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Journal of Microbiological Methods

Fabio Arena, Tommaso Giani, Alberto Antonelli, Olga Lorenza Colavecchio, Patrizia Pecile, Bruno Viaggi, Riccardo Favilli, Gian Maria Rossolini
We evaluated the performance of an automated, rapid (TAT 4-8 h), liquid-culture method for carbapenem-resistant Enterobacteriaceae (CRE) detection from rectal swabs, in a setting of KPC-producing Klebsiella pneumoniae endemicity. With 600 samples (22 positive for CRE, 3.7%), the system sensitivity and specificity, at 8 h, were 100% and 99.2%, respectively.
March 7, 2018: Journal of Microbiological Methods
Tatsuya Tominaga
Bacteria of the genera Klebsiella and Raoultella, which are present in foods and the natural environment, are associated with health hazards in humans. In the present study, two types of strips-based methods were developed to detect these bacteria simply and quickly. One method used lateral-flow test strips (LFTS) in combination with anti-Klebsiella antibodies labeled with palladium nanoparticles that bind to target bacteria, allowing their visualization. In the other, the antibodies were immobilized on nitrocellulose membranes, and urease activity was measured using an ion sensitive field effect transistor pH sensor...
March 6, 2018: Journal of Microbiological Methods
Adilya Dagkesamanskaya, Krzysztof Langer, Alexandra Tauzin, Catherine Rouzeau, Delphine Lestrade, Gabrielle Potocki-Veronese, Laurent Boitard, Jérôme Bibette, Jean Baudry, Denis Pompon, Véronique Anton-Leberre
Application of droplet-based microfluidics for the screening of microbial libraries is one of the important ongoing developments in functional genomics/metagenomics. In this article, we propose a new method that can be employed for high-throughput profiling of cell growth. It consists of light-driven labelling droplets that contain growing cells directly in a microfluidics observation chamber, followed by recovery of the labelled cells. This method is based on intracellular expression of green-to-red switchable fluorescent proteins...
March 5, 2018: Journal of Microbiological Methods
Hemjot Kaur, Laura Dize, Beatriz Munoz, Charlotte Gaydos, Sheila West
PURPOSE: Serological testing for antibodies to Chlamydia trachomatis pgp3 is being evaluated as a tool to use for trachoma surveillance. There are limited data on the reproducibility of the test results using a multiplex platform. METHODS: We tested the reproducibility of a serologic test for C. trachomatis pgp3 in 6 dried blood spots collected from a random sample of 45 children from a trachoma endemic area. The spots were tested on a multiplex bead array platform, using one bead set twice, using another bead set at the same time as the first, and using the same bead set twice on different days separated by several months...
March 1, 2018: Journal of Microbiological Methods
Anuradha Ravi, Ekaterina Avershina, Inga Leena Angell, Jane Ludvigsen, Prashanth Manohar, Sumathi Padmanaban, Ramesh Nachimuthu, Lars Snipen, Knut Rudi
Use of the 16S rRNA gene in microbiota studies is limited by the lack of taxonomic and functional resolution. High resolution analyses are particularly important for understanding transmission and persistence of bacteria. The aim of our work was therefore to compare a novel reduced metagenome sequencing (RMS) approach with 16S rRNA gene sequencing to determine both the metagenome genetic diversity and the mother-to-child sharing of the microbiota in a cohort of 17 mother-child pairs. We found that although both approaches gave comparable results with respect to sample separation and taxonomy, RMS gave higher resolution and the potential for genomic-/functional assignment...
March 1, 2018: Journal of Microbiological Methods
Kai-Chih Chang, Chin-Yi Chung, Chen-Hsing Yeh, Kuo-Hsiu Hsu, Ya-Ching Chin, Sin-Siang Huang, Bo-Rong Liu, Hsi-An Chen, Anren Hu, Po-Chi Soo, Wen-Ping Peng
The appearance and spread of carbapenem-resistant Acinetobacter baumannii (CRAB) pose a challenge for optimization of antibiotic therapies and outbreak preventions. The carbapenemase production can be detected through culture-based methods (e.g. Modified Hodge Test-MHT) and DNA based methods (e.g. Polymerase Chain Reaction-PCR). The culture-based methods are time-consuming, whereas those of PCR assays need only a few hours but due to its specificity, can only detect known genetic targets encoding carbapenem-resistance genes...
February 27, 2018: Journal of Microbiological Methods
Guillaume Gautier, Thomas Guillard, Bianca Podac, Béatrice Bercot, Véronique Vernet-Garnier, Christophe de Champs
A new phenotypic method for detecting carbapenemases has been adapted (assembling of two MAST® kits, including one that contains faropenem to which a temocillin disk has been added) then assessed using 101 bacterial strains (Enterobacteriaceae with assays on Pseudomonas aeruginosa and Acinetobacter baumannii) including 62 which produce genetically identified carbapenemases. Concerning Carbapenemase-Producing Enterobacteriaceae (CPE), there is 100% sensitivity for Klebsiella pneumoniae carbapenemase (KPC, Ambler class A) and OXA-48 (Ambler class D), and 91% for metallo-beta-lactamase (MBL, Ambler class B), with a 97% sensitivity for all carbapenemases, with a specificity of 100%...
February 24, 2018: Journal of Microbiological Methods
Zhirong Li, Xiaolei Liu, Jianhong Zhao, Kaiyue Xu, Tiantian Tian, Jing Yang, Cuixin Qiang, Dongyan Shi, Honglian Wei, Suju Sun, Qingqing Cui, Ruxin Li, Yanan Niu, Bixing Huang
Clostridium difficile is the causative pathogen for antibiotic-related nosocomial diarrhea. For epidemiological study and identification of virulent clones, a new binary typing method was developed for C. difficile in this study. The usefulness of this newly developed optimized 10-loci binary typing method was compared with two widely used methods ribotyping and multilocus sequence typing (MLST) in 189 C. difficile samples. The binary typing, ribotyping and MLST typed the samples into 53 binary types (BTs), 26 ribotypes (RTs), and 33 MLST sequence types (STs), respectively...
February 24, 2018: Journal of Microbiological Methods
Villa-Rodríguez Eber, Ibarra-Gámez José Cuauhtemoc, de Los Santos-Villalobos Sergio
A suitable technique (lysozyme combined with Trizol reagent) was developed to improve the RNA yield, purity and integrity from Bacillus subtilis, under different bacterial growth stages. The obtained RNA was intact, having the required characteristics for downstream applications.
February 20, 2018: Journal of Microbiological Methods
Gabriela C Alonso, Ana C Pavarina, Tábata V Sousa, Marlise I Klein
Biofilm production contributes to several human diseases, including oral candidiasis. Among the Candida species, Candida albicans is the most prevalent. The expression of virulence genes is implicated in the pathogenic potential of Candida biofilms. However, the evaluation of microbial gene expression from in vivo biofilm samples is not trivial, specifically, assessment via quantitative PCR (qPCR) can be a challenge because of several species present in clinical samples. Hence, the necessity of primers specificity...
February 14, 2018: Journal of Microbiological Methods
Karsten Zecher, Vishwa Prasad Aitha, Kirsten Heuer, Herbert Ahlers, Katrin Roland, Michael Fiedel, Bodo Philipp
Marine biofouling on artificial surfaces such as ship hulls or fish farming nets causes enormous economic damage. The time for the developmental process of antifouling coatings can be shortened by reliable laboratory assays. For designing such test systems, it is important that toxic effects can be excluded, that multiple parameters can be addressed simultaneously and that mechanistic aspects can be included. In this study, a multi-step approach for testing antifouling coatings was established employing photoautotrophic biofilm formation of marine microorganisms in micro- and mesoscoms...
February 10, 2018: Journal of Microbiological Methods
Bassam A Elgamoudi, Julian M Ketley, Victoria Korolik
Chemotactic behaviour is an important part of the lifestyle of motile bacteria and enables cells to respond to various environmental stimuli. The Hard Agar Plug (HAP) method is used to study the chemotactic behaviour of bacteria, including the fastidious microaerophile Campylobacter jejuni, an intestinal pathogen of humans. However, the traditional HAP assay is not quantitative, is unsuitable for chemotaxis observation over short time periods and for the investigation of repellent taxis, and is prone to false-positive and -negative results...
February 8, 2018: Journal of Microbiological Methods
Anu Hynninen, Marian Külaviir, Kalle Kirsimäe
Scanning electron microscopy (SEM) is a powerful tool for observing microbe-mineral interactions in situ. Despite its wide usage in geomicrobiology there is no consensus on how the samples should be handled before visualizing in SEM. We compared response of artificial laboratory-grown bacterial community and natural in situ microbes on terrestrial basalt to different sample pre-treatment methods with the aim to preserve microbe-mineral interaction interface. Air-drying was the only method that maintained the location of loosely attached bacteria on a mineral surface, whereas chemical fixation and drying dislocated the cells...
February 8, 2018: Journal of Microbiological Methods
Vincent van Almsick, Beniam Ghebremedhin, Niels Pfennigwerth, Parviz Ahmad-Nejad
Accurate detection of carbapenem-resistant Enterobacteriaceae (CRE) and carbapenemase-producing carbapenem-resistant Acinetobacter spp. (CP-CRA) constitutes a major challenge in laboratory diagnostics. We developed a bioluminescence-based carbapenem susceptibility detection assay (BCDA) which allows identification of CRE (carbapenemase-producing-CRE (CP-CRE) as well as non-carbapenemase-producing-CRE (non-CP-CRE) and CP-CRA in 2.5 h from culture media. This laboratory method was evaluated with CP-CRE and CP-CRA isolates producing different β-lactamases of different Ambler classes (A, n = 16; B, n = 25; D, n = 67) and 22 non-CP-CRE...
February 7, 2018: Journal of Microbiological Methods
Matthijs Oyaert, Britt Van Meensel, Reinoud Cartuyvels, Johan Frans, Wim Laffut, Patricia Vandecandelaere, Hans De Beenhouwer
The BILULU study group consists of seven microbiologists of hospital laboratories located in the region of Flanders (Belgium). A major goal of the group is to standardize diagnostic microbiology procedures based on available evidence and, in the absence of evidence, based on general microbiological principles and expert opinion. Scientific evidence of current urine culture guidelines is incomplete and at some points guidelines don't indicate clear choice. The aim of this project was to develop a clear and unambiguous step-by-step guideline regarding the work-up of urine cultures...
February 7, 2018: Journal of Microbiological Methods
Michaela Simon, Katharina Richert, Niels Pfennigwerth, Yvonne Pfeifer, Udo Reischl, Sören Gatermann, André Gessner, Jonathan Jantsch
No abstract text is available yet for this article.
February 7, 2018: Journal of Microbiological Methods
Yenenesh K Tekletsion, Hannah Christensen, Adam Finn
Detection of bacterial gene transcripts in low density mucosal samples is challenging. We evaluated the NanoString nCounter system for transcript detection in Neisseria meningitidis (Nm) cultures. The method was sensitive, reproducible (R2 = 0.99) and demonstrated changes in gene expression. Studying Nm transcripts from pharyngeal samples may be feasible using this approach.
February 6, 2018: Journal of Microbiological Methods
Tashmin Rampersad, Mantha Makume, Parveen Sobia, A Willem Sturm
MICs for eleven anti-TB drugs with M. tuberculosis isolates were obtained by means of agar dilution with multi-point inoculation. The results were compared with classic agar dilution and the MTT assay. The multi-point inoculation method was reproducible with all drugs and correlated with classic agar dilution and MTT assay. This methodology can be used for routine breakpoint drug susceptibility testing (DST) and for MIC determination.
February 1, 2018: Journal of Microbiological Methods
Philip J Johnson, Leeza L Hargreaves, Chelsea N Zobrist, Aaron C Ericsson
While recent advances in culture-independent sequencing approaches have revitalized the field of microbiology, rapid collection and preservation of microbial DNA in samples like feces is critical to avoid degradation of target DNA via nuclease activity and proliferation of aerotolerant microbes. Common laboratory practices to ameliorate such changes rely on prompt freezing of samples or dispersion in nuclease-inhibiting reagents. As many of the microbial enzymes associated with nuclease activity and bacterial proliferation are hydrolases, prompt desiccation of samples offers an attractive alternative to freezing and liquid reagents for field collection of samples in remote areas...
February 1, 2018: Journal of Microbiological Methods
Sujeesh Sebastian, Rajesh Malhotra, Vishnubhatla Sreenivas, Arti Kapil, Rama Chaudhry, Benu Dhawan
INTRODUCTION: Accurate and prompt microbiological diagnosis of prosthetic joint infection (PJI) is crucial for successful antimicrobial treatment. Studies have shown the diagnostic utility of sonication of explanted implants in total joint arthroplasty but all did not use consensus statements for defining PJI. We evaluated the diagnostic utility of culture of samples obtained by sonication of explanted implants compared with periprosthetic tissue cultures (PTC) for the diagnosis of PJI using Musculoskeletal Infection Society (MSIS) consensus criteria...
January 31, 2018: Journal of Microbiological Methods
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