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Transmission, infection, SIngle nucleotide polymorphism

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https://www.readbyqxmd.com/read/29208056/importation-mitigation-and-genomic-epidemiology-of-candida-auris-at-a-large-teaching-hospital
#1
Emil P Lesho, Melissa Z Bronstein, Patrick McGann, Jason Stam, Yoon Kwak, Rosslyn Maybank, Jodi McNamara, Megan Callahan, Jean Campbell, Mary K Hinkle, Edward E Walsh
OBJECTIVE Candida auris (CA) is an emerging multidrug-resistant pathogen associated with increased mortality. The environment may play a role, but transmission dynamics remain poorly understood. We sought to limit environmental and patient CA contamination following a sustained unsuspected exposure. DESIGN Quasi-experimental observation. SETTING A 528-bed teaching hospital. PATIENTS The index case patient and 17 collocated ward mates. INTERVENTION Immediately after confirmation of CA in the bloodstream and urine of a patient admitted 6 days previously, active surveillance, enhanced transmission-based precautions, environmental cleaning with peracetic acid-hydrogen peroxide and ultraviolet light, and patient relocation were undertaken...
December 6, 2017: Infection Control and Hospital Epidemiology
https://www.readbyqxmd.com/read/29178620/comparative-genomics-of-spiraeoideae-infecting-erwinia-amylovora-strains-revealed-high-genetic-diversity-and-identified-the-genetic-basis-of-a-low-virulence-strain
#2
Quan Zeng, Zhouqi Cui, Jie Wang, Kevin L Childs, George W Sundin, Daniel R Cooley, Ching-Hong Yang, Elizabeth Garofalo, Alan Eaton, Regan B Huntley, Xiaochen Yuan, Neil P Schultes
Erwinia amylovora is the causal agent of fire blight, one of the most devastating diseases of apple and pear. E. amylovora is thought to have originated in North America and has now spread to at least 50 countries worldwide. Understanding the diversity of the pathogen population and the transmission to different geographical regions is important for the future mitigation of this disease. In this research, we performed a comprehensive comparative genomic study of the Spiraeoideae-infecting (SI) E. amylovora population in North America and Europe...
November 27, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29106592/intrahost-genetic-diversity-of-bacterial-symbionts-exhibits-evidence-of-mixed-infections-and-recombinant-haplotypes
#3
Shelbi L Russell, Colleen M Cavanaugh
Even the simplest microbial-eukaryotic mutualisms are comprised of entire populations of symbionts at the level of the host individual. Early work suggested that these intrahost populations maintain low genetic diversity as a result of transmission bottlenecks or to avoid competition between symbiont genotypes. However, the amount of genetic diversity among symbionts within a single host remains largely unexplored. To address this, we investigated the chemosynthetic symbiosis between the bivalve Solemya velum and its intracellular bacterial symbionts, which exhibits evidence of both vertical and horizontal transmission...
November 1, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29095965/frequent-undetected-mrsa-ward-based-transmission-linked-to-patient-sharing-between-hospitals
#4
Olga Tosas Auguet, Richard A Stabler, Jason Betley, Mark D Preston, Mandeep Dhaliwal, Michael Gaunt, Avgousta Ioannou, Nergish Desai, Tacim Karadag, Rahul Batra, Jonathan A Otter, Helene Marbach, Taane G Clark, Jonathan D Edgeworth
Background: Recent evidence suggests hospital transmission of methicillin-resistant Staphylococcus aureus (MRSA) is uncommon in UK centers that have implemented sustained infection control programmes. We investigated whether a healthcare-network analysis could shed light on transmission paths currently sustaining MRSA levels in UK hospitals. Methods: A cross-sectional observational study was performed in two NHS hospital groups and a general district hospital in South-East London...
October 31, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29077712/quantifying-connectivity-between-local-plasmodium-falciparum-malaria-parasite-populations-using-identity-by-descent
#5
Aimee R Taylor, Stephen F Schaffner, Gustavo C Cerqueira, Standwell C Nkhoma, Timothy J C Anderson, Kanlaya Sriprawat, Aung Pyae Phyo, François Nosten, Daniel E Neafsey, Caroline O Buckee
With the rapidly increasing abundance and accessibility of genomic data, there is a growing interest in using population genetic approaches to characterize fine-scale dispersal of organisms, providing insight into biological processes across a broad range of fields including ecology, evolution and epidemiology. For sexually recombining haploid organisms such as the human malaria parasite P. falciparum, however, there have been no systematic assessments of the type of data and methods required to resolve fine scale connectivity...
October 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29061159/genetic-polymorphisms-of-hla-dp-and-isolated-anti-hbc-are-important-subsets-of-occult-hepatitis-b-infection-in-indonesian-blood-donors-a-case-control-study
#6
Yan Mardian, Yoshihiko Yano, Widya Wasityastuti, Neneng Ratnasari, Yujiao Liang, Wahyu Aristyaning Putri, Teguh Triyono, Yoshitake Hayashi
BACKGROUND: Occult hepatitis B infection (OBI) is defined as the presence of hepatitis B virus (HBV) DNA in the serum and/or liver in HBsAg-negative individuals. OBI is associated with the risk of viral transmission, especially in developing countries, and with progressive liver disease and reactivation in immunosuppressive patients. The objective of this study was to evaluate the relation of OBI to HLA-DP single nucleotide polymorphisms (SNPs) encoding antigen-binding sites for the immune response to HBV infection...
October 23, 2017: Virology Journal
https://www.readbyqxmd.com/read/28954067/profile-of-hiv-subtypes-in-hiv-hbv-and-hiv-hcv-coinfected-patients-in-southern-brazil
#7
Valéria Miranda Avanzi, Bianca Arão Vicente, Nayara Carvalho Polido Beloto, Monica Maria Gomes-da-Silva, Clea Elisa Lopes Ribeiro, Felipe Francisco Tuon, Luine Rosele Renaud Vidal, Meri Bordignon Nogueira, Sonia Mara Raboni
INTRODUCTION: HIV and viral hepatitis infections are major causes of chronic disease worldwide and have some similarities with regard to routes of transmission, epidemiology, front barriers faced during access of treatment, and strategies for a global public health response. The objective was to describe the HIV-1 subtypes, viral tropism and single-nucleotide polymorphisms (SNPs) of interleukin 28B (IL28B) from a case series of HIV/viral hepatitis coinfected patients from southern Brazil...
July 2017: Revista da Sociedade Brasileira de Medicina Tropical
https://www.readbyqxmd.com/read/28944299/geographic-genetic-analysis-of-plasmodium-falciparum-parasite-populations-from-surveys-of-primary-school-children-in-western-kenya
#8
Irene Omedo, Polycarp Mogeni, Kirk Rockett, Alice Kamau, Christina Hubbart, Anna Jeffreys, Lynette Isabella Ochola-Oyier, Etienne P de Villiers, Caroline W Gitonga, Abdisalan M Noor, Robert W Snow, Dominic Kwiatkowski, Philip Bejon
Background. Malaria control, and finally malaria elimination, requires the identification and targeting of residual foci or hotspots of transmission. However, the level of parasite mixing within and between geographical locations is likely to impact the effectiveness and durability of control interventions and thus should be taken into consideration when developing control programs. Methods. In order to determine the geographic-genetic patterns of Plasmodium falciparum parasite populations at a sub-national level in Kenya, we used the Sequenom platform to genotype 111 genome-wide distributed single nucleotide polymorphic (SNP) positions in 2486 isolates collected from children in 95 primary schools in western Kenya...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28820758/lack-of-association-between-interleukin-28b-polymorphism-and-vertical-transmission-of-hepatitis-c
#9
Afrodite Psaros Einberg, Ann-Sofi Duberg, Olga Filipovich, Jessica Nyström, Anton Zhirkov, Erwin Daniel Brenndörfer, Lars Frelin, Elena Rukoiatkina, Yuriy Lobzin, Matti Sällberg, Björn Fischler, Anton Lutckii
OBJECTIVES: Single genetic nucleotide polymorphism (rs12979860) near the gene for Interleukin 28B (IL28B), is known to be of importance for frequency of spontaneous clearance and treatment outcome in interferon based therapies in patients with hepatitis C virus (HCV) infection. The aim of this study was to investigate if IL28B polymorphism in children and/or their mothers plays a role in vertical transmission of HCV (HCV-VT). METHODS: Plasma samples from 59 infected women, 76 uninfected children born to infected mothers, and 47 children with known vertically transmitted HCV infection, were analysed for IL28B polymorphism and classified by the IL28B genotype (C/C, C/T and T/T) as well as by viral genotype...
August 17, 2017: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/28807917/bedaquiline-inhibits-the-atp-synthase-in-mycobacterium-abscessus-and-is-effective-in-infected-zebrafish
#10
Christian Dupont, Albertus Viljoen, Sangeeta Thomas, Françoise Roquet-Banères, Jean-Louis Herrmann, Kevin Pethe, Laurent Kremer
Pulmonary infections caused by Mycobacterium abscessus are emerging as a global threat, especially in cystic fibrosis patients. Further intensifying the concern of M. abscessus infection is the recent evidence of human-to-human transmission of the infection. M. abscessus is a naturally multidrug-resistant fast-growing pathogen for which pharmacological options are limited. Repurposing antitubercular drugs represents an attractive option for the development of chemotherapeutic alternatives against M. abscessus infections...
November 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28730622/susceptibility-to-hiv-1-infection-is-influenced-by-toll-like-receptor-2-196-to-174-polymorphism-in-north-indian-population
#11
Sanjukta Vidyant, Animesh Chatterjee, Vikas Agarwal, Tapan N Dhole
INTRODUCTION: Toll like receptors (TLRs) are pattern recognition receptors, recognize molecular patterns of pathogens and play an important role in innate immunity. Recent studies have identified that single nucleotide polymorphism (SNPs) in TLR gene impairs the response to TLR ligands in some individuals and is associated with susceptibility to various infectious diseases. AIM: The aim of the present study is to investigate the role of four SNPs in the TLR2 gene, -196 to -174 Ins/Del, 2258 G/A (Arg753Gln), 2029 C/T (Arg677Trp) and 1892 C/A (Pro631His) with susceptibility and progression to HIV-1 in North Indian individuals...
July 20, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28666475/a-model-to-estimate-effects-of-snps-on-host-susceptibility-and-infectivity-for-an-endemic-infectious-disease
#12
Floor Biemans, Mart C M de Jong, Piter Bijma
BACKGROUND: Infectious diseases in farm animals affect animal health, decrease animal welfare and can affect human health. Selection and breeding of host individuals with desirable traits regarding infectious diseases can help to fight disease transmission, which is affected by two types of (genetic) traits: host susceptibility and host infectivity. Quantitative genetic studies on infectious diseases generally connect an individual's disease status to its own genotype, and therefore capture genetic effects on susceptibility only...
June 30, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28575285/comparison-of-control-of-clostridium-difficile-infection-in-six-english-hospitals-using-whole-genome-sequencing
#13
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...
August 1, 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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