Journal of Microbiological Methods

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 to obtain reproducible and accurate results. Herein, we report an improved qPCR method for bacterial quantification of Gardnerella vaginalis, Prevotella bivia, and Fannyhessea vaginae, three key-bacterial vaginosis (BV)-associated bacteria (BVAB) thought to play important roles in the pathogenesis of this common vaginal infection...

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. Sixty-four clinical isolates were identified to species by NMTMS, and mutations associated with clarithromycin resistance were detected...

In the filamentous fungus Talaromyces cellulolyticus, 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 for integration into the intact chromosome, we found that homologous recombination between linear DNA fragments in T...

Gracilibacillus halotolerans, 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, G. halotolerans growth optimization was tested to determine the ideal saline concentration. In addition, a variety of G. halotolerans'-derived survival strategies were reviewed. The major findings of the current study includes the optimal laboratory growth condition for G...

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.

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 the dephosphorylation of phytic acid and its salts, with various resulting myo-inositol phosphates and phosphoric acid...

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. Listeria monocytogenes, Salmonella enterica, and Escherichia coli 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 Listeria monocytogenes, Escherichia coli and Salmonella enterica in 100 minced beef samples collected from different butchers and markets situated in the central districts of Erzurum province was performed by Real-Time PCR without pre-enrichment and DNA isolation...

Ralstonia solanacearum (RS) is a widely recognized phytopathogenic bacterium which is responsible for causing devastating losses in a wide range of economically significant crops. Timely and accurate detection of this pathogen is pivotal to implementing effective disease management strategies and preventing crop losses. This review provides a comprehensive overview of recent advances in immuno-based detection methods for RS. The review begins by introducing RS, highlighting its destructive potential and the need for point-of-care detection techniques...

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 and bacterial co-incubation with antibiotics are accomplished based on a common PCR instrument. ID of three bacteria is based on specific conserved DNA sequence fragment (gltA for A...

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.

Research interest in ecological significance, toxicity, and potential applications of cyanobacterial metabolites has grown as a result of the current extensive cyanobacterial blooms in water bodies. Under favourable conditions, specific cyanobacterial species release cyanotoxins, hepatotoxins, dermatoxins, neurotoxins, and cytotoxins, creating a heightened threat to aquatic ecosystems and human health. Wastewater treatment plants (WWTPs) offer one of the best culture media for cyanobacterial development and synthesis of cyanotoxins by providing optimum environmental conditions, including temperature, light intensity, lengthy water residence time, and nutrient-rich habitat...

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, and lower equipment requirements, making it a promising tool for use in basic livestock units where resources and infrastructure may be limited...

Fourier transform infrared spectroscopy (FTIR) is an alternative microbial identification technique due to its faster analysis times and lower cost compared to molecular methods. In this study, forty-three fungal strains isolated from different Turkish traditional mold-ripened cheeses representing nine different Penicillium species (P. roqueforti, P. corylophilum, P. before, P. crustosum, P. spinulosum, P. rubens, P. brevicompactum, P. paneum, and P. solitum) were analyzed by using FTIR HTS-XT (High Throughput Screening Extension) method in the 4000-400 cm-1 wavenumber range...

Cystic fibrosis (CF) is a genetic disorder of the respiratory system caused by mutation of the Cystic Fibrosis Trans-Membrane Conductance Regulator (CFTR) gene that affects a huge number of people worldwide. It results in difficulty breathing due to a large accumulation of mucus in the respiratory tract, resulting in serious bacterial infections, and subsequent death. Traditional drug-based treatments face hindered penetration at the site of action due to the thick mucus layer. Nanotechnology offers possibilities for developing advanced and effective treatment platforms by focusing on drugs that can penetrate the dense mucus layer, fighting against the underlying bacterial infections, and targeting the genetic cause of the disease...

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 at different concentrations. AgNPs + carriers polymer films were characterized at 0.2, 0.4, and 0.6% concentrations using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), field emission gun-scanning electron microscope (FEG-SEM), thermogravimetric analyzer (TGA), differential scanning calorimetry (DSC), and migration in acidic and non-acidic simulants...

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 the study. Out of the 78 serum samples tested, a total of 17, 26, and 47 samples turned out to be positive by IFAT, IgM ELISA, and Weil Felix test, respectively...

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 animals (52 serum samples) (naturally infected); G2 - non-vaccinated animals (28 serum samples) positive in RBT (Rose Bengal test) and 2ME (2-mercaptoethanol test) selected from positive herds; G3 - animals from a brucellosis-free area (32 serum samples); G4 - S19 vaccinated heifers (114 serum samples); G5 - RB51 vaccinated heifers (60 serum samples); G6 - animals inoculated with inactivated Yersinia enterocolitica O:9 (42 serum samples)...

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 potential risk associated with cross-resistance to antibiotics due to biocide use. The primary aim of this work was to develop a repeat-exposure method for predicting bacterial resistance to microbicides, including their cross-resistance to antibiotics...

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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 the performance of these swabs before incorporating into an environmental monitoring procedure. The overall effectiveness of a swab is determined by two factors: the number of bacteria that a swab can uptake from a surface and the number of picked-up bacteria the swab can elute into a releasing buffer...