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Multiplex PCR

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https://www.readbyqxmd.com/read/29352043/prognostic-implications-of-multiplex-detection-of-kras-mutations-in-cell-free-dna-from-patients-with-pancreatic-ductal-adenocarcinoma
#1
Min Kyeong Kim, Sang Myung Woo, Boram Park, Kyong-Ah Yoon, Yun-Hee Kim, Jungnam Joo, Woo Jin Lee, Sung-Sik Han, Sang-Jae Park, Sun-Young Kong
BACKGROUND: Cell-free DNA (cfDNA) is known to provide potential biomarkers for predicting clinical outcome, but its value in pancreatic ductal adenocarcinoma (PDAC) has not been fully evaluated. The aim of this study was to evaluate the clinical applicability of quantitative analysis of multiplex KRAS mutations in cell-free DNA from patients with PDAC. METHODS: A total of 106 patients with PDAC were enrolled in this prospective study. The concentration and fraction of KRAS mutations were determined through multiplex detection of KRAS mutations in plasma samples by use of a droplet digital PCR kit (Bio-Rad)...
January 19, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29351318/invasive-bacterial-disease-trends-and-characterization-of-group-b-streptococcal-isolates-among-young-infants-in-southern-mozambique-2001-2015
#2
Betuel Sigaúque, Miwako Kobayashi, Delfino Vubil, Ariel Nhacolo, Alberto Chaúque, Benild Moaine, Sérgio Massora, Inácio Mandomando, Tacilta Nhampossa, Quique Bassat, Fabiana Pimenta, Clara Menéndez, Maria da Gloria Carvalho, Eusebio Macete, Stephanie J Schrag
BACKGROUND: Maternal group B streptococcal (GBS) vaccines under development hold promise to prevent GBS disease in young infants. Sub-Saharan Africa has the highest estimated disease burden, although data on incidence and circulating strains are limited. We described invasive bacterial disease (IBD) trends among infants <90 days in rural Mozambique during 2001-2015, with a focus on GBS epidemiology and strain characteristics. METHODS: Community-level birth and mortality data were obtained from Manhiça's demographic surveillance system...
2018: PloS One
https://www.readbyqxmd.com/read/29350545/sensitive-multiplex-real-time-rt-qpcr-assay-for-the-detection-of-filoviruses
#3
Vladimir G Dedkov, N'Faly Magassouba, Marina V Safonova, Sergey A Bodnev, Oleg V Pyankov, Jacob Camara, Bakary Sylla, Alexander P Agafonov, Victor V Maleev, German A Shipulin
Filoviruses are important etiological agents of emergent diseases with high mortality rates. Traditionally, filovirus fever diseases have primarily been a burden of African countries; however, global interconnectedness has increased the probability of the worldwide spread of filoviruses. Therefore, national healthcare organizations need tools for managing filovirus risk, including diagnostic kits based on real-time reverse transcription PCR (RT-qPCR), as this is the most suitable method for diagnosing filovirus fever diseases...
January 19, 2018: Health Security
https://www.readbyqxmd.com/read/29350524/development-of-a-multiplexed-microsphere-pcr-for-rapid-culture-free-detection-and-gram-typing-of-bacteria-in-human-blood-samples
#4
Fang Liang, Daniel J Browne, Megan J Gray, Kate H Gartlan, David D Smith, Ross Barnard, Geoff R Hill, Simon Robert Corrie, Kate Markey
Blood stream infection is a significant clinical problem, particularly in vulnerable patient groups such as those undergoing chemotherapy and bone marrow transplantation. Clinical diagnostics for suspected blood stream infection remain centered around blood culture (highly variable timing, hours to days), and empiric use of broad-spectrum antibiotics is often employed for patients presenting with febrile neutropenia. Gram-typing provides the first opportunity to target therapy (e.g. combinations containing vancomycin or teicoplanin for Gram-positives; piperacillin-tazobactam or a carbapenem for Gram-negatives), however current approaches require blood culture...
January 19, 2018: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29350137/multiplex-pcr-based-next-generation-sequencing-and-global-diversity-of-seoul-virus-in-humans-and-rats
#5
Won-Keun Kim, Jin Sun No, Seung-Ho Lee, Dong Hyun Song, Daesang Lee, Jeong-Ah Kim, Se Hun Gu, Sunhye Park, Seong Tae Jeong, Heung-Chul Kim, Terry A Klein, Michael R Wiley, Gustavo Palacios, Jin-Won Song
Seoul virus (SEOV) poses a worldwide public health threat. This virus, which is harbored by Rattus norvegicus and R. rattus rats, is the causative agent of hemorrhagic fever with renal syndrome (HFRS) in humans, which has been reported in Asia, Europe, the Americas, and Africa. Defining SEOV genome sequences plays a critical role in development of preventive and therapeutic strategies against the unique worldwide hantavirus. We applied multiplex PCR-based next-generation sequencing to obtain SEOV genome sequences from clinical and reservoir host specimens...
February 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29348835/simultaneous-quantification-of-dna-damage-and-mitochondrial-copy-number-by-long-run-dna-damage-quantification-lord-q
#6
Benjamin Dannenmann, Simon Lehle, Sebastian Lorscheid, Stephan M Huber, Frank Essmann, Klaus Schulze-Osthoff
DNA damage and changes in the mitochondrial DNA content have been implicated in ageing and cancer development. To prevent genomic instability and tumorigenesis, cells must maintain the integrity of their nuclear and mitochondrial DNA. Advances in the research of DNA damage protection and genomic stability, however, also depend on the availability of techniques that can reliably quantify alterations of mitochondrial DNA copy numbers and DNA lesions in an accurate high-throughput manner. Unfortunately, no such method has been established yet...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348433/speciation-of-common-gram-negative-pathogens-using-a-highly-multiplexed-high-resolution-melt-curve-assay
#7
Thomas Edwards, Shugo Sasaki, Christopher Williams, Glyn Hobbs, Nicholas A Feasey, Katie Evans, Emily R Adams
The identification of the bacterial species responsible for an infection remains an important step for the selection of antimicrobial therapy. Gram-negative bacteria are an important source of hospital and community acquired infections and frequently antimicrobial resistant. Speciation of bacteria is typically carried out by biochemical profiling of organisms isolated from clinical specimens, which is time consuming and delays the initiation of tailored treatment. Whilst molecular methods such as PCR have been used, they often struggle with the challenge of detecting and discriminating a wide range of targets...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343540/point-counterpoint-meningitis-encephalitis-syndromic-testing-in-the-clinical-laboratory
#8
Jennifer Dien Bard, Kevin Alby
"I'm not telling you it's going to be easy. I'm telling you it's going to be worth it"- Art WilliamsFor the most part, syndromic testing by multiplex molecular panels has been a welcome addition to the diagnostic laboratory. The first three panels available addressed syndromes associated with upper respiratory tract infections, bloodstream infections and gastroenteritis, with adoption of the first two panels being the most widespread. Multiple studies have been published on the performance characteristics of these syndromic panels as well as the impact on turn-around-time (TAT), increased pathogen detection, and antimicrobial use...
January 17, 2018: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29341220/prevalence-of-rhodococcus-equi-from-the-nasal-cavity-of-1-010-apparently-healthy-horses
#9
L T Gressler, G Machado, B P da Silveira, N D Cohen, L G Corbellini, V B Leotti, G N Diehl, L C Dos Santos, A Castagna de Vargas
BACKGROUND: Rhodococcus equi is an important cause of foal pneumonia. While its isolation from different sources has been widely evaluated, there is a need to better understand the R. equi epidemiology from samples of the nasal cavity of healthy horses. OBJECTIVES: To determine the prevalence of R. equi from the nasal cavity of healthy horses, along with its virulence profile, antimicrobial susceptibility, and environmental variables associated. STUDY DESIGN: Cross-sectional study...
January 17, 2018: Equine Veterinary Journal
https://www.readbyqxmd.com/read/29339418/an-evolutionary-biochemical-connection-between-promoter-and-primer-dependent-polymerases-revealed-by-selective-evolution-of-ligands-by-exponential-enrichment-selex
#10
Katherine J Fenstermacher, Vasudevan Achuthan, Thomas D Schneider, Jeffrey J DeStefano
DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified Selective Evolution of Ligands by Exponential Enrichment (SELEX) approach...
January 16, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29337224/an-experimental-study-for-rapid-detection-and-quantification-of-endodontic-microbiota-following-photo-activated-disinfection-via-new-multiplex-real-time-pcr-assay
#11
Maryam Pourhajibagher, Reza Raoofian, Roghayeh Ghorbanzadeh, Abbas Bahador
BACKGROUND: The infected root canal system harbors one of the highest accumulations of polymicrobial infections. Since the eradication of endopathogenic microbiota is a major goal in endodontic infection therapy, photo-activated disinfection (PAD) can be used as an alternative therapeutic method in endodontic treatment. Compared to cultivation-based approaches, molecular techniques are more reliable for identifying microbial agents associated with endodontic infections. The purpose of this study was to evaluate the ability of designed multiplex real-time PCR protocol for the rapid detection and quantification of six common microorganisms involved in endodontic infection before and after the PAD...
January 11, 2018: Photodiagnosis and Photodynamic Therapy
https://www.readbyqxmd.com/read/29333787/detection-of-ureaplasma-species-by-a-semi-quantitative-pcr-test-in-urine-samples-can-it-predict-clinical-significance
#12
Merav Strauss, Raul Colodner, Dana Sagas, Azmi Adawi, Hanna Edelstein, Bibiana Chazan
BACKGROUND: Ureaplasma species (Usp) are the most prevalent genital Mycoplasma isolated from the urogenital tract of both men and women. Usp may be commensals in the genital tract but may also be contributors to a number of pathological conditions of the genital tract. Because they can also just colonize the genital tract of healthy people, their pathogenic role can be difficult to prove. OBJECTIVES: The aim of the study was to evaluate the efficacy of a quantitative polymerase chain reaction (qPCR) method for the discrimination between infection and colonization by measuring prevalence of Usp in asymptomatic versus symptomatic patients...
January 2018: Israel Medical Association Journal: IMAJ
https://www.readbyqxmd.com/read/29332209/the-rapid-diagnosis-of-viral-respiratory-tract-infections-and-its-impact-on-antimicrobial-stewardship-programs
#13
Şiran Keske, Önder Ergönül, Faik Tutucu, Doruk Karaaslan, Erhan Palaoğlu, Füsun Can
We aimed to describe the potential benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use among the inpatients presenting with influenza-like illness (ILI). We included patients from inpatient and outpatient departments who had ILI and performed MRT between 1 January 2015 and 31 December 2016 in a 265-bed private hospital in Istanbul. At the end of 2015, we implemented antimicrobial stewardship including systematic use of MRT. Then, we compared our observations between the year 2015 and the year 2016...
January 13, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29330014/frequency-of-red-blood-cell-genotypes-in-multi-transfused-patients-and-blood-donors-from-minas-gerais-southeast-brazil
#14
Vitor Mendonça Alves, Fernanda Bernadelli De Vito, Paulo Roberto Juliano Martins, Sheila Soares Silva, Lilian Castilho, Helio Moraes-Souza
BACKGROUND AND OBJECTIVES: The frequency of red blood cell (RBC) antigens in Brazil varies due to differences in the ethnic groups in different regions; however, these studies have not been performed in Minas Gerais, where African admixture is more prevalent in comparison with other states. Due to these facts, this study aimed to determine the frequency of RBC genotypes on Rh, Kell, Duffy and Kidd systems in blood donors and multi-transfused patients from Minas Gerais, Southeast Brazil...
December 16, 2017: Transfusion and Apheresis Science
https://www.readbyqxmd.com/read/29329588/accuracy-of-four-mononucleotide-repeat-markers-for-the-identification-of-dna-mismatch-repair-deficiency-in-solid-tumors
#15
Yuko Takehara, Takeshi Nagasaka, Akihiro Nyuya, Tomoko Haruma, Junko Haraga, Yoshiko Mori, Keiichiro Nakamura, Toshiyoshi Fujiwara, C Richard Boland, Ajay Goel
BACKGROUND: To screen tumors with microsatellite instability (MSI) arising due to DNA mismatch repair deficiency (dMMR), a panel of five quasi-monomorphic mononucleotide-repeat markers amplified in a multiplex PCR (Pentaplex) are commonly used. In spite of its several strengths, the pentaplex assay is not robust at detecting the loss of MSH6-deficiency (dMSH6). In order to overcome this challenge, we designed this study to develop and optimize a panel of four quasi-monomorphic mononucleotide-repeat markers (Tetraplex) for identifying solid tumors with dMMR, especially dMSH6...
January 12, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29329337/mitochondrial-dna-ancestry-hpv-infection-and-the-risk-of-cervical-cancer-in-a-multiethnic-population-of-northeastern-argentina
#16
Ines Badano, Daiana J Sanabria, Maria E Totaro, Samara Rubinstein, Juan A Gili, Domingo J Liotta, Maria A Picconi, Rodolfo H Campos, Theodore G Schurr
BACKGROUND: Misiones Province in northeastern Argentina is considered to be a region with a high prevalence of HPV infection and a high mortality rate due to cervical cancer. The reasons for this epidemiological trend are not completely understood. To gain insight into this problem, we explored the relationship between mitochondrial DNA (mtDNA) ancestry, HPV infection, and development of cervical lesions/cancer in women from the city of Posadas in Misiones Province. METHODS: Two hundred and sixty-one women, including 92 cases of patients diagnosed with cervical lesions and 169 controls, were analyzed...
2018: PloS One
https://www.readbyqxmd.com/read/29329324/variability-and-cost-implications-of-three-generations-of-the-roche-lightcycler%C3%A2-480
#17
Maria Dullaert-de Boer, Onno W Akkerman, Marloes Vermeer, Dorine L J Hess, Huib A M Kerstjens, Richard M Anthony, Tjip S van der Werf, Dick van Soolingen, Adri G M van der Zanden
Real time PCR has become a dominant method for the highly sensitive detection of pathogens in clinical material. Real time PCR can generate a fluorescence signal by using fluorescence labelled probes, allowing us to detect and semi quantify the amount of amplified DNA. Here we test the variability of the detection system and cost implications of three different versions of the LightCycler® 480 (LC480), focusing on the intensity of fluorescence and Cq in monoplex and multiplex rtPCRs. For gastro-intestinal pathogens there was no correlation between the intensity of fluorescence and the Cq value in the different LC480 types...
2018: PloS One
https://www.readbyqxmd.com/read/29323541/development-of-a-targeted-next-generation-sequencing-assay-to-detect-diagnostically-relevant-mutations-of-jak2-calr-and-mpl-in-myeloproliferative-neoplasms
#18
Thomas Frawley, Cathal P O'Brien, Eibhlin Conneally, Elisabeth Vandenberghe, Melanie Percy, Stephen E Langabeer, Karl Haslam
BACKGROUND: The classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), consisting of polycythemia vera, essential thrombocythemia, and primary myelofibrosis, are a heterogeneous group of neoplasms that harbor driver mutations in the JAK2, CALR, and MPL genes. The detection of these mutations has been incorporated into the recent World Health Organization (WHO) diagnostic criteria for MPN. Given a pressing clinical need to screen for these mutations in a routine diagnostic setting, a targeted next-generation sequencing (NGS) assay for the detection of MPN-associated mutations located in JAK2 exon 14, JAK2 exon 12, CALR exon 9, and MPL exon 10 was developed to provide a single platform alternative to reflexive, stepwise diagnostic algorithms...
January 11, 2018: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/29323070/is-diabetes-mellitus-an-important-risk-factor-for-the-antibiotic-resistance-in-extraintestinal-pathogenic-escherichia-coli
#19
Arindam Chakraborty, Shalini Shenoy, Prabha Adhikari, Vishwas Saralaya, Satish Rao
Escherichia coli is a major cause of extraintestinal infections in all age group. However, the infection becomes more severe when patients have some underlying condition such as Diabetes Mellitus. The aim of the study was to determine whether diabetic mellitus may act as an important risk factor for the E. coli to express drug resistance property. This descriptive study was carried out in a multi-specialty tertiary care hospital. One hundred and twenty-seven E. coli isolates from diabetic patients, and one hundred seventy-three isolates from nondiabetic patients were studied...
October 2017: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/29320875/characterization-of-bacteriophages-and-their-carriage-in-staphylococcus-aureus-isolated-from-broilers-in-poland
#20
A Marek, E Pyzik, D Stępień-Pyśniak, R Urban-Chmiel, A Nowaczek
1. The objective of this study was the isolation and morphological characterisation of temperate bacteriophages induced from Staphylococcus aureus strains isolated from clinical samples from broiler chickens and turkeys. 2. Eighty-five S. aureus strains were tested for susceptibility to oxacillin in order to determine which were multi-resistant. A total of 24 strains showed resistance to methicillin. 3. Thirty-one bacteriophages that were lytic against S. aureus strains were isolated and the host range of the bacteriophages was evaluated...
January 11, 2018: British Poultry Science
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