4,336 results match your criteria Journal of Microbiological Methods [Journal]


Development of a multiplex PCR assay based on the pilA gene sequences to detect different types of Acidovorax citrulli.

J Microbiol Methods 2019 Feb 8. Epub 2019 Feb 8.

State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences, Institute of Plant Protection, Beijing, China. Electronic address:

Bacterial fruit blotch (BFB) of cucurbits, caused by Acidovorax citrulli, is a major threat to commercial watermelon and melon production worldwide. At present, there are at least two genetically distinct sub-populations (group I and II) of A. citrulli that differ in host preference among cucurbit species and copper sensitivity. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.02.003DOI Listing
February 2019

Potential in vivo transfer of a bla-harbouring plasmid established by combining long- and short-read sequencing.

J Microbiol Methods 2019 Feb 7. Epub 2019 Feb 7.

Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium. Electronic address:

Horizontal transfer of plasmid-mediated antibiotic resistance has rarely been documented in vivo. Utilizing long-read (Oxford Nanopore) and short-read (Illumina) sequencing, we confirmed that a gut-colonizing Escherichia coli and a hypervirulent Klebsiella pneumoniae ST23, isolated from a surgical site culture of a patient receiving cefuroxime therapy, harboured a 100% identical bla-harbouring plasmid, indicative of a potential transfer in vivo. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.02.004DOI Listing
February 2019

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

J Microbiol Methods 2019 Feb 6. Epub 2019 Feb 6.

Universidade Federal de São Carlos (UFSCar), Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, São Carlos, SP 13565-905, Brazil. Electronic address:

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 inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.02.005DOI Listing
February 2019

Antifungal efficacy of Itraconazole loaded PLGA-nanoparticles stabilized by vitamin-E TPGS: In vitro and ex vivo studies.

J Microbiol Methods 2019 Feb 6. Epub 2019 Feb 6.

Nanobiotechnology Unit, Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box: 2457, Riyadh 11451, Saudi Arabia. Electronic address:

Itraconazole (ITZ) loaded Poly-(D, L-lactic-co-glycolic acid, PLGA) nanoparticles (PLGA-NPs) stabilized by D-α-Tocopherol polyethylene-glycol succinate-1000 (TPGS) were developed by nanoprecipitation and single emulsion solvent evaporation methods to improve antifungal activity of ITZ by enhancing its solubility, and hence bioavailability. Encapsulation efficiency, drug loading, in-vitro release, ex-vivo permeation and antifungal activity were performed for the optimized PLGA-NPs. Characterization of PLGA-NPs were performed by scanning electron microscopy, dynamic light scattering, differential scanning calorimetry, Fourier transform infrared spectroscopy, and powder X-ray diffractometry. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.020DOI Listing
February 2019

An immunoliposome-based immunochromatographic strip assay for the rapid detection of Cronobacter species.

J Microbiol Methods 2019 Feb 6. Epub 2019 Feb 6.

Department of Food Science and Technology, Yeungnam University, Gyeongsan-si, Gyeongsangbuk-do 38541, Republic of Korea. Electronic address:

Cronobacter species are foodborne pathogens that pose a high risk in infant formula and can cause fatality rates of 40-80% in infected infants. To develop a rapid and easy detection method for Cronobacter species, especially in powdered infant formula (PIF), an immunoliposome-based immunochromatographic strip assay was developed using an anti-Cronobacter immunoglobulin G (IgG)-conjugated liposome and an anti-Cronobacter IgG-coated nitrocellulose membrane. The developed assay could detect Cronobacter species in both pure culture and artificially contaminated PIF. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.02.006DOI Listing
February 2019

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

J Microbiol Methods 2019 Feb 6. Epub 2019 Feb 6.

Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute of Genetics and Selection of Industrial Microorganisms of National Research Center "Kurchatov Institute", 1-st Dorozhny pr., 1, Moscow 117545, Russia. Electronic address:

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. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.022DOI Listing
February 2019

Estimation of fungal biomass using multiphase artificial neural network based dynamic soft sensor.

Authors:
M Chitra N Pappa

J Microbiol Methods 2019 Feb 5. Epub 2019 Feb 5.

Department of Instrumentation Engineering, Madras Institute of Technology (MIT) Campus, Anna University Chennai, India. Electronic address:

Interest in low cost cellulase production has become a major challenge in recent years for biorefineries. Fed-batch fermentation of Trichoderma strains for the production of low cost cellulase is carried out on complex media that has various soluble and insoluble substrates. The lack of direct estimation of biomass in the presence of insoluble substrates is one of the major concerns for controlling bioprocesses in industries. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.02.002DOI Listing
February 2019

A simple and rapid colorimetric method for the estimation of chitosan produced by microbial degradation of chitin waste.

J Microbiol Methods 2019 Feb 3;158:66-70. Epub 2019 Feb 3.

School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India; School of Law, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India. Electronic address:

Chitin is one of the most abundant biopolymers present in the environment. Chitosan being its major derivative can be obtained by hydrolysis of chitin, especially by microbial degradation. Estimation of resulting chitosan produced by chitin degradation is crucial to the process. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.02.001DOI Listing
February 2019
2 Reads

A rapid method to detect and estimate the activity of the enzyme, alcohol oxidase by the use of two chemical complexes - acetylacetone (3,5-diacetyl-1,4-dihydrolutidine) and acetylacetanilide (3,5-di-N-phenylacetyl-1,4-dihydrolutidine).

J Microbiol Methods 2019 Feb 2;158:71-79. Epub 2019 Feb 2.

Biorefining Research Institute, Lakehead University, Thunder Bay, Ontario P7B 5E1, Canada.

A rapid and sensitive method has been devised in order to detect and estimate the synthesis of the enzyme alcohol oxidase (AOX) by fungi, by way of the use of two chemical complexes, namely, acetylacetone (3,5-diacetyl-1,4-dihydrolutidine) and acetylacetanilide (3,5-di-N-phenylacetyl-1,4-dihydrolutidine). This method involves the use of the AOX enzyme that could specifically oxidize methanol, giving rise to equimolar equivalents each of formaldehyde (HCHO) and hydrogen peroxide (HO) as the end products. Further, the formaldehyde, thus produced was allowed to interact with the neutral solutions of acetylacetone and the ammonium salt, gradually developing a yellow color, owing to the synthesis and release of 3,5-diacetyl-1,4-dihydrolutidine (yellow product; λ = 420 nm; λ = 390/470 nm) and the product, so generated was quantified spectrophotometrically by measureing its absorbance at 412 nm. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.021DOI Listing
February 2019

An efficient strategy for screening polyunsaturated fatty acid-producing oleaginous filamentous fungi from soil.

J Microbiol Methods 2019 Jan 29;158:80-85. Epub 2019 Jan 29.

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA. Electronic address:

Screening oleaginous microorganisms capable of accumulating considerable lipids is essential for industrial lipid production. Here we demonstrated forty-seven filamentous fungal isolates were obtained from eight soil samples using a new screening strategy with both triphenyltetrazolium chloride (TTC), a redox indicator used for testing oil presence, and cerulenin, an inhibitor of fatty acid synthase (FAS), supplemented in screening medium. Among these fungal isolates, nineteen have high lipid content (>20% dry biomass weight) and were affiliated with the genus Mortierella by morphology identification and phylogenetic analysis based on ITS gene sequences. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.023DOI Listing
January 2019
1 Read

A multiplexed, indirect enzyme-linked immunoassay for the detection and differentiation of E. coli from other Enterobacteriaceae and P. aeruginosa from other glucose non-fermenters.

J Microbiol Methods 2019 Jan 29;158:52-58. Epub 2019 Jan 29.

School of Public Health, Division of Infectious Disease and Vaccinology, University of California, Berkeley, CA 94720, USA. Electronic address:

Gram-negative bacteria (GNB) are important causes of community (CA) and hospital (HA)- associated infections. Here we describe the development of an indirect ELISA (I-ELISA), which can be used to detect and differentiate the Enterobacteriaceae Escherichia coli, and glucose non-fermenter Pseudomonas aeruginosa from other GNB species. The I-ELISA utilizes six antibodies for bacterial speciation, which were grouped according to their bacterial targets; Enterobacteriaceae (SL-EntA and CH1810 mAb), Escherichia coli (SL-EcA and 6103-46 mAb), Pseudomonas aeruginosa (SL-PaA and SL-PaB). Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.014DOI Listing
January 2019

Performance evaluation of the βLACTA™ Test for rapid detection of ceftazidime resistance in Pseudomonas aeruginosa isolates from cystic fibrosis patients.

J Microbiol Methods 2019 Jan 29;158:21-24. Epub 2019 Jan 29.

Service de Microbiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France; INSERM UMRS 1138, Centre de Recherche des Cordeliers, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, Centre de Recherche des Cordeliers, Paris, France. Electronic address:

The chromogenic βLACTA™ test was evaluated to detect ceftazidime resistance in P. aeruginosa isolates from patients with cystic fibrosis. Best results were obtained after one hour of incubation with low sensitivity (64. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.019DOI Listing
January 2019
1 Read

Diagnostic accuracy of loop-mediated isothermal amplification assay for extra-pulmonary tuberculosis in Indian population.

J Microbiol Methods 2019 Jan 28;158:59-65. Epub 2019 Jan 28.

Department of Paediatrics, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India.

Background: Confirmatory diagnosis of extra-pulmonary tuberculosis remains a true challenge owing to difficulty in procuring appropriate specimen, inefficient laboratory methods and paucibacillary nature of infection. These obstructions become all the very difficult in pediatric EPTB cases, due to non-specific clinical signs and symptoms, low sensitivity of smear microscopy and culture, lack of awareness among clinicians, etc. AIM OF THE STUDY: The present study aimed to evaluate the diagnostic accuracy of rapid and cost-effective loop-mediated isothermal amplification (LAMP) assay for EPTB diagnosis in children. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01677012183087
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http://dx.doi.org/10.1016/j.mimet.2019.01.016DOI Listing
January 2019
5 Reads

A rapid throughput assay for screening (R)-2-(4-hydroxyphenoxy)propionic acid producing microbes.

J Microbiol Methods 2019 Jan 29;158:44-51. Epub 2019 Jan 29.

Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China; Engineering Research Center of Bioconversion, Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, China.

(R)-2-(4-hydroxyphenoxy)propionic acid ((R)-HPOPA) is an important intermediate for the synthesis of optically pure aryloxyphenoxypropionic acid herbicides. Regioselective hydroxylation of (R)-2-phenoxypropionic acid ((R)-POPA) by microbes is one of the most useful methods for the industrial production of (R)-HPOPA. In this study, we designed and optimized a rapid throughput assay for screening (R)-HPOPA producing bacterial/fungal strains which can regioselectively hydroxylate (R)-POPA. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.015DOI Listing
January 2019

Sensitive and rapid visual detection of Salmonella Typhimurium in milk based on recombinase polymerase amplification with lateral flow dipsticks.

J Microbiol Methods 2019 Jan 29;158:25-32. Epub 2019 Jan 29.

School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China.

Salmonella Typhimurium (S. Typhimurium) can cause serious foodborne diseases. In this study, an assay combining recombinase polymerase amplification (RPA) with lateral flow dipsticks (LFD) was developed to detect S. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.018DOI Listing
January 2019
1 Read

Molecular characterization of intact cell-derived and cell-free bacterial DNA from carious dentine samples.

J Microbiol Methods 2019 Jan 23;158:33-43. Epub 2019 Jan 23.

Department of Cariology, Endodontology and Periodontology, University of Leipzig, Liebigstr. 12, 04103 Leipzig, Germany.

Microbial analyzes of carious dentine samples, especially in terms of interventions, represent a challenge due to difficulties in carious dentine sampling particularly with small bacterial DNA contents. Therefore, information about the quantitative reduction of bacterial DNA as well as microbial shifts and differences in diversity correlating with treatment interventions are scarce. In this study, carious dentine samples were collected in a first step in the course of a selective caries excavation at two different deep dentine caries lesions in three patients. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.012DOI Listing
January 2019
2 Reads

Rapid detection of Lactobacillus crispatus and Lactobacillus iners in vaginal specimens by loop-mediated isothermal amplification.

J Microbiol Methods 2019 Jan 22;158:18-20. Epub 2019 Jan 22.

Department of Microbiology, Meiji Pharmaceutical University, 2-522-1, Noshio, Kiyose, Tokyo 204-8588, Japan. Electronic address:

A rapid detection method for Lactobacillus crispatus and Lactobacillus iners, which are important for maintaining a healthy vaginal environment, was developed using loop-mediated isothermal amplification (LAMP). The LAMP assay had a lower limit of detection of 10 fg DNA and could detect both species within 45 min. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.011DOI Listing
January 2019

Effects of sample preservation on marine microbial diversity analysis.

J Microbiol Methods 2019 Jan 21;158:6-13. Epub 2019 Jan 21.

Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States. Electronic address:

Three replicate seawater samples were collected on three different days, filtered immediately and preserved with one of two guanidinium thiocyanate-based preservatives (DNAzol™ or RNA Lysis Buffer™ plus β-mercaptoethanol (RLA+)) and were kept frozen while being shipped to a lab. In parallel, a carboy of seawater was collected on each of the three days and maintained at ambient temperature while being shipped to a lab. Upon receipt the samples were filtered and treated in the same manner as for immediate preservation. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.006DOI Listing
January 2019

HPLC quantitation of aflatoxin B from fungal mycelium culture.

J Microbiol Methods 2019 Jan 22;158:14-17. Epub 2019 Jan 22.

Center for Integrated Fungal Research, Program of Genetics, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA. Electronic address:

Aflatoxins are mycotoxins that contaminate agricultural products when infected by toxigenic Aspergillus flavus. Methods for quantifying aflatoxin from culture using chromatography are available but are not optimized for population studies. We provide details of a method for preparation and quantitation of aflatoxin B from fungal cultures that satisfy those needs. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.008DOI Listing
January 2019

Development of a rapid RNA extraction procedure from urediniospores of the leaf rust fungus, Puccinia triticina.

J Microbiol Methods 2019 Jan 22;158:1-5. Epub 2019 Jan 22.

Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India. Electronic address:

Obtaining high quality RNA in good quantities is often a requirement for plant-pathogen interaction studies, so it becomes very essential that a highly efficient method should be deployed to isolate RNA from minute quantities of fungal spores. The methods available to date, either require a high quantity of spores or the use of expensive chemicals. The protocol discussed here for RNA isolation from Puccinia triticina pathotype 77-5 urediniospores utilizes TRI Reagent as extraction buffer that is widely used for RNA isolation from plant tissues. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.010DOI Listing
January 2019
2.026 Impact Factor

Assessment of white rot fungus mediated hardwood degradation by FTIR spectroscopy and multivariate analysis.

J Microbiol Methods 2019 Feb 16;157:123-130. Epub 2019 Jan 16.

Department of Microbiology, N. V. Patel College of Pure and Applied Sciences, Vallabh Vidyanagar, Anand 388 120, Gujarat, India. Electronic address:

Evaluating the biomass degradation using fast, validate and sensitive techniques for exploratory purposes of biofuel production has been developed since last decade. Thus, we assessed the degradation of two Indian hardwoods using FTIR and chemometric approaches. Two white rot fungi, namely Pseudolagarobasidium acaciicola AGST3 and Tricholoma giganteum AGDR1, were selected among twenty-one fungal isolates for higher hardwood degradation. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.007DOI Listing
February 2019

Development and evaluation of a novel Campylobacter spp. enrichment medium.

J Microbiol Methods 2019 Feb 11;157:117-122. Epub 2019 Jan 11.

Pamukkale University, Technology Faculty, Denizli, Turkey.

Although rapid detection kits continue to be developed and used, the classical culture method is still accepted as a gold standard. Therefore accelerating the classical culture methods safely is important for the detection of Campylobacter. The aim of this study is to design and compare a novel developed medium with other confirmed media in naturally and experimentally contaminated food matrices. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.004DOI Listing
February 2019

Evaluation of the FilmArray™ Meningitis/Encephalitis panel with focus on bacteria and Cryptococcus spp.

J Microbiol Methods 2019 Feb 10;157:113-116. Epub 2019 Jan 10.

Department of Laboratory Medicine, Clinical Microbiology, University Hospital, Örebro SE-701 85, Sweden; Department of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro SE-701 82, Sweden. Electronic address:

Purpose: Molecular methods provide fast and accurate detection of both bacteria and viruses in the cerebrospinal fluid (CSF) causing infection in the central nervous system (CNS). In the present study we evaluated the bacterial detection performance of the fully automated FilmArray™ Meningitis/Encephalitis (ME) panel (bioMérieux) by comparing it with culture and multiplexed in-house PCR.

Methods: Three sample types were analysed; Contrived samples with known bacterial/fungal concentration (n = 29), clinical samples from patients with verified cause of CNS infection (n = 17) and external quality assessment (EQA) samples (n = 11). Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.003DOI Listing
February 2019

Prevention of EHEC infection by chitosan nano-structure coupled with synthetic recombinant antigen.

J Microbiol Methods 2019 Feb 8;157:100-107. Epub 2019 Jan 8.

Department of agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran. Electronic address:

One of highly effective methods for prevention and control of Entrohemorragic Esherichia coli (EHEC) infections is to use vaccination against extremely immunogenic part of attachment factors. In this study rEIT (EspA, Intimin, Tir) was produced in bacteria and then encapsulated with chitosan nanoparticle as a candidate nanovaccine. A chimeric trivalent recombinant protein which was previously found to provide reasonable immunogenicity against E. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.002DOI Listing
February 2019
2 Reads
2.026 Impact Factor

Comparison of Neisseria gonorrhoeae minimum inhibitory concentrations obtained using agar dilution versus microbroth dilution methods.

J Microbiol Methods 2019 Feb 7;157:93-99. Epub 2019 Jan 7.

AMRI, 1001 Main Street, Suite 7, Buffalo, NY 14203, USA. Electronic address:

With increasing antibiotic resistance observed amongst clinical isolates of Neisseria gonorrhoeae, the second most prevalent sexually transmitted bacterial disease in the United States, there is still a need for antimicrobial susceptibility testing (AST). The current method recommended by the Clinical and Laboratory Standards Institute is agar dilution. In this study, we show that a commercially available version of Fastidious Broth is capable of supporting N. Read More

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http://dx.doi.org/10.1016/j.mimet.2019.01.001DOI Listing
February 2019

From days to hours: Can MALDI-TOF MS system replace both conventional and molecular typing methods with new cut off level for Vancomycin Resistant Enterococcus faecium.

J Microbiol Methods 2018 Dec 31. Epub 2018 Dec 31.

Department of Medical Microbiology, Yuzuncu Yil University School of Medicine, Ankara, Turkey.

Vancomycin-Resistant E. faecium (VRE) strains from clinical specimens were identified by conventional methods before. Following the phenotype-based identification, all strains were also identified using both BD Phoenix and VITEK MS bioMérieux System. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.015DOI Listing
December 2018

Technical and economic efficiency of methods for extracting genomic DNA from Meloidogyne javanica.

J Microbiol Methods 2019 Feb 26;157:108-112. Epub 2018 Dec 26.

Departamento de Entomologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa 36570-900, Minas Gerais, Brazil.

Plant parasitic nematodes reduce the production of agricultural crops. Species diagnosis is essential to predict losses, determine economic damage levels and develop integrated pest management programs. DNA extraction techniques need to be improved for precise and rapid molecular diagnosis of nematodes. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.022DOI Listing
February 2019

Targeting discriminatory SNPs in Salmonella enterica serovar Heidelberg genomes using RNase H2-dependent PCR.

J Microbiol Methods 2019 Feb 25;157:81-87. Epub 2018 Dec 25.

National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada. Electronic address:

We report a novel RNase H2-dependent PCR (rhPCR) genotyping assay for a small number of discriminatory single-nucleotide polymorphisms (SNPs) that identify lineages and sub-lineages of the highly clonal pathogen Salmonella Heidelberg (SH). Standard PCR primers targeting numerous SNP locations were initially designed in silico, modified to be RNase H2-compatible, and then optimized by laboratory testing. Optimization often required repeated cycling through variations in primer design, assay conditions, reagent concentrations and selection of alternative SNP targets. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.021DOI Listing
February 2019
1 Read

Selenite enrichment broth to improve the sensitivity in molecular diagnostics of Salmonella.

J Microbiol Methods 2019 Feb 23;157:59-64. Epub 2018 Dec 23.

Laboratory for Medical Microbiology and Public Health, LabMicTA, Hengelo, The Netherlands; Medical Microbiology VieCuri, Venlo, The Netherlands; Laurentius Hospital, Department of Medical Microbiology, Roermond, The Netherlands. Electronic address:

Selenite enrichment broth (SEB) is used to optimize the recovery of Salmonella enterica subspecies enterica from stool samples. Compared to a direct culture approach, it enhances culture yield by reducing growth of faecal coliforms and faecal streptococci. Over the course of seven years from 2000 to 2017, 47,235 faecal samples were tested with a Salmonella PCR. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.018DOI Listing
February 2019

Comparative performance of TCBS and TSA for the enumeration of trh+ Vibrio parahaemolyticus by direct colony hybridization.

J Microbiol Methods 2019 Feb 19;157:37-42. Epub 2018 Dec 19.

Division of Infectious Diseases, Nitte University Centre for Science Education and Research, NITTE (Deemed to be University), Paneer Campus, Deralakatte, Mangaluru 575018, India. Electronic address:

Vibrio parahaemolyticus is one of the important foodborne pathogens is of public health concern due to the emergence of pandemic strains causing disease outbreaks worldwide. We evaluated the DNA based colony hybridization technique for the detection and enumeration of total and pathogenic V. parahaemolyticus from the bivalve shellfish, clam using non-radioactive, enzyme-labeled probe targeting the tlh and trh genes, respectively. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.020DOI Listing
February 2019

Quantification of Legionella DNA certified reference material by digital droplet PCR.

J Microbiol Methods 2019 Feb 19;157:50-53. Epub 2018 Dec 19.

Bio-Rad, Food Science Division, Marnes-la-Coquette, France.

A value was assigned in 2009 to the Legionella DNA Certified Reference Material, and the stability study conducted using quantitative PCR found a low level of degradation. Herein, the Digital Droplet PCR method for Legionella DNA was qualified and used to provide absolute quantification of the CRM. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01677012183086
Publisher Site
http://dx.doi.org/10.1016/j.mimet.2018.12.019DOI Listing
February 2019
8 Reads

A comparison of flocked nylon swabs and non-flocked rayon swabs for detection of respiratory bacteria in nasopharyngeal carriage in Australian Indigenous children.

J Microbiol Methods 2019 Feb 19;157:47-49. Epub 2018 Dec 19.

Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

This study compared flocked (nylon) swabs and (non-flocked) rayon swabs for the detection of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis in nasopharyngeal samples from 20 enrolled Indigenous children under the age of 6 years living in remote Australian Aboriginal communities, and determined which swab the child or parent perceived to be more comfortable. There was no evidence of a significant difference between flocked and rayon swabs in the recovery of common respiratory bacteria. Rayon swabs detected presence of S. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.013DOI Listing
February 2019

Real-time recombinase polymerase amplification assay for the rapid and sensitive detection of Campylobacter jejuni in food samples.

J Microbiol Methods 2019 Feb 18;157:31-36. Epub 2018 Dec 18.

Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, No. 318 Hepingxilu Road, Shijiazhuang, Hebei Province 050051, People's Republic of China; Hebei Academy of Inspection and Quarantine Science and Technology, No. 318 Hepingxilu Road, Shijiazhuang, Hebei Province 050051, People's Republic of China. Electronic address:

Campylobacter jejuni (C. jejuni), a foodborne pathogen, is a major contributor to human bacterial gastroenteritis worldwide and detrimental to public health. It is crucial for initiating appropriate outbreak control strategies to rapidly detect C. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.017DOI Listing
February 2019

A simple and reliable method for the quantitative evaluation of anthocyanin adsorption by wine yeasts.

J Microbiol Methods 2019 Feb 18;157:88-92. Epub 2018 Dec 18.

Institute of Biotechnology, University of Caxias do Sul, R. Francisco G. Vargas, 1130, 95070-560 Caxias do Sul, RS, Brazil.

Yeast pigments adsorption can modify wine color intensity and is considered an important trait in wine yeasts. The existing methods for the evaluation of yeast adsorption are laborious, time consuming, need confirmation experiments, or are difficult to apply for a large number of strains generated in breeding programs. In this study, a new test is proposed to measure yeast pigments adsorption and wine color in a single experiment. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.016DOI Listing
February 2019

Development of a multiplex PCR assay for the detection of major virulence genes in Vibrio cholerae including non-O1 and non-O139 serogroups.

J Microbiol Methods 2019 Feb 18;157:54-58. Epub 2018 Dec 18.

International Prevention of Epidemics, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan. Electronic address:

Vibrio cholerae strains producing cholera toxin (CT) and toxin co-regulated pilus (TCP) and belonging to O1 and O139 serogroups are responsible for cholera. However, non-CT producing V. cholerae from non-O1/non-O139 serogroups have been increasingly isolated from diarrheal stools and extra-intestinal infections. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.012DOI Listing
February 2019
1 Read
2.026 Impact Factor

A metagenomic analysis of the pre-enrichment step for the isolation of Salmonella spp. from pig feces.

J Microbiol Methods 2019 Feb 18;157:43-46. Epub 2018 Dec 18.

Chaire de recherche en salubrité des viandes, Faculté de médecine vétérinaire, Département de pathologie et microbiologie, Université de Montréal, 3200 rue Sicotte, Saint-Hyacinthe, QC, J2S 7C6, Canada.

The bacterial short pre-enrichment culture step is important for the proper detection and isolation of Salmonella spp. from pig feces. Using metagenomics, we showed that pre-enrichment of Salmonella was favored not only by inhibiting the growth of competing bacteria but also by increasing its fitness. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.014DOI Listing
February 2019

Real-time PCR quantification of Fusarium avenaceum in soil and seeds.

J Microbiol Methods 2019 Feb 17;157:21-30. Epub 2018 Dec 17.

USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, USA. Electronic address:

The pathogenic fungus Fusarium avenaceum infects a broad range of plant hosts across the globe. While primarily soilborne, F. avenaceum can colonize all plant tissues, including buds, seeds, fruits, stems, crowns, and roots, resulting in significant crop yield reductions and economic losses for growers. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01677012183085
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http://dx.doi.org/10.1016/j.mimet.2018.12.009DOI Listing
February 2019
8 Reads

Direct antimicrobial susceptibility tests of bacteria and yeasts from positive blood cultures by using serum separator gel tubes and MALDI-TOF MS.

J Microbiol Methods 2019 Feb 15;157:16-20. Epub 2018 Dec 15.

Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Zhejiang, China. Electronic address:

Early and appropriate antimicrobial treatment can effectively reduce the mortality rate caused by bloodstream infections (BSIs) and is critical for favorable patient outcomes. In general, >90% of positive blood cultures will show positive results within 48 h after incubation in the BACTECTM FX system. However, an additional 6-8 h are required to obtain clones of the bacterium and another 10-24 h to obtain antimicrobial susceptibility test (AST) results. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01677012183057
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http://dx.doi.org/10.1016/j.mimet.2018.12.011DOI Listing
February 2019
4 Reads

High fidelity recovery of airborne microbial genetic materials by direct condensation capture into genomic preservatives.

J Microbiol Methods 2019 Feb 14;157:1-3. Epub 2018 Dec 14.

University of Colorado, Environmental Engineering Program, Boulder, CO, USA. Electronic address:

A condensation growth tube was adapted to capture bacterial bioaerosols directly into genomic preservatives. As judged by quantitative PCR and direct microscopy, bioaerosol condensation capture conserves airborne microbes' genomes as they exist in the atmospheric environment. This method circumvents the collection stresses bioaerosols experience on air filters, impactors and impingers. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.010DOI Listing
February 2019

Biogenic nanomaterials: Synthesis, characterization, growth mechanism, and biomedical applications.

J Microbiol Methods 2019 Feb 13;157:65-80. Epub 2018 Dec 13.

School of Pharmacy, Sungkyunkwan University, 2066 Seoburo, Jangan-gu, Suwon, Gyeonggido 16419, Republic of Korea. Electronic address:

The biosynthesis of nanomaterials is a huge and intensifying field of research due to their application in various areas, in particular the biomedical and pharmaceutical fields. In this review, we focused on the biosynthesis of both metallic and semiconductor nanomaterials and their application in biomedicine and pharmaceutics. In order to meet an exponentially increasing need for nanostructured materials, the biological route for the synthesis of nanomaterials will have to be explored, offering advantages over chemical and physical methods as a simpler, more cost effective, and environmentally friendly method, and for which there is no need to use high pressure and temperatures or toxic chemicals. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01677012183038
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http://dx.doi.org/10.1016/j.mimet.2018.12.008DOI Listing
February 2019
14 Reads

Is sonication of antibiotic-loaded cement spacers useful in two-stage revision of prosthetic joint infection?

J Microbiol Methods 2019 Jan 12;156:81-84. Epub 2018 Dec 12.

IRCSS Istituto Ortopedico Rizzoli, Bologna, Italy.

Background: In a two-stage exchange protocol for prosthetic joint infection (PJI), bacteria surviving over the antibiotic-loaded cement spacers may cause the persistence of infection with renewed clinical symptoms following the surgery. Culture after sonication of removed prosthesis is more sensitive than conventional periprosthetic tissue culture for the microbiological diagnosis of PJI. The aim of this study was to assess whether sonication of the spacer at the time of the second-stage procedure may improve the diagnosis of persistent PJI. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.006DOI Listing
January 2019
1 Read

Real-time dynamic analysis with low-field nuclear magnetic resonance of residual oil and sophorolipids concentrations in the fermentation process of Starmerella bombicola.

J Microbiol Methods 2019 Feb 12;157:9-15. Epub 2018 Dec 12.

State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China. Electronic address:

The yeast Starmerella bombicola is known to produce sophorolipids (SLs) by fermentation method. In the fermentative production of SLs, at least three phases i.e. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.007DOI Listing
February 2019
1 Read
2.026 Impact Factor

A performance evaluation of an immuno-latex chromatography card for the rapid detection of Candida spp.

J Microbiol Methods 2019 Feb 10;157:4-8. Epub 2018 Dec 10.

Department of Clinical Laboratory, the First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, China.

This report evaluates the performance and species specificity of an immuno-latex chromatography card (ICC) for rapid detection of Candida spp. Double-manipulator single-blind Gram staining smear examination (GSSE) and ICC were used to analyze 354 vaginal discharge specimens (VDS) (including 98 tested as positive by GSSE) from women with suspected candidal vaginitis, simulated specimens with a concentration gradient, and vaginitis causing organism suspensions (0.9% NaCl) of 22 species from nine genera. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01677012183045
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http://dx.doi.org/10.1016/j.mimet.2018.12.005DOI Listing
February 2019
3 Reads

Optimization of viability qPCR for selective detection of membrane-intact Legionella pneumophila.

J Microbiol Methods 2019 Jan 5;156:68-76. Epub 2018 Dec 5.

IWW Water Centre, Applied Microbiology, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany. Electronic address:

Although a number of viability qPCR assays have been reported to selectively detect signals from membrane-intact Legionella pneumophila, the efficient suppression of amplification of DNA from dead membrane-compromised bacteria remains an ongoing challenge. This research aimed at establishing a new oligonucleotide combination that allows for a better exclusion of dead Legionella pneumophila on basis of the mip gene. Propidium monoazide (PMA) was chosen as viability dye. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.003DOI Listing
January 2019

Multiplex real-time PCR assays to detect Stenotrophomonas maltophilia carrying sul1, sul2, and sul3 genes.

J Microbiol Methods 2019 Jan 5;156:52-59. Epub 2018 Dec 5.

Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China. Electronic address:

Nosocomial infections caused by Stenotrophomonas maltophilia resistant to SXT are increasingly reported worldwide. In this study, a novel melting-curve based multiplex real-time PCR assay for the simultaneous detection of the ssrA and sul1, sul2 and sul3 genes was first established. The assays were performed on a Roche LightCycler® 480 II system. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.002DOI Listing
January 2019

Optimisation of a propidium monoazide based method to determine the viability of microbes in faecal slurries for transplantation.

J Microbiol Methods 2019 Jan 4;156:40-45. Epub 2018 Dec 4.

The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.

The efficacy of faecal microbiota transplantation (FMT) as a therapeutic intervention may depend on the viability of the microorganisms in faecal slurries (FS) prepared from donor stool. However, determining the viability of these organisms is challenging. Most microorganisms in stool are refractory to culture using standard techniques, and culture-independent PCR-based methods derive signal from both viable and non-viable cells. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.001DOI Listing
January 2019

Improvement of electroporation-mediated transformation efficiency for a Bifidobacterium strain to a reproducibly high level.

J Microbiol Methods 2018 Dec 4. Epub 2018 Dec 4.

Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Republic of Korea; Research Center, BIFIDO Co., Ltd, Hongcheon 205-804, Republic of Korea. Electronic address:

Bifidobacteria are representative probiotics which are defined as live microorganisms that confer a health benefit on the host. Because of their safety and healthfulness when applied to humans, bifidobacteria are suitable as genetically engineered bacteria for applications to benefit human physiology and pathology. However, molecular biological studies of bifidobacteria have been limited due to insufficient genetic tools including effective transformation methods. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.11.019DOI Listing
December 2018

Validation of a novel molecular diagnostic panel for pediatric musculoskeletal infections: Integration of the Cepheid Xpert MRSA/SA SSTI and laboratory-developed real-time PCR assays for clindamycin resistance genes and Kingella kingae detection.

J Microbiol Methods 2019 Jan 7;156:60-67. Epub 2018 Dec 7.

Division of Pediatric Infectious Diseases, Children's Hospital Colorado, 13123 East 16th Avenue, Aurora, CO 80045, USA. Electronic address:

Background: Pathogen detection in pediatric patients with musculoskeletal infections relies on conventional bacterial culture, which is slow and can delay antimicrobial optimization. The ability to rapidly identify causative agents and antimicrobial resistance genes in these infections may improve clinical care.

Methods: Convenience specimens from bone and joint samples submitted for culture to Children's Hospital Colorado (CHCO) from June 2012 to October 2016 were evaluated using a "Musculoskeletal Diagnostic Panel" (MDP) consisting of the Xpert MRSA/SA SSTI real-time PCR (qPCR, Cepheid) and laboratory-developed qPCRs for Kingella kingae detection and erm genes A, B, and C which confer clindamycin resistance. Read More

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http://dx.doi.org/10.1016/j.mimet.2018.12.004DOI Listing
January 2019
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Evaluation of the automated BD Phoenix CPO Detect panel in combination with the β-CARBA assay for detection and classification of carbapenemase-producing Enterobacterales.

J Microbiol Methods 2019 Jan 3;156:29-33. Epub 2018 Dec 3.

Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, Franz-Josef-Strauß-Allee 11, D-93053 Regensburg, Germany.

Recently, the CPO Detect panel for the detection of carbapenemase-producing, Gram-negative bacteria was introduced for the Phoenix semi-automated antimicrobial susceptibility testing system. The CPO Detect assay aims to detect carbapenemase activity (P/N test) and to type carbapenemase producers according to the Ambler classification (Ambler test). The P/N test-based detection of carbapenemase producers was 100% sensitive and 55. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01677012183072
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http://dx.doi.org/10.1016/j.mimet.2018.11.024DOI Listing
January 2019
9 Reads

Fluorescence polarization assay: Diagnostic evaluation for porcine brucellosis.

J Microbiol Methods 2019 Jan 3;156:46-51. Epub 2018 Dec 3.

Indian Council Agricultural Research-National Institute of Veterinary Epidemiology and Disease Informatics, Yelahanka, Bengaluru 560064, India. Electronic address:

Brucellosis in pigs, caused by the bacterium Brucella suis, is an important zoonotic infection. In the present study, fluorescence polarization assay (FPA) was standardized and compared with indirect enzyme linked immunosorbent assay (iELISA) and competitive ELISA (cELISA) for diagnosis of porcine brucellosis. Test performances were evaluated using representative panel (n = 100), samples from swine brucellosis outbreak (n = 300), samples from brucellosis suspected animals (n = 291) and sera samples from apparently healthy animals (n = 1121). Read More

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https://linkinghub.elsevier.com/retrieve/pii/S01677012183079
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http://dx.doi.org/10.1016/j.mimet.2018.11.023DOI Listing
January 2019
12 Reads
2.026 Impact Factor