lewis; R.J. Ganley
Source:
Journal of microbiological methods 2021 v.189 pp. 106299
ISSN:
0167-7012
Subject:
DNA; Phytophthora; Pinus radiata; Pseudotsuga menziesii; biosecurity; detection limit; diagnostic techniques; fungi; genes; nucleotide sequences; pathogens; quantitative polymerase chain reaction; sequence analysis
Abstract:
... Phytophthora pluvialis was first described in 2013 and is the causal agent of red needle cast (RNC) in Pinus radiata as well as infection in Douglas fir (Pseudotsuga menziesii). A species-specific PCR is necessary for detection of this pathogen and diagnosis of RNC.To design and validate a species-specific molecular assay for P. pluvialis using isolates from infected pine needles.Species-specific ...
DOI:
10.1016/j.mimet.2021.106299

47. Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification

Author:
Jordan Cannon; Robert A. Sanford; Lynn Connor; Wendy H. Yang; Joanne Chee-Sanford
Source:
Journal of microbiological methods 2019 v.160 pp. 49-59
ISSN:
0167-7012
Subject:
DNA; DNA primers; ammonification; ammonium; bacteria; cytochrome c; gene amplification; genes; genetic traits; groundwater; heme; high-throughput nucleotide sequencing; nitrate reduction; nitrite reductase; nitrites; phylogeny; quantitative polymerase chain reaction; terrestrial ecosystems; translation (genetics)
Abstract:
... Dissimilatory nitrate reduction to ammonium (DNRA) is now known to be a more prevalent process in terrestrial ecosystems than previously thought. The key enzyme, a pentaheme cytochrome c nitrite reductase NrfA associated with respiratory nitrite ammonification, is encoded by the nrfA gene in a broad phylogeny of bacteria. The lack of reliable and comprehensive molecular tools to detect diverse nrf ...
DOI:
10.1016/j.mimet.2019.03.020
CHORUS:
10.1016/j.mimet.2019.03.020
Chorus Open Access:
10.1016/j.mimet.2019.03.020

48. Optimization of pre- treatments with Propidium Monoazide and PEMAX™ before real-time quantitative PCR for detection and quantification of viable Helicobacter pylori cells

Author:
Irene Hortelano; María Yolanda Moreno; Jorge García-Hernández; María Antonia Ferrús
Source:
Journal of microbiological methods 2021 v.185 pp. 106223
ISSN:
0167-7012
Subject:
DNA; Helicobacter pylori; disinfection; genomics; propidium; public health; quantitative polymerase chain reaction
Abstract:
... Accurate detection of H. pylori in different environmental and clinical samples is essential for public health strtdudies. Now, a big effort is being made to design PCR methodologies that allow for the detection of viable and viable but non-culturable (VBNC) H. pylori cells, by achieving complete exclusion of dead cells amplification signals. The use of DNA intercalating dyes has been proposed. Ho ...
DOI:
10.1016/j.mimet.2021.106223

49. PCR procedures to amplify GC-rich DNA sequences of Mycobacterium bovis

Author:
Nadia Assal; Min Lin
Source:
Journal of microbiological methods 2021 v.181 pp. 106121
ISSN:
0167-7012
Subject:
DNA; Listeria monocytogenes; Mycobacterium bovis; denaturation; genes
Abstract:
... Amplification of high GC content genes by PCR is a major challenge during the creation of recombinant GC-rich DNA constructs. This may be due to the difficulty in DNA denaturation or the possibility of forming secondary structures from DNA templates. Tools have been described to address the technical problems associated with the amplification of shorter sequences (<1000 bp). However, obstacles of ...
DOI:
10.1016/j.mimet.2020.106121

50. Precise, direct, and rapid detection of Shigella Spa gene by a novel unmodified AuNPs-based optical genosensing system

Author:
Narges Elahi; Mohammad Hadi Baghersad; Mehdi Kamali
Source:
Journal of microbiological methods 2019 v.162 pp. 42-49
ISSN:
0167-7012
Subject:
DNA; Shigella; bacteria; biosensors; cost effectiveness; detection limit; genes; infectious diseases; nucleotide sequences; polymerase chain reaction; rapid methods; screening
Abstract:
... Early detection of infectious bacteria is a necessity for combating infectious diseases. Due to low infectious dose of Shigella, rapid and sensitive detection is needed. Compared to the presented genes, Spa gene can be introduced as a novel sequence for all species of Shigella detection. Herein, the possibility of Spa genes for detection of four species of Shigella was investigated for the first t ...
DOI:
10.1016/j.mimet.2019.05.007