Journal name: Journal of microbiological methods

1. A European multicenter evaluation study to investigate the performance on commercially available selective agar plates for the detection of carbapenemase producing Enterobacteriaceae

Author:: Cindy Dierikx; Stefan Börjesson; Agnès Perrin-Guyomard; Marisa Haenni; Madelaine Norström; Hege H. Divon; Hanna Karin Ilag; Sophie A. Granier; Annette Hammerum; Jette Sejer Kjeldgaard; Natalie Pauly; Luke Randall; Muna F. Anjum; Aleksandra Smialowska; Alessia Franco; Kees Veldman; Jannice Schau Slettemeås; One Health EJP IMPART project
Source:: Journal of microbiological methods 2022 v.193 pp. 106418
ISSN:: 0167-7012
Subject:: Enterobacteriaceae; agar; beta-lactamase; carbapenems; cecum; flora; food safety; genotyping; peptones; species identification; swine; turkey meat
Abstract:: ... The European Food Safety Authority (EFSA) advised to prioritize monitoring carbapenemase producing Enterobacteriaceae (CPE) in food producing animals. Therefore, this study evaluated the performance of different commercially available selective agars for the detection of CPE using spiked pig caecal and turkey meat samples and the proposed EFSA cultivation protocol. Eleven laboratories from nine co ...
DOI:: 10.1016/j.mimet.2022.106418
: https://doi.org/10.1016/j.mimet.2022.106418

2. A fluorescent aptasensor for the detection of Aflatoxin B1 by graphene oxide mediated quenching and release of fluorescence

Author:: Sai Keerthana Setlem; Bhairab Mondal; Shylaja Ramlal
Source:: Journal of microbiological methods 2022 v.193 pp. 106414
ISSN:: 0167-7012
Subject:: adsorption; aflatoxin B1; aptasensors; bioassays; desorption; detection limit; fluorescence; fluorescent dyes; food safety; graphene oxide; industry; oligonucleotides; peanuts; trade
Abstract:: ... Aflatoxin B1 contamination in food and agro commodities has been major concern of global food safety and trade industry. There is an urgent need to develop sensitive and on-site detection methods for aflatoxins mainly, AFB1 monitoring. In the present study, a fluorophore (Alexa Fluor 488) based aptamer biosensor was devised in combination with graphene oxide (GO) for the detection of Aflatoxin B1 ...
DOI:: 10.1016/j.mimet.2022.106414
: https://doi.org/10.1016/j.mimet.2022.106414

3. A multistep enrichment process with custom growth medium improves resuscitation of chlorine-stressed coliforms from secondary sewage effluents

Author:: Jennifer M. Mobberley; Scott K. Cooley; Mark W. Widder; Shelby M. Phillips; Angela M. Melville; Linda M. Brennan; Valerie T. Divito; William H. van der Schalie; Richard M. Ozanich; Janine R. Hutchison
Source:: Journal of microbiological methods 2022 v.192 pp. 106364
ISSN:: 0167-7012
Subject:: chlorine; culture media; growth promotion; magnesium chloride; sewage; sodium pyruvate; trace elements; trehalose
Abstract:: ... Resuscitation and detection of stressed total coliforms in chlorinated water samples is needed to assess and prevent health effects from adverse exposure. In this study, we report that the addition of a growth enhancer mix consisting of trehalose, sodium pyruvate, magnesium chloride, and 1× trace mineral supplement improved growth of microorganisms from chlorinated secondary effluent in the base m ...
DOI:: 10.1016/j.mimet.2021.106364
: https://doi.org/10.1016/j.mimet.2021.106364

4. A panoptic review of techniques for finfish disease diagnosis: The status quo and future perspectives

Author:: Tina Kollannoor Johny; Thangaraj Raja Swaminathan; Neeraj Sood; Pravata Kumar Pradhan; Kuldeep Kumar Lal
Source:: Journal of microbiological methods 2022 v.196 pp. 106477
ISSN:: 0167-7012
Subject:: aquaculture; diagnostic techniques; disease diagnosis; fish; fish health; flow cytometry; fluorescent antibody technique; immunohistochemistry; point-of-care systems; sustainable development
Abstract:: ... Disease outbreaks caused by bacterial and viral pathogens is a major impediment to the sustainable growth of aquaculture. Rapid and accurate diagnosis of pathogens is crucial for the successful maintenance of fish health and productivity in aquaculture. This review manuscript provides a brief description of conventional disease diagnosis techniques and a detailed description of immunological techn ...
DOI:: 10.1016/j.mimet.2022.106477
: https://doi.org/10.1016/j.mimet.2022.106477

5. A simple method for purification of epsilon toxin of Clostridium perfringens type D for serum neutralization assay

Author:: Lida Abdolmohammadi Khiav; Anahita Emadi; Azadeh Zahmatkesh
Source:: Journal of microbiological methods 2022 v.193 pp. 106395
ISSN:: 0167-7012
Subject:: ammonium sulfate; blood serum; cell culture; chromatography; cost effectiveness; disease prevention; enterotoxemia; lethal dose; neutralization; neutralization tests; phosphates; polyacrylamide gel electrophoresis; purification methods; small ruminants; toxins; vaccination; vaccines
Abstract:: ... Enterotoxaemia, a disease that affects domestic ruminants, is caused by the epsilon toxin of Clostridium perfringens type D and B. Control and prophylaxis are based on systemic vaccination of small ruminant herds with epsilon toxoid. Purified epsilon toxin is an essential material for vaccine evaluation. It is also necessary for diagnosis of enterotoxaemia disease in the field by in vitro tests in ...
DOI:: 10.1016/j.mimet.2021.106395
: https://doi.org/10.1016/j.mimet.2021.106395

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

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

7. A study of various factors affecting satellitism tests of Haemophilus influenzae and Haemophilus parainfluenzae using Staphylococcus aureus as the source of NAD

Author:: Yu Xi; Hexuan Wang; Shanmei Wang; Xuxiao Wu; Zeyu Wang
Source:: Journal of microbiological methods 2022 v.193 pp. 106417
ISSN:: 0167-7012
Subject:: Haemophilus influenzae; Haemophilus parainfluenzae; NAD (coenzyme); Staphylococcus aureus; agar
Abstract:: ... Many factors affecting satellitism tests are unclear, and it is difficult to avoid misidentification, even if the medium is properly selected. We investigated the factors causing false-positive results for Haemophilus influenzae and false-negative results for Haemophilus parainfluenzae in the satellitism tests using Staphylococcus aureus as the source of nicotinamide adenine dinucleotide (NAD). H. ...
DOI:: 10.1016/j.mimet.2022.106417
: https://doi.org/10.1016/j.mimet.2022.106417

8. A two-step bioluminescence assay for optimizing antibacterial coating of hollow-fiber membranes with polydopamine in an integrative approach

Author:: Michael Czieborowski; Antoine J.B. Kemperman; Erik Rolevink; Janieke Blom; Tymen Visser; Bodo Philipp
Source:: Journal of microbiological methods 2022 v.196 pp. 106452
ISSN:: 0167-7012
Subject:: biofilm; bioluminescence; bioluminescence assay; dopamine; polymerization; sodium; ultrafiltration
Abstract:: ... Pure-water filtration membranes are often fouled by bacterial biofilms. Antibacterial coatings for preventing biofilm formation on such membranes should not rely on leaching of inhibiting compounds but should only be effective on surface contact. Certified assays for antibacterial coatings do not sufficiently exclude leaching effects and involve nutrient-rich cultivation media that do not correspo ...
DOI:: 10.1016/j.mimet.2022.106452
: https://doi.org/10.1016/j.mimet.2022.106452

9. Accurate classification of Listeria species by MALDI-TOF mass spectrometry incorporating denoising autoencoder and machine learning

Author:: Yunhong Li; Zeyu Gan; Xi Zhou; Zhiwei Chen
Source:: Journal of microbiological methods 2022 v.192 pp. 106378
ISSN:: 0167-7012
Subject:: Food and Drug Administration; Listeria monocytogenes; data collection; food industry; food safety; listeriosis; matrix-assisted laser desorption-ionization mass spectrometry; pathogens; statistics; support vector machines
Abstract:: ... Listeria monocytogenes belongs to the category of facultative anaerobic bacteria, and is the pathogen of listeriosis, potentially lethal disease for humans. There are many similarities between L. monocytogenes and other non-pathogenic Listeria species, which causes great difficulties for their correct identification. The level of L. monocytogenes contamination in food remains high according to sta ...
DOI:: 10.1016/j.mimet.2021.106378
: https://doi.org/10.1016/j.mimet.2021.106378

10. Accurate qPCR quantification in polymicrobial communities requires assessment of gDNA extraction efficiency

Author:: Nuno Cerca; Ângela Lima; Angela França
Source:: Journal of microbiological methods 2022 v.194 pp. 106421
ISSN:: 0167-7012
Subject:: journals; methodology; microbial load
Abstract:: ... qPCR absolute quantification requires the assessment of PCR reaction efficiency. This is achieved by performing serial dilutions of gDNA. Herein, we demonstrate that when quantifying bacterial load in mixed samples, reaction efficiency should not be used as a calibration curve since gDNA isolation efficiency is neglected, significantly impacting quantification. ...
DOI:: 10.1016/j.mimet.2022.106421
: https://doi.org/10.1016/j.mimet.2022.106421

11. Adaptation and validation of a method for evaluating the bactericidal activity of ethyl alcohol in gel format 70% (w/w)

Author:: Amanda Fermiano da Cruz; Alessandra Oliveira de Abreu; Paula Araujo de Souza; Bianca Deveza; Carolaine Totelote Medeiros; Verônica Santos Sousa; Bruna Peres Sabagh; Maria Helena Simões Villas Bôas
Source:: Journal of microbiological methods 2022 v.193 pp. 106402
ISSN:: 0167-7012
Subject:: Pseudomonas aeruginosa; Salmonella enterica; Staphylococcus aureus; aerosols; analytical methods; antibacterial properties; disinfectants; equipment; ethanol; gels; microbial activity; microbiological quality; monitoring; quality control; Brazil
Abstract:: ... Ethyl alcohol 70% (w/w) is a broad-spectrum bactericidal agent that is mandatorily marketed as a gel in Brazil since 2002. However, there is no method described for the microbiological quality control of surface disinfectants in the form of gel, which makes it impossible to monitor the effectiveness of these products by the Health Surveillance. Thus, the present study aimed to adapt an analytical ...
DOI:: 10.1016/j.mimet.2021.106402
: https://doi.org/10.1016/j.mimet.2021.106402

12. 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
: https://doi.org/10.1016/j.mimet.2022.106437

13. Analysis of DNA extraction methods for detection of Treponema pallidum: A comparison of three methods

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

14. Antimicrobial susceptibility testing determined by Alfred 60/AST (Alifax®) in a multi-sites lab: performance's evaluation and optimization of workflow

Author:: R. Cupaiolo; S. Cherkaoui; G. Serrano; N. Dauby; A. Georgala; S. Blumental; E. Maillart; M. Hites; M. Hallin; D. Martiny
Source:: Journal of microbiological methods 2022 v.194 pp. 106433
ISSN:: 0167-7012
Subject:: Enterococcus; antibiotic resistance; automation; bacteremia; blood; blood flow; blood volume; clindamycin; disk diffusion antimicrobial test; meropenem
Abstract:: ... New techniques are needed to speed-up the identification and antimicrobial susceptibility testing (AST) of bacteria associated with bloodstream infections. Alfred 60/AST (Alifax®, Polverara, Italy) performs AST by light scattering directly from positive blood cultures. We evaluated Alfred 60/AST performances for 4 months. Each new episode of bacteraemia was included and AST were compared to either ...
DOI:: 10.1016/j.mimet.2022.106433
: https://doi.org/10.1016/j.mimet.2022.106433

15. Application of proper orthogonal decomposition for evaluation of coherent structures and energy contents in microbial biofilms

Author:: Daniel Montelongo-Jauregui; Adesile Ajisafe; Mary Ann Jabra-Rizk; Ahmed S. Sultan
Source:: Journal of microbiological methods 2022 v.194 pp. 106420
ISSN:: 0167-7012
Subject:: Candida albicans; acoustics; biofilm; biosensors; energy; fluid mechanics; fungi; models; pathogens; polysaccharides; reflectance
Abstract:: ... Microbial biofilms are structured communities of surface-associated microbial populations embedded in a matrix of extracellular polysaccharides that provide protection for biofilm cells. Among the wide plethora of microbial species adept at forming biofilms, the fungal pathogen Candida albicans (C. albicans), is one of the most notable. C. albicans biofilm development occurs in a series of sequent ...
DOI:: 10.1016/j.mimet.2022.106420
: https://doi.org/10.1016/j.mimet.2022.106420

16. Assessment of VITEK® 2, MALDI-TOF MS and full gene 16S rRNA sequencing for aerobic endospore-forming bacteria isolated from a pharmaceutical facility

Author:: Luciana Veloso da Costa; Rebeca Vitoria da Silva Lage de Miranda; Erica Louro da Fonseca; Natalia Pedra Gonçalves; Cristhiane Moura Falavina dos Reis; Adriana Marques Frazão; Fernanda Ventura Cruz; Marcelo Luiz Lima Brandão; Juliana Nunes Ramos; Verônica Viana Vieira
Source:: Journal of microbiological methods 2022 v.194 pp. 106419
ISSN:: 0167-7012
Subject:: databases; endospore forming bacteria; genes; journals; methodology; nucleotide sequences
Abstract:: ... VITEK®2, MALDI-TOF MS and 16S rRNA sequencing were evaluated for the identification of aerobic endospore-forming bacteria (AEB) from a pharmaceutical facility. MALDI-TOF MS demonstrated higher accuracy compared to VITEK®2, although both databases were insufficient to identify AEB species. Sequencing was the best methodology, but unable to identify closely related species. ...
DOI:: 10.1016/j.mimet.2022.106419
: https://doi.org/10.1016/j.mimet.2022.106419

17. Bacterial and fungal disinfection via ozonation in air

Author:: Emmanuel I. Epelle; Andrew Macfarlane; Michael Cusack; Anthony Burns; Bathini Thissera; William Mackay; Mostafa E. Rateb; Mohammed Yaseen
Source:: Journal of microbiological methods 2022 v.194 pp. 106431
ISSN:: 0167-7012
Subject:: Aspergillus fumigatus; Candida albicans; Escherichia coli; Staphylococcus aureus; air; cost effectiveness; disinfection; exposure duration; fabrics; fungi; ozonation; ozone; pandemic; water treatment
Abstract:: ... Ozone treatment is an eco-friendly and cost-effective approach to achieve material disinfection, and this disinfection method is of utmost importance in the present global pandemic. The efficacy of ozone's oxidative potential on common microorganisms has been extensively studied, particularly in the food and water treatment industries. However, little is still understood regarding its antimicrobia ...
DOI:: 10.1016/j.mimet.2022.106431
: https://doi.org/10.1016/j.mimet.2022.106431

18. Bioremediation of oily seawater by Bacteria immobilization on a novel carrier material containing nutrients

Author:: Qun Luo; Lina Liu; Dengyong Hou
Source:: Journal of microbiological methods 2022 v.192 pp. 106392
ISSN:: 0167-7012
Subject:: biodegradability; biodegradation; bioremediation; calcium alginate; diesel fuel; gas chromatography-mass spectrometry; oils; rhubarb; rice; seawater
Abstract:: ... A novel carrier material was obtained by coating puffed rhubarb rice (PRR) with calcium alginate (CA) membrane. The carrier material was prepared to contain oil-degrading bacterial strains and inorganic nutrients through entrapping them in different locations. This formulation possessed floatability, biodegradability and nutrient slow-release properties. Therefore, it could be applied for oil biod ...
DOI:: 10.1016/j.mimet.2021.106392
: https://doi.org/10.1016/j.mimet.2021.106392

19. Chemical susceptibility testing of non-tuberculous mycobacterium strains and other aquatic bacteria: Results of a study for the development of a more sensitive and simple method for the detection of NTM in environmental samples

Author:: Savina Ditommaso; Monica Giacomuzzi; Gabriele Memoli; Jacopo Garlasco; Antonio Curtoni; Marco Iannaccone; Carla Maria Zotti
Source:: Journal of microbiological methods 2022 v.193 pp. 106405
ISSN:: 0167-7012
Subject:: Burkholderia multivorans; Methylobacterium; Mycobacterium chelonae; Mycobacterium chimaera; acetylcysteine; agar; cetylpyridinium chloride; culture media; decontamination; sodium hydroxide
Abstract:: ... The methods employed to detect non-tuberculous mycobacteria on environmental samples are essentially those classically used in clinical microbiology, which envisage a decontamination step to reduce the overgrowth of non-mycobacterial organisms before plating them on the culture medium. The aim of this study was to propose alternative culture techniques to improve non-tuberculous mycobacteria detec ...
DOI:: 10.1016/j.mimet.2021.106405
: https://doi.org/10.1016/j.mimet.2021.106405

20. 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
: https://doi.org/10.1016/j.mimet.2022.106474

21. Comparative performance of different antigens on the lateral flow assay (LFA) platform for the rapid serodiagnosis of paratuberculosis

Author:: Mukta Jain; Amit Kumar Singh; Amit Kumar; Saurabh Gupta; Rathnagiri Polavarapu; Jagdip Singh Sohal
Source:: Journal of microbiological methods 2022 v.192 pp. 106367
ISSN:: 0167-7012
Subject:: antigens; blood serum; bovine tuberculosis; cattle; cross reaction; detection limit; diagnostic techniques; issues and policy; paratuberculosis; point-of-care systems; polymerase chain reaction; serodiagnosis; tissue culture
Abstract:: ... Paratuberculosis is a globally prevalent disease, that adversely affects the economy of livestock farming. Control is largely based on early detection followed by ‘Test and Cull’ or ‘Test and Segregate’ Policy. Implementation of paratuberculosis control is a special challenge due to the non-availability of point of care diagnostics (PoCD). Therefore, the present study aimed to optimize and evaluat ...
DOI:: 10.1016/j.mimet.2021.106367
: https://doi.org/10.1016/j.mimet.2021.106367

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

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

23. Comparison of peaks in the matrix-assisted laser desorption ionization time-of-flight mass spectrometry spectra of Staphylococcus aureus grown on various blood agar plates

Author:: Jung-Min Kim; Sung Hee Chung; Inhee Kim; Jae-Seok Kim
Source:: Journal of microbiological methods 2022 v.196 pp. 106471
ISSN:: 0167-7012
Subject:: agar; bacterial proteins; culture media; genes; matrix-assisted laser desorption-ionization mass spectrometry; methicillin; methicillin-resistant Staphylococcus aureus; protein synthesis; yeast extract
Abstract:: ... Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification in clinical laboratories. Bacterial protein expression may differ according to their growth conditions, especially the culture medium composition. We aimed to study the peak variations of Staphylococcus aureus grown on various blood agar plates (BAP), especiall ...
DOI:: 10.1016/j.mimet.2022.106471
: https://doi.org/10.1016/j.mimet.2022.106471

24. Comparison of the complete filtration method using an automated feces analyzer with three manual methods for stool examinations

Author:: Peechana Aiadsakun; Wilaiwan Sriwimol; Nannapas Thongbun; Bancha Rui-on; Kulathida Thiparaksaphan; Churai Phainuice; Chonnikarn Nuhom
Source:: Journal of microbiological methods 2022 v.192 pp. 106394
ISSN:: 0167-7012
Subject:: Ascaris lumbricoides; Blastocystis; Entamoeba histolytica; Giardia lamblia; Strongyloides stercoralis; Trichuris trichiura; automation; fecal examination; feces; filtration; formalin; hookworms; yeasts
Abstract:: ... Conventional diagnostic techniques using manual methods for stool examination have important limitations. Hence there is a need for improved technologies in routine clinical practice. This study aimed to compare detection rates, agreements, and diagnostic performances for stool examinations in all parameters of the complete filtration method using the Sciendox Feces Analysis System-50 automated fe ...
DOI:: 10.1016/j.mimet.2021.106394
: https://doi.org/10.1016/j.mimet.2021.106394

25. Current methods for the diagnosis of leptospirosis: Issues and challenges

Author:: Gillaine Vail Pinto; Kuppusamy Senthilkumar; Praveen Rai; Shama Prakash Kabekkodu; Indrani Karunasagar; Ballamoole Krishna Kumar
Source:: Journal of microbiological methods 2022 v.195 pp. 106438
ISSN:: 0167-7012
Subject:: Leptospira interrogans; antibiotics; leptospirosis; public health; rain; rapid methods; therapeutics; zoonoses
Abstract:: ... Leptospirosis is a re-emerging anthropo-zoonotic infection of worldwide significance caused by the pathogenic spirochete (Leptospira interrogans) of the genus Leptospira, predominant in tropical/temperate regions and endemic to areas receiving heavy rainfall and flooding. Clinical presentation is similar to that of other febrile illnesses exhibiting mild symptoms which are often self-limiting. Hen ...
DOI:: 10.1016/j.mimet.2022.106438
: https://doi.org/10.1016/j.mimet.2022.106438

26. Determination by isothermal microcalorimetry of the sensitivity of phytopathogenic fungi of tropical fruits against an ethanolic extract of jackfruit leaf (Artocarpus heterophyllus Lam.)

Author:: Leonardo Covarrubias-Rivera; Rafael López-Cruz; Juan Arturo Ragazzo-Sánchez; Maricarmen Iñiguez-Moreno; Montserrat Calderón-Santoyo
Source:: Journal of microbiological methods 2022 v.195 pp. 106457
ISSN:: 0167-7012
Subject:: Artocarpus heterophyllus; agar; antifungal properties; calorimetry; heat; jackfruits; leaves
Abstract:: ... Conventional microbiological methods to evaluate the in vitro antifungal activity of bioactive compounds usually consume a long time. It is also difficult to calculate different kinetic parameters. For this reason, this study aimed to evaluate the sensitivity of phytopathogenic fungi to an ethanolic extract of jackfruit leaf by the poison agar and isothermal microcalorimetry (IMC) tests. The kinet ...
DOI:: 10.1016/j.mimet.2022.106457
: https://doi.org/10.1016/j.mimet.2022.106457

27. Determination of streptomycin and doxycycline using LC/MS towards an effective treatment against an experimental Brucella abortus infection in mice

Author:: Eugenia Sancho; Fabio Granados-Chinchilla; Elías Barquero-Calvo
Source:: Journal of microbiological methods 2022 v.194 pp. 106436
ISSN:: 0167-7012
Subject:: Brucella melitensis biovar Abortus; animal models; bone marrow; brucellosis; defatting; doxycycline; freeze drying; liquid chromatography; liver; mass spectrometry; metabolism; mice; streptomycin; therapeutics
Abstract:: ... Herein we described a versatile liquid chromatographic method for detection and quantification of the total levels of two antimicrobials [i.e., streptomycin (STM) and doxycycline (DOX)], in mice plasma and selected tissues, with the aid of a single quadrupole as a detection method. The method included a few sample preparation steps, including freeze-drying and in situ triphasic solvent-assisted de ...
DOI:: 10.1016/j.mimet.2022.106436
: https://doi.org/10.1016/j.mimet.2022.106436

28. Development and evaluation of a sensitive recombinase aided amplification assay for rapid detection of Vibrio parahaemolyticus

Author:: Zhi-shan Feng; Jing-yi Li; Jing-yun Zhang; Feng-yu Li; Hong-xia Guan; Rui-qing Zhang; Hong Liu; Qi Guo; Xin-xin Shen; Biao Kan; Xue-jun Ma
Source:: Journal of microbiological methods 2022 v.193 pp. 106404
ISSN:: 0167-7012
Subject:: Vibrio parahaemolyticus; fish; gastroenteritis; pathogens; plasmids; quantitative polymerase chain reaction; rapid methods; recombinases
Abstract:: ... Vibrio parahaemolyticus (V. parahaemolyticus) is a widely distributed pathogen in the coastal areas, which causes food poisoning and leads to gastroenteritis and sepsis. Therefore, developing a simple, sensitive, and rapid detection method for V. parahaemolyticus is a major concern globally. This study established a sensitive and rapid technique based on recombinase aided amplification (RAA) to de ...
DOI:: 10.1016/j.mimet.2021.106404
: https://doi.org/10.1016/j.mimet.2021.106404

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

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

30. Do it yourself! – Initial experiences with self-synthesized CsTFA for RNA-SIP analyses

Author:: Severin Weis; Susanne Jacksch; Marius Welkerling; Magnus S. Schmidt; Markus Egert
Source:: Journal of microbiological methods 2022 v.194 pp. 106432
ISSN:: 0167-7012
Subject:: RNA; carbonates; centrifugation; cesium; stable isotopes
Abstract:: ... Cesium trifluoroacetate (CsTFA) is a gradient medium for isopycnic centrifugation in RNA-based Stable Isotope Probing (RNA-SIP), an important means to link the structure and function of microbial communities. We report a protocol to easily synthesize CsTFA from cesium carbonate (Cs₂CO₃) and trifluoroacetic acid (TFA) and show that self-synthesized CsTFA performs similarly to commercial CsTFA in th ...
DOI:: 10.1016/j.mimet.2022.106432
: https://doi.org/10.1016/j.mimet.2022.106432

31. Electrotransformation of thermophilic bacterium Caldimonas manganoxidans

Author:: Takamitsu Arai; Shimpei Aikawa; Kumar Sudesh; Toshiaki Kondo; Akihiko Kosugi
Source:: Journal of microbiological methods 2022 v.192 pp. 106375
ISSN:: 0167-7012
Subject:: Caldimonas; Escherichia coli; bacterial growth; bioplastics; electroporation; genetic engineering; plasmids; thermophilic bacteria
Abstract:: ... Caldimonas manganoxidans is a Gram-negative, thermophilic, bioplastic-producing bacterium that is a promising strain to overcome the drawbacks of existing bioplastic manufacturing methods. However, genetic manipulation of this species has not previously been studied. Here, we developed an optimized electrotransformation protocol for C. manganoxidans by screening conditions, including the bacterial ...
DOI:: 10.1016/j.mimet.2021.106375
: https://doi.org/10.1016/j.mimet.2021.106375

32. Establishment of a TaqMan-MGB probe multiplex real-time PCR system for one-step levofloxacin and clarithromycin resistant Helicobacter pylori detection

Author:: Yan Zhao; Yang Li; Zhixian Luan; Cuiping Ma; Lin Yang; Wang Zhang; Chao Shi
Source:: Journal of microbiological methods 2022 v.192 pp. 106393
ISSN:: 0167-7012
Subject:: Helicobacter pylori; antibiotic resistance; biopsy; clarithromycin; gender; levofloxacin; mutation; patients; plasmids; quantitative polymerase chain reaction; statistics
Abstract:: ... Due to the abuse of antibiotics, the prevalence of antibiotic resistant Helicobacter pylori strains continues to increase. Therefore, antibiotic resistance assessment is now essential in addition to general H. pylori diagnosis in medical institutions to fulfill clinicians administering effective antibiotic regimens. However, the conventional antibiotic resistance assessment methods, such as in vit ...
DOI:: 10.1016/j.mimet.2021.106393
: https://doi.org/10.1016/j.mimet.2021.106393

33. Evaluating acute toxicity in enriched nitrifying cultures: Lessons learned

Author:: Carla Lopez; Charles W. Knapp
Source:: Journal of microbiological methods 2022 v.192 pp. 106377
ISSN:: 0167-7012
Subject:: acetone; acute effects; acute toxicity; aeration; air; ammonia; bacterial communities; biomass; centrifugation; experimental design; inoculum; nitrification; nitrites; toxicity testing; wastewater treatment
Abstract:: ... Toxicological batch assays are essential to assess a compound's acute effect on microorganisms. This methodology is frequently employed to evaluate the effect of contaminants in sensitive microbial communities from wastewater treatment plants (WWTPs), such as autotrophic nitrifying populations. However, despite nitrifying batch assays being commonly mentioned in the literature, their experimental ...
DOI:: 10.1016/j.mimet.2021.106377
: https://doi.org/10.1016/j.mimet.2021.106377

34. Evaluation of VITEK® 2 and MALDI-TOF/MS automated methodologies in the identification of atypical Listeria spp. isolated from food in different regions of Brazil

Author:: Cristhiane M.F. dos Reis; Gustavo Luis de P.A. Ramos; Rodrigo de Castro Lisbôa Pereira; Deyse Christina Vallim; Leonardo Emanuel de Oliveira Costa
Source:: Journal of microbiological methods 2022 v.194 pp. 106434
ISSN:: 0167-7012
Subject:: Listeria grayi; Listeria innocua; Listeria monocytogenes; Listeria welshimeri; automation; elderly; foodborne illness; listeriosis; mortality; pathogens; polymerase chain reaction; Brazil
Abstract:: ... Listeria monocytogenes is a pathogen responsible for listeriosis, a foodborne disease with high mortality rates (20–30%). It mainly affects the elderly, pregnant women, and immunocompromised people. Although not pathogenic, the isolation and identification of Listeria innocua are critical since they can indicate L. monocytogenes' presence as they are closely related and widely distributed in the e ...
DOI:: 10.1016/j.mimet.2022.106434
: https://doi.org/10.1016/j.mimet.2022.106434

35. Evaluation of anti-LipL32 carbon nanotube immunofluorescence probe (carbo-lip) and comparison with MAT, IgM ELISA, IgM spot test and culture for early detection of leptospirosis at local hospital

Author:: K. Sapna; A. Ashaiba; T.N. Ravi Kumar; V. Shashidhar; A.B. Arun; K. Sudhakara Prasad
Source:: Journal of microbiological methods 2022 v.195 pp. 106448
ISSN:: 0167-7012
Subject:: Leptospira; agglutination tests; carbon nanotubes; diagnostic techniques; fluorescent antibody technique; fluorescent dyes; hospitals; leptospirosis; public health
Abstract:: ... Leptospirosis is an emerging public health problem affecting people mainly from tropical and subtropical regions. Therefore, there is a need for rapid and sensitive tests for proper and prompt treatment. Recently we have demonstrated Carbo-Lip probe, which was fabricated through immuno recognition method with fluorescent dye functionalized LipL32 monoclonal antibodies, secondary antibody and Lepto ...
DOI:: 10.1016/j.mimet.2022.106448
: https://doi.org/10.1016/j.mimet.2022.106448

36. Evaluation of commercial ELISA kits for diagnosis of brucellosis in cattle and buffaloes in different epidemiological scenarios

Author:: Laxmi Narayan Sarangi; Kota Sri Naga Leela Surendra; Samir Kumar Rana; Thodangala Naveena; Amitesh Prasad; Nadikerianda Muthappa Ponnanna; Girish Kumar Sharma
Source:: Journal of microbiological methods 2022 v.195 pp. 106449
ISSN:: 0167-7012
Subject:: agglutination tests; brucellosis; cattle; India
Abstract:: ... Seven ELISA kits were evaluated for the fitness of purpose in diagnosing brucellosis among cattle and buffaloes in the endemic scenarios of India. The sera (675 numbers) for the study were sourced from brucellosis-free as well as infected herds. The diagnostic sensitivity (dsn) and specificity (dsp) of the kits were determined by three approaches: based on the results of the Rose Bengal test, hist ...
DOI:: 10.1016/j.mimet.2022.106449
: https://doi.org/10.1016/j.mimet.2022.106449

37. Evaluation of the clinical sensitivity and specificity of the BD Max™ Enteric Bacterial Panel for molecular detection of pathogens for acute gastroenteritis in the Singaporean population

Author:: Seok Hwee Koo; Ying Xuan Heng; Boran Jiang; Lily Siew Yong Ng; Diana Miao Fang Sim; Thean Yen Tan
Source:: Journal of microbiological methods 2022 pp. 106478
ISSN:: 0167-7012
Subject:: Aeromonas; Campylobacter; Plesiomonas shigelloides; Salmonella; Shiga toxin-producing Escherichia coli; Singapore; Vibrio parahaemolyticus; bacterial culture; epidemiology; gastroenteritis; labor; reference standards
Abstract:: ... Acute gastroenteritis (AGE) is caused by a wide range of pathogens. Culture methods for the detection of bacterial pathogens is time consuming and labour intensive. This study compared a same-day-to-result commercial molecular method using BD Max™ Enteric Bacterial Panel against conventional culture and laboratory-developed PCR assays (LDTs), and characterised the epidemiology of bacterial AGE in ...
DOI:: 10.1016/j.mimet.2022.106478
: https://doi.org/10.1016/j.mimet.2022.106478

38. Evaluation of various phenotypic methods for differentiation of Candida dubliniensis from Candida albicans

Author:: Abiroo Jan; Gulnaz Bashir; Insha Altaf; Bashir A. Fomda; Sabiya Hamid; Kownsar Jan
Source:: Journal of microbiological methods 2022 v.193 pp. 106400
ISSN:: 0167-7012
Subject:: Candida albicans; agar; color; cost effectiveness; heat tolerance; hyphae; phenotype; polymerase chain reaction; salt tolerance; tobacco; xylose; Ireland
Abstract:: ... Candida dubliniensis was first identified by Sullivan et al. (1995) in Dublin, Ireland. Its clinical significance is associated with development of fluconazole-resistance and invasive diseases in immunocompromised hosts. C. dubliniensis share many features with C. albicans so has been overlooked and misidentified for a long time. Evaluation of various phenotypic tests with polymerase chain reactio ...
DOI:: 10.1016/j.mimet.2021.106400
: https://doi.org/10.1016/j.mimet.2021.106400

39. Experimental validation under controlled conditions of real time PCR to quantify arbuscular mycorrhizal colonization in root

Author:: Bruna Arruda; Yasmin Florentino Rodrigues; Wilfrand Ferney Bejarano Herrera; Agnès Robin; Simone Raposo Cotta; Fernando Dini Andreote
Source:: Journal of microbiological methods 2022 v.192 pp. 106382
ISSN:: 0167-7012
Subject:: microscopy; quantitative polymerase chain reaction; vesicular arbuscular mycorrhizae
Abstract:: ... Mycorrhizal colonization of roots is traditionally evaluated by empirical methods, such as root microscopy. We compared this method with data from using a real time PCR technique, and determined the correlation between methods, indicating particularities of a promising system for a quick and accurate molecular diagnostic of arbuscular mycorrhization. ...
DOI:: 10.1016/j.mimet.2021.106382
: https://doi.org/10.1016/j.mimet.2021.106382

40. Formalin-fixed paraffin-embedded tissues for microbiome analysis in rainbow trout (Oncorhynchus mykiss)

Author:: Roberto Cruz-Flores; Mónica Hernández Rodríguez; Jesús Salvador Olivier Guirado Flores; Arun K. Dhar
Source:: Journal of microbiological methods 2022 v.192 pp. 106389
ISSN:: 0167-7012
Subject:: Oncorhynchus mykiss; digestive system; histology; intestinal microorganisms; microbiome
Abstract:: ... The gut microbiomes of rainbow trout (Oncorhynchus mykiss) reared at 16° and 22 °C were determined using formalin-fixed paraffin-embedded tissues (FFPE) and compared to fresh frozen tissue. The data revealed microbiomes could be successfully determined using FFPE tissue opening a new horizon in studying intestinal microbiota using archived histological samples. ...
DOI:: 10.1016/j.mimet.2021.106389
: https://doi.org/10.1016/j.mimet.2021.106389

41. Green synthesis, characterization of silver nanoparticals for biomedical application and environmental remediation

Author:: Victoria Vorobyova; Georgii Vasyliev; Dmitriy Uschapovskiy; Khrokalo Lyudmyla; Margarita Skiba
Source:: Journal of microbiological methods 2022 v.193 pp. 106384
ISSN:: 0167-7012
Subject:: Bacillus subtilis; Candida albicans; Escherichia coli; X-ray diffraction; antibacterial properties; biosynthesis; electrochemistry; energy-dispersive X-ray analysis; grapes; nanosilver; nylon; oxidation; oxygen; photocatalysis; remediation; silver; tandem mass spectrometry; ultrasonics; ultraviolet-visible spectroscopy; zeta potential
Abstract:: ... Production of silver nanoparticles (Ag-NPs) to increase photocatalytic activity of commercial TiO₂ (P25) and antibacterial activity of surgical sutures was studied. А new method of “green” synthesis of Ag-NPs from aqueous extract of grape skin (oxidation product), which is pre-processed by oxygen and ultrasound is reported. Also, a new method of electrochemical modification of surgical sutures was ...
DOI:: 10.1016/j.mimet.2021.106384
: https://doi.org/10.1016/j.mimet.2021.106384

42. High throughput pH bioassay demonstrates pH adaptation of Rhizobium strains isolated from the nodules of Trifolium subterraneum and T. repens

Author:: Anish S. Shah; Steve A. Wakelin; Derrick J. Moot; Céline Blond; Alasdair Noble; Hayley J. Ridgway
Source:: Journal of microbiological methods 2022 v.195 pp. 106455
ISSN:: 0167-7012
Subject:: Rhizobium; Trifolium repens; Trifolium subterraneum; bioassays; mannitol; soil pH; yeasts
Abstract:: ... The purpose of developing this high throughput assay was to determine whether there was evidence of pH adaptation in strains of rhizobia which nodulate subterranean clover (SC) and white clover (WC), and whether this was related to the pH of the soil of origin. pH is a first-order factor influencing the niche preferences of soil microorganisms and has been convincingly shown to be a key driver of ...
DOI:: 10.1016/j.mimet.2022.106455
: https://doi.org/10.1016/j.mimet.2022.106455

43. Identification of two potential aetiological agents of chronic diarrhoea in an immunocompromised patient in Cuba using conventional and molecular diagnostic techniques

Author:: Luis Enrique Jerez Puebla; Fidel A. Núñez Fernández; Iraís Atencio Millán; Jorge Pérez Avila; Jorge Fraga Nodarse; Iredys Cruz Rodríguez; Laura Rodríguez Moreno; Yanet Fresco Sampedro; Lucy J. Robertson
Source:: Journal of microbiological methods 2022 v.192 pp. 106376
ISSN:: 0167-7012
Subject:: Enterocytozoon bieneusi; diagnostic techniques; diarrhea; microscopy; patients; Cuba
Abstract:: ... The aetiology of diarrhoea in a patient in Cuba with HIV was investigated. Although molecular diagnostics are still not used in many under-resourced settings, here traditional methods were supported by use of PCR. This approach enabled detection of a dual infection (Cystoisospora belli and Enterocytozoon bieneusi), the latter of which was not identified by microscopy with Didier's trichromic stain ...
DOI:: 10.1016/j.mimet.2021.106376
: https://doi.org/10.1016/j.mimet.2021.106376

44. Insight into the biotechnology potential of Alicyclobacillus tolerans from whole genome sequence analysis and genome-scale metabolic network modeling.

Author:: Enuh Blaise Manga; Belma Nural Yaman; Pınar Aytar Çelik
Source:: Journal of microbiological methods 2022 pp. 106459
ISSN:: 0167-7012
Subject:: Alicyclobacillus; acid mine drainage; bacteria; biochemical pathways; bioinformatics; bioleaching; biotechnology; carbon; computer simulation; energy; genomics; mathematical models; metabolism; nucleic acids; nucleotide sequences; phenotype; pyrite; sequence analysis
Abstract:: ... Extremophilic bacteria have numerous uncovered biotechnological potentials. Acidophilic bacteria are important iron oxidizers that are valuable in bioleaching and in studying extreme environments on earth and in space. Despite their obvious potential, little is known about the genetic traits that underpin their metabolic functions, which are equally poorly understood from a mechanistic perspective ...
DOI:: 10.1016/j.mimet.2022.106459
: https://doi.org/10.1016/j.mimet.2022.106459

45. Interlaboratory evaluations of a standardized quantitative test method for determining the bactericidal and tuberculocidal efficacy of antimicrobial substances on hard non-porous surfaces

Author:: Stephen F. Tomasino; Rebecca M. Pines; Darla M. Goeres; Albert E. Parker
Source:: Journal of microbiological methods 2022 v.196 pp. 106460
ISSN:: 0167-7012
Subject:: Mycobacterium terrae; Pseudomonas aeruginosa; Staphylococcus aureus; disease control; liquids; markets; quantitative analysis; stainless steel; statistical analysis
Abstract:: ... The development, validation, and use of new quantitative methodologies for testing the effectiveness of antimicrobial products are necessary to meet the regulatory challenges associated with an ever-changing marketplace, novel product claims, new infection control practices, and the emergence of new clinical pathogens. A series of four interlaboratory studies were conducted in a standardized manne ...
DOI:: 10.1016/j.mimet.2022.106460
: https://doi.org/10.1016/j.mimet.2022.106460

46. Is skipping the definition of primary and secondary models possible? Prediction of Escherichia coli O157 growth by machine learning

Author:: Kento Koyama; Kyosuke Kubo; Satoko Hiura; Shige Koseki
Source:: Journal of microbiological methods 2022 v.192 pp. 106366
ISSN:: 0167-7012
Subject:: Escherichia coli O157; mathematical theory; model validation; normal distribution; population growth; prediction; predictive microbiology; regression analysis
Abstract:: ... To predict bacterial population behavior in food, statistical models with specific function form have been applied in the field of predictive microbiology. Modelers need to consider the linear or non-linear relationship between the response and explanatory variables in the statistical modeling approach. In the present study, we focused on machine learning methods to skip definition of primary and ...
DOI:: 10.1016/j.mimet.2021.106366
: https://doi.org/10.1016/j.mimet.2021.106366

47. Low-cost, specific PCR assays to identify the main aflatoxigenic species of Aspergillus section Flavi

Author:: Josué J. Silva; Maria H.P. Fungaro; Taynara Souza Soto; Marta H. Taniwaki; Beatriz T. Iamanaka
Source:: Journal of microbiological methods 2022 v.196 pp. 106470
ISSN:: 0167-7012
Subject:: DNA-directed RNA polymerase; aflatoxins; cryptic species; food contamination; fungi; loci; metabolites
Abstract:: ... Aflatoxins are fungal metabolites that are present as contaminants in food globally. Most aflatoxigenic species belong to Aspergillus section Flavi, and the main ones are grouped in the A. flavus clade, where many cryptic species that are difficult to discriminate are found. In this study, we investigated inter- and intraspecific diversity of the A. flavus clade to develop low-cost, species-specif ...
DOI:: 10.1016/j.mimet.2022.106470
: https://doi.org/10.1016/j.mimet.2022.106470

48. Machine learning approach for predicting the antifungal effect of gilaburu (Viburnum opulus) fruit extracts on Fusarium spp. isolated from diseased potato tubers

Author:: Alper Zongur; Hatice Kavuncuoglu; Erhan Kavuncuoglu; Tugba Dursun Capar; Hasan Yalcin; Mehmet Akif Buzpinar
Source:: Journal of microbiological methods 2022 v.192 pp. 106379
ISSN:: 0167-7012
Subject:: Viburnum opulus; acetone; antifungal properties; ethanol; food microbiology; fruits; fungal growth; methanol; neural networks; potatoes
Abstract:: ... This work addresses the mathematical model building to detect the diameter of the inhibition zone of gilaburu (Viburnum opulus L.) extract against eight different Fusarium strains isolated from diseased potato tubers. Gilaburu extracts were obtained with acetone, ethanol or methanol. The isolated Fusarium strains were: F. solani, F. oxysporum, F. sambucinum, F. graminearum, F. coeruleum, F. sulphu ...
DOI:: 10.1016/j.mimet.2021.106379
: https://doi.org/10.1016/j.mimet.2021.106379

49. Measurement of lactose concentration in milk by using engineered bacteria producing lycopene

Author:: Yinjie Li; Qunqun Guo; Tingting Zhang; Chao Wang; Hong Yang; Guicai Du; Ronggui Li
Source:: Journal of microbiological methods 2022 v.194 pp. 106390
ISSN:: 0167-7012
Subject:: Escherichia coli; bacterial culture; genetic transformation; high performance liquid chromatography; lactose; lycopene; milk; phenotype; plasmids; spectrophotometers
Abstract:: ... Lycopene is an orange–red carotenoid, which confers a visual phenotype to assess genetic transformation of microorganisms. In this study, the lycopene synthesis pathway was constructed in engineered Escherichia coli BL21 (DE3) by transforming plasmid pET-15b-crtBEI, wherein crtB, crtE, and crtI could be expressed under the control of the T7 promoter and lacO operator and lycopene could be accumula ...
DOI:: 10.1016/j.mimet.2021.106390
: https://doi.org/10.1016/j.mimet.2021.106390

50. Methodology to streamline flow cytometric-based detection of early stage Plasmodium parasitemia in mice

Author:: Mohan Liu; Matthew J. Liao; Christopher J. Fisher; Rodolfo D. Vicetti Miguel; Thomas L. Cherpes
Source:: Journal of microbiological methods 2022 v.195 pp. 106439
ISSN:: 0167-7012
Subject:: Plasmodium berghei; fluorescence; laminar flow; malaria; mice; parasitemia; therapeutics
Abstract:: ... Murine infection models are needed to develop therapeutics and vaccines to combat the Plasmodium parasites causing malaria. Herein, we describe an easy to perform flow cytometry-based methodology for detecting green fluorescent protein-expressing Plasmodium berghei in the peripheral red blood cells (RBC) of mice. This methodology uses one-step staining and simplified gating strategies to streamlin ...
DOI:: 10.1016/j.mimet.2022.106439
: https://doi.org/10.1016/j.mimet.2022.106439

51. 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
: https://doi.org/10.1016/j.mimet.2022.106476

52. Multi-dimensional nanoscale liquid chromatography and nano-electrospray ion-trap mass spectrometry for detection of Clostridium botulinum type C and the produced botulinum neurotoxin type C complex

Author:: Tanja Plößl; Nada Vujtovic-Ockenga; Corinna Kehrenberg; Bernd Klaubert
Source:: Journal of microbiological methods 2022 v.193 pp. 106397
ISSN:: 0167-7012
Subject:: Clostridium botulinum C; bacteria; bacteriophages; bioassays; biosynthesis; botulinum toxin; botulism; fish; grass sickness; liquid chromatography; mice; neurotoxins; poultry; toxicity; veterinary medicine
Abstract:: ... Botulinum neurotoxin types C, D and their mosaic forms C/D and D/C produced mainly by Clostridium botulinum types C and D cause botulism in animals and belong to the most toxic substances for poultry and fish. In addition to intoxications, also toxoinfections with C. botulinum types C and D play a role that should not be underestimated, especially in veterinary medicine. Contrary to other botulinu ...
DOI:: 10.1016/j.mimet.2021.106397
: https://doi.org/10.1016/j.mimet.2021.106397

53. Nanoparticle immuno-fluorescent probes as a method for detection of viable E. coli O157:H7

Author:: Nasruddeen Al-Awwal; Mehdi Masjedi; Majed El-Dweik; Stephen H. Anderson; Jamshid Ansari
Source:: Journal of microbiological methods 2022 v.193 pp. 106403
ISSN:: 0167-7012
Subject:: Escherichia coli O157; Salmonella enterica; antibodies; biosensors; dyes; fluorescence; fluorescence microscopy; isothiocyanates; nanogold; photons; transmission electron microscopy; ultraviolet-visible spectroscopy; wavelengths
Abstract:: ... Development of revolutionary sensitive biosensors for detecting the presence of harmful biological species in the environment is a necessity for countering disease outbreaks. This work examined the interaction of fluorescence-labeled antibody on amine functionalized gold nanoparticles (GNP) as a model system. The synthesized tetramethylrhodamine isothiocyanate (TRITC) labeled antibody-amine functi ...
DOI:: 10.1016/j.mimet.2021.106403
CHORUS:: 10.1016/j.mimet.2021.106403
: https://doi.org/10.1016/j.mimet.2021.106403

54. Novel microaerobic agar plate method delivers highly selective and accurate enumeration of probiotic lactobacilli in freeze-dried blends containing bifidobacteria

Author:: Phillip M. Byrd; Vincenzo Fallico; Peipei Tang; Connie Wong
Source:: Journal of microbiological methods 2022 v.195 pp. 106451
ISSN:: 0167-7012
Subject:: Bifidobacterium; Lactobacillus; agar; antibiotics; carbon dioxide; dietary supplements; food industry; freeze drying; oxygen; probiotics
Abstract:: ... The enumeration of viable bacteria is an essential metric in the dietary supplement and food industry to ensure quality of probiotic products. However, selective enumeration of lactobacilli in probiotic freeze-dried blends containing bifidobacteria is difficult to achieve with current Lactobacillus-specific agars (i.e., Rogosa and LAMVAB). Using a panel of Bifidobacterium and Lactobacillus commerc ...
DOI:: 10.1016/j.mimet.2022.106451
: https://doi.org/10.1016/j.mimet.2022.106451

55. Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms

Author:: Alison M. Cupples; Jean-Rene Thelusmond
Source:: Journal of microbiological methods 2022 v.193 pp. 106401
ISSN:: 0167-7012
Subject:: Geobacter; Mycobacterium; ammonia; data collection; databases; genes; methane monooxygenase (particulate); methane monooxygenase (soluble); methanotrophs; oxidation; phenol; phylotype; pollution; soil; soil ecology; toluene; xylene
Abstract:: ... Cometabolic oxidation involves the oxidation of chemicals often by monooxygenases or dioxygenases and can be a removal process for environmental contaminants such as trichloroethene (TCE) or 1,4-dioxane. Information on the occurrence of these genes and their associated microorganisms in environmental samples has the potential to enhance our understanding of contaminant removal. The overall aims we ...
DOI:: 10.1016/j.mimet.2021.106401
: https://doi.org/10.1016/j.mimet.2021.106401

56. Preservation of Streptococcus pneumoniae quality control strains using chocolate agar blocks in glycerol at minus 70 degrees celsius

Author:: Sindhulina Chandrasingh; Mahalaxmi Subramaniam; Sreeja Nair
Source:: Journal of microbiological methods 2022 v.196 pp. 106469
ISSN:: 0167-7012
Subject:: Streptococcus pneumoniae; culture media; glycerol; quality control; viability
Abstract:: ... We present a method for storage of the quality control strain of S. pneumoniae that could be used in low resource settings. Small blocks of chocolate agar with growth were placed in glycerol (60%V/V) and stored at minus 70 °C. Viability and cultural characteristics were maintained for the testing period of 10 months. The wide availability of both chocolate agar and glycerol make this a suitable al ...
DOI:: 10.1016/j.mimet.2022.106469
: https://doi.org/10.1016/j.mimet.2022.106469

57. Probe-based qPCR assay enables the rapid and specific detection of bacterial degrading genes for the pesticide metaldehyde in soil

Author:: Víctor M. Castro-Gutierrez; Francis Hassard; James W.B. Moir
Source:: Journal of microbiological methods 2022 v.195 pp. 106447
ISSN:: 0167-7012
Subject:: biodegradation; compliance; metaldehyde; molluscicides; multigene family; pollutants; quantitative polymerase chain reaction; sand; soil; water purification
Abstract:: ... Metaldehyde, a molluscicide pesticide, has been identified as a pollutant of concern due to its repeated detection in drinking water, thereby generating numerous compliance failures for water utilities. Biological degradation potential for metaldehyde is widespread in soils, occurring at different rates, but to date, no molecular methods for its assessment have been reported. Here, three genes bel ...
DOI:: 10.1016/j.mimet.2022.106447
: https://doi.org/10.1016/j.mimet.2022.106447

58. Pulling needles out of a haystack: Subtractive community metatranscriptomics retrieves anaerobic o-xylene degradation pathway genes out of a mixed microbial culture

Author:: Karen Rossmassler; Jean F. Challacombe; Susan K. De Long
Source:: Journal of microbiological methods 2022 pp. 106481
ISSN:: 0167-7012
Subject:: biodegradation; biomarkers; microbial culture; microbiome; reverse transcriptase polymerase chain reaction; suppression subtractive hybridization; toluene; transcriptomics; xylene
Abstract:: ... For many contaminants, biomarker genes are unknown or assays are unavailable, and most biomarker assays target the first pathway step. Herein, we obtained sequences for all of the genes in a previously hypothesized o-xylene degradation pathway based on similarities to analogous genes in a known toluene degradation pathway. Comparative metatranscriptomics resulted in sequences for genes annotated a ...
DOI:: 10.1016/j.mimet.2022.106481
: https://doi.org/10.1016/j.mimet.2022.106481

59. Quantification of cyanobacterial cyclic di-guanosine monophosphate (c-di-GMP) by liquid chromatography electrospray ionization tandem mass spectrometry

Author:: Marina Kameda; Robert A. Kanaly; Mei Harada; Setsuyuki Aoki; Hideyuki Tukada; Shinsuke Kutsuna
Source:: Journal of microbiological methods 2022 v.196 pp. 106468
ISSN:: 0167-7012
Subject:: Synechococcus sp. PCC 7942; cost effectiveness; cyclic AMP; cyclic GMP; electrospray ionization mass spectrometry; flocculation; liquid chromatography; methanol; phototaxis; solvents; tandem mass spectrometry
Abstract:: ... Cyclic di-guanosine monophosphate (c-di-GMP) is a second messenger found ubiquitously in bacteria. This signaling molecule regulates a variety of physiological activities such as phototaxis and flocculation in cyanobacteria and is critical for their environmental adaptation. Although genes encoding the enzymes for synthesis and/or degradation of c-di-GMP are found in the genomes of both multicellu ...
DOI:: 10.1016/j.mimet.2022.106468
: https://doi.org/10.1016/j.mimet.2022.106468

60. Rapid and specific detection of Mycoplasma gallisepticum and Mycoplasma synoviae infection in poultry using single and duplex PCR assays

Author:: Jay Prakash Yadav; Yarvendra Singh; Naresh Jindal; N.K. Mahajan
Source:: Journal of microbiological methods 2022 v.192 pp. 106365
ISSN:: 0167-7012
Subject:: Mycoplasma gallisepticum; Mycoplasma synoviae; air; birds; confidence interval; flocks; genes; hemagglutinins; intergenic DNA; mycoplasmosis; necropsy; poultry; poultry industry; respiratory tract diseases; India
Abstract:: ... Avian mycoplasmosis, mainly caused by Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS), is an economically important disease of poultry industry. The present study was aimed to develop duplex PCR as a rapid, specific and economical method for accurate detection of MG and MS in poultry and its comparison with single (monoplex) MG/MS PCR. During present investigation, a total of 146 poultr ...
DOI:: 10.1016/j.mimet.2021.106365
: https://doi.org/10.1016/j.mimet.2021.106365

61. Rapid cell counting and viability detection method of Escherichia coli Nissle using image cytometry

Author:: Michele Perry; Mary McDonald; Anders Lund; Mrinalini Nikrad; Denise Wong; William L. Rice; Leo Li-Ying Chan
Source:: Journal of microbiological methods 2022 v.192 pp. 106381
ISSN:: 0167-7012
Subject:: Escherichia coli; biopharmaceutical industry; biopharmaceuticals; fluorescence; viability
Abstract:: ... The improvement of cell enumeration methods for the counting of Escherichia coli (E. coli) is important as E. coli gains in popularity as a basis for biopharmaceutical applications. In the biopharmaceutical industry, enumerating, characterizing, and dosing the accurate number of cells is imperative. In this work, we demonstrate the utilization of a chip-based image cytometer using a thin-gap, low ...
DOI:: 10.1016/j.mimet.2021.106381
: https://doi.org/10.1016/j.mimet.2021.106381

62. Rapid detection and discrimination of potentially toxigenic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis by multiplex real-time PCR and amplicon melting curve analysis

Author:: Jun Kawase; Tomotake Sakai; Masaaki Iwaki; Kaoru Umeda; Aiko Fukuma; Naoki Fujisawa; Yuta Kawakami; Hiroki Hayashi; Mieko Wada
Source:: Journal of microbiological methods 2022 v.195 pp. 106454
ISSN:: 0167-7012
Subject:: Corynebacterium pseudotuberculosis; Corynebacterium ulcerans; diphtheria toxin; genes; quantitative polymerase chain reaction; rapid methods
Abstract:: ... We developed a multiplex real-time PCR assay with amplicon melting curve analysis to rapidly discriminate Corynebacterium ulcerans from Corynebacterium pseudotuberculosis and detect the bacterial diphtheria toxin gene. This assay should be a valuable tool for identification of potentially toxigenic C. ulcerans. ...
DOI:: 10.1016/j.mimet.2022.106454
: https://doi.org/10.1016/j.mimet.2022.106454

63. Rapid detection of KPC-producing Klebsiella pneumoniae in China based on MALDI-TOF MS

Author:: Yun Huang; Juan Li; Qianyu Wang; Kewen Tang; Congrong Li
Source:: Journal of microbiological methods 2022 v.192 pp. 106385
ISSN:: 0167-7012
Subject:: Klebsiella pneumoniae; algorithms; automation; computer software; cross infection; disease control; drug resistance; genes; patients; public health; China
Abstract:: ... Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) represent a serious threat to public health and their timely detection is essential for patient management and the prevention of nosocomial infections. Here, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to rapidly identify dominant KPC-Kp in China, by using an automated dete ...
DOI:: 10.1016/j.mimet.2021.106385
: https://doi.org/10.1016/j.mimet.2021.106385

64. Real-time quantitative PCR method for detection and quantification of Clostridioides difficile cells and spores

Author:: Christina M. Kohler; Ana G. Quintanar Alfaro; Randall T. Hayden; Elisa B. Margolis
Source:: Journal of microbiological methods 2022 v.196 pp. 106458
ISSN:: 0167-7012
Subject:: Clostridium difficile; genes; quantitative polymerase chain reaction
Abstract:: ... A quantitative PCR method was developed for the detection of Clostridioides difficile Chaperonin-60 gene. The method had a specificity for C. difficile strains of clinical and epidemiological importance and allowed for quantification of C. difficile cells and spores. ...
DOI:: 10.1016/j.mimet.2022.106458
: https://doi.org/10.1016/j.mimet.2022.106458

65. Research on the optimization, key chemical constituents and antibacterial activity of the essential oil extraction process of Thuja koraiensis Nakai

Author:: Cong Fu; Xuehan Lan; Jingqi Yuan; Chenghong Li; Liming Li; Zhongliang Yu; Tingting Tan; Mengqi Yuan; Fengguo Du
Source:: Journal of microbiological methods 2022 v.194 pp. 106435
ISSN:: 0167-7012
Subject:: Bacillus subtilis; Escherichia coli; Staphylococcus aureus; Thuja; acetates; antibacterial properties; essential oils; gas chromatography-mass spectrometry; insects; lipid content; minimum inhibitory concentration; odors; response surface methodology; steam distillation; system optimization; trees
Abstract:: ... Thuja koraiensis Nakai is a kind of precious economic tree species with fragrance, ornamental and medicinal functions. The essential oil has the satisfactory antibacterial activity. In this paper, the essential oil from the branches and leaves of Thuja koraiensis Nakai was studied by optimization of extraction process, and the optimized parameters mainly include solid-liquid ratio, NaCl concentrat ...
DOI:: 10.1016/j.mimet.2022.106435
: https://doi.org/10.1016/j.mimet.2022.106435

66. Role of temperature, nutrition, oxygen, osmolality, and bacterial strain in inducing a viable but non-culturable state in Campylobacter jejuni

Author:: Sayo Yagi; Ayaka Okada; Yasuo Inoshima
Source:: Journal of microbiological methods 2022 v.195 pp. 106456
ISSN:: 0167-7012
Subject:: Campylobacter jejuni; food pathogens; monitoring; nutrition; osmolality; oxygen; temperature
Abstract:: ... Campylobacter jejuni is a globally important foodborne pathogen that can exist environmentally in a viable but non-culturable (VBNC) state, leading to missed detection of VBNC cells in food and false results in epidemiological surveillance. To establish a method for its resuscitation from the VBNC state and enable better detection, the mechanisms by which C. jejuni are induced into the VBNC state ...
DOI:: 10.1016/j.mimet.2022.106456
: https://doi.org/10.1016/j.mimet.2022.106456

67. Screening of immune-enhancing Lactobacillus in mice by using a cell-line

Author:: Xiaomin Yu; Yu Zhang; Feng Xu; Degang Dong; Wanchun Wang; Xiaoli Wu
Source:: Journal of microbiological methods 2022 v.192 pp. 106380
ISSN:: 0167-7012
Subject:: Lactobacillus paracasei; blood serum; cell culture; colon; cyclophosphamide; epithelium; immune response; interleukin-2; interleukin-6; mice; splenocytes
Abstract:: ... In this study, we found that it is possible to screen Lactobacillus strains that enhance the immune function of mice using HCT-8 cells. Lactobacillus were co-incubated with intestinal epithelial HCT-8 cells to detect and screen the strains that induced more interleukin-6 (IL-6) in the culture supernatant. Simultaneously, a mouse model of low immunity was established to administer the screened lact ...
DOI:: 10.1016/j.mimet.2021.106380
: https://doi.org/10.1016/j.mimet.2021.106380

68. Single-round multiplex PCR with species-specific mitochondrial primers of P. falciparum, P. vivax/P. simium and P. malariae/P. brasilianum: Comparison with standard techniques

Author:: Wilson Domingues; Emilly Henrique dos Santos; Lidia Yamamoto; Silvia Maria Di Santi; Kelly Aparecida Kanunfre; Thelma Suely Okay
Source:: Journal of microbiological methods 2022 v.193 pp. 106398
ISSN:: 0167-7012
Subject:: Babesia canis subsp. vogeli; Bartonella henselae; Chagas disease; Plasmodium falciparum; Rickettsia; anemia; leishmaniasis; malaria; microscopy; mitochondria; parasites; polymerase chain reaction; schistosomiasis
Abstract:: ... A single-round multiplex PCR (mPCR) with species-specific primers (SSP) of three mitochondrial genes of Plasmodium, namely COX I, COX III and CYT B, was compared to microscopy and 18S rRNA semi-nested PCR, nested-PCR and Real Time PCRs (*PCRs). Each parasite has between 20 and 150 mitochondria and each mitochondria has one copy of each target gene, while 18S rRNA gene is repeated 4 to 8 times. The ...
DOI:: 10.1016/j.mimet.2021.106398
: https://doi.org/10.1016/j.mimet.2021.106398

69. Spectinomycin, gentamicin, and routine disc diffusion testing: An alternative for the treatment and monitoring of multidrug-resistant Neisseria gonorrhoeae?

Author:: Jéssica Motta Martins; Mara Cristina Scheffer; Hanalydia de Melo Machado; Marcos André Schörner; Lisléia Golfetto; Thais Matos Santos; Fernando Hartmann Barazzetti; Victor Cavadas Barreto de Albuquerque; Maria Luiza Bazzo
Source:: Journal of microbiological methods 2022 pp. 106480
ISSN:: 0167-7012
Subject:: Neisseria gonorrhoeae; agar; antibiotic resistance; azithromycin; ceftriaxone; ciprofloxacin; gentamicin; laboratory diagnosis; multiple drug resistance; public health; spectinomycin; Brazil
Abstract:: ... Neisseria gonorrhoeae is a major concern of public health due to its extraordinary capacity to develop and acquire resistance to different antimicrobials used to treat gonorrhoea. Limited treatment options and uncontrolled transmission have raised the need to assess the antimicrobial susceptibility profile of the isolates and to establish affordable alternatives for laboratory diagnosis. This stud ...
DOI:: 10.1016/j.mimet.2022.106480
: https://doi.org/10.1016/j.mimet.2022.106480

70. Standardisation and validation of an in-house quantitative real-time polymerase chain reaction (qPCR) assay for the diagnosis of Clostridioides difficile infection

Author:: Adriane C. Maestri; Sonia M. Raboni; Laura L. Cogo; Marisa V. Rossi; Keite S. Nogueira
Source:: Journal of microbiological methods 2022 v.193 pp. 106399
ISSN:: 0167-7012
Subject:: Clostridium difficile; algorithms; cross infection; diagnostic techniques; diarrhea; enteropathogens; genes; glutamate dehydrogenase; hydrolysis; laboratory diagnosis; quantitative polymerase chain reaction; toxins
Abstract:: ... Clostridioides difficile is an emerging enteric pathogen that causes nosocomial diarrhoea in adults. The excessive cost of commercial molecular tests restricts the access of developing countries to its diagnosis. This study aimed to develop and validate in-house quantitative polymerase chain reaction (qPCR) targeting the C. difficile toxin B gene (tcdB) using two detection methodologies—SYBR Green ...
DOI:: 10.1016/j.mimet.2021.106399
: https://doi.org/10.1016/j.mimet.2021.106399

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

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

72. 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
: https://doi.org/10.1016/j.mimet.2021.106391

73. The AMR-ARRAY: A modular bead array detecting β-lactam, (fluoro) quinolone, colistin, aminoglycoside and macrolide resistance determinants in Gram-negative bacteria

Author:: Michaël Timmermans; Samuel Latour; Pieter-Jan Ceyssens; Cristina Garcia-Graells; Carole Kowalewicz; David Fretin; Olivier Denis; Pierre Wattiau; Cécile Boland
Source:: Journal of microbiological methods 2022 v.196 pp. 106472
ISSN:: 0167-7012
Subject:: Escherichia coli; Salmonella; Shigella; aminoglycosides; antibiotic resistance; colistin; computer software; ligases; macrolides; quinolones; sequence analysis
Abstract:: ... The aim of this study was to develop a highly multiplexed bead array to detect genes and/or mutations frequently associated with resistance to antimicrobials of the β-lactam, (fluoro)quinolone, colistin, macrolide and aminoglycoside families in Enterobacteriaceae such as Escherichia coli, Shigella spp. and Salmonella spp. Ligase Chain Reaction and the Luminex® technology were combined in a 53-plex ...
DOI:: 10.1016/j.mimet.2022.106472
: https://doi.org/10.1016/j.mimet.2022.106472

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

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

75. Transposition of insertion sequences by dielectric barrier discharge plasma and gamma irradiation in the radiation-resistant bacterium Deinococcus geothermalis

Author:: Qianying Ye; Eunjung Shin; Chanjae Lee; Nakjun Choi; Yeonho Kim; Ki Sun Yoon; Sung-Jae Lee
Source:: Journal of microbiological methods 2022 v.196 pp. 106473
ISSN:: 0167-7012
Subject:: Deinococcus geothermalis; Deinococcus radiodurans; Deinococcus radiopugnans; bacteria; biosynthesis; carotenoids; cystine; gamma radiation; hydrogen peroxide; oxidative stress; phenotypic selection; phytoene synthase; protein deficiencies; reactive nitrogen species
Abstract:: ... Insertion sequences (ISs) of the radiation-resistant bacterium Deinococcus geothermalis are transposed into other loci by oxidative stress through hydrogen peroxide treatment. Gamma irradiation and dielectric barrier discharge (DBD) plasma radiation are known to produce a variety of oxidative stress agents such as reactive oxygen species and reactive nitrogen species. Therefore, to determine wheth ...
DOI:: 10.1016/j.mimet.2022.106473
: https://doi.org/10.1016/j.mimet.2022.106473

76. Validation of a cariogenic biofilm model by evaluating the effect of fluoride on enamel demineralization

Author:: Lina M. Marin; Jaime A. Cury; Walter L. Siqueira
Source:: Journal of microbiological methods 2022 v.192 pp. 106386
ISSN:: 0167-7012
Subject:: Streptococcus mutans; biofilm; culture media; dose response; enamel; fluorides; glucose; models; peptides; sucrose; water solubility
Abstract:: ... In vitro biofilm models have been extensively used, but only few of the models available to date had been validated in terms of the dose-response effect of anti-caries and/or antimicrobial substances. Additionally, none of the validated models allow the use of microliter volumes of the treatment solutions, needed mainly to test (screen) novel but expensive substances under development. This study ...
DOI:: 10.1016/j.mimet.2021.106386
: https://doi.org/10.1016/j.mimet.2021.106386

77. A LAMP-based system for rapid detection of eight common pathogens causing lower respiratory tract infections

Author:: Yuying Si; Tong Zhang; Nianzhen Chen; Yu Cheng; Lan Wang; Jiayi Yuan; Gen Li; Ming Zong; Guodong Sui; Lieying Fan
Source:: Journal of microbiological methods 2021 v.190 pp. 106339
ISSN:: 0167-7012
Subject:: Acinetobacter baumannii; Escherichia coli; Haemophilus influenzae; Klebsiella pneumoniae; Moraxella catarrhalis; Pseudomonas aeruginosa; Staphylococcus aureus; Streptococcus pneumoniae; diagnostic techniques; loop-mediated isothermal amplification; morbidity; mortality; rapid methods; respiratory system
Abstract:: ... Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality worldwide and lack a rapid diagnostic method. To improve the diagnosis of LRTIs, we established an available loop-mediated isothermal amplification (LAMP) assay for the detection of eight common lower respiratory pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Stap ...
DOI:: 10.1016/j.mimet.2021.106339
: https://doi.org/10.1016/j.mimet.2021.106339

78. A dynamic resazurin microassay allowing accurate quantification of cells and suitable for acid-forming bacteria

Author:: Maritxu Labadie; Irina Randrianjatovo-Gbalou; Meriem Zaidi-Ait-Salem; Valérie Dossat-Létisse; Catherine Fontagné-Faucher; Claire-Emmanuelle Marcato-Romain
Source:: Journal of microbiological methods 2021 v.183 pp. 106172
ISSN:: 0167-7012
Subject:: Bacillus licheniformis; acidity; fluorescence; lactic acid
Abstract:: ... A resazurin micro-assay was developed to quantify acidifying bacteria. The resorufin fluorescent signal was measured over time and the determined time to reach the max slope (TMS) was plotted against CFU (colony forming unit) counts. This dynamic assay enabled to quantify nine lactic acid bacteria and a Bacillus licheniformis strain despite the increasing acidity of the medium. ...
DOI:: 10.1016/j.mimet.2021.106172
: https://doi.org/10.1016/j.mimet.2021.106172

79. A high-throughput virulence screening method for the Ralstonia solanacearum species complex

Author:: Jeffrey K. Schachterle; Qi Huang
Source:: Journal of microbiological methods 2021 v.187 pp. 106270
ISSN:: 0167-7012
Subject:: Nicotiana glutinosa; Ralstonia solanacearum; bacterial growth; bacterial wilt; brown rot disease; high-throughput screening methods; host-pathogen relationships; inoculation methods; inoculum; mutants; plant pathogenic bacteria; seedlings; virulence
Abstract:: ... Ralstonia solanacearum species complex strains are the causative agents for wilting diseases of many plants, including the economically important brown rot of potato. We developed a high-throughput virulence screen that is implemented in 96-well microtiter plates using seedlings grown in soft water agar to save space, effort, and resources. Nicotiana glutinosa was determined to be the most effecti ...
Handle:: 10113/7418056
DOI:: 10.1016/j.mimet.2021.106270
: https://doi.org/10.1016/j.mimet.2021.106270

80. A highly sensitive and specific method to evaluate viable fungal burden of Aspergillus fumigatus in mice by RT-qPCR for 18S ribosomal RNA

Author:: Yuuta Ukai; Yuri Nishiyama; Kenichi Okazaki; Hideki Maki; Akira Naito
Source:: Journal of microbiological methods 2021 v.184 pp. 106214
ISSN:: 0167-7012
Subject:: Aspergillus fumigatus; antifungal agents; antifungal properties; aspergillosis; blood serum; fungi; galactomannans; hyphae; mice; reverse transcriptase polymerase chain reaction; ribosomal DNA; ribosomal RNA
Abstract:: ... Potent fungicidal activity is one of the key factors of antifungals to overcome invasive pulmonary aspergillosis (IPA). To date, quantification of Aspergillus DNA in the lungs and galactomannan (GM) in serum or bronchoalveolar lavage fluid have been developed as general methods for measuring fungal burden in IPA animal models. However, GM quantification is not supposed to be a suitable method for ...
DOI:: 10.1016/j.mimet.2021.106214
: https://doi.org/10.1016/j.mimet.2021.106214

81. A low pH-based rapid and direct colorimetric sensing of bacteria using unmodified gold nanoparticles

Author:: Juan Du; Ziyue Yu; Zheyuan Hu; Jing Chen; Jin Zhao; Yanhong Bai
Source:: Journal of microbiological methods 2021 v.180 pp. 106110
ISSN:: 0167-7012
Subject:: Bacillus subtilis; Escherichia coli O157; Pseudomonas aeruginosa; Salmonella Typhimurium; Shigella flexneri; Staphylococcus aureus; Vibrio parahaemolyticus; absorbance; color; colorimetry; detection limit; diagnostic techniques; nanogold
Abstract:: ... Herein we report a novel strategy for the detection of bacteria using unfunctionalized gold nanoparticles (AuNPs), which was utilized as a colorimetric sensor. The UV–vis absorbance of AuNPs showed red shift due to the interactions between bacteria and AuNPs in the high acidic environment, producing a distinct color change which can be visually detected by naked-eye. The proposed low pH-based colo ...
DOI:: 10.1016/j.mimet.2020.106110
: https://doi.org/10.1016/j.mimet.2020.106110

82. A method for correcting underestimation of enteric pathogen genome quantities in environmental samples

Author:: Pengbo Liu; Nuhu Amin; Rana Miah; Tim Foster; Suraja Raj; Maria Julia Bianca Corpuz; Mahbubur Rahman; Juliet Willetts; Christine L. Moe
Source:: Journal of microbiological methods 2021 v.189 pp. 106320
ISSN:: 0167-7012
Subject:: Giardia; Norovirus; Salmonella Typhi; Shigella; Vibrio cholerae; enteropathogens; genome; quantitative polymerase chain reaction; risk; risk assessment; sediments; ultrafiltration; Bangladesh
Abstract:: ... Exposure to enteric pathogens in the environment poses a serious risk for infection and disease. The accurate detection and quantification of enteric pathogens in environmental samples is critical for understanding pathogen transport and fate and developing risk assessment models. In this study, we successfully applied TaqMan real-time PCR assays to quantitatively detect five human-specific pathog ...
DOI:: 10.1016/j.mimet.2021.106320
: https://doi.org/10.1016/j.mimet.2021.106320

83. A method for high-throughput image-based antifungal screening

Author:: Rosalie Sabburg; Aphrika Gregson; Andrew S. Urquhart; Elizabeth A.B. Aitken; Linda Smith; Louise F. Thatcher; Donald M. Gardiner
Source:: Journal of microbiological methods 2021 v.190 pp. 106342
ISSN:: 0167-7012
Subject:: broths; fungal growth; fungi; inoculum; journals; screening; spores
Abstract:: ... Robust antifungal screening is technically challenging particularly for filamentous fungi. We present a method for undertaking antifungal screening assays that builds upon existing broth dilution protocols and incorporates time resolved image-based assessment of fungal growth. We show that the method performs with different fungi, particularly those for which spores can be used as inoculum, and wi ...
DOI:: 10.1016/j.mimet.2021.106342
: https://doi.org/10.1016/j.mimet.2021.106342

84. A molecular assay for rapidly distinguishing the AviPro SALMONELLA VAC T vaccine strain from wild-type field isolates

Author:: Pieter-Jan Ceyssens; An Van den Bossche; Lac Kim Phan; Koenraad Van Hoorde; Wesley Mattheus
Source:: Journal of microbiological methods 2021 v.184 pp. 106190
ISSN:: 0167-7012
Subject:: Salmonella; antibiotic resistance; phenotype; vaccines; virulence
Abstract:: ... Rapid differentiation of the AviPro Salmonella VAC T strain from wild-type Salmonella ser. Typhimurium isolates is essential for the monitoring of veterinary isolates and targeted control actions. The distinction between the two strain types is routinely made by phenotypic antimicrobial resistance testing, but this sometime leads to ambiguous results with major economic implications. In this study ...
DOI:: 10.1016/j.mimet.2021.106190
: https://doi.org/10.1016/j.mimet.2021.106190

85. A myo-inositol bioassay utilizing an auxotrophic strain of S. cerevisiae

Author:: Mahmoud Suliman; Michael W. Schmidtke; Miriam L. Greenberg
Source:: Journal of microbiological methods 2021 v.189 pp. 106300
ISSN:: 0167-7012
Subject:: auxotrophs; bioassays; biosynthesis; equipment; mammals; myo-inositol; tandem mass spectrometry
Abstract:: ... Myo-inositol is a six‑carbon sugar that is essential for the growth of mammalian cells and must be obtained through either extracellular uptake or de novo biosynthesis. The physiological importance of myo-inositol stems from its incorporation into phosphoinositides and inositol phosphates, which serve a variety of signaling, regulatory, and structural roles in cells. To study myo-inositol metaboli ...
DOI:: 10.1016/j.mimet.2021.106300
: https://doi.org/10.1016/j.mimet.2021.106300

86. A new MALDI-TOF approach for the quick sequence type identification of Legionella pneumophila

Author:: Susana Blanco; Cristina Sanz; María P. Gutiérrez; María Simarro; Irene López; Isabel Escribano; José M. Eiros; Pilar Zarzosa; Antonio Orduña; Juan C. López; Gabriel A. March
Source:: Journal of microbiological methods 2021 v.188 pp. 106292
ISSN:: 0167-7012
Subject:: Legionella pneumophila; agar; biomarkers
Abstract:: ... Recently, MALDI-TOF has emerged as a quick tool for bacterial typing. The aim was to evaluate if MALDI-TOF based typing of Legionella pneumophila can achieve the same discriminatory power as that of the Sequence Based Typing (SBT) method.The Sequence Type (ST) was obtained from the 90 strains included in the training set and an in-house MALDI-TOF library based on the Main Spectra Profile (MSP) was ...
DOI:: 10.1016/j.mimet.2021.106292
: https://doi.org/10.1016/j.mimet.2021.106292

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

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

88. A novel bioreactor for the stable growth of Ureaplasma parvum and Ureaplasma urealyticum

Author:: Derek Fleming; Melissa Karau; Robin Patel
Source:: Journal of microbiological methods 2021 v.181 pp. 106131
ISSN:: 0167-7012
Subject:: Ureaplasma parvum; Ureaplasma urealyticum; bioreactors; liquids
Abstract:: ... Ureaplasma species, including Ureaplasma parvum and Ureaplasma urealyticum, are challenging to culture and maintain. Here, we describe a novel bioreactor for growing high-titer liquid Ureaplasma cultures in a stable manner. ...
DOI:: 10.1016/j.mimet.2020.106131
: https://doi.org/10.1016/j.mimet.2020.106131

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

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

90. A novel technique capable of taking ‘protected’ biopsies for reliable assessment of the distribution of microbiota along the colonic mucosa

Author:: Floortje Strobbe; Mèlanie V. Bénard; Noortje G. Rossen; Willem M. de Vos; Nitin Kumar; Trevor D. Lawley; Erwin G. Zoetendal; Floor Hugenholtz; Cyriel Y. Ponsioen
Source:: Journal of microbiological methods 2021 v.185 pp. 106204
ISSN:: 0167-7012
Subject:: biopsy; colon; intestinal microorganisms; mucosa
Abstract:: ... We evaluated a novel ‘protected’ biopsy method to reliably ascertain the spatial distribution of the mucosa-adherent colonic microbiota. Apart from minor differences at genus level, overall similarities along the colon were high between the various areas, irrespective of protected or unprotected sampling. ...
DOI:: 10.1016/j.mimet.2021.106204
: https://doi.org/10.1016/j.mimet.2021.106204

91. A rapid screening method to evaluate acidifying activity by lactic acid bacteria

Author:: S.C. Ribeiro; M.C. Coelho; C.C.G. Silva
Source:: Journal of microbiological methods 2021 v.185 pp. 106227
ISSN:: 0167-7012
Subject:: absorbance; acidification; colorimetry; dyes; equations; fermentation; fermented milk; glass electrodes; lactic acid; pH; regression analysis; spectroscopy; whey
Abstract:: ... The determination of pH in fermented milk is an important parameter for monitoring the production of acid by lactic acid bacteria (LAB). In this work, a colorimetric method is proposed that allows a fast determination of LAB acidification ability by evaluation of pH drop in whey fermentation. The proposed method uses spectrophotometry to measure the pH change by bacteria and uses bromocresol purpl ...
DOI:: 10.1016/j.mimet.2021.106227
: https://doi.org/10.1016/j.mimet.2021.106227

92. A rapid, antibiotic susceptibility test for multidrug-resistant, Gram-negative bacterial uropathogens using the biochemical assay, DETECT

Author:: Nicole Jackson; Clarissa A. Borges; Nicole J. Tarlton; Angel Resendez; Aubrianne K. Milton; Tara R. de Boer; Cheyenne R. Butcher; Niren Murthy; Lee W. Riley
Source:: Journal of microbiological methods 2021 v.182 pp. 106160
ISSN:: 0167-7012
Subject:: Escherichia coli; Gram-negative bacteria; Klebsiella pneumoniae; antibiotic resistance; ciprofloxacin; multiple drug resistance; nitrofurantoin; rapid methods; sulfamethoxazole; trimethoprim; urinary tract
Abstract:: ... The increasing prevalence of extended spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC (pAmpC) β-lactamases among Enterobacterales threatens our ability to treat urinary tract infections (UTIs). These organisms are resistant to most β-lactam antibiotics and are frequently multidrug-resistant (MDR). Consequently, they are often resistant to antibiotics used to empirically treat UTIs. The lac ...
DOI:: 10.1016/j.mimet.2021.106160
: https://doi.org/10.1016/j.mimet.2021.106160

93. A review of molecular identification tools for the opisthorchioidea

Author:: Maureen Duflot; Thomas Setbon; Graziella Midelet; Thomas Brauge; Mélanie Gay
Source:: Journal of microbiological methods 2021 v.187 pp. 106258
ISSN:: 0167-7012
Subject:: Clonorchis sinensis; Heterophyidae; Opisthorchis viverrini; aquatic environment; freshwater; genes; genomics; mitochondria; parasites; people; public health
Abstract:: ... The superfamily Opisthorchioidea encompasses the families Cryptogonimidae, Opisthorchiidae and Heterophyidae. These parasites depend on the aquatic environment and include marine and freshwater species. Some species, such as Clonorchis sinensis and Opisthorchis viverrini, have a high impact on public health with millions of infected people worldwide and have thus been the object of many studies an ...
DOI:: 10.1016/j.mimet.2021.106258
: https://doi.org/10.1016/j.mimet.2021.106258

94. 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
: https://doi.org/10.1016/j.mimet.2021.106269

95. A screening method for decoloration of xenobiotic dyes by fungi

Author:: Brigit van Brenk; Han A.B. Wösten
Source:: Journal of microbiological methods 2021 v.188 pp. 106301
ISSN:: 0167-7012
Subject:: Schizophyllum commune; color; decolorization; gentian violet; malachite green; models; quantitative analysis; scanners; wood; xenobiotics
Abstract:: ... Wood degrading fungi are often screened for their ability to degrade xenobiotics such as dyes. Dye decoloration by these fungi on solid media could until now only be assessed qualitatively. We here describe a fast quantitative method to screen for dye decoloration on such media. Decoloration of crystal violet (CV), malachite green (MG), orange G (OG), rose bengal (RB) and remazol brilliant blue R ...
DOI:: 10.1016/j.mimet.2021.106301
: https://doi.org/10.1016/j.mimet.2021.106301

96. A sensitive EZMTT method provides microscale, quantitative and high-throughput evaluation of drug efficacy in the treatment of Mycobacterium tuberculosis infectious diseases

Author:: Li Xie; Zhao Chen; Wei Liu; Dongshi Gu; Yan Yu; Xinrou Chen; Yefei Wu; Ning Xu; Jie Xie; Gang Zhao; Benfang Helen Ruan
Source:: Journal of microbiological methods 2021 v.181 pp. 106136
ISSN:: 0167-7012
Subject:: Mycobacterium tuberculosis; biosafety; drug resistance; drugs; liquids; public health; tetrazolium; water solubility
Abstract:: ... Drug resistance has become a serious public health problem in mycobacterial infectious diseases. Here, we investigated a water soluble tetrazolium salt (EZMTT)-based detection method to provide an easy, safe and quantitative antimycobacterial susceptibility test (AMST) method, especially for targeting early detection of loss of drug susceptibility in mycobacteria. After a single addition of the EZ ...
DOI:: 10.1016/j.mimet.2021.106136
: https://doi.org/10.1016/j.mimet.2021.106136

97. A short history of methods used to measure bathing beach water quality

Author:: Al Dufour
Source:: Journal of microbiological methods 2021 v.181 pp. 106134
ISSN:: 0167-7012
Subject:: beaches; density; filters; journals; most probable number technique; trays; water quality
Abstract:: ... The enumeration of fecal indicators of bathing beach water to determine quality have been used since the mid-20th century. In the 1930s and as late the 1970s, the Most Probable Number procedure for estimating microbial densities in water was in general use. The most probable number procedure was replaced as a method of choice by the membrane filter procedure. The membrane filter had been developed ...
DOI:: 10.1016/j.mimet.2021.106134
: https://doi.org/10.1016/j.mimet.2021.106134

98. A simple and novel method for the production of polyethylene terephthalate containing agar plates for the growth and detection of bacteria able to hydrolyze this plastic

Author:: Colin Charnock
Source:: Journal of microbiological methods 2021 v.185 pp. 106222
ISSN:: 0167-7012
Subject:: agar; hydrolysis; manufacturing; plastics; polyethylene terephthalates; waste management
Abstract:: ... Polyethylene terephthalate is used in the manufacture of many products. Microbes able to hydrolyze the plastic are known, and offer promise for practical waste management. Screening for hydrolysis usually involves unwieldy culturing in the presence of film. A rapid screening method based on culturing on agar plates is here described. ...
DOI:: 10.1016/j.mimet.2021.106222
: https://doi.org/10.1016/j.mimet.2021.106222

99. A simple method for the cultivation of the “unculturable” asterinaceous fungi (Asterinales/Dothideomycetes)

Author:: André Luiz Firmino; Olinto Liparini Pereira
Source:: Journal of microbiological methods 2021 v.187 pp. 106272
ISSN:: 0167-7012
Subject:: Dothideomycetes; ascospores; mycelium; phylogeny; physiology
Abstract:: ... Although asterinaceous fungi have been studied for many years, all previous attempts to isolate, cultivate, and propagate these fungi in vitro have failed. This paper provides the first reports of in vitro isolation of representative strains of species belonging to five fungi from different genera belonging to Asterinales. To confirm if the sequences of DNA obtained from the mycelia are the same o ...
DOI:: 10.1016/j.mimet.2021.106272
: https://doi.org/10.1016/j.mimet.2021.106272

100. A simple, efficient and cost-effective method for medium- to longterm maintenance and storage of Mycobacterium abscessus complex organisms

Author:: John E. Moore; Beverley C. Millar
Source:: Journal of microbiological methods 2021 v.188 pp. 106295
ISSN:: 0167-7012
Subject:: Mycobacterium abscessus; agar; ambient temperature; blood; casein; cost effectiveness; eggs; glucose; pH; plate count; viability; yeast extract
Abstract:: ... Traditional culture of non-tuberculous mycobacteria (NTMs) has involved egg-based formulations (Lowenstein-Jensen medium, Ogawa Egg medium) or defined media (Middlebrook formulations), which have disadvatages of composition complexity, availability and cost. Previously, the commercial agar formulation, Standard Plate Count (SPC) agar [Yeast extract 2.5 g/L, pancreatic digest of casein 5.0 g/L, glu ...
DOI:: 10.1016/j.mimet.2021.106295
: https://doi.org/10.1016/j.mimet.2021.106295

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1. A European multicenter evaluation study to investigate the performance on commercially available selective agar plates for the detection of carbapenemase producing Enterobacteriaceae

2. A fluorescent aptasensor for the detection of Aflatoxin B1 by graphene oxide mediated quenching and release of fluorescence

3. A multistep enrichment process with custom growth medium improves resuscitation of chlorine-stressed coliforms from secondary sewage effluents

4. A panoptic review of techniques for finfish disease diagnosis: The status quo and future perspectives

5. A simple method for purification of epsilon toxin of Clostridium perfringens type D for serum neutralization assay

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

7. A study of various factors affecting satellitism tests of Haemophilus influenzae and Haemophilus parainfluenzae using Staphylococcus aureus as the source of NAD

8. A two-step bioluminescence assay for optimizing antibacterial coating of hollow-fiber membranes with polydopamine in an integrative approach

9. Accurate classification of Listeria species by MALDI-TOF mass spectrometry incorporating denoising autoencoder and machine learning

10. Accurate qPCR quantification in polymicrobial communities requires assessment of gDNA extraction efficiency

11. Adaptation and validation of a method for evaluating the bactericidal activity of ethyl alcohol in gel format 70% (w/w)

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

13. Analysis of DNA extraction methods for detection of Treponema pallidum: A comparison of three methods

14. Antimicrobial susceptibility testing determined by Alfred 60/AST (Alifax®) in a multi-sites lab: performance's evaluation and optimization of workflow

15. Application of proper orthogonal decomposition for evaluation of coherent structures and energy contents in microbial biofilms

16. Assessment of VITEK® 2, MALDI-TOF MS and full gene 16S rRNA sequencing for aerobic endospore-forming bacteria isolated from a pharmaceutical facility

17. Bacterial and fungal disinfection via ozonation in air

18. Bioremediation of oily seawater by Bacteria immobilization on a novel carrier material containing nutrients

19. Chemical susceptibility testing of non-tuberculous mycobacterium strains and other aquatic bacteria: Results of a study for the development of a more sensitive and simple method for the detection of NTM in environmental samples

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

21. Comparative performance of different antigens on the lateral flow assay (LFA) platform for the rapid serodiagnosis of paratuberculosis

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

23. Comparison of peaks in the matrix-assisted laser desorption ionization time-of-flight mass spectrometry spectra of Staphylococcus aureus grown on various blood agar plates

24. Comparison of the complete filtration method using an automated feces analyzer with three manual methods for stool examinations

25. Current methods for the diagnosis of leptospirosis: Issues and challenges

26. Determination by isothermal microcalorimetry of the sensitivity of phytopathogenic fungi of tropical fruits against an ethanolic extract of jackfruit leaf (Artocarpus heterophyllus Lam.)

27. Determination of streptomycin and doxycycline using LC/MS towards an effective treatment against an experimental Brucella abortus infection in mice

28. Development and evaluation of a sensitive recombinase aided amplification assay for rapid detection of Vibrio parahaemolyticus

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

30. Do it yourself! – Initial experiences with self-synthesized CsTFA for RNA-SIP analyses

31. Electrotransformation of thermophilic bacterium Caldimonas manganoxidans

32. Establishment of a TaqMan-MGB probe multiplex real-time PCR system for one-step levofloxacin and clarithromycin resistant Helicobacter pylori detection

33. Evaluating acute toxicity in enriched nitrifying cultures: Lessons learned

34. Evaluation of VITEK® 2 and MALDI-TOF/MS automated methodologies in the identification of atypical Listeria spp. isolated from food in different regions of Brazil

35. Evaluation of anti-LipL32 carbon nanotube immunofluorescence probe (carbo-lip) and comparison with MAT, IgM ELISA, IgM spot test and culture for early detection of leptospirosis at local hospital

36. Evaluation of commercial ELISA kits for diagnosis of brucellosis in cattle and buffaloes in different epidemiological scenarios

37. Evaluation of the clinical sensitivity and specificity of the BD Max™ Enteric Bacterial Panel for molecular detection of pathogens for acute gastroenteritis in the Singaporean population

38. Evaluation of various phenotypic methods for differentiation of Candida dubliniensis from Candida albicans

39. Experimental validation under controlled conditions of real time PCR to quantify arbuscular mycorrhizal colonization in root

40. Formalin-fixed paraffin-embedded tissues for microbiome analysis in rainbow trout (Oncorhynchus mykiss)

41. Green synthesis, characterization of silver nanoparticals for biomedical application and environmental remediation

42. High throughput pH bioassay demonstrates pH adaptation of Rhizobium strains isolated from the nodules of Trifolium subterraneum and T. repens

43. Identification of two potential aetiological agents of chronic diarrhoea in an immunocompromised patient in Cuba using conventional and molecular diagnostic techniques

44. Insight into the biotechnology potential of Alicyclobacillus tolerans from whole genome sequence analysis and genome-scale metabolic network modeling.

45. Interlaboratory evaluations of a standardized quantitative test method for determining the bactericidal and tuberculocidal efficacy of antimicrobial substances on hard non-porous surfaces

46. Is skipping the definition of primary and secondary models possible? Prediction of Escherichia coli O157 growth by machine learning

47. Low-cost, specific PCR assays to identify the main aflatoxigenic species of Aspergillus section Flavi

48. Machine learning approach for predicting the antifungal effect of gilaburu (Viburnum opulus) fruit extracts on Fusarium spp. isolated from diseased potato tubers

49. Measurement of lactose concentration in milk by using engineered bacteria producing lycopene

50. Methodology to streamline flow cytometric-based detection of early stage Plasmodium parasitemia in mice

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

52. Multi-dimensional nanoscale liquid chromatography and nano-electrospray ion-trap mass spectrometry for detection of Clostridium botulinum type C and the produced botulinum neurotoxin type C complex

53. Nanoparticle immuno-fluorescent probes as a method for detection of viable E. coli O157:H7

54. Novel microaerobic agar plate method delivers highly selective and accurate enumeration of probiotic lactobacilli in freeze-dried blends containing bifidobacteria

55. Predicting the occurrence of monooxygenases and their associated phylotypes in soil microcosms

56. Preservation of Streptococcus pneumoniae quality control strains using chocolate agar blocks in glycerol at minus 70 degrees celsius

57. Probe-based qPCR assay enables the rapid and specific detection of bacterial degrading genes for the pesticide metaldehyde in soil

58. Pulling needles out of a haystack: Subtractive community metatranscriptomics retrieves anaerobic o-xylene degradation pathway genes out of a mixed microbial culture

59. Quantification of cyanobacterial cyclic di-guanosine monophosphate (c-di-GMP) by liquid chromatography electrospray ionization tandem mass spectrometry

60. Rapid and specific detection of Mycoplasma gallisepticum and Mycoplasma synoviae infection in poultry using single and duplex PCR assays

61. Rapid cell counting and viability detection method of Escherichia coli Nissle using image cytometry

62. Rapid detection and discrimination of potentially toxigenic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis by multiplex real-time PCR and amplicon melting curve analysis

63. Rapid detection of KPC-producing Klebsiella pneumoniae in China based on MALDI-TOF MS

64. Real-time quantitative PCR method for detection and quantification of Clostridioides difficile cells and spores

65. Research on the optimization, key chemical constituents and antibacterial activity of the essential oil extraction process of Thuja koraiensis Nakai

66. Role of temperature, nutrition, oxygen, osmolality, and bacterial strain in inducing a viable but non-culturable state in Campylobacter jejuni

67. Screening of immune-enhancing Lactobacillus in mice by using a cell-line

68. Single-round multiplex PCR with species-specific mitochondrial primers of P. falciparum, P. vivax/P. simium and P. malariae/P. brasilianum: Comparison with standard techniques

69. Spectinomycin, gentamicin, and routine disc diffusion testing: An alternative for the treatment and monitoring of multidrug-resistant Neisseria gonorrhoeae?

70. Standardisation and validation of an in-house quantitative real-time polymerase chain reaction (qPCR) assay for the diagnosis of Clostridioides difficile infection