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https://www.readbyqxmd.com/read/28239513/rapid-molecular-detection-of-zika-virus-in-acute-phase-urine-samples-using-the-recombinase-polymerase-amplification-assay
#1
Ahmed Abd El Wahed, Sabri Saeed Sanabani, Oumar Faye, Rodrigo Pessôa, João Veras Patriota, Ricardo Rodrigues Giorgi, Pranav Patel, Susanne Böhlken-Fascher, Olfert Landt, Matthias Niedrig, Paolo Marinho de Andrade Zanotto, Claus Peter Czerny, Amadou A Sall, Manfred Weidmann
BACKGROUND: Currently the detection of Zika virus (ZIKV) in patient samples is done by real-time RT-PCR. Samples collected from rural area are sent to highly equipped laboratories for screening. A rapid point-of-care test is needed to detect the virus, especially at low resource settings. METHODOLOGY/PRINCIPAL FINDINGS: In this report, we describe the development of a reverse transcription isothermal recombinase polymerase amplification (RT-RPA) assay for the identification of ZIKV...
January 25, 2017: PLoS Currents
https://www.readbyqxmd.com/read/28238416/quantitative-multiplexed-tandem-pcr-for-direct-detection-of-bacteraemia-in-critically-ill-patients
#2
Andrew N Ginn, Briony Hazelton, Shereen Shoma, Martin Cullen, Thomas Solano, Jonathan R Iredell
Culture remains the gold standard for diagnosis of blood stream infections (BSI), but its clinical utility is limited by slow turnaround times. Here we describe a method for rapid quantitative detection of bacterial DNA directly extracted from whole blood using a multiplexed tandem real-time PCR (MT-PCR) assay targeting Staphylococcus, Streptococcus, Pseudomonas, Enterococcus and Enterobacteriaceae 16S rDNA genes. Results were available less than 3.5 hours after blood collection with all five bacterial targets having limits of detection between 10(1) and 10(3) CFU/mL...
February 23, 2017: Pathology
https://www.readbyqxmd.com/read/28238388/multicenter-evaluation-of-the-revised-rida%C3%A2-quick-test-n1402-for-rapid-detection-of-norovirus-in-a-diagnostic-laboratory-setting
#3
Stijn Jonckheere, Nadine Botteldoorn, Patricia Vandecandelaere, Johan Frans, Wim Laffut, Guy Coppens, Anne Vankeerberghen, Hans De Beenhouwer
The updated RIDA® QUICK (N1402) immunochromatographic assay (R-Biopharm) for detection of norovirus was evaluated during a prospective, multicenter study using 771 stool samples from patients with gastroenteritis. Compared to real-time reverse transcriptase polymerase chain reaction (RT-rtPCR) as gold standard, the RIDA® QUICK had an overall sensitivity of 72.8% (91/125) and a specificity of 99.5% (640/643). Genotype analysis of the polymerase (ORF1) and capsid (ORF2) region of the genome indicated that the RIDA® QUICK assay could detect a broad range of genotypes including new variants (15 of 125 positive samples) which were detected by an in-house SYBR®Green RT-rtPCR, but not by the RIDA® GENE PCR PG1415 (R-Biopharm) and mostly not by the RIDA® GENE PCR PG1405 and the Xpert® Norovirus assay (Cepheid)...
February 12, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28238212/development-a-rapid-and-accurate-multiplex-real-time-pcr-method-for-the-detection-chlamydia-trachomatis-and-mycoplasma-hominis
#4
Roya Safarkar, Jalil Fallah Mehrabadi, Zahra Noormohammadi, Reza Mirnejad
BACKGROUND: Sexually transmitted diseases easily spread among sexually active people and often have no symptoms. Rapid and accurate method for detecting these infections are necessary in early stages. The traditional detection methods of them are difficult and time-consuming. METHODS: In this study, multiplex real time PCR was optimized for rapid identification of Chlamydia trachomatis and Mycoplasma hominis in a single tube and was performed with our designed primers...
February 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28237995/development-of-strain-specific-primers-for-identification-of-bifidobacterium-bifidum-bgn4
#5
So Youn Youn, Geun Eog Ji, Yoo Ri Han, Myeong Soo Park
Bifidobacterium bifidum BGN4 (BGN4) has many proven beneficial effects including antiallergy and anti-cancer properties. It has been commercialized and used in several probiotic products and thus, strain-specific identification of this strain is very valuable for further strain dependent physiological study. For this purpose, we developed novel multiplex polymerase chain reaction (PCR) primer sets for strain specific detection of BGN4 in the commercial product and fecal sample of animal model. The primer set was tested on seven strains of B...
February 24, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28237777/integrin-linked-kinase-improves-functional-recovery-of-diabetic-cystopathy-and-mesenchymal-stem-cell-survival-and-engraftment-in-rats
#6
Yi Huang, Liucheng Ding, Yunpeng Shao, Zhengsen Chen, Baixin Shen, Yinchao Ma, Lijie Zhu, Zhongqing Wei
OBJECTIVES: Diabetic cystopathy (DCP), characterized by peripheral neuropathy-associated bladder dysfunction, is a common urinary complication in patients with diabetes (~80%). Bone marrow mesenchymal stem cell (BMMSC) transplantation, a new and emerging regenerative therapy, provides a curative option for DCP. However, the application of this therapy is limited by the low survival rate and engraftment of transplanted stem cells. This study was undertaken to determine whether integrin-linked kinase (ILK) overexpression would improve stem cell survival and engraftment after BMMSC transplantation...
February 22, 2017: Canadian Journal of Diabetes
https://www.readbyqxmd.com/read/28237624/three-year-evaluation-of-xpert-mtb-rif-in-a-low-prevalence-tuberculosis-setting-a-scottish-perspective
#7
Benjamin J Parcell, Anna Jarchow-MacDonald, Amie-Louise Seagar, Ian Laurenson, Gordon J Prescott, Michael Lockhart
OBJECTIVES: Xpert MTB/RIF (Cepheid) is a rapid molecular assay shown to be sensitive and specific for pulmonary tuberculosis (TB) diagnosis in highly endemic countries. We evaluated its diagnostic performance in a low TB prevalence setting, examined rifampicin resistance detection and quantitative capabilities predicting graded auramine microscopy and time to positivity (TTP) of culture. METHODS: Xpert MTB/RIF was used to test respiratory samples over a 3 year period...
February 22, 2017: Journal of Infection
https://www.readbyqxmd.com/read/28237380/newborn-dried-blood-spot-polymerase-chain-reaction-to-identify-infants-with-congenital-cytomegalovirus-associated-sensorineural-hearing-loss
#8
Shannon A Ross, Amina Ahmed, April L Palmer, Marian G Michaels, Pablo J Sánchez, Audra Stewart, David I Bernstein, Kristina Feja, Karen B Fowler, Suresh B Boppana
OBJECTIVE: To determine the utility of dried blood spot (DBS) polymerase chain reaction (PCR) in identifying infants with cytomegalovirus (CMV) infection-associated sensorineural hearing loss (SNHL). STUDY DESIGN: Newborns at 7 US hospitals between March 2007 and March 2012 were screened for CMV by saliva rapid culture and/or PCR. Infected infants were monitored for SNHL during the first 4 years of life to determine sensitivity, specificity, and positive and negative likelihood ratios of DBS PCR for identifying CMV-associated SNHL...
February 22, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28230980/chitosan-modified-filter-paper-for-nucleic-acid-extraction-and-in-situ-pcr-on-a-thermoplastic-microchip
#9
Wupeng Gan, Yin Gu, Junping Han, Caixia Li, Jing Sun, Peng Liu
Plastic microfluidic devices with embedded chitosan-modified Fusion 5 filter paper (unmodified one purchased from GE Healthcare) have been successfully developed for DNA extraction and concentration, utilizing two different mechanisms for DNA capture: the physical entanglement of long-chain DNA molecules with the fiber matrix of the filter paper and the electrostatic adsorption of DNA to the chitosan-modified filter fibers. This new method not only provided a high DNA extraction efficiency at a pH of 5 by synergistically combining these two capture mechanisms together, but also resisted the elution of DNA from filters at a pH >8 due to the entanglement of DNA with fibers...
February 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28230741/high-frequency-repetitive-transcranial-magnetic-stimulation-rtms-improves-functional-recovery-by-enhancing-neurogenesis-and-activating-bdnf-trkb-signaling-in-ischemic-rats
#10
Jing Luo, Haiqing Zheng, Liying Zhang, Qingjie Zhang, Lili Li, Zhong Pei, Xiquan Hu
Repetitive transcranial magnetic stimulation (rTMS) has rapidly become an attractive therapeutic approach for stroke. However, the mechanisms underlying this remain elusive. This study aimed to investigate whether high-frequency rTMS improves functional recovery mediated by enhanced neurogenesis and activation of brain-derived neurotrophic factor (BDNF)/tropomyosin-related kinase B (TrkB) pathway and to compare the effect of conventional 20 Hz rTMS and intermittent theta burst stimulation (iTBS) on ischemic rats...
February 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28229213/development-of-a-rapid-identification-method-for-the-differentiation-of-enterococcus-species-using-a-species-specific-multiplex-pcr-based-on-comparative-genomics
#11
Jongbin Park, Gwi-Deuk Jin, Jae In Pak, Jihyun Won, Eun Bae Kim
Enterococci are lactic acid bacteria that are commonly found in food and in animal gut. Since 16 S ribosomal RNA (rRNA) sequences, genetic markers for bacterial identification, are similar among several Enterococcus species, it is very difficult to determine the correct species based on only 16 S rRNA sequences. Therefore, we developed a rapid method for the identification of different Enterococcus species using comparative genomics. We compared 38 genomes of 13 Enterococcus species retrieved from the National Center of Biotechnology Information database and identified 25,623 orthologs...
February 22, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28228179/serological-evidence-of-lyssavirus-infection-among-bats-in-nagaland-a-north-eastern-state-in-india
#12
R S Mani, D P Dovih, M A Ashwini, B Chattopadhyay, P K Harsha, K M Garg, S Sudarshan, R Puttaswamaiah, U Ramakrishnan, S N Madhusudana
Bats are known to be reservoirs of several medically important viruses including lyssaviruses. However, no systematic surveillance for bat rabies has been carried out in India, a canine rabies endemic country with a high burden of human rabies. Surveillance for rabies virus (RABV) infection in bats was therefore carried out in Nagaland, a north-eastern state in India at sites with intense human-bat interfaces during traditional bat harvests. Brain tissues and sera from bats were tested for evidence of infection due to RABV...
February 23, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28228113/validation-of-an-ngs-mutation-detection-panel-for-melanoma
#13
Anne Reiman, Hugh Kikuchi, Daniela Scocchia, Peter Smith, Yee Wah Tsang, David Snead, Ian A Cree
BACKGROUND: Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as immunotherapy. METHODS: While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential advantages in turnaround time...
February 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28225788/molecular-detection-and-genotyping-of-enteroviruses-from-csf-samples-of-patients-with-suspected-sepsis-like-illness-and-or-aseptic-meningitis-from-2012-to-2015-in-west-bank-palestine
#14
Kamal Dumaidi, Amer Al-Jawabreh
BACKGROUND: Human enteroviruses (HEVs) are the most frequently reported cause of aseptic meningitis with or without CSF pleocytosis in childhood. Rapid detection and genotype of HEVs is essential to determine the causative agent and variant causing sepsis-like illness and/or aseptic meningitis. AIM: To investigate the molecular epidemiology of enteroviruses (EVs) among patients with sepsis-like illness and/or aseptic meningitis admitted to three major hospitals in West Bank, Palestine from 2012 to 2015...
2017: PloS One
https://www.readbyqxmd.com/read/28225779/combined-small-rna-and-degradome-sequencing-reveals-complex-microrna-regulation-of-catechin-biosynthesis-in-tea-camellia-sinensis
#15
Ping Sun, Chunzhen Cheng, Yuling Lin, Qiufang Zhu, Jinke Lin, Zhongxiong Lai
MicroRNAs are endogenous non-coding small RNAs playing crucial regulatory roles in plants. Tea, a globally popular non-alcoholic drink, is rich in health-enhancing catechins. In this study, 69 conserved and 47 novel miRNAs targeting 644 genes were identified by high-throughout sequencing. Predicted target genes of miRNAs were mainly involved in plant growth, signal transduction, morphogenesis and defense. To further identify targets of tea miRNAs, degradome sequencing and RNA ligase-mediated rapid amplification of 5'cDNA ends (RLM-RACE) were applied...
2017: PloS One
https://www.readbyqxmd.com/read/28224727/molecular-identification-and-distribution-of-non-tuberculous-mycobacteria-isolated-from-clinical-specimens-by-pcr-sequencing-method-in-west-of-iran
#16
Mahsa Dastranj, Abbas Farahani, Abdolrazagh Hashemi Shahraki, Sara Atashi, Parviz Mohajeri
BACKGROUND AND AIMS: Infections by Non-tuberculous Mycobacteria (NTM) has rapidly increased in recent years, due to high infection rates related to the populations at risk like immunocompromised individuals, patients predisposed by prior pulmonary. The aim of this study was to investigate the presence of NTM in clinical samples and genetic diversity using 16S rRNA and rpoB sequence analysis. METHODS: A cross-sectional study was conducted on 45 diverse isolates collected from sputum in two years 2014-2015 using standard decontamination procedure...
February 22, 2017: Clinical Respiratory Journal
https://www.readbyqxmd.com/read/28223146/identification-of-a-novel-cosavirus-species-in-feces-of-children-and-its-relationship-with-acute-gastroenteritis-in-china
#17
Jie-Mei Yu, Yuan-Yun Ao, Li-Li Li, Zhao-Jun Duan
OBJECTIVES: To assess the prevalence of human cosavirus (HCosV) in China and to determine the association of a novel HCosV (Cosa-CHN) with acute gastroenteritis (AGE) . METHODS: A case-control study with 461 paired stool samples from diarrhea and healthy children was conducted. Real-time PCR and nested PCR were used to detect the HCosVs. Rapid-amplification of cDNA ends was employed to obtain the ends of the Cosa-CHN. RESULTS: Known HCosVs were detected in two control samples, while Cosa-CHN was detected in eight (1...
February 18, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28222780/advanced-biosensors-for-detection-of-pathogens-related-to-livestock-and-poultry
#18
REVIEW
Jasmina Vidic, Marisa Manzano, Chung-Ming Chang, Nicole Jaffrezic-Renault
Infectious animal diseases caused by pathogenic microorganisms such as bacteria and viruses threaten the health and well-being of wildlife, livestock, and human populations, limit productivity and increase significantly economic losses to each sector. The pathogen detection is an important step for the diagnostics, successful treatment of animal infection diseases and control management in farms and field conditions. Current techniques employed to diagnose pathogens in livestock and poultry include classical plate-based methods and conventional biochemical methods as enzyme-linked immunosorbent assays (ELISA)...
February 21, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28221970/genomic-tools-for-customized-recovery-and-detection-of-foodborne-shiga-toxigenic-escherichia-coli
#19
Michael Knowles, Sara Stinson, Dominic Lambert, Catherine Carrillo, Adam Koziol, Martine Gauthier, Burton Blais
Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-associated clinical samples, may serve as the basis for customization of selective enrichment media, facilitating its recovery from samples in a food safety investigation. Different possibilities for AMR analyses include the use of comprehensive AMR gene databases such as the Comprehensive Antibiotic Resistance Database, which can be mined with in-house bioinformatics alignment tools (e...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221954/molecular-detection-of-the-three-major-pathogenic-vibrio-species-from-seafood-products-and-sediments-in-tunisia-using-real-time-pcr
#20
Morsi Gdoura, Hanen Sellami, Hanen Nasfi, Rahma Trabelsi, Sabeur Mansour, Touraya Attia, Siwar Nsaibia, Tatiana Vallaeys, Radhouane Gdoura, Mariam Siala
: Vibrio spp. have emerged as a serious threat to human health worldwide. V. parahaemolyticus , V. cholerae , and V. vulnificus pose a considerable public health risk in Tunisia because they cause sporadic and epidemic foodborne infections associated with the consumption of raw or undercooked contaminated seafood. More recently, toxR-positive V. alginolyticus was also reported to be a potential source of contaminated seafood. A total of 247 samples, including 113 fishes ( Labrus viridis , Penaeus kerathurus , Diplodus annularis , Diplodus sparaillon , Scorparna porcus , Sarpa salpa , Dentex dentex , Scorparna scrofa , Sardinella aurita , Trachurus trachurus , Synodus saurus , Pagellus erythrinus , and Metapenaeus monoceros ), 83 clams ( Ruditapes decussatus species), 30 seawater samples, and 21 sediment samples were analyzed using traditional culture methods (ISO/TS 21872-1; International Organization for Standardization 2007) and a conventional PCR method for Vibrio spp...
December 2016: Journal of Food Protection
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