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Molecular-epidemiology

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https://www.readbyqxmd.com/read/29782370/a-common-polymorphism-in-the-scn5a-gene-is-associated-with-dilated-cardiomyopathy
#1
Cristina Mazzaccara, Giuseppe Limongelli, Mario Petretta, Rossella Vastarella, Giuseppe Pacileo, Domenico Bonaduce, Francesco Salvatore, Giulia Frisso
AIMS: SCN5A is a disease-causing gene associated with familial dilated cardiomyopathy (FDC). We examined the possible association between a common polymorphism in the SCN5A gene (c.1673A>G-p.H558R; rs1805124) and the risk of dilated cardiomyopathy (DCM) occurrence. METHODS: We genotyped 185 DCM cases (familial DCM, idiopathic DCM and postischemic DCM) and 251 controls for the p.H558R polymorphism in the SCN5A gene, to test the association of the molecular epidemiology of the individuals with the presence/absence of various types of DCM...
May 17, 2018: Journal of Cardiovascular Medicine
https://www.readbyqxmd.com/read/29780013/use-of-internal-transcribed-spacer-sequence-polymorphisms-as-a-method-for-trichomonas-vaginalis-genotyping
#2
Hatice Ertabaklar, Sema Ertuğ, Serçin Özlem Çalışkan, Erdoğan Malatyalı, Bülent Bozdoğan
OBJECTIVE: Trichomonas vaginalis is the most common non-viral, sexually transmitted pathogen with a worldwide distribution. The aim of the present study was to design a new genotyping tool for T. vaginalis isolates using internal transcribed spacer (ITS) sequences. METHODS: First, a total of 20 cryopreserved T. vaginalis isolates were thawed and genomic DNA was isolated from fresh cultures. A polymerase chain reaction (PCR) was performed to amplify the ITS regions and the amplicons were sequenced...
March 2018: Türkiye Parazitolojii Dergisi
https://www.readbyqxmd.com/read/29779780/on-sunspots-click-science-and-molecular-iconography
#3
Igor Mokrousov
CRISPR-spoligotyping and MIRU-VNTR typing, SITVIT_WEB and MIRU-VNTRplus are the methods and online resources most widely used for Mycobacterium tuberculosis genotype family assignment and clustering analysis. They have been proven invaluable for molecular epidemiological studies of this important human pathogen in setting up the terminology and classification framework. However, they are inherently limited by insufficient knowledge of evolution of the targeted genome loci (especially, CRISPR). The situation is aggravated by the dogmatic, iconographic perception of these increasingly user-friendly online tools...
May 2018: Tuberculosis
https://www.readbyqxmd.com/read/29778701/natural-history-of-avian-papillomaviruses
#4
REVIEW
Daniel A Truchado, Richard A J Williams, Laura Benítez
Papillomaviruses (Family: Papillomaviridae) are small non-enveloped viruses that cause skin and mucosa infections in diverse vertebrates. The vast majority have been detected in mammals. However, the number of papillomaviruses described in birds is growing, especially because of metagenomic studies. Seven complete genomes and one partial sequence have been described, corresponding to five papillomavirus genera. These have been detected from various sample types, including skin, internal epithelium, and faecal material, from seven highly diverse wild and captive avian species...
May 17, 2018: Virus Research
https://www.readbyqxmd.com/read/29777337/molecular-epidemiology-of-parasitic-protozoa-and-ehrlichia-canis-in-wildlife-in-madrid-central-spain
#5
Angel Criado-Fornelio, T Martín-Pérez, C Verdú-Expósito, S A Reinoso-Ortiz, J Pérez-Serrano
Wildlife species are involved in the transmission of diverse pathogens. This study aimed to monitor raccoons (Procyon lotor), American minks (Neovison vison), and red foxes (Vulpes vulpes) as potential reservoirs in central Spain. Specifically, 200 spleen and fecal samples (from 194 raccoons, 3 minks, and 3 foxes) were analyzed molecularly by PCR/qPCR and sequencing for the presence of piroplasmids, Hepatozoon spp., Toxoplasma gondii, and Ehrlichia canis infections in the Community of Madrid (Spain). Biological samples were obtained in the years 2014, 2015, and 2016...
May 18, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29776807/public-health-surveillance-of-multidrug-resistant-clones-of-neisseria-gonorrhoeae-in-europe-a-genomic-survey
#6
Simon R Harris, Michelle J Cole, Gianfranco Spiteri, Leonor Sánchez-Busó, Daniel Golparian, Susanne Jacobsson, Richard Goater, Khalil Abudahab, Corin A Yeats, Beatrice Bercot, Maria José Borrego, Brendan Crowley, Paola Stefanelli, Francesco Tripodo, Raquel Abad, David M Aanensen, Magnus Unemo
BACKGROUND: Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and to predict and infer transmission of antimicrobial resistance, and can enhance infection control through linkage with epidemiological data. We used WGS, in conjunction with linked epidemiological and phenotypic data, to describe the gonococcal population in 20 European countries. We aimed to detail changes in phenotypic antimicrobial resistance levels (and the reasons for these changes) and strain distribution (with a focus on antimicrobial resistance strains in risk groups), and to predict antimicrobial resistance from WGS data...
May 15, 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29774858/genomic-epidemiology-of-global-carbapenemase-producing-enterobacter-spp-2008-2014
#7
Gisele Peirano, Yasufumi Matsumura, Mark D Adams, Patricia Bradford, Mary Motyl, Liang Chen, Barry N Kreiswirth, Johann D D Pitout
We performed whole-genome sequencing on 170 clinical carbapenemase-producing Enterobacter spp. isolates collected globally during 2008-2014. The most common carbapenemase was VIM, followed by New Delhi metallo-β-lactamase (NDM), Klebsiella pneumoniae carbapenemase, oxacillin 48, and IMP. The isolates were of predominantly 2 species (E. xiangfangensis and E. hormaechei subsp. steigerwaltii) and 4 global clones (sequence type [ST] 114, ST93, ST90, and ST78) with different clades within ST114 and ST90. Particular genetic structures surrounding carbapenemase genes were circulating locally in various institutions within the same or between different STs in Greece, Guatemala, Italy, Spain, Serbia, and Vietnam...
June 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29774212/alkaline-peptone-water-based-enrichment-method-for-mcr-3-from-acute-diarrheic-outpatient-gut-samples
#8
Qiaoling Sun, Yanyan Hu, Hongwei Zhou, Lingbin Shu, Hanyu Wang, Zixian Huang, Rong Zhang
A third plasmid-mediated colistin resistance gene, mcr-3 , is increasingly being reported in Enterobacteriaceae and Aeromonas spp. from animals and humans. To investigate the molecular epidemiology of mcr in the gut flora of Chinese outpatients, 152 stool specimens were randomly collected from outpatients in our hospital from May to June, 2017. Stool specimens enriched in alkaline peptone water or Luria-Bertani (LB) broth were screened for mcr-1, mcr-2 , and mcr-3 using polymerase chain reaction (PCR)-based assays...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29774093/distribution-of-virulence-associated-genes-and-antimicrobial-susceptibility-in-clinical-acinetobacter-baumannii-isolates
#9
Chao Liu, Yaowen Chang, Ying Xu, Yun Luo, Linrong Wu, Zhanjun Mei, Shigang Li, Rui Wang, Xu Jia
Acinetobacter baumannii is undoubtedly one of the most clinically significant pathogens. The multidrug resistance and virulence potential of A. baumannii are responsible for hospital-acquired nosocomial infections. Unlike numerous investigations on the drug-resistant epidemiology of A. baumanni , virulence molecular epidemiology is less studied. Here, we collected 88 A. baumannii clinical isolates, tested their antimicrobial susceptibility to 10 commonly used antibiotics and analyzed the distribution of 9 selected virulence-associated genes, aims to investigate the primary characteristics of the virulence-associated genes that exist in clinically multidrug resistant (MDR) and non-MDR isolates of A...
April 24, 2018: Oncotarget
https://www.readbyqxmd.com/read/29772466/research-on-the-contamination-levels-of-norovirus-in-food-facilities-using-groundwater-in-south-korea-2015-2016
#10
Jeong Su Lee, In Sun Joo, Si Yeon Ju, Min Hee Jeong, Yun-Hee Song, Hyo Sun Kwak
Norovirus (NoV) is a major pathogenic virus that is responsible for foodborne and waterborne gastroenteritis outbreaks. Groundwater is an important source of drinking water and is used in agriculture and food manufacturing processes. This study investigated norovirus contamination of groundwater treatment systems at 1360 sites in seven metropolitan areas and nine provinces in 2015-2016. Temperature, pH, residual chlorine, and turbidity content were assessed to analyze the water quality. In 2015, six sites were positive for the presence of NoV (0...
May 11, 2018: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29772398/molecular-epidemiology-and-characterization-of-picobirnaviruses-in-small-ruminant-populations-in-india
#11
Yashpal Singh Malik, Shubhankar Sircar, Kuldeep Dhama, Rashmi Singh, Souvik Ghosh, Krisztián Bányai, Anastasia N Vlasova, Touil Nadia, Raj Kumar Singh
Picobirnavirus (PBV) is recognized as a putative cause of diarrhea and respiratory illnesses. Although PBV has been reported in several mammalian (including humans) and avian host species, data pertaining to its presence in small ruminants are limited. We report, here, PBV infection in small ruminants (ovine and caprine), in India. From January 2015 to December 2017, 400 samples were tested for the presence of PBV, using an RT-PCR assay specific for the genome segment-2. The overall rate of PBV infection was 35...
May 14, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29771992/first-description-of-echinococcus-ortleppi-and-cystic-echinococcosis-infection-status-in-chile
#12
Felipe Corrêa, Caroll Stoore, Pamina Horlacher, Mauricio Jiménez, Christian Hidalgo, Cristian A Alvarez Rojas, Guilherme Figueiredo Barros, Henrique Bunselmeyer Ferreira, Marcela Hernández, Gonzalo Cabrera, Rodolfo Paredes
Cystic echinococcosis (CE), a parasitic disease caused by the cestode Echinococcus granulosus sensu lato (s.l.), is a worldwide zoonotic infection. Although endemic in Chile, information on the molecular characteristics of CE in livestock remains scarce. Therefore we aimed to describe the status of infection with E. granulosus s.l. in cattle from central Chile and also to contribute to the study of the molecular epidemiology of this parasite. According to our results, the prevalence of CE is 18.84% in cattle, similar to previous reports from Chile, suggesting that the prevalence in Santiago Metropolitan area has not changed in the last 30 years...
2018: PloS One
https://www.readbyqxmd.com/read/29770590/genomic-and-antigenic-characterization-of-porcine-epidemic-diarrhoea-virus-strains-isolated-from-south-korea-2017
#13
Sunhee Lee, Changhee Lee
Porcine epidemic diarrhoea virus (PEDV) is a globally emerging and re-emerging enteric coronavirus in pigs causing serious economic threats to the world swine industry. Since the re-emergence of massive PEDV outbreaks in South Korea in 2013-2014, domestic pig farms have continued to experience PED epidemics or endemics. This study represents the molecular characterization of PEDV isolates identified in diarrhoeic animals collected across the country in 2017. Initial sequencing analysis of the full-length S genes revealed that 70% of the 2017 isolates (7/10) belong to the G2b subgroup, while the remaining isolates were classified as G1b...
May 16, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29770205/beginning-at-the-ends-telomeres-and-human-disease
#14
REVIEW
Sharon A Savage
Studies of rare and common illnesses have led to remarkable progress in the understanding of the role of telomeres (nucleoprotein complexes at chromosome ends essential for chromosomal integrity) in human disease. Telomere biology disorders encompass a growing spectrum of conditions caused by rare pathogenic germline variants in genes encoding essential aspects of telomere function. Dyskeratosis congenita, a disorder at the severe end of this spectrum, typically presents in childhood with the classic triad of abnormal skin pigmentation, nail dystrophy, and oral leukoplakia, accompanied by a very high risk of bone marrow failure, cancer, pulmonary fibrosis, and other medical problems...
2018: F1000Research
https://www.readbyqxmd.com/read/29763630/clinical-and-molecular-epidemiologic-characteristics-of-carbapenem-resistant-klebsiella-pneumoniae-infection-colonization-among-neonates-in-china
#15
Dandan Yin, Lei Zhang, Aimin Wang, Leiyan He, Yun Cao, Fupin Hu, Chuanqing Wang
BACKGROUND: The spread of carbapenem-resistant Klebsiella pneumoniae (CR-KPN) is a major concern, but data on CR-KPN infection/colonization in paediatric populations are limited. AIM: This study aimed to analyze epidemiologic and clinical characteristics, therapeutic options of CR-KPN infections in neonates in China. METHODS: A retrospective study was performed at the Children's Hospital of Fudan University, including 88 neonates with CR-KPN admitted between November 2015 and October 2016...
May 12, 2018: Journal of Hospital Infection
https://www.readbyqxmd.com/read/29763627/evaluation-of-minion-nanopore-sequencing-for-rapid-enterovirus-genotyping
#16
Emily Rames, Joanne Macdonald
Enteroviruses (EV) are associated with a range of serious infections, including aseptic meningitis, hand foot and mouth disease, myocarditis, acute flaccid paralysis and encephalitis. Improved methods for assessing EV genotypic diversity could assist molecular epidemiology studies, clinical diagnosis and environmental surveillance. We report new methods for EV genome amplification, and subsequent genotyping using the miniaturised MinION sequencing device. Importantly, this next-generation sequencer enabled correct strain-level assignment of identity for the EV-A71 isolate assessed, where strains with up to 99...
May 12, 2018: Virus Research
https://www.readbyqxmd.com/read/29760959/molecular-epidemiology-of-multidrug-resistant-bacteria-isolated-from-libyan-and-syrian-patients-with-war-injuries-in-two-bundeswehr-hospitals-in-germany
#17
Hagen Frickmann, Thomas Köller, Ralf Matthias Hagen, Klaus-Peter Ebert, Martin Müller, Werner Wenzel, Renate Gatzer, Ulrich Schotte, Alfred Binder, Romy Skusa, Philipp Warnke, Andreas Podbielski, Christian Rückert, Bernd Kreikemeyer
Introduction: We assessed the molecular epidemiology of multidrug-resistant bacteria colonizing or infecting war-injured patients from Libya and Syria who were treated at the Bundeswehr hospitals Hamburg and Westerstede, Germany. Methods: Enterobacteriaceae and Gram-negative rod-shaped nonfermentative bacteria with resistance against third-generation methoxyimino cephalosporins or carbapenems as well as methicillin-resistant Staphylococcus aureus (MRSA) from war-injured patients from Libya and Syria were assessed by molecular typing, i...
April 2018: European Journal of Microbiology & Immunology
https://www.readbyqxmd.com/read/29755603/bacterial-crispr-regions-general-features-and-their-potential-for-epidemiological-molecular-typing-studies
#18
REVIEW
Zahra Karimi, Ali Ahmadi, Ali Najafi, Reza Ranjbar
Introduction: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods: These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements...
2018: Open Microbiology Journal
https://www.readbyqxmd.com/read/29753103/genetic-diversity-of-human-sapovirus-across-the-americas
#19
Marta Diez-Valcarce, Christina J Castro, Rachel L Marine, Natasha Halasa, Holger Mayta, Mayuko Saito, Laura Tsaknaridis, Chao-Yang Pan, Filemon Bucardo, Sylvia Becker-Dreps, Maria Renee Lopez, Laura Cristal Magaña, Terry Fei Fan Ng, Jan Vinjé
BACKGROUND: Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. OBJECTIVE/STUDY DESIGN: To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US)...
May 6, 2018: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/29752274/molecular-epidemiology-of-shiga-toxin-producing-escherichia-coli-stec-on-new-zealand-dairy-farms-application-of-a-culture-independent-assay-and-whole-genome-sequencing
#20
A Springer Browne, Anne C Midwinter, Helen Withers, Adrian L Cookson, Patrick J Biggs, Jonathan C Marshall, Jackie Benschop, Steve Hathaway, Neville A Haack, Rukhshana N Akhter, Nigel P French
New Zealand has a relatively high incidence of human cases of Shiga toxin-producing Escherichia coli (STEC), with 8.9 STEC cases per 100,000 people reported in 2016. Previous research showed living near cattle and contact with cattle feces as significant risk factors for STEC infections in humans in New Zealand, but infection was not linked to food-associated factors. During the 2014 spring calving season, a random stratified cross-sectional study of dairy farms (n=102) in six regions across New Zealand assessed the prevalence of the 'Top 7' STEC (serogroups O157, O26, O45, O103, O111, O121, O145) in young calves (n=1,508) using a culture-independent diagnostic test (PCR/MALDI-TOF)...
May 11, 2018: Applied and Environmental Microbiology
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