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Comparing DNA isolation and sequencing strategies for 16S rRNA gene amplicon analysis in biofilm containing environments J. Microbiol. Methods (IF 2.2) Pub Date : 2024-03-16 Ilgaz Cakin, Barbara Morrissey, Matthew Gordon, Paul P.J. Gaffney, Lucio Marcello, Kenneth Macgregor, Mark A. Taggart
Bacteria are primarily responsible for biological water treatment processes in constructed wetland systems. Gravel in constructed wetlands serves as an essential substrate onto which complex bacterial biofilms may successfully grow and evolve. To fully understand the bacterial community in these systems it is crucial to properly isolate biofilms and process DNA from such substrates. This study looked
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Cell-free synthesis of the Salmonella specific broad host range bacteriophage, felixO1 J. Microbiol. Methods (IF 2.2) Pub Date : 2024-03-12 John A. McFarlane, David Garenne, Vincent Noireaux, Steven D. Bowden
Phage-based biocontrol of foodborne is limited by the requisite use of to propagate the phages. This limitation can be circumvented by producing phages using a cell-free gene expression system (CFE) with a non-pathogenic chassis. Here, we produce the phage felixO1 using an -based CFE system.
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Factors affecting the quality and reproducibility of MALDI-TOF MS identification for human Capnocytophaga species J. Microbiol. Methods (IF 2.2) Pub Date : 2024-03-08 Ahmed Algahawi, Inka Harju, Eija Könönen, Kaisu Rantakokko-Jalava, Mervi Gürsoy
Reproducibility and quality of MALDI-TOF MS spectra are critical in the identification process, however, information on the factors affecting the identification scores are scarce. Here, we studied the influence of various factors during the identification process of human oral species. The influence of two incubation times, plate-spotting reproducibility of two examiners, extraction technique, storage
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The performance of a fully automated urine particle analyzer, Sysmex UF-5000, in detecting fastidious bacteria in urine samples J. Microbiol. Methods (IF 2.2) Pub Date : 2024-03-06 Masako Kaido, Mitsuru Yasuda, Masahiro Hayashi, Hazuki Ohashi, Hirotoshi Ohta, Yasumasa Akai, Kaori Tanaka, Takashi Deguchi
Several types of fastidious bacteria can cause tract infections. We evaluated the performance of counting fastidious bacteria using a Fully Automated Urine Particle Analyzer UF-5000. The results showed that UF-5000 counts fastidious bacteria in urine without the need for culture using measurement principles based on flow cytometry.
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Optimisation of DNA electroporation protocols for different plant-associated bacteria J. Microbiol. Methods (IF 2.2) Pub Date : 2024-03-06 Edson Yu Sin Kim, Emanuel Maltempi de Souza, Marcelo Müller-Santos
Electroporation is a vital process that facilitates the use of modern recombineering and other high-throughput techniques in a wide array of microorganisms, including non-model bacteria like plant growth-promoting bacteria (PGPB). These microorganisms play a significant role in plant health by colonizing plants and promoting growth through nutrient exchange and hormonal regulation. In this study, we
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Host specific Eimeria genus diagnosis and qPCR development in Ovis aries and Capra hircus J. Microbiol. Methods (IF 2.2) Pub Date : 2024-03-06 Shijie Li, Yichen Jian, Kaihui Zhang, Xiaoying Li, Rongjun Wang, Longxian Zhang, Fuchun Jian
The objective of the present study was to develop a real-time PCR (qPCR) technique for the diagnosis of spp. in and . The qPCR technique was developed using SYBR Green, resulting in a PCR with high sensitivity, specificity, and reproducibility.
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Development of a multiplex droplet digital PCR assay for simultaneous detection and quantification of Escherichia coli, E. marmotae, and E. ruysiae in water samples J. Microbiol. Methods (IF 2.2) Pub Date : 2024-03-01 Marie Moinet, Rose M. Collis, Lynn Rogers, Megan L. Devane, Patrick J. Biggs, Rebecca Stott, Jonathan Marshall, Richard Muirhead, Adrian L. Cookson
are widely used by water quality managers as Fecal Indicator Bacteria, but current quantification methods do not differentiate them from benign, environmental species such as (formerly named cryptic clade V) or (cryptic clades III and IV). Reliable and specific techniques for their identification are required to avoid confounding microbial water quality assessments. To address this, a multiplex droplet
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Occurrence of Rhodococcus sp. RR1 prmA and Rhodococcus jostii RHA1 prmA across microbial communities and their enumeration during 1,4-dioxane biodegradation J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-23 Zohre Eshghdoostkhatami, Alison M. Cupples
1,4-Dioxane, a likely human carcinogen, is a co-contaminant at many chlorinated solvent contaminated sites. Conventional treatment technologies, such as carbon sorption or air stripping, are largely ineffective, and so many researchers have explored bioremediation for site clean-up. An important step towards this involves examining the occurrence of the functional genes associated with 1,4-dioxane
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Bacteria as a source of biopigments and their potential applications J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-20 Moitrayee Devi, Elancheran Ramakrishnan, Suresh Deka, Deep Prakash Parasar
From the prehistoric period, the utilization of pigments as colouring agents was an integral part of human life. Early people may have utilized paint for aesthetic motives, according to archaeologists. The pigments are either naturally derived or synthesized in the laboratory. Different studies reported that certain synthetic colouring compounds were toxic and had adverse health and environmental effects
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Fluorine materials scavenge excess carbon dioxide and promote Escherichia coli growth J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-13 Yoshihisa Yamashige, Shojiro Kikuchi, Ryosuke Hosoki, Koji Kawada, Katsuaki Izawa, Masahiko Harata, Yuichi Ogawa
Fluorinated solvents have been used as oxygen carriers in closed microbial cultures to sustain aerobic conditions. However, the growth-promoting effects of fluorinated solvents remain unclear. Therefore, this study aimed to elucidate the mechanism by which fluorinated solvents promote microbial growth and to explore alternative materials that can be easily isolated after culture. and HFE-7200, a fluorinated
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Enhancing sensitivity of qPCR assays targeting Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae by using a mutant Taq DNA polymerase J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-13 Selin Nar Otgun, Canan Zohre Ketre Kolukirik, Nuriye Unal Sahin, Mustafa Kolukirik, Gozde Girgin Ozgumus, Meral Turan, Mert Elmas, Selcuk Kilic
, and are important causes of bacterial meningitis. In this study, the DNA binding site of the wild type Taq DNA polymerase was modified to produce a mutant enzyme with enhanced DNA affinity and PCR performance. The engineered and the wild type enzymes were integrated into qPCR-based assays for molecular detection of , , , and serogroups and serotypes of these three pathogens. Bio-Speedy® Bacterial
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Determination of foodborne pathogens in minced beef by real-time PCR without culture enrichment J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-09 Busra Turanoglu, Mehmet Akif Omeroglu, Mustafa Ozkan Baltaci, Gulsah Adiguzel, Ahmet Adiguzel
Meat provides the necessary environment for the growth of foodborne pathogens due to its features such as being rich in protein and having sufficient water activity. , , and O157:H7, which can be transmitted through many foods, including water, and cause serious diseases, are among the significant pathogens. In the current study. Detection of , and in 100 minced beef samples collected from different
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Rapid and sensitive detection of Salmonella in agro-Food and environmental samples: A review of advances in rapid tests and biosensors J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-09 Siti Nur Hazwani Oslan, Nik Yusnoraini Yusof, Si Jie Lim, Nurul Hawa Ahmad
is as an intracellular bacterium, causing many human fatalities when the host-specific serotypes reach the host gastrointestinal tract. Nontyphoidal are responsible for numerous foodborne outbreaks and product recalls worldwide whereas typhoidal are responsible for Typhoid fever cases in developing countries. Yet, -related foodborne disease outbreaks through its food and water contaminations have urged
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Optimized bacterial absolute quantification method by qPCR using an exogenous bacterial culture as a normalization strategy in triple-species BV-like biofilms J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-06 Inês Lameira, Ana S. Pinto, Ângela Lima, Christina A. Muzny, Nuno Cerca
Quantitative Polymerase Chain Reaction (qPCR) is a widely used method in molecular biology to quantify target DNA sequences. Despite its accuracy, there are important experimental controls that should be considered to avoid biased results. One of them is gDNA loss during extraction, which is higher among samples with lower bacterial concentrations. Improvement in qPCR quantification procedures is mandatory
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Rapid detection of clarithromycin resistance in clinical samples of nontuberculous mycobacteria by nucleotide MALDI-TOF MS J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-05 Li Wang, Peng Wang, Jing-Hui Yang, Xiao-Cui Wu, Fang-You Yu, Jin Gu, Wei Sha
The multidrug resistance of nontuberculous mycobacteria (NTM) poses a significant therapeutic challenge. Rapid and reliable drug susceptibility testing is urgently needed for evidence-based treatment decision, especially for macrolides. This study evaluated the utility of nucleotide matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (NMTMS) in detecting clarithromycin resistance
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Electron microscopic observation of Mycobacterium avium subsp. paratuberculosis in cattle feces after a novel purification using liquid paraffin J. Microbiol. Methods (IF 2.2) Pub Date : 2024-01-30 Masatoshi Fujihara, Daisuke Kondoh, Shigeru Matsuzawa, Ikunori Naito
We developed a novel method for purifying acid-fast bacteria from feces. The method enabled the observation of characteristic clumps of Mycobacterium avium subsp. paratuberculosis (MAP) under electron microscopy by removing contaminants and other bacteria. Further refinement of this method will contribute to efficient and effective MAP detection.
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In vivo assembly of genetic constructs in filamentous fungus Talaromyces cellulolyticus J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-04 Alexandra P. Orleneva, Petr N. Teslya, Vsevolod A. Serebrianyi
In the filamentous fungus , similar to other filamentous fungi, non-homologous recombination predominates over homologous recombination. For instance, to achieve an acceptable integration frequency of a genetic construct into a target site on the intact chromosome, the flanking sequences directing this integration should be approximately 2.5 kb in length. However, despite the requirement of long flanks
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Short communication: Investigating optimal laboratory growth conditions of Gracilibacillus halotolerans in media supplemented with salt J. Microbiol. Methods (IF 2.2) Pub Date : 2024-02-02 Isaac N. Young, Victor M. Jimenez Jr
, a new and relatively unstudied extremophile, extracted from the Great Salt Lake USA, survives in an extreme saline environment. Uncovering optimal laboratory growth conditions can be useful to improve treatment strategies against antibiotic resistance and biofilm formation. In the current study, growth optimization was tested to determine the ideal saline concentration. In addition, a variety of
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Investigation of the potential of yeast strains for phytase biosynthesis in a two-step screening procedure J. Microbiol. Methods (IF 2.2) Pub Date : 2024-01-23 Danail Georgiev, Milena Kostova, Ana Caroline de Oliveira, Yordan Muhovski
Research into phytase production is useful for improving the efficiency of animal production, reducing environmental impact, and contributing to the development of sustainable and efficient animal production systems. This study aims to investigate the potential of yeast strains for phytase biosynthesis in nutrient media. Phytase is a phosphomonoesterase (E.C 3.1.3.8) catalyzing in a ladder-like manner
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Recent advances in immuno-based methods for the detection of Ralstonia solanacearum J. Microbiol. Methods (IF 2.2) Pub Date : 2024-01-10 Shalini Bhatt, Neha Faridi, S. Merwyn P. Raj, Ankur Agarwal, Mayank Punetha
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Application of cell-free plasma next-generation sequencing technology in the diagnosis and management of pediatric meningitis J. Microbiol. Methods (IF 2.2) Pub Date : 2023-12-31 Nicole Duster, Nanda Ramchandar, Jennifer Foley, Lauge Farnaes, Nicole G. Coufal
This retrospective study evaluates the clinical utility of CFPNGS in the diagnosis and management of pediatric meningitis. CFPNGS identified a causative pathogen in 36% of 28 subjects, compared to 50% for diverse conventional testing (57% combined). CFPNGS may be considered as an adjunct to standard testing.
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Integrating rapid pathogen identification and antimicrobial susceptibility testing through multiplex TaqMan qPCR assay J. Microbiol. Methods (IF 2.2) Pub Date : 2024-01-02 Libo Xie, Min Yang, Min Liu, Qianyuan Li, Chunhua Luo, Jun Luo
Timely bacterial identification (ID) and antimicrobial susceptibility testing (AST) are of significance for therapy of bacteria-infected patients. In the present study, we developed a multiplex TaqMan qPCR assay for rapid and accurate ID and AST of three common hospital acquired pneumonia species, namely Acinetobacter baumannii, Klebsiella pneumoniae and Staphylococcus aureus. In this assay, DNA extraction
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Development of loop-mediated isothermal amplification for detection of Mycoplasma ovipneumoniae in goats, Capra hircus J. Microbiol. Methods (IF 2.2) Pub Date : 2023-12-28 Miti Borang, Rathish Ramachandran Latha, Pradeep Mampilli, Deepa Padinjare Melepat, Vijayakumar Kaithathara
Mycoplasma ovipneumoniae is an important pathogen that causes respiratory disease in goats and sheep, leading to significant economic losses in the livestock industry. A quick and robust diagnostic test will aid in early diagnosis and treatment of the disease. Loop-mediated isothermal amplification (LAMP) offers several advantages over traditional PCR, including faster amplification, simpler operation
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Cyanotoxins availability and detection methods in wastewater treatment plants: A review J. Microbiol. Methods (IF 2.2) Pub Date : 2023-12-28 K.G.L. Manjitha, B.G.N. Sewwandi
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A rapid spectroscopic method for the identification of the filamentous fungi isolated from Turkish traditional mold-ripened cheeses J. Microbiol. Methods (IF 2.2) Pub Date : 2023-12-28 Hatice Ebrar Kirtil, Nur Cebi, Rusen Metin Yildirim, Banu Metin, Muhammet Arici
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Nanoparticle-based platforms for targeted drug delivery to the pulmonary system as therapeutics to curb cystic fibrosis: A review J. Microbiol. Methods (IF 2.2) Pub Date : 2023-12-20 Sujoy Rano, Ahana Bhaduri, Mukesh Singh
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Antimicrobial potential of linear low-density polyethylene food packaging with Ag nanoparticles in different carriers (Silica and Hydroxyapatite) J. Microbiol. Methods (IF 2.2) Pub Date : 2023-12-19 Sabrina da Costa Brito, Vinicius Alex Cano Pereira, Ana Carolina Figueiredo Prado, Thais Juliana Tobias, Elaine Cristina Paris, Marcos David Ferreira
Silver nanoparticles incorporation into polymeric packaging aims to prevent microbiological contamination in food products, thus ensuring superior food safety and preservation. In this context, this study aimed to verify the antimicrobial efficacy of linear low-density polyethylene (LLDPE) films incorporated with silver nanoparticles (AgNPs) dispersed in silica (SiO2) and hydroxyapatite (HAP) carriers
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Comparative analysis of diagnostic assays for scrub typhus: Unveiling enhanced approaches for accurate detection J. Microbiol. Methods (IF 2.2) Pub Date : 2023-12-13 Shruti S. Barbuddhe, Yogesh T. Thorat, Piyush Kulkarni, Shilpshri V. Shinde, Sandeep P. Chaudhari, Nitin V. Kurkure, Radhakrishna Sahu, Deepak B. Rawool
The study comparatively evaluated serological assays, namely, Weil Felix assay, and IgM ELISA with the gold-standard immunofluorescence test (IFAT) for the sensitive and specific serodiagnosis of scrub typhus infection in occupationally exposed groups of humans. A total of 78 serum samples collected from persons affected with various ailments and belonging to different risk groups were screened in
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Use of recombinant malate dehydrogenase (MDH) and superoxide dismutase (SOD) [CuZn] as antigens in indirect ELISA for diagnosis of bovine brucellosis J. Microbiol. Methods (IF 2.2) Pub Date : 2023-12-14 Rafaella Silva Andrade, Angélica Rosa Faria, Hélida Monteiro Andrade, Júlio Sílvio de Sousa Bueno Filho, Herman Sander Mansur, Alexandra Ancelmo Piscitelli Mansur, Andrey Pereira Lage, Elaine Maria Seles Dorneles
The objective of this study was to validate an indirect enzyme-linked immunoassay (iELISA) using the recombinant proteins, malate dehydrogenase (MDH) and superoxide dismutase (SOD) [CuZn], as antigens and to evaluate its ability to discriminate antibodies produced by vaccination from those induced by infection in the diagnosis of bovine brucellosis. Sera from six groups were evaluated: G1 – culture-positive
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Performance evaluation of commercially available swabs for environmental monitoring: Uptake and release efficiency J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-29 Thisara M. Kumarajith, Michael Breadmore, Shane M. Powell
Safety and the quality of products rely on proper cleanliness procedures and good manufacturing practices in the production environment. The use of swabs for the collection of samples from surfaces has been a common practice in industries, medicine and forensic studies. To accommodate these different purposes, many varieties of swabs have been introduced into the market, and it is important to assess
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An efficient targeted gene deletion approach for Cochliobolus heterostrophus using Agrobacterium tumefaciens-mediated transformation J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-28 Jiaying Sun, Rui Yang, Yujia Liu, Zengran Zhou, Jiaqi Jia, Hongming Huang, Shuqin Xiao, Chunsheng Xue
Cochliobolus heterostrophus is a plant pathogenic fungus of southern corn leaf blight, which has been regarded as a model necrotrophic plant pathogen. Many methods have been developed to knock out targeted genes in C. heterostrophus, of which the most widely-used one is protoplast-mediated transformation. However, there are several problems of this method associated with protoplast preparation, DNA
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Assay of cellulose 1,4-β-cellobiosidase activity in soil J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-27 Hussein Alserae, Shiping Deng
As the most abundant biopolymer on earth, cellulose undergoes degradation by a diverse set of enzymes with varying specificities that act in synergism. An assay protocol was developed to detect and quantify activity of cellulose 1,4-β-cellobiosidase (EC 3.2.1.91) in soil. The optimum pH and temperature for β-cellobiosidase activity were approximately pH 5.5 and 60 °C, respectively. In the tested six
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Corrigendum to “Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples” [Journal of Microbiological Methods volume 215 (2023) 106850] J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-30 Malin Bomberg, Hanna Miettinen
Abstract not available
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Bacterial worth in genotoxicity assessment studies J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-24 Nidhi Mishra, Rashmi Srivastava
Bacterial-based genotoxicity test systems play a significant role in the detection and evaluation of genotoxicity in vitro and have gained importance due to attributes like wide applicability, speed, high sensitivity, good reproducibility, and simplicity. The Salmonella microsomal mutagenicity assay was created by Ames and colleagues at the beginning of the 1970s, and it was based on the fundamental
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One-pot rapid visual detection of E. coli O157:H7 by label-free AuNP-based plasmonic-aptasensor in water sample J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-29 Hadi Shirzad, Mohammad Panji, Seyed Amin Mousavi Nezhad, Pouya Houshmand, Iradj Ashrafi Tamai
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Rapid method for detection of Vibrio cholerae from drinking water with nanomaterials enhancing electrochemical biosensor J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-27 Sumeyra Savas, Melike Saricam
Cholera is a potentially fatal diarrheal disease caused by Vibrio cholerae and is spread to humans from contaminated food and water. In order to prevent spread of epidemic chlorea, the development of novel sensitive, selective, user-friendly, cost-effective and rapid detection systems to detect of V. cholerae are necessary. Therefore, in this study, it was aimed to develop a specific, electrochemical
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Measuring effect of mutations & conditions on microbial respiratory rates J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-27 Sarah Piccirillo, Saul M. Honigberg
Cellular respiration is central to a wide range of cellular processes. In microorganisms, the effect of a mutation or an environmental condition on the rate of respiration is usually determined by measuring oxygen consumption in the media. We describe this method and discuss caveats and controls for the method.
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A simple method for the preparation of single cells and regeneration of colonies of Botryococcus braunii NIES836 J. Microbiol. Methods (IF 2.2) Pub Date : 2023-11-22 Kengo Murayama, Takashi Ohtsuki
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Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-30 Malin Bomberg, Hanna Miettinen
Microorganisms in flotation and minerals processing may significantly affect the grade and yield of metal concentrates. However, studying the phenomena requires working techniques to detach microorganisms and their DNA from mineral particles to which they strongly adhere. We developed a new method utilizing the competitive properties of anionic nanocellulose to block sorption of DNA to and detach microbial
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Agrobacterium tumefaciens-mediated transformation of Nigrospora sp. isolated from switchgrass leaves and antagonistic toward plant pathogens J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-30 Summi Dutta, Gabriella Houdinet, Gitanjali NandaKafle, Arjun Kafle, Christine V. Hawkes, Kevin Garcia
Nigrospora is a diverse genus of fungi colonizing plants through endophytic, pathogenic, or saprobic interactions. Endophytic isolates can improve growth and development of host plants, as well as their resistance to microbial pathogens, but exactly how they do so remains poorly understood. Developing a reliable transformation method is crucial to investigate these mechanisms, in particular to identify
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Repeat-exposure in vitro protocol to assess the risk of antimicrobial resistance (AMR) development from use of personal care products: Case study using an antibacterial liquid handwash J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-30 J.A. Shepherd, M.D. Parker
The global crisis we are facing with regard to antibiotic resistance has been largely attributed to the overuse and misuse of antibiotics in healthcare and agriculture. However, there is also growing global concern about cross-resistance between biocides and antibiotics. This has made clear the need for more research in this area along with easy-to-perform, but realistic, methods to characterise the
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Development of a molecular marker for the Pi1 gene based on the association of the SNAP protocol with the touch-up gradient amplification method J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-17 Klaus Konrad Scheuermann, Adriana Pereira
Genetic resistance is the most effective and eco-friendly approach to combat rice blast. The application of resistance genes may be facilitated by the availability of molecular markers that allow marker-assisted selection during the breeding process. The Pi1 gene, considered to be a broad-spectrum resistance gene, might contribute to enhancing resistance to rice blast, but it lacks a suitable marker
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Detergent-free parasite transformation and replication assay for drug screening against intracellular Leishmania amastigotes J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-21 Sergio Sifontes-Rodríguez, Alma Reyna Escalona-Montaño, Daniel Andrés Sánchez-Almaraz, Ofelia Pérez-Olvera, María Magdalena Aguirre-García
Leishmaniasis is an infectious disease caused by protozoan species in the genera Leishmania and Endotrypanum. Current antileishmanial drugs are limited due to adverse effects, variable efficacy, the development of resistant parasites, high cost, parenteral administration and lack of availability in endemic areas. Therefore, active searching for new antileishmanial drugs has been done for years, mainly
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Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-21 Hongqin Zhao, Yanhong Zhao, Nana Yan, Yu Wang, Wushuang Li, Jiangman Zhao, Yue Xu, Hui Tang, Xunchao Liu
Metagenomic next-generation sequencing (mNGS) is widely used as a more promising technology than conventional tests. However, its clinical utility in the context of bronchoalveolar lavage fluid (BALF) samples for discriminating between non-severe and severe pneumonia is not well established. Thus, this study aimed to investigate the diagnostic performance of mNGS on BALF samples from 100 individuals
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Evaluation of RapidChek® SELECT™ for the detection of Salmonella spp. in environmental samples from a veterinary hospital J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-16 Daniela C. Pena-Hernandez, Jessica Joneson, Rebecca P. Wilkes, G. Kenitra Hendrix
Nosocomial salmonellosis in hospitalized animals is a recognized hazard, especially in large animal clinics. A standardized culture protocol (SCP) for detecting Salmonella spp. in environmental samples using a 48-h enrichment step results in a 5-day turnaround time for negative results. The RapidChek® SELECT™ Salmonella (RCSS) test system offers detection of organisms in 22–44 h through double enrichment
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Integration of 16S rRNA gene sequencing and LC/MS-based metabolomic analysis of early biomarkers of acute ischaemic stroke in Tibetan miniature pigs J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-18 Yajin Guan, Tianping Liu, Fei Xu, Shuilin Xie, Weiwang Gu, Yanan Bie
Acute ischaemic stroke (AIS) is a complex, systemic, pathological, and physiological process. Systemic inflammatory responses and disorders of the gut microbiome contribute to increased mortality and disability following AIS. We conducted 16S high-throughput sequencing and ultra-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry-based non-targeted metabolomic analyses
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A novel method for determining viable bacteria from a mixture of dead and viable bacteria: Delayed real-time PCR (DR-PCR) method J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-17 Akira Imakiire, Sakiko Soutome, Yuichi Nakamura, Moeko Nakamatsu, Keiichiro Miura, Yuki Sakamoto, Masahiro Umeda
Aspiration pneumonia can occur in perioperative and older patients, and various oral care methods have been used to prevent it. To validate the effective oral care methods, measuring bacterial counts before and after oral care is necessary. However, isolating and quantifying viable bacteria from those that are inactivated by agents used in oral care is not possible. In this study, we developed a novel
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Agrobacterium tumefaciens-mediated transformation of the white-rot fungus Dichomitus squalens J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-11 Jing Li, Min Wu, Yasuo Igarashi, Feng Luo, Peng Chang
Dichomitus squalens is an efficient white-rot fungus that generates a wide range of extracellular enzymes to degrade lignocellulose in nature. Although a protoplast-mediated transformation method for D. squalens has been developed, the transformation efficiency remains low. Here, we established a highly efficient Agrobacterium tumefaciens-mediated transformation (ATMT) procedure for D. squalens by
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CAR1 as a new selective marker for genetic engineering of wine yeasts J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-10 Valery N. Urakov, Andrey V. Mardanov, Alexander I. Alexandrov, Aleksandr O. Ruzhitskiy, Nikolai V. Ravin, Vitaly V. Kushnirov
A common problem in engineering industrial yeasts, and wine yeasts in particular, is the lack or scarcity of selective markers for introducing desired genetic changes. Almost all such markers, which are usually auxotrophic mutations, would reduce the growth characteristics of yeast strains. However, a potentially useful marker could be the CAR1 gene encoding arginase, the deletion of which reduces
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Application of flow cytometry for rapid, high-throughput, multiparametric analysis of environmental microbiomes J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-11 Madhumita Priyadarsini, Jeetesh Kushwaha, Kailash Pati Pandey, Jyoti Rani, Abhishek S. Dhoble
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An experimental setup and segmentation method for CFU counting on agar plate for the assessment of drinking water J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-04 Prachi Arora, Suman Tewary, Srinivasan Krishnamurthi, Neelam Kumari
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An improved MTT colorimetric method for rapid viable bacteria counting J. Microbiol. Methods (IF 2.2) Pub Date : 2023-10-05 Wenliang Xu, Danxia Shi, Kuanmin Chen, Jon Palmer, David G. Popovich
The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay has been employed in the analysis of bacterial growth. In comparison to experiments conducted on mammalian cells, the MTT bacterial assay encounters a greater number of interfering factors and obstacles that impact the accuracy of results. In this study, we have elucidated an improved MTT assay protocol and put forth an equation
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Improvement of the mismatch amplification mutation assay-PCR for discrimination between Streptococcus suis serotypes 2 and 1/2 J. Microbiol. Methods (IF 2.2) Pub Date : 2023-09-30 Erina Okuhama-Yoshida, Mizuki Nakayama, Miki Hattori, Daisuke Takamatsu, Masatoshi Okura
A mismatch amplification mutation assay (MAMA)-PCR, which detects a single-nucleotide polymorphism contributed to serological difference between Streptococcus suis serotypes 2 and 1/2, is used to discriminate between these serotypes. The present study reports unusual serotype 1/2 isolates untypable by the MAMA-PCR and improvement of the MAMA-PCR for typing such isolates.
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Validation of digital PCR assay for the quantification of Mycobacterium avium subsp. paratuberculosis in bovine faeces according to the ISO 20395:2019 J. Microbiol. Methods (IF 2.2) Pub Date : 2023-09-20 Simone Russo, Claudia Cortimiglia, Anita Filippi, Giorgia Palladini, Chiara Garbarino, Elisa Massella, Matteo Ricchi
Paratuberculosis is an enteric disease caused by Mycobacterium avium subs. Paratuberculosis (MAP). Quantifying the load of MAP in faeces samples offers the advantage of determining the stage of infection and planning control measures. Currently, detection of MAP in faecal specimens relies on cultural assays and quantitative PCR (qPCR), but both methods have limitations such as prolonged isolation times
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Quantitative investigation of the bacterial content of periodontal abscess samples by real-time PCR J. Microbiol. Methods (IF 2.2) Pub Date : 2023-09-22 Ercan Ergün, Emine Toraman, Özlem Barış, Harun Budak, Turgut Demir
Objectives Periodontal abscesses, which are part of the acute periodontal disease group characterized by the destruction of periodontal tissue with deep periodontal pockets, bleeding on probing, suppuration, and localized pus accumulation, cause rapid destruction of tooth-supporting tissues. This study aimed to evaluate the microbial content of periodontal abscesses by specific and culture-independent
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Rapid identification of Salmonella serovars Enteritidis and Typhimurium using whole cell matrix assisted laser desorption ionization – Time of flight mass spectrometry (MALDI-TOF MS) coupled with multivariate analysis and artificial intelligence J. Microbiol. Methods (IF 2.2) Pub Date : 2023-09-23 Anli Gao, Jennifer Fischer-Jenssen, Durda Slavic, Kimani Rutherford, Sarah Lippert, Emily Wilson, Shu Chen, Carlos G. Leon-Velarde, Perry Martos
Salmonella is a common food-borne pathogen with Enteritidis and Typhimurium being among the most important serovars causing numerous outbreaks. A rapid method was investigated to identify these serovars using whole-cell MALDI-TOF MS coupled with multivariate analysis and artificial intelligence and 113 Salmonella strains, including 38 Enteritidis (SE), 38 Typhimurium (ST) and 37 strains from 32 other
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Assessment of the capacity of Whatman filter papers as support to store stools for the molecular diagnostic testing of soil-transmitted helminthiasis J. Microbiol. Methods (IF 2.2) Pub Date : 2023-09-16 Cyrille Nguemnang Kamdem, Pythagore Soubgwi Fogue, Auvaker Arnol Zebaze Tiofack, Estelle Mezajou Mewamba, Loic Edmond Tekeu Mengoue, Macaire Hilaire Womeni, Gustave Simo
Storage of stools for the detection of soil-transmitted helminths (STH) remains challenging for the molecular diagnostic testing of STH infections. This study aimed to overcome this challenge by assessing the capacity of Whatman filter papers to store stools for the molecular detection of STHs. Stool samples were collected from school-aged children of soil-transmitted helminthiasis endemic areas of
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Evaluation of metagenomic assembly methods for the detection and characterization of antimicrobial resistance determinants and associated mobilizable elements J. Microbiol. Methods (IF 2.2) Pub Date : 2023-09-10 Catrione Lee, Rodrigo Ortega Polo, Rahat Zaheer, Gary Van Domselaar, Athanasios Zovoilis, Tim A. McAllister
Antimicrobial resistance genes (ARGs) can be transferred between members of a bacterial population by mobile genetic elements (MGE). Understanding the risk of these transfer events is important in monitoring and predicting antimicrobial resistance (AMR), especially in the context of a One Health Continuum. However, there is no universally accepted method for detection of ARGs and MGEs, and especially
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A new killing assay with the Caenorhabditis elegans PX627 mutant to assess the virulence of uropathogenic Escherichia coli strains J. Microbiol. Methods (IF 2.2) Pub Date : 2023-09-15 Hela Harbeoui, Patrick Di Martino, Gilles Mayot
The nematode Caenorhabditis elegans (C. elegans) is a prime invertebrate host model for studying uropathogenic Escherichia coli (UPEC) pathogenesis. The aim of this work was to develop a new C. elegans killing assay based on feeding bacteria by the nematode throughout its life from the egg. With this model, the lifespan of C. elegans rrf-3, temperature-sterile, mutant, and PX627, auxin-inducible infertile