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Transmission, infection, SIngle nucleotide polymorphism

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https://www.readbyqxmd.com/read/28575285/comparison-of-control-of-clostridium-difficile-infection-in-six-english-hospitals-using-whole-genome-sequencing
#1
David W Eyre, Warren N Fawley, Anu Rajgopal, Christopher Settle, Kalani Mortimer, Simon D Goldenberg, Susan Dawson, Derrick W Crook, Tim E A Peto, A Sarah Walker, Mark H Wilcox
Background.: Variation in Clostridium difficile infection (CDI) rates between healthcare institutions suggests overall incidence could be reduced if the lowest rates could be achieved more widely. Methods.: We used whole-genome sequencing (WGS) of consecutive C. difficile isolates from 6 English hospitals over 1 year (2013-14) to compare infection control performance. Fecal samples with a positive initial screen for C. difficile were sequenced. Within each hospital, we estimated the proportion of cases plausibly acquired from previous cases...
May 29, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28547382/comparative-analysis-of-cherry-virus-a-genome-sequences-assembled-from-deep-sequencing-data
#2
Prasad Kesanakurti, Mark Belton, Hanaa Saeed, Heidi Rast, Ian Boyes, Michael Rott
Cherry virus A (CVA) is a ubiquitous graft-transmissible virus that mainly infects Prunus spp. Next-generation sequencing was applied to 39 tree fruit specimens infected with CVA, and 75 full and 16 partial-length CVA genome sequences were assembled. Phylogenetic analysis of these and 11 previously sequenced CVA genomes resulted in six major clusters with no observable relationship between the host and the assembled genome sequences. Recombination analysis detected four recombinants. Consistent single-nucleotide polymorphism (SNP) patterns were observed between the 75 full-length genomes and their sequence clouds, which supports a quasispecies model for CVA evolution...
May 25, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28490578/investigating-clinical-issues-by-genotyping-of-medically-important-fungi-why-and-how
#3
REVIEW
Alexandre Alanio, Marie Desnos-Ollivier, Dea Garcia-Hermoso, Stéphane Bretagne
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes...
July 2017: Clinical Microbiology Reviews
https://www.readbyqxmd.com/read/28484440/in-depth-characterization-and-functional-analysis-of-clonal-variants-in-a-mycobacterium-tuberculosis-strain-prone-to-microevolution
#4
Yurena Navarro, Laura Pérez-Lago, Marta Herranz, Olalla Sierra, Iñaki Comas, Javier Sicilia, Emilio Bouza, Darío García de Viedma
The role of clonal complexity has gradually been accepted in infection by Mycobacterium tuberculosis (MTB), although analyses of this issue are limited. We performed an in-depth study of a case of recurrent MTB infection by integrating genotyping, whole genome sequencing, analysis of gene expression and infectivity in in vitro and in vivo models. Four different clonal variants were identified from independent intrapatient evolutionary branches. One of the single-nucleotide polymorphisms in the variants mapped in mce3R, which encodes a repressor of an operon involved in virulence, and affected expression of the operon...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28475785/mrsa-transmission-dynamics-among-interconnected-acute-intermediate-term-and-long-term-healthcare-facilities-in-singapore
#5
Angela Chow, Vanessa W Lim, Ateeb Khan, Kerry Pettigrew, David C B Lye, Kala Kanagasabai, Kelvin Phua, Prabha Krishnan, Brenda Ang, Kalisvar Marimuthu, Pei-Yun Hon, Jocelyn Koh, Ian Leong, Julian Parkhill, Li-Yang Hsu, Matthew T G Holden
Background: Methicillin-resistant Staphylococcus aureus (MRSA) is the most common healthcare-associated multidrug-resistant organism. Despite the interconnectedness between acute care hospitals (ACHs) and intermediate- and long-term care facilities (ILTCFs), the transmission dynamics of MRSA between healthcare settings is not well understood. Methods: We conducted a cross-sectional study in a network comprising an ACH and 5 closely affiliated ILTCFs in Singapore...
May 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28420399/distinct-parasite-populations-infect-individuals-identified-through-passive-and-active-case-detection-in-a-region-of-declining-malaria-transmission-in-southern-zambia
#6
Kelly M Searle, Ben Katowa, Tamaki Kobayashi, Mwiche N S Siame, Sungano Mharakurwa, Giovanna Carpi, Douglas E Norris, Jennifer C Stevenson, Philip E Thuma, William J Moss
BACKGROUND: Substantial reductions in the burden of malaria have been documented in parts of sub-Saharan Africa, with elimination strategies and goals being formulated in some regions. Within this context, understanding the epidemiology of low-level malaria transmission is crucial to achieving and sustaining elimination. A 24 single-nucleotide-polymorphism Plasmodium falciparum molecular barcode was used to characterize parasite populations from infected individuals identified through passive and active case detection in an area approaching malaria elimination in southern Zambia...
April 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28348875/short-term-evolution-of-shiga-toxin-producing-escherichia-coli-o157-h7-between-two-food-borne-outbreaks
#7
Lauren A Cowley, Timothy J Dallman, Stephen Fitzgerald, Neil Irvine, Paul J Rooney, Sean P McAteer, Martin Day, Neil T Perry, James L Bono, Claire Jenkins, David L Gally
Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC O157:H7 that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided the outbreak strains into two sub-clusters separated by only three single-nucleotide polymorphisms in the core genome while traditional typing identified them as separate phage types, PT8 and PT54. Isolates did not cluster with local strains but with those associated with foreign travel to the Middle East/North Africa...
September 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28267758/whole-genome-analysis-of-mycobacteria-from-birds-at-the-san-diego-zoo
#8
Wayne Pfeiffer, Josephine Braun, Jennifer Burchell, Carmel L Witte, Bruce A Rideout
METHODS: Mycobacteria isolated from more than 100 birds diagnosed with avian mycobacteriosis at the San Diego Zoo and its Safari Park were cultured postmortem and had their whole genomes sequenced. Computational workflows were developed and applied to identify the mycobacterial species in each DNA sample, to find single-nucleotide polymorphisms (SNPs) between samples of the same species, to further differentiate SNPs between as many as three different genotypes within a single sample, and to identify which samples are closely clustered genomically...
2017: PloS One
https://www.readbyqxmd.com/read/28242664/the-two-component-system-chtrs-contributes-to-chlorhexidine-tolerance-in-enterococcus-faecium
#9
Ana M Guzmán Prieto, Jessica Wijngaarden, Johanna C Braat, Malbert R C Rogers, Eline Majoor, Ellen C Brouwer, Xinglin Zhang, Jumamurat R Bayjanov, Marc J M Bonten, Rob J L Willems, Willem van Schaik
Enterococcus faecium is one of the primary causes of nosocomial infections. Disinfectants are commonly used to prevent infections with multidrug-resistant E. faecium in hospitals. Worryingly, E. faecium strains that exhibit tolerance to disinfectants have already been described. We aimed to identify and characterize E. faecium genes that contribute to tolerance to the disinfectant chlorhexidine (CHX). We used a transposon mutant library, constructed in a multidrug-resistant E. faecium bloodstream isolate, to perform a genome-wide screen to identify genetic determinants involved in tolerance to CHX...
May 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28241747/screening-of-tnf%C3%AE-il-10-and-tlr4-single-nucleotide-polymorphisms-in-individuals-with-asymptomatic-and-chronic-cutaneous-leishmaniasis-in-colombia-a-pilot-study
#10
Angélica Mera-Ramírez, Andrés Castillo, Yenifer Orobio, María Adelaida Gómez, Carolina Gallego-Marin
BACKGROUND: Clinical manifestations of cutaneous leishmaniasis (CL) caused by Leishmania (Viannia) range from asymptomatic infection to self-limited, or chronic (non-healing) cutaneous lesions. Given the critical role of the immune response in the clinical outcome of CL, it is plausible that functional polymorphisms in immune-related genes contribute to define the clinical manifestations of human infection. METHODS: DNA samples from a retrospective cohort of individuals from an endemic area of L...
February 28, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28214367/population-genetic-structure-and-adaptation-of-malaria-parasites-on-the-edge-of-endemic-distribution
#11
Craig W Duffy, Hampate Ba, Samuel Assefa, Ambroise D Ahouidi, Yacine B Deh, Abderahmane Tandia, Freja C M Kirsebom, Dominic P Kwiatkowski, David J Conway
To determine whether the major human malaria parasite Plasmodium falciparum exhibits fragmented population structure or local adaptation at the northern limit of its African distribution where the dry Sahel zone meets the Sahara, samples were collected from diverse locations within Mauritania over a range of ~1000 km. Microsatellite genotypes were obtained for 203 clinical infection samples from eight locations, and Illumina paired-end sequences were obtained to yield high coverage genomewide single nucleotide polymorphism (SNP) data for 65 clinical infection samples from four locations...
June 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28194548/investigation-of-intra-herd-spread-of-mycobacterium-caprae-in-cattle-by-generation-and-use-of-a-whole-genome-sequence
#12
S Broeckl, S Krebs, A Varadharajan, R K Straubinger, H Blum, M Buettner
Single nucleotide polymorphisms (SNPs) calculated from whole genome sequencing (WGS) are ideally suited to study evolutionary relationships of pathogens and their epidemiology. Mycobacterium caprae infections have been documented frequently in cattle and red deer along the Bavarian and Austrian Alps during the last decade. However, little is still known about the transmission within cattle holdings and possible alterations of the genomes of M. caprae during such events. The aim of this study was to study the molecular epidemiology of bovine tuberculosis (bTB) in selected herds based on isolate-specific genome-wide SNPs and to perform a phylogenetic network analysis...
February 13, 2017: Veterinary Research Communications
https://www.readbyqxmd.com/read/28125584/the-real-mccoil-a-method-for-the-concurrent-estimation-of-the-complexity-of-infection-and-snp-allele-frequency-for-malaria-parasites
#13
Hsiao-Han Chang, Colin J Worby, Adoke Yeka, Joaniter Nankabirwa, Moses R Kamya, Sarah G Staedke, Grant Dorsey, Maxwell Murphy, Daniel E Neafsey, Anna E Jeffreys, Christina Hubbart, Kirk A Rockett, Roberto Amato, Dominic P Kwiatkowski, Caroline O Buckee, Bryan Greenhouse
As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28109869/outcomes-infectiousness-and-transmission-dynamics-of-patients-with-extensively-drug-resistant-tuberculosis-and-home-discharged-patients-with-programmatically-incurable-tuberculosis-a-prospective-cohort-study
#14
Keertan Dheda, Jason D Limberis, Elize Pietersen, Jody Phelan, Aliasgar Esmail, Maia Lesosky, Kevin P Fennelly, Julian Te Riele, Barbara Mastrapa, Elizabeth M Streicher, Tania Dolby, Abdallah M Abdallah, Fathia Ben-Rached, John Simpson, Liezel Smith, Tawanda Gumbo, Paul van Helden, Frederick A Sirgel, Ruth McNerney, Grant Theron, Arnab Pain, Taane G Clark, Robin M Warren
BACKGROUND: The emergence of programmatically incurable tuberculosis threatens to destabilise control efforts. The aim of this study was to collect prospective patient-level data to inform treatment and containment strategies. METHODS: In a prospective cohort study, 273 South African patients with extensively drug-resistant tuberculosis, or resistance beyond extensively drug-resistant tuberculosis, were followed up over a period of 6 years. Transmission dynamics, infectiousness, and drug susceptibility were analysed in a subset of patients from the Western Cape using whole-genome sequencing (WGS; n=149), a cough aerosol sampling system (CASS; n=26), and phenotypic testing for 18 drugs (n=179)...
January 18, 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#15
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28093076/genetic-source-tracking-of-an-anthrax-outbreak-in-shaanxi-province-china
#16
Dong-Li Liu, Jian-Chun Wei, Qiu-Lan Chen, Xue-Jun Guo, En-Min Zhang, Li He, Xu-Dong Liang, Guo-Zhu Ma, Ti-Cao Zhou, Wen-Wu Yin, Wei Liu, Kai Liu, Yi Shi, Jian-Jun Ji, Hui-Juan Zhang, Lin Ma, Fa-Xin Zhang, Zhi-Kai Zhang, Hang Zhou, Hong-Jie Yu, Biao Kan, Jian-Guo Xu, Feng Liu, Wei Li
BACKGROUND: Anthrax is an acute zoonotic infectious disease caused by the bacterium known as Bacillus anthracis. From 26 July to 8 August 2015, an outbreak with 20 suspected cutaneous anthrax cases was reported in Ganquan County, Shaanxi province in China. The genetic source tracking analysis of the anthrax outbreak was performed by molecular epidemiological methods in this study. METHODS: Three molecular typing methods, namely canonical single nucleotide polymorphisms (canSNP), multiple-locus variable-number tandem repeat analysis (MLVA), and single nucleotide repeat (SNR) analysis, were used to investigate the possible source of transmission and identify the genetic relationship among the strains isolated from human cases and diseased animals during the outbreak...
January 17, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/27997331/detection-of-multiple-parallel-transmission-outbreak-of-streptococcus-suis-human-infection-by-use-of-genome-epidemiology-china-2005
#17
Pengcheng Du, Han Zheng, Jieping Zhou, Ruiting Lan, Changyun Ye, Huaiqi Jing, Dong Jin, Zhigang Cui, Xuemei Bai, Jianming Liang, Jiantao Liu, Lei Xu, Wen Zhang, Chen Chen, Jianguo Xu
Streptococcus suis sequence type 7 emerged and caused 2 of the largest human infection outbreaks in China in 1998 and 2005. To determine the major risk factors and source of the infections, we analyzed whole genomes of 95 outbreak-associated isolates, identified 160 single nucleotide polymorphisms, and classified them into 6 clades. Molecular clock analysis revealed that clade 1 (responsible for the 1998 outbreak) emerged in October 1997. Clades 2-6 (responsible for the 2005 outbreak) emerged separately during February 2002-August 2004...
February 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/27988485/simultaneous-emergence-of-multidrug-resistant-candida-auris-on-3-continents-confirmed-by-whole-genome-sequencing-and-epidemiological-analyses
#18
Shawn R Lockhart, Kizee A Etienne, Snigdha Vallabhaneni, Joveria Farooqi, Anuradha Chowdhary, Nelesh P Govender, Arnaldo Lopes Colombo, Belinda Calvo, Christina A Cuomo, Christopher A Desjardins, Elizabeth L Berkow, Mariana Castanheira, Rindidzani E Magobo, Kauser Jabeen, Rana J Asghar, Jacques F Meis, Brendan Jackson, Tom Chiller, Anastasia P Litvintseva
BACKGROUND: Candida auris, a multidrug-resistant yeast that causes invasive infections, was first described in 2009 in Japan and has since been reported from several countries. METHODS: To understand the global emergence and epidemiology of C. auris, we obtained isolates from 54 patients with C. auris infection from Pakistan, India, South Africa, and Venezuela during 2012-2015 and the type specimen from Japan. Patient information was available for 41 of the isolates...
January 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/27825828/dissecting-malaria-biology-and-epidemiology-using-population-genetics-and-genomics
#19
REVIEW
Sarah Auburn, Alyssa E Barry
Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies...
February 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/27821902/rantes-gene-polymorphisms-associated-with-hiv-1-infections-in-kenyan-population
#20
COMPARATIVE STUDY
Shem P M Mutuiri, Helen L Kutima, Lamech M Mwapagha, James K Munyao, Anthony Kebira Nyamache, Irene Wanjiru, Samoel A Khamadi
Previous studies have reported that two single nucleotide polymorphisms (SNPs) in the RANTES gene promoter region, -403G/A and -28C/G, are associated with a slower rate of decline in CD4+ T cell count. In addition, as a ligand of the major HIV coreceptor CCR5, it is known to block HIV-CCR5 interactions in the course of the HIV infection cycle. This study was carried out with the aim of determining the occurrence of single nucleotide polymorphisms (SNPs) -403G > A and -28C > G in the promoter region of RANTES, in a subset of the Kenyan population...
2016: Disease Markers
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