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Multiplex PCR

Elena García-Payá, Marta Fernández, Sergio Padilla, José A García, Catalina Robledano, Victoria Ortiz DE LA Tabla, Félix Gutiérrez, Mar Masiá
OBJECTIVE: The protective effect of ART has not yet been definitively established in men who have sex with men (MSM). We aimed to characterize the factors associated with persistent HIV-1 RNA rectal shedding. METHODS: Prospective study including virologically-suppressed MSM from an HIV cohort. High-resolution anoscopy (HRA) was performed for screening of anal dysplasia, and rectal sampling for HIV-1 RNA quantification and sexually-transmitted infections (STIs) investigation through multiplex PCR...
March 15, 2018: AIDS
Xianhua Wang, Aiguo Ma, Xiuxia Han, Aishan Litifu, Feng Xue
Seven single-nucleotide polymorphism (SNP) sites located in ASAP1 gene have been found associated with tuberculosis (TB) susceptibility by genome-wide association studies in Russia. The case-control study was carried out to test whether these seven SNPs were associated with susceptibility to TB in a Chinese Xinjiang Muslim population. The seven SNPs were genotyped in a case-control design that included 780 Xinjiang Muslim subjects (400 TB patients and 380 controls). Multiplex PCR and direct sequencing were used to detect ASAP1 gene polymorphisms...
April 2018: Experimental and Therapeutic Medicine
M-A Dagnelie, A Khammari, B Dréno, S Corvec
BACKGROUND: The Gram-positive, anaerobic-aerotolerant bacterium Cutibacterium acnes is a commensal of human healthy skin, subdivided into six main phylogenetic groups or phylotypes: IA1, IA2, IB, IC, II and III. To decipher how far C. acnes specific subgroups are involved in disease physiopathology, different molecular typing methods have been developed to identify these subgroups (i.e. phylotypes, clonal complexes, SLST-types). However, as there were several molecular typing methods developed over the last decade, comparing the results from one article to another became a difficult task...
March 12, 2018: Clinical Microbiology and Infection
Kotoe Iesato, Tsukasa Hori, Yuko Yoto, Masaki Yamamoto, Natsuko Inazawa, Kenichi Kamo, Hiroshi Ikeda, Satoshi Iyama, Naoki Hatakeyama, Akihiro Iguchi, Junichi Sugita, Ryoji Kobayashi, Nobuhiro Suzuki, Hiroyuki Tsutsumi
BACKGROUND: Patients undergoing hematopoietic stem cell transplantation (HSCT) frequently experience HHV-6 reactivation typically during early phase following HSCT. However, the long-term clinical complications and prognosis among such patients remain unclear. METHODS: Between September 2010 and October 2012, whole blood samples from 105 patients collected weekly from prior to 6 weeks after HSCT underwent multiplex polymerase chain reaction (PCR) to screen for viral DNA, followed by real-time PCR for quantitative estimation...
March 14, 2018: Pediatrics International: Official Journal of the Japan Pediatric Society
Sumire Terasawa, Asuka Kato, Haruki Nishizawa, Takema Kato, Hikari Yoshizawa, Yoshiteru Noda, Jun Miyazaki, Mayuko Ito, Takao Sekiya, Takuma Fujii, Hiroki Kurahashi
Thanatophoric dysplasia (TD) and achondroplasia (ACH) are allelic disorders caused by a constitutively active mutation in the FGFR3 gene. Because TD is a lethal disorder and ACH is non-lethal, they need to be distinguished after ultrasound identification of fetal growth retardation with short limbs. Accordingly, we have developed a noninvasive prenatal test using cell-free fetal DNA in the maternal circulation to distinguish TD and ACH. A multiplex PCR system encompassing five mutation hotspots in the FGFR3 gene allowed us to efficiently identify the responsible mutation in cell-free DNA in all examined pregnancies with a suspected TD or ACH fetus...
March 14, 2018: Congenital Anomalies
Ngan Thi Kim Pham, Aksara Thongprachum, Quang Duy Trinh, Shoko Okitsu, Shihoko Komine-Aizawa, Hiroyuki Shimizu, Satoshi Hayakawa, Hiroshi Ushijima
Of 972 stool samples collected from infants and children with acute gastroenteritis in six different regions (Hokkaido, Tokyo, Shizuoka, Kyoto, Osaka, and Saga) of Japan during 2-year period from July 2014 to June 2016, 63 samples (6.5%) determined to be positive for enterovirus by multiplex RT-PCR were subjected to genotype determination based on the partial VP1 region using the CODEHOP method. Sixty-two strains were succeeded in genotyping and seventeen EV types were identified. The majority of the studied strains belonged to EV-A (30 of 62; 48...
March 11, 2018: Infection, Genetics and Evolution
Íñigo Corral, Susana Sainz de la Maza, Mario Rodríguez, Michal-Maciej Kawiorski, María-José López-Martínez, Juan-Carlos Galán
Neurological manifestations associated with HHV-7 have been described in primary infection in children, and very occasionally in immunocompromised adult patients. However, the role of HHV-7 reactivation as a cause of central nervous system (CNS) diseases in immunocompetent adults has not yet been defined. We retrospectively analyzed clinical and microbiological features of adults with neurological symptoms who underwent lumbar puncture and a multiplex polymerase chain reaction (PCR) for herpesviruses (HHV-1-8) and enteroviruses performed in cerebrospinal fluid (CSF), during a 4-year period...
March 13, 2018: Journal of Neurovirology
D Zidekova, I Waczulikova, L Dolesova, L Vavrova, O Hamidova, R Lohajova Behulova, M Konecny
The average risk of breast cancer in general Slovak population of women is 4-5% and the risk of ovarian cancer is 2%. Probability of breast/ovarian cancer development is higher in individuals carrying a causative germline DNA variant in BRCA1 or BRCA2 gene responsible for hereditary breast/ovarian cancer (HBOC). Although a major proportion of inherited breast/ovarian cancers are due to the mentioned causal mutations, a number of new genes have emerged. Here we describe a rapid, multiplex and comprehensive approach for the detection of pathogenic variants in BRCA1 and BRCA2 genes which most frequently occur in Slovak HBOC population...
2018: Neoplasma
Benedikt G Brink, Justin Meskas, Ryan R Brinkman
Motivation: Droplet digital PCR (ddPCR) is an emerging technology for quantifying DNA. By partitioning the target DNA into ∼20000 droplets, each serving as its own PCR reaction compartment, a very high sensitivity of DNA quantification can be achieved. However, manual analysis of the data is time consuming and algorithms for automated analysis of non-orthogonal, multiplexed ddPCR data are unavailable, presenting a major bottleneck for the advancement of ddPCR transitioning from low-throughput to high- throughput...
March 9, 2018: Bioinformatics
Bernard Louizette Christophe, Mariana Mott, Gabriela da Cunha, Juliana Caierão, Pedro D Azevedo, Cícero Dias
PURPOSE: Invasive pneumococcal disease (IPD) in the elderly is an important public health issue due to the increased proportion of this population in many countries including Brazil. We aimed to characterise pneumococci isolates in adults >50 years with IPD, following the introduction of the 10-valent pneumococcal conjugate vaccine (PCV10) as part of the National Childhood Immunisation Program for children ≤2 years in March 2010. METHODOLOGY: Between 2013 and 2015, pneumococcal isolates were collected and serotypes were determined using multiplex PCR and/or Quellung reaction...
March 13, 2018: Journal of Medical Microbiology
Nicole M Bzdyl, Nadezda Urosevic, Ben Payne, Ray Brockenshire, Michael McIntyre, Michael J Leung, Graham Weaire-Buchanan, Elizabeth Geelhoed, Timothy J J Inglis
PURPOSE: In this field trial of rapid blood culture identification (BCID), we aimed to determine whether the improved speed and accuracy of specific BCID predicted in our earlier pilot study could be obtained in regional hospitals by deploying a multiplex PCR FilmArray (Biomerieux, France) capability in their laboratories. METHODS: We trained local hospital laboratory staff to operate the FilmArray equipment and act on the results. To do this, we integrated the multiplex PCR into the standard laboratory blood culture workflow and reporting procedure...
March 13, 2018: Journal of Medical Microbiology
Anshu Babbar, Andreas Itzek, Dietmar H Pieper, D Patric Nitsche-Schmitz
Streptococcus dysgalactiae subsp. equisimilis (SDSE), belonging to the group C and G streptococci, are human pathogens reported to cause clinical manifestations similar to infections caused by Streptococcus pyogenes. To scrutinize the distribution of gene coding for S. pyogenes virulence factors in SDSE, 255 isolates were collected from humans infected with SDSE in Vellore, a region in southern India, with high incidence of SDSE infections. Initial evaluation indicated SDSE isolates comprising of 82.35% group G and 17...
March 12, 2018: Folia Microbiologica
Suparak Para, Punchalee Mungkalasut, Makamas Chanda, Issarang Nuchprayoon, Srivicha Krudsood, Chalisa Louicharoen Cheepsunthorn
Background: The protective effect of α-thalassemia, a common hematological disorder in Southeast Asia, against Plasmodium falciparum malaria has been well established. However, there is much less understanding of the effect of α-thalassemia against P. vivax . Here, we aimed to investigate the proportion of α-thalassemia including the impact of α-thalassemia and HbE on the parasitemia of P. vivax in Southeast Asian malaria patients in Thailand. Methods: A total of 210 malaria patients, admitted to the Hospital for Tropical Diseases, Thailand during 2011-2012, consisting of 159 Myanmeses, 13 Karens, 26 Thais, 3 Mons, 3 Laotians, and 6 Cambodians were recruited...
2018: Mediterranean Journal of Hematology and Infectious Diseases
Phuong L Trinh, Yen Pham
Numerous studies have identified Nucleophosmin 1 ( NPM1 ) and Fms -like tyrosine kinase 3 ( FLT3 ) as the most frequently mutated genes in Acute Myeloid Leukemia (AML) patients. Mutations occurring in these genes, including NPM1+4 (tetranucleotide insertions), FLT3-ITD (internal tandem duplications), and FLT3-TKD (tyrosine kinase domain point mutations) account for approximately 80% of all mutations found in normal karyotype AML (AML-NK) cases. Different methods have been established to detect the three listed mutations, in which, PCR-based techniques are the most widely used due to their efficiency...
January 2018: Annals of Clinical and Laboratory Science
Starling A Sim, Vivian K Y Leung, David Ritchie, Monica A Slavin, Sheena G Sullivan, Benjamin W Teh
BACKGROUND: Viral respiratory tract infections (vRTI) are a significant cause of morbidity and mortality in patients undergoing allogeneic haematopoietic stem cell transplantation (alloHSCT). This study aimed to assess the epidemiological characteristics, risk factors, and outcomes of vRTI occurring from conditioning to 100 days after HSCT in the era of molecular testing. METHODS: This study was a retrospective record review of alloHSCT patients at Royal Melbourne Hospital from January 2010 to December 2015...
March 9, 2018: Biology of Blood and Marrow Transplantation
Yuk-Fai Lau, Wee-Hong Victor Koh, Clement Kan, Poh-Choo Alethea Dua, Ai-Sim Elizabeth Lim, Chin-Wen Jasper Liaw, Qiu-Han Gao, Jeremiah Chng, Vernon J Lee, Boon-Huan Tan, Jin-Phang Loh
BACKGROUND: Respiratory illnesses have been identified as a significant factor leading to lost training time and morbidity among Singapore military recruits. A surveillance programme has been put in place to determine etiological agents responsible for febrile, as well as afebrile respiratory illnesses in a military camp. The goal of the study is to better understand the epidemiology of these diseases and identify potential countermeasures to protect military recruits against them. METHODS: From Jan 2016 - Jan 2017, a total of 2647 respiratory cases were enrolled into the surveillance programme...
March 12, 2018: BMC Infectious Diseases
Dechao Xu, Yiyi Ma, Xiangchen Gu, Rongrong Bian, Yunhui Lu, Xiaohong Xing, Changlin Mei
BACKGROUND/AIMS: Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder with mutations in PKD1 or PKD2. This study aimed to identify novel PKD1 and PKD2 mutations in Chinese patients with ADPKD. METHODS: Mutational analyses of both PKD genes were performed in 120 Chinese families with inherited ADPKD using long-range PCR and targeted next-generation sequencing approaches. Sanger sequencing was performed to check the positive mutations, while multiplex ligation-dependent probe amplification was adopted to examine those without mutations for the presence of large deletions...
March 6, 2018: Kidney & Blood Pressure Research
Ana Kovacic, Martina Seruga Music, Svjetlana Dekic, Marija Tonkic, Anita Novak, Zana Rubic, Jasna Hrenovic, Ivana Goic-Barisic
Acinetobacter baumannii origin and its epidemiology is under a great concern worldwide since this microorganism has become a leading nosocomial pathogen of the 21th century among the "ESKAPE" group of microorganisms. The aim of the study was to monitor and explore the epidemiology of this important hospital pathogen in the second largest clinical university hospital in Croatia. The presence of A. baumannii in hospital wastewater, as a route for possible transmission outside of the hospital setting, as well as its survival in environmental conditions including seawater, was investigated...
December 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
Chong Shi, Shazhou An, Zhengpei Yao, Carolyn A Young, Daniel G Panaccione, Stephen T Lee, Christopher L Schardl, Chunjie Li
Cool-season grasses (Poaceae subfamily Poöideae) are an important forage component for livestock in western China, and many have seed-transmitted symbionts of the genus Epichloë, fungal endophytes that are broadly distributed geographically and in many tribes of the Poöideae. Epichloë strains can produce any of several classes of alkaloids, of which ergot alkaloids and indole-diterpenes can be toxic to mammalian and invertebrate herbivores, whereas lolines and peramine are more selective against invertebrates...
January 25, 2018: Mycologia
Alejandro Garrido-Maestu, Sarah Azinheiro, Joana Carvalho, Marta Prado
Listeria monocytogenes continues to be one of the most important foodborne pathogens worldwide, either due to its incidence and/or to its high mortality rate. In the present study, a filtration-based protocol was applied for the screening of viable bacteria. Additionally, a complete method (enrichment, filtration, DNA extraction and real-time PCR detection) was evaluated in order to determine the capacity of this protocol to detect viable L. monocytogenes in food samples. A new multiplex qPCR detection system was designed, including an internal amplification control, both targets were detected with hydrolysis probes...
August 2018: Food Microbiology
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