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1. Classification of gases around Pseudomonas aeruginosa and Acinetobacter baumannii by infrared spectroscopy

Author:
Masato Yamamoto; Satoru Arata; Kunihiko Fukuchi; Hidehiko Honda; Hirokazu Kobayashi; Masahiro Inagaki
Source:
Journal of microbiological methods 2022 v.196 pp. 106474
ISSN:
0167-7012
Subject:
Acinetobacter baumannii; Pseudomonas aeruginosa; absorption; air; humans; infrared spectroscopy
Abstract:
... Gas samples were collected from the air surrounding single and mixed laboratory cultures, and preliminary data on human breath samples were also obtained. The infrared spectra of a variety of gasses were measured at high resolution (0.5 cm⁻¹) to obtain information about the infrared absorption bands to be used as indicators. These key bands enable bacterial classification, and the discrimination r ...
DOI:
10.1016/j.mimet.2022.106474

2. Diagnosis of brucellosis disease using data mining: A case study on patients of a hospital in Tehran

Author:
Mohammad Vahid Sebt; Sirous Jafari; Milad Khavaninzadeh; Ali Shavandi
Source:
Journal of microbiological methods 2022 v.199 pp. 106530
ISSN:
0167-7012
Subject:
Bayesian theory; Brucella; algorithms; appetite; arthritis; blood; brucellosis; case studies; data collection; decision making; decision support systems; fever; hospitals; humans; livestock; pathogens; patients; therapeutics; vaccines; zoonoses
Abstract:
... Brucellosis is a common zoonotic infection of humans from livestock. This bacterial infection is acquired from infected animals and their products. The pathogen of this disease is a genus of bacilli called Brucella, and no effective vaccine has been discovered yet for the prevention of human brucellosis. The present study is mainly conducted to diagnose brucellosis accurately and timely, using Dat ...
DOI:
10.1016/j.mimet.2022.106530

3. Machine learning-based typing of Salmonella enterica O-serogroups by the Fourier-Transform Infrared (FTIR) Spectroscopy-based IR Biotyper system

Author:
Miriam Cordovana; Norman Mauder; Olivier Join-Lambert; François Gravey; Simon LeHello; Michel Auzou; Monica Pitti; Simona Zoppi; Michael Buhl; Joerg Steinmann; Hagen Frickmann; Denise Dekker; Yumiko Funashima; Zenzo Nagasawa; József Soki; László Orosz; Alida C. Veloo; Ulrik S. Justesen; Hanne M. Holt; Andrea Liberatore; Simone Ambretti; Stefano Pongolini; Laura Soliani; Andreas Wille; Sandra Rojak; Ralf Matthias Hagen; Jürgen May; A.B. Pranada; Markus Kostrzewa
Source:
Journal of microbiological methods 2022 v.201 pp. 106564
ISSN:
0167-7012
Subject:
Fourier transform infrared spectroscopy; Japan; Salmonella enterica; absorption; agar; automation; computer software; cost effectiveness; human resources; humans; public health; serotypes; support vector machines; Europe
Abstract:
... Salmonella enterica is among the major burdens for public health at global level. Typing of salmonellae below the species level is fundamental for different purposes, but traditional methods are expensive, technically demanding, and time-consuming, and therefore limited to reference centers. Fourier transform infrared (FTIR) spectroscopy is an alternative method for bacterial typing, successfully ...
DOI:
10.1016/j.mimet.2022.106564

4. Microbiome analysis from formalin-fixed paraffin-embedded tissues: Current challenges and future perspectives

Author:
Roberto Cruz-Flores; Jesús Antonio López-Carvallo; Jorge Cáceres-Martínez; Arun K. Dhar
Source:
Journal of microbiological methods 2022 v.196 pp. 106476
ISSN:
0167-7012
Subject:
animal pathology; humans; laser capture microdissection; microbiome; pollution; spatial variation
Abstract:
... Formalin-fixed paraffin-embedded (FFPE) tissues stored in thousands of human and animal pathology laboratories around the globe represent mines of stored genetic information. In recent years, the use of FFPE tissues as a viable source of DNA for diverse genetic studies has attracted attention for interrogating microbiomes from this sample type. These studies have proven that 16S rRNA amplicon sequ ...
DOI:
10.1016/j.mimet.2022.106476

5. Reducing human DNA bias in cystic fibrosis airway specimens for microbiome analysis

Author:
Karolina Klosinska; Emma Reece; Elaine Kenny; Julie Renwick
Source:
Journal of microbiological methods 2022 v.200 pp. 106540
ISSN:
0167-7012
Subject:
biomass; cystic fibrosis; genes; humans; microbiology; microbiome; saponins; species diversity
Abstract:
... Next generation sequencing (NGS) has transformed our understanding of airway microbiology, however there are methodology limitations that require consideration. The presence of high concentrations of human DNA in clinical specimens can significantly impact sequencing of the microbiome, especially in low biomass samples. Here we compared three different methods (0.025% saponin, NEBNext Microbiome D ...
DOI:
10.1016/j.mimet.2022.106540

6. 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

7. An agar-based bioassay for accurate screening of the total antioxidant capacity of lactic acid bacteria cell-free supernatants

Author:
Hasna Hanchi; Khaled Sebei; Walid Mottawea; Imad Al Kasaa; Riadh Hammami
Source:
Journal of microbiological methods 2022 v.195 pp. 106437
ISSN:
0167-7012
Subject:
agar; analysis of variance; antioxidant activity; ascorbic acid; bioassays; color; cost effectiveness; humans; intestines; lactic acid; probiotics
Abstract:
... This study aims to develop a new, simple, and efficient method for estimating the total antioxidant capacity of lactic acid bacteria-cell free supernatant. The bioassay is based on diffusion and reduction of permanganate in agar medium under acidic conditions where the Mn7+ ions are quantitatively oxidized to Mn2+ and shift from an intense purple color to colorless. Hence, the reaction enables fas ...
DOI:
10.1016/j.mimet.2022.106437

8. Assessment of stool collection and storage conditions for in vitro human gut model studies

Author:
Grace A.I. Newland; Glenn R. Gibson; Frances L. Jackson; Anisha Wijeyesekera
Source:
Journal of microbiological methods 2021 v.185 pp. 106230
ISSN:
0167-7012
Subject:
batch fermentation; breast milk; culture media; digestive system; feces; humans; hybridization; ice; intestinal microorganisms; magnetism; oligosaccharides
Abstract:
... The role of the gut microbiota in health and disease is becoming increasingly apparent. Faeces is the most accessible sample to collect from human volunteers for studying the gut microbiota. However, the impact of stool collection and storage conditions on microbial and metabolic profiles have not been fully evaluated. By understanding the effect of different stool collection and storage condition ...
DOI:
10.1016/j.mimet.2021.106230

9. 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

10. CtNorm: Real time PCR cycle of threshold (Ct) normalization algorithm

Author:
Amin Ramezani
Source:
Journal of microbiological methods 2021 v.187 pp. 106267
ISSN:
0167-7012
Subject:
algorithms; genes; humans; quantitative polymerase chain reaction
Abstract:
... In relative quantification with Real Time PCR (qRT-PCR,), accurate analysis requires equal amplification efficiency for both genes (Gene of interest and reference gene) and equal threshold values for all the samples. In this quantification method the expression level in treated samples will be calculated in comparison to the control group. We conducted the present study to design an algorithm for ...
DOI:
10.1016/j.mimet.2021.106267

11. 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

12. 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

13. Identifying septic pollution exposure routes during a waterborne norovirus outbreak - A new application for human-associated microbial source tracking qPCR

Author:
Mia C. Mattioli; Katharine M. Benedict; Jennifer Murphy; Amy Kahler; Kelly E. Kline; Allison Longenberger; Patrick K. Mitchell; Sharon Watkins; Philip Berger; Orin C. Shanks; Catherine E. Barrett; Leslie Barclay; Aron J. Hall; Vincent Hill; Andre Weltman
Source:
Journal of microbiological methods 2021 v.180 pp. 106091
ISSN:
0167-7012
Subject:
Norovirus; bedrock; exposure pathways; genetic markers; groundwater; groundwater contamination; hand washing; humans; hygiene; land evaluation; pollutants; public health; risk; septic systems; Pennsylvania
Abstract:
... In June 2017, the Pennsylvania Department of Health (PADOH) was notified of multiple norovirus outbreaks associated with 179 ill individuals who attended separate events held at an outdoor venue and campground over a month period. Epidemiologic investigations were unable to identify a single exposure route and therefore unable to determine whether there was a persistent contamination source to tar ...
DOI:
10.1016/j.mimet.2020.106091

14. Influence of the expression vector and its elements on recombinant human prolactin synthesis in Escherichia coli; co-directional orientation of replication and transcription is highly critical

Author:
Regina Affonso; Miriam Fussae Suzuki; Geraldo Santana Magalhães; Paolo Bartolini
Source:
Journal of microbiological methods 2021 v.191 pp. 106340
ISSN:
0167-7012
Subject:
Escherichia coli; antibiotic resistance genes; genetic background; genetic vectors; humans; prolactin; protein synthesis
Abstract:
... The aim of the present work was to define a bacterial expression system that is particularly efficient for the synthesis of recombinant human prolactin (hPRL). In previous work, based on experiments that were basically carried out in parallel with the present ones, the synthesis of rec-hPRL by the p1813-hPRL vector in E. coli HB2151 was >500 mg/L, while it was much lower here (2.5–4-fold), in the ...
DOI:
10.1016/j.mimet.2021.106340

15. Simulation of the mucosal environment in the re-construction of the synthetic gut microbial ecosystem

Author:
Humphrey A. Mabwi; Emmanuel Hitayezu; Intan Rizki Mauliasari; Kilaza Samson Mwaikono; Hyo Shin Yoon; Erick V.G. Komba; Cheol-Ho Pan; Kwang Hyun Cha
Source:
Journal of microbiological methods 2021 v.191 pp. 106351
ISSN:
0167-7012
Subject:
Bifidobacterium; Clostridium; Collinsella; Enterococcus; Roseburia; cell movement; digestive system; gels; gene expression; human health; humans; intestinal microorganisms; liquids; metabolism; microbial biomass; microbial communities; microbiome; prediction
Abstract:
... Human gut surface-attached mucosal microbiota plays significant roles in human health and diseases. This study sought to simulate the mucosal environment using mucin-agar gel and synthetic mucosal microbial community in vitro. To select suitable culture media, microbial communities were assembled and cultured in seven different media at 37 °C for 36 h. Among the seven media, Bryant & Burkey (BB) a ...
DOI:
10.1016/j.mimet.2021.106351

16. 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

17. 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

18. Antibacterial-coated silk surgical sutures by ex situ deposition of silver nanoparticles synthesized with Eucalyptus camaldulensis eradicates infections

Author:
Dwi Marlina Syukri; Ozioma Forstinus Nwabor; Sudarshan Singh; Julalak Chorachoo Ontong; Suttiwan Wunnoo; Supakit Paosen; Soraiham Munah; Supayang Piyawan Voravuthikunchai
Source:
Journal of microbiological methods 2020 v.174 pp. 105955
ISSN:
0167-7012
Subject:
Acinetobacter baumannii; Escherichia coli; Eucalyptus camaldulensis; Klebsiella pneumoniae; Pseudomonas aeruginosa; Staphylococcus aureus; antibacterial properties; biosynthesis; cell viability; hospitals; humans; keratinocytes; microbial contamination; nanosilver; pathogens; silk; surface roughness
Abstract:
... Surgical site infection arising from microbial contamination of surgical wounds is a major cause of surgical complications and prolong hospital stay. In this study, silver nanoparticles (AgNPs) biosynthesized using Eucalyptus camaldulensis extract were deposited on silk surgical sutures by ex situ method. Adherence of AgNPs to the surface of sutures was observed, with significantly reduced surface ...
DOI:
10.1016/j.mimet.2020.105955

19. Automatic Bacillus anthracis bacteria detection and segmentation in microscopic images using UNet++

Author:
Fatemeh Hoorali; Hossein Khosravi; Bagher Moradi
Source:
Journal of microbiological methods 2020 v.177 pp. 106056
ISSN:
0167-7012
Subject:
Bacillus anthracis; anthrax; artificial intelligence; automation; data collection; humans; patch test
Abstract:
... Anthrax is one of the important diseases in humans and animals, caused by the gram-positive bacteria spores called Bacillus anthracis. The disease is still one of the health problems of developing countries. Due to fatigue and decreased visual acuity, microscopic diagnosis of diseases by humans may not be of good quality. In this paper, for the first time, a system for automatic and rapid diagnosi ...
DOI:
10.1016/j.mimet.2020.106056

20. Comparative evaluation of nucleic acid stabilizing reagents for RNA- and DNA-based Leishmania detection in blood as proxy for visceral burdens

Author:
Eline Eberhardt; Rik Hendrickx; Magali Van den Kerkhof; Severine Monnerat; Fabiana Alves; Sarah Hendrickx; Louis Maes; Guy Caljon
Source:
Journal of microbiological methods 2020 v.173 pp. 105935
ISSN:
0167-7012
Subject:
5' untranslated regions; Leishmania; Mesocricetus auratus; animal models; blood groups; clinical trials; erythrocytes; hamsters; hemoparasites; humans; immunosuppression; kinetoplast DNA; patients; pyrazoles; quantitative polymerase chain reaction; stabilizers; storage temperature; visceral leishmaniasis
Abstract:
... Molecular detection techniques using peripheral blood are preferred over invasive tissue aspiration for the diagnosis and post-treatment follow-up of visceral leishmaniasis (VL) patients. This study aims to identify suitable stabilizing reagents to prevent DNA and RNA degradation during storage and transport to specialized laboratories where molecular diagnosis is performed.The stabilizing capacit ...
DOI:
10.1016/j.mimet.2020.105935

21. 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

22. Evaluation of pooled human urine and synthetic alternatives in a dynamic bladder infection in vitro model simulating oral fosfomycin therapy

Author:
Iain J. Abbott; Elke van Gorp; Rixt A. Wijma; Joseph Meletiadis; Johan W. Mouton; Anton Y. Peleg
Source:
Journal of microbiological methods 2020 v.171 pp. 105861
ISSN:
0167-7012
Subject:
Enterobacteriaceae; agar; bacterial growth; bladder; culture media; dynamic testing; fosfomycin; glucose 6-phosphate; humans; minimum inhibitory concentration; simulation models; therapeutics; urinary tract diseases; urine
Abstract:
... The impact of the bladder environment on fosfomycin activity and treatment response is uncertain. Standard laboratory media does not reflect the biomatrix of urine, where limited nutritional factors are important for growth and antimicrobial kill rates. We compared fosfomycin activity against Enterobacteriaceae in laboratory media, human urine and synthetic alternatives. Sixteen clinical isolates ...
DOI:
10.1016/j.mimet.2020.105861

23. Identification new potential multidrug resistance proteins of Saccharomyces cerevisiae

Author:
V.M. Grechko; D.E. Podolsky; V.T. Cheshchevik
Source:
Journal of microbiological methods 2020 v.176 pp. 106029
ISSN:
0167-7012
Subject:
P-glycoproteins; Saccharomyces cerevisiae; cell membranes; cluster analysis; genes; humans; hydrophobicity; multiple drug resistance; phenotype; phylogeny; substrate specificity; xenobiotics; yeasts
Abstract:
... ABC (ATP-binding cassette) proteins can transport metabolic molecules and removes metabolic products and xenobiotics from the cell. The important problem is to study activity and search inhibitors of ABC proteins. There is a problem that ABC-proteins can transport hydrophobic drugs across the cell membrane due to their high substrate specificity. According to published data, Saccharomyces cerevisi ...
DOI:
10.1016/j.mimet.2020.106029

24. Is it possible to shorten serum bactericidal testing?

Author:
Paterova Pavla; Radocha Jakub; Buchta Vladimir; Zavrelova Alzbeta; Malakova Jana; Zak Pavel; Zemlickova Helena
Source:
Journal of microbiological methods 2020 v.168 pp. 105775
ISSN:
0167-7012
Subject:
Escherichia coli; antibiotics; blood serum; colorimetry; humans; patients; therapeutics; turbidity; wavelengths
Abstract:
... Serum bactericidal test represents an alternative possibility for optimization of antibiotic treatment. The paper aimed to confirm non-inferiority of bactericidal testing using the broth dilution method according to the CLSI method (M21A) in comparison with turbidimetric and colorimetric modifications. We tested human blood sera (n = 76) of ten hematological patients, their blood was withdrawn pri ...
DOI:
10.1016/j.mimet.2019.105775

25. Optimization of 16S rRNA gene analysis for use in the diagnostic clinical microbiology service

Author:
Dan Sune; Helene Rydberg; Åsa Nilsdotter Augustinsson; Lena Serrander; Malin Bergman Jungeström
Source:
Journal of microbiological methods 2020 v.170 pp. 105854
ISSN:
0167-7012
Subject:
DNA; bacteria; false positive results; genes; humans; oligodeoxyribonucleotides; patients; polymerase chain reaction; prospective studies; ribosomal RNA; sequence analysis; tissue culture
Abstract:
... Broad-range amplification and sequencing of the 16S rRNA gene, directly from clinical samples, is a method that potentially allows detection of any cultivable or non-cultivable bacteria. However, the method is prone to false positive results due to PCR contamination. Another concern is the human DNA abundance compared to bacterial DNA in samples from sterile sites. Those factors may decrease the s ...
DOI:
10.1016/j.mimet.2020.105854

26. Optimization of electrotransformation (ETF) conditions in lactic acid bacteria (LAB)

Author:
Chao Wang; Yanhua Cui; Xiaojun Qu
Source:
Journal of microbiological methods 2020 v.174 pp. 105944
ISSN:
0167-7012
Subject:
animal husbandry; cell walls; electroporation; food industry; genes; genetic conjugation; heat treatment; humans; lactic acid; medicine; metabolome; plasmids
Abstract:
... Lactic acid bacteria (LAB) play important roles in the food industry, animal husbandry and medicine which are closely related to human life. Modern gene engineering technology is the major means to reveal gene functions, study metabolic pathways and metabolomes of strains and improve the properties of strains. However, up to now, the molecular technologies that can be applied to LAB are still very ...
DOI:
10.1016/j.mimet.2020.105944

27. Ruggedness testing of liquid chromatography-tandem mass spectrometry system components using microbiome-relevant methods and matrices

Author:
Thomas D. Horvath; Sigmund J. Haidacher; Numan Oezguen; Kathleen M. Hoch; Jennifer M. Auchtung; Anthony M. Haag
Source:
Journal of microbiological methods 2020 v.177 pp. 106020
ISSN:
0167-7012
Subject:
bile; bile acids; calibration; computer software; culture media; feces; humans; liquid chromatography; metabolism; metabolomics; microbiome; tandem mass spectrometry
Abstract:
... Recently, an opportunity to perform a broad ruggedness assessment of our liquid chromatography-tandem mass spectrometry (LC-MS/MS) system presented itself during the analytical planning phase of a large-scale human fecal microbiome study. The specific aim of this project was to study the microbial-mediated metabolism of a targeted set of bile acids/salts by mixed bacterial communities cultured fro ...
DOI:
10.1016/j.mimet.2020.106020

28. Sequence-enabled community-based microbial source tracking in surface waters using machine learning classification: A review

Author:
Prince P. Mathai; Christopher Staley; Michael J. Sadowsky
Source:
Journal of microbiological methods 2020 v.177 pp. 106050
ISSN:
0167-7012
Subject:
Bayesian theory; DNA; humans; microbial communities
Abstract:
... The development of Microbial Source Tracking (MST) technologies was borne out of necessity. This was largely due to the: 1) inadequacies of the fecal indicator bacterial paradigm, 2) fact that many fecal bacteria can survive and often grow in the environment, 3) inability of traditional microbiological methods to attribute source, 4) lack of correspondence between numbers of fecal indicator bacter ...
DOI:
10.1016/j.mimet.2020.106050

29. Utilization of multiple microbial tools to evaluate efficacy of restoration strategies to improve recreational water quality at a Lake Michigan Beach (Racine, WI)

Author:
Julie Kinzelman; M.N. Byappanahalli; M.B. Nevers; D. Shively; S. Kurdas; C. Nakatsu
Source:
Journal of microbiological methods 2020 v.178 pp. 106049
ISSN:
0167-7012
Subject:
Escherichia coli; bacterial communities; coastal water; constructed wetlands; humans; hydrometeorology; lakes; microbial contamination; pollution; public health; rain; rivers; shorelines; stormwater; water quality; wind; Lake Michigan; Wisconsin
Abstract:
... Hydro-meteorological conditions facilitate transport of fecal indicator bacteria (FIB) to the nearshore environment, affecting recreational water quality. North Beach (Racine, Wisconsin, United States), is an exemplar public beach site along Lake Michigan, where precipitation-mediated surface runoff, wave encroachment, stormwater and tributary outflow were demonstrated to contribute to beach advis ...
DOI:
10.1016/j.mimet.2020.106049

30. A fungal based synthesis method for copper nanoparticles with the determination of anticancer, antidiabetic and antibacterial activities

Author:
Sadaf Noor; Ziaullah Shah; Aneela Javed; Amjad Ali; Syed Bilal Hussain; Sidra Zafar; Hazrat Ali; Syed Aun Muhammad
Source:
Journal of microbiological methods 2020 v.174 pp. 105966
ISSN:
0167-7012
Subject:
Aspergillus niger; Bacillus subtilis; Escherichia coli; Klebsiella pneumoniae; Micrococcus luteus; Staphylococcus aureus; agar; alpha-glucosidase; antibacterial properties; copper nanoparticles; cost effectiveness; cytotoxicity; drug delivery systems; fungi; glycemic effect; hepatoma; humans; inhibitory concentration 50; neoplasm cells; ultraviolet-visible spectroscopy
Abstract:
... Biological procedures for the synthesis of copper nanoparticles (CuNPs) are eco-friendly, cost-effective, and easily scalable as compared to chemical and physical methods.In the present study, a simple fungus based synthesis method was used for copper nanoparticles. After morphological and molecular characterization of fungal strains, Aspergillus niger strain STA9 was used for CuNPs synthesis. Par ...
DOI:
10.1016/j.mimet.2020.105966

31. A loop-mediated isothermal amplification (LAMP) assay for the consensus detection of human pathogenic Campylobacter species

Author:
Uma S. Babu; Lisa M. Harrison; Mark K. Mammel; Elmer C. Bigley; Kelli L. Hiett; Kannan V. Balan
Source:
Journal of microbiological methods 2020 v.176 pp. 106009
ISSN:
0167-7012
Subject:
Arcobacter; Campylobacter coli; Campylobacter fetus; Campylobacter jejuni; Escherichia coli; Helicobacter; Salmonella; Shigella; color; colorimetry; cost effectiveness; gene amplification; heat tolerance; humans; loop-mediated isothermal amplification; monitoring; restriction endonucleases; spinach; thermosensitivity
Abstract:
... Most rapid identification methods for Campylobacter are designed to detect thermotolerant Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli). A growing number of thermosensitive Campylobacter species are now gaining recognition as emerging human pathogens. Methods are lacking for the rapid screening of these emerging species. Loop-mediated Isothermal Amplification (LAMP) is a nuclei ...
DOI:
10.1016/j.mimet.2020.106009

32. A novel pharmaceutical approach for the analytical validation of probiotic bacterial count by flow cytometry

Author:
Luca Michelutti; Michela Bulfoni; Emanuele Nencioni
Source:
Journal of microbiological methods 2020 v.170 pp. 105834
ISSN:
0167-7012
Subject:
Bifidobacterium; Lactobacillus; acidification; bacteria; biochemical pathways; cell viability; chemical species; computer software; data analysis; dietary supplements; drugs; fermentation; flow cytometry; fluorescent dyes; humans; oxygen; plate count; probiotics; propidium; thiazoles
Abstract:
... Introduction: Flow cytometry is a powerful and sensitive technique able to characterize single cells within a heterogeneous population. Different fluorescent dyes can be combined and used together to analyze a great variety of parameters simultaneously. In particular, flow-cytometry allows to measure viability and vitality of probiotics measuring their metabolic activity, fermentation capacity, ac ...
DOI:
10.1016/j.mimet.2020.105834

33. A novel recombinant multiepitope protein candidate for the diagnosis of brucellosis: A pilot study

Author:
Dehui Yin; Qiongqiong Bai; Jinpeng Zhang; Kun Xu; Juan Li
Source:
Journal of microbiological methods 2020 v.174 pp. 105964
ISSN:
0167-7012
Subject:
Brucella; Escherichia coli; agglutination; brucellosis; colorimetry; genes; humans; hydrophilicity; immunodominant epitopes; lipopolysaccharides; outer membrane proteins; serodiagnosis; zoonoses
Abstract:
... Brucellosis is a zoonotic disease transmitted to humans from infected animals. As a systemic disease, it can harm any organ or system of the host body. Human brucellosis presents with various clinical symptoms, which makes diagnosis challenging. Serological diagnosis of brucellosis is based on ELISA or agglutination tests, which use colorimetry to detect antibodies generated against lipopolysaccha ...
DOI:
10.1016/j.mimet.2020.105964

34. Anaerobic bioburden in transport solution of human cardiovascular tissues

Author:
Victoria Stadler Tasca Ribeiro; Letícia Kraft; Paula Hansen Suss; Juliette Cieslinski; Luciana Cristina Wollmann; Felipe Francisco Tuon
Source:
Journal of microbiological methods 2019 pp. -
ISSN:
0167-7012
Subject:
Clostridium perfringens; allografting; anaerobes; automation; bacteria; blood; bottles; heart; humans; matrix-assisted laser desorption-ionization mass spectrometry; microbial load; microfiltration; oxygen; tissue transplantation; tissues
Abstract:
... Although reports of infections caused by anaerobes after tissue transplantation are uncommon, contamination of allografts may result in substantial complications. Anaerobic incubation and testing of organ transport solution (TS) are not routine. The aim of this study was to determine the bioburden of strict anaerobic bacteria and oxygen tension of heart-TS. Forty TS from different donors were eval ...
DOI:
10.1016/j.mimet.2019.105723

35. Baby-SPIME: A dynamic in vitro piglet model mimicking gut microbiota during the weaning process

Author:
Sandrine Dufourny; Nadia Everaert; Sarah Lebrun; Caroline Douny; Marie-Louise Scippo; Bing Li; Bernard Taminiau; Massimo Marzorati; José Wavreille; Eric Froidmont; Pierre Rondia; Véronique Delcenserie
Source:
Journal of microbiological methods 2019 v.167 pp. 105735
ISSN:
0167-7012
Subject:
Bacteroides; Bifidobacterium; Fusobacterium; Lactobacillus; Megasphaera; Mitsuokella; Prevotella; acetates; animal models; bioreactors; butyric acid; colon; delta-Proteobacteria; fermentation; gamma-Proteobacteria; humans; ileum; in vitro digestion; intestinal microorganisms; metabolites; microbial communities; piglets; propionic acid; weaning
Abstract:
... The study aimed to adapt the SHIME® model, developed to simulate human digestion and fermentation, to a baby-SPIME (baby Simulator of Pig Intestinal Microbial Ecosystem). What constitutes a unique feature of this model is its twofold objective of introducing an ileal microbial community and mimicking a dietary weaning transition. This model should then be ideally suited to test the dietary weaning ...
DOI:
10.1016/j.mimet.2019.105735

36. Biomarker discovery in the biofilm-forming process of Burkholderia pseudomallei by mass-spectrometry

Author:
Piyapong Hadpanus; Permkun Permsirivisarn; Sitthiruk Roytrakul; Sumalee Tungpradabkul
Source:
Journal of microbiological methods 2019 v.159 pp. 26-33
ISSN:
0167-7012
Subject:
Burkholderia pseudomallei; antibiotic resistance; antibiotics; bacteria; biofilm; biomarkers; enzymes; humans; matrix-assisted laser desorption-ionization mass spectrometry; melioidosis; proteomics
Abstract:
... A serious human infectious disease called Melioidosis is a result of Burkholderia pseudomallei infection. Treatment for infected individuals is difficult due to a wide range of ineffective antibiotics including a high level of antibiotic tolerance which has been known to be caused by biofilm production. However, biofilm forming processes of this bacterium are not well documented despite multiple-m ...
DOI:
10.1016/j.mimet.2019.02.011

37. Development of a new serological assay for the diagnosis of Clostridium difficile infections with prognostic value

Author:
Felix von Bechtolsheim; Adorjan Varga; Laszlo Szereday; Beata Polgar; Timea Balassa; Bela Kocsis; Zoltan Peterfi; Eva Miko
Source:
Journal of microbiological methods 2019 v.167 pp. 105777
ISSN:
0167-7012
Subject:
Clostridium difficile; antibodies; blood serum; clinical trials; enzyme-linked immunosorbent assay; humans; humoral immunity; immune response; nutritional status; patients; prognosis; protective effect; risk; virulence
Abstract:
... The most common hospital-acquired enteral infection is caused by Clostridium difficile. Unfortunately, Clostridium difficile infections (CDI) are of high risk to recur and little is known about how to predict recurrences. Previous findings have shown that high risk for recurrence correlates with low levels of C. difficile toxin-A and -B specific antibodies suggesting the protective role of humoral ...
DOI:
10.1016/j.mimet.2019.105777

38. Evaluation of denaturing gradient gel electrophoresis (DGGE) and next generation sequencing (NGS) in combination with enrichment culture techniques to identify bacteria in commercial microbial-based products

Author:
R.M. Subasinghe; A.D. Samarajeewa; R. Scroggins; L.A. Beaudette
Source:
Journal of microbiological methods 2019 v.161 pp. 118-130
ISSN:
0167-7012
Subject:
Enterococcus; Escherichia; Morganella; Proteus; Shigella; Vagococcus; azides; bacteria; compliance; denaturing gradient gel electrophoresis; enrichment culture; environmental assessment; glucose; high-throughput nucleotide sequencing; humans; laws and regulations; peptones; ribosomal DNA; risk assessment; temperature; variance; virulent strains
Abstract:
... Identification of bacteria in new or existing commercial microbial-based products (MBPs) is important for compliance with government regulations and for human and environmental risk assessment. Research was performed to develop effective methods to identify bacteria present in a MBP using a combined approach of conventional enrichment culture technique and denaturing gradient gel electrophoresis ( ...
DOI:
10.1016/j.mimet.2019.04.017

39. Evaluation of the GeneFields® EHEC/SS PCR dipstick DNA chromatography kit for the detection of enteric bacterial pathogens in stool specimens of healthy humans

Author:
Hiroki Maruoka; Atsushi Hinenoya; Noritomo Yasuda; Atsuyoshi Takeda; Shin Inoue; Tomoko Sumi; Kazuaki Koitabashi; Hiroshi Yasue; Kazuhiko Kogou; Shinji Yamasaki
Source:
Journal of microbiological methods 2019 v.161 pp. 111-117
ISSN:
0167-7012
Subject:
DNA; Salmonella enterica; Shigella; bacteria; chromatography; detection limit; enterohemorrhagic Escherichia coli; feces; genes; genetic testing; humans; pathogens; quantitative polymerase chain reaction
Abstract:
... We developed a new GeneFields® EHEC/SS PCR dipstick DNA chromatography kit for the simultaneously detection of invA, ipaH, and stx genes in Salmonella enterica (56 strains), Shigella spp. (44), and enterohemorrhagic Escherichia coli (EHEC) (28), respectively, and evaluated the sensitivity and specificity with other bacteria (57) by this kit. The sensitivity and specificity were 100%, respectively. ...
DOI:
10.1016/j.mimet.2019.04.016

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

Author:
Min Ju Park; Myeong Soo Park; Geun Eog Ji
Source:
Journal of microbiological methods 2019 v.159 pp. 112-119
ISSN:
0167-7012
Subject:
Bifidobacterium bifidum; bacteria; bacterial growth; cell membrane structures; cell walls; developmental stages; electrical properties; electroporation; genetic engineering; genetically engineered microorganisms; human physiology; humans; plasmids; probiotics; sodium chloride
Abstract:
... 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 in ...
DOI:
10.1016/j.mimet.2018.11.019

41. Induction of EGFP expression in Pichia pastoris during co-culture with human endothelial cell line

Author:
Der Thor; Nan Xiao; Ryan Yu; Anita Jivan; Bomi Cha
Source:
Journal of microbiological methods 2019 v.161 pp. 28-34
ISSN:
0167-7012
Subject:
viability; human cell lines; green fluorescent protein; protein synthesis; endothelial cells; Komagataella pastoris; humans; coculture; recombinant proteins; yeasts
Abstract:
... While Pichia pastoris has been developed into a versatile recombinant protein expression system, there are only few studies that have investigated the efficacious use of this yeast with human cells. In this study, we demonstrated that P. pastoris can be cultured under mammalian cell culture conditions and co-cultured with human endothelial cells. Co-cultures did not affect endothelial cell morphol ...
DOI:
10.1016/j.mimet.2019.04.006

42. Osteoarticular infections: Blood as a determinant factor in the isolation of Kingella kingae

Author:
Antoni Noguera-Julian; Manuel Monsonis; Guillermo Ludwig; David Moreno-Romo; Amadéu Gené-Giralt
Source:
Journal of microbiological methods 2019 v.161 pp. 8-11
ISSN:
0167-7012
Subject:
Kingella kingae; blood; bottles; humans
Abstract:
... We assessed the capacity of Kingella kingae to grow in blood culture bottles (BCB), taking into account the concentrations of the microorganism and blood in the culture medium.An initial suspension (McFarland 0.5) of 32 strains of K. kingae was serially diluted. One mL of the initial suspension and 1 mL of the subsequent dilutions were inoculated in two BCB, together with 1 mL of human blood in th ...
DOI:
10.1016/j.mimet.2019.04.009

43. Plesiomonas shigelloides sipD mutant, generated by an efficient gene transfer system, is less invasive

Author:
Daoyi Xi; Fuyi Jing; Qian Liu; Boyang Cao
Source:
Journal of microbiological methods 2019 v.159 pp. 75-80
ISSN:
0167-7012
Subject:
Plesiomonas shigelloides; Salmonella; diarrhea; gene transfer; genetic engineering; human cell lines; humans; mutants; pathogenicity islands; pathogens; plasmid vectors; serotypes; type III secretion system
Abstract:
... Plesiomonas shigelloides is widely associated with human diarrheal disease. Research on this pathogen has been hampered by the absence of an effective genetic manipulation system. In the present study, an efficient and precise conjugation transfer procedure, mediated by suicide vector pRE112 was used to overcome this limitation. The efficiency of generating double recombinants was average 74.3%, a ...
DOI:
10.1016/j.mimet.2019.02.017

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

Author:
Yunyun Geng; Guanhui Liu; Libing Liu; Qiaoen Deng; Liwei Zhao; Xiao Xia Sun; Jinfeng Wang; Baohua Zhao; Jianchang Wang
Source:
Journal of microbiological methods 2019 v.157 pp. 31-36
ISSN:
0167-7012
Subject:
Campylobacter jejuni; breast meat; chicken meat; food pathogens; gastroenteritis; genes; humans; milk contamination; public health; quantitative polymerase chain reaction
Abstract:
... 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. jejuni. As a novel isothermal gene amplification technique, recombinase polymerase amplification (RPA) has been developed for the molecular detection of ...
DOI:
10.1016/j.mimet.2018.12.017

45. Silver enhanced nano-gold dot blot immunoassay for leptospirosis

Author:
Veerapandian Raja; Muthu Prasad; Palanisamy Bothammal; Perumal Saranya; Krishnamoorthi Sumaiya; Charles Solomon Akino Mercy; Kalimuthusamy Natarajaseenivasan
Source:
Journal of microbiological methods 2019 v.156 pp. 20-22
ISSN:
0167-7012
Subject:
diagnostic techniques; humans; immunoassays; leptospirosis; nanogold; nanosilver; peroxidase; urine; zoonoses
Abstract:
... Leptospirosis is a widespread zoonotic disease and lacks in efficient diagnostic tools. In the present study, a nanogold based dot blot immunoassay was developed and evaluated for the detection of leptospirosis in human urine samples. This method was found to be rapid (<4 h) with higher sensitivity (>4.2–14.6%) than horse radish peroxidase (HRP) conjugated dot blot assay. ...
DOI:
10.1016/j.mimet.2018.11.021

46. A novel microbiological medium for the growth of periodontitis associated pathogens

Author:
Niall A. Hickey; Kathryn A. Whitehead; Liliana Shalamanova; Jonathan A. Butler; Rebecca L. Taylor
Source:
Journal of microbiological methods 2019 v.163 pp. 105647
ISSN:
0167-7012
Subject:
cell viability; humans; microorganisms; pathogens; periodontitis
Abstract:
... A novel microbiological medium designed to be more representative of gingival crevicular fluid. Chosen representative periodontal microorganisms showed good growth with minimal effect on human cell viability. This will enable more comparisons between different periodontitis associated organisms and their potential role in host health and systemic disease. ...
DOI:
10.1016/j.mimet.2019.105647

47. A review on various maleic anhydride antimicrobial polymers

Author:
Akshatha Nagaraja; Manohara Dhulappa Jalageri; Yashoda Malgar Puttaiahgowda; Kakarla Raghava Reddy; Anjanapura V. Raghu
Source:
Journal of microbiological methods 2019 v.163 pp. 105650
ISSN:
0167-7012
Subject:
anti-infective agents; chemical bonding; chemical structure; disinfectants; health effects assessments; humans; industry; maleic anhydrides; microorganisms; pathogens; polymers
Abstract:
... The basic requirement of human beings is better health but the serious health effects and numerous infections caused by rapid growth of harmful pathogens resulting in a large number of deaths and is a significant challenge to modern science. Microbes infecting humans can be stopped in two ways: disinfectants and antimicrobial agents. There is considerable interest from both academics and industry ...
DOI:
10.1016/j.mimet.2019.105650

48. A systematic review on the role of GRA proteins of Toxoplasma gondii in host immunization

Author:
Fatemeh Rezaei; Mahdi Sharif; Shahabeddin Sarvi; Seyed Hossein Hejazi; Sargis Aghayan; Abdol Sattar Pagheh; Samira Dodangeh; Ahmad Daryani
Source:
Journal of microbiological methods 2019 pp. -
ISSN:
0167-7012
Subject:
Toxoplasma gondii; antigens; databases; human diseases; humans; immune response; immunization; immunogenicity; laboratory animals; mice; parasites; proteins; systematic review; vaccines; virulence
Abstract:
... Toxoplasma gondii is a widespread obligatory intracellular parasite infecting humans and most of all other warm-blooded animals. Currently there is no any accepted vaccine for prevention of T. gondii infection. Many studies are focused on using of various excretory secretory antigens (ESA); and among them dense granule antigens (GRAs) being involved in parasite survival, virulence and replication ...
DOI:
10.1016/j.mimet.2019.105696

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

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

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

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