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Transmission, infection, SIngle nucleotide polymorphism

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https://www.readbyqxmd.com/read/29367612/use-of-whole-genome-sequencing-to-investigate-an-increase-in-neisseria-gonorrhoeae-infection-among-women-in-urban-areas-of-australia
#1
Cameron Buckley, Brian M Forde, Ella Trembizki, Monica M Lahra, Scott A Beatson, David M Whiley
Increasing rates of gonorrhoea have been observed among women within the Australian state of New South Wales. Here, we applied whole genome sequencing (WGS) to better understand the associated networks and transmission dynamics. Ninety-four isolates of a particular N. gonorrhoeae genotype (G122) associated with women (years 2012 to 2014) underwent phylogenetic analysis using core single nucleotide polymorphisms. WGS data revealed five main clusters, all of which were heterogeneous in terms of patient age and site of infection...
January 24, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29366468/evaluation-of-wgs-based-approaches-for-investigating-a-food-borne-outbreak-caused-by-salmonella-enterica-serovar-derby-in-germany
#2
Sandra Simon, Eva Trost, Jennifer Bender, Stephan Fuchs, Burkhard Malorny, Wolfgang Rabsch, Rita Prager, Erhard Tietze, Antje Flieger
In Germany salmonellosis still represents the 2nd most common bacterial foodborne disease. The majority of infections are caused by Salmonella (S.) Typhimurium and S. Enteritidis followed by a variety of other broad host-range serovars. Salmonella Derby is one of the five top-ranked serovars isolated from humans and it represents one of the most prevalent serovars in pigs, thus bearing the potential risk for transmission to humans upon consumption of pig meat and products thereof. From November 2013 to January 2014 S...
May 2018: Food Microbiology
https://www.readbyqxmd.com/read/29362238/adaptive-evolution-of-rh5-in-ape-plasmodium-species-of-the-laverania-subgenus
#3
Lindsey J Plenderleith, Weimin Liu, Oscar A MacLean, Yingying Li, Dorothy E Loy, Sesh A Sundararaman, Frederic Bibollet-Ruche, Gerald H Learn, Beatrice H Hahn, Paul M Sharp
Plasmodium falciparum, the major cause of malaria morbidity and mortality in humans, has been shown to have emerged after cross-species transmission of one of six host-specific parasites (subgenus Laverania) infecting wild chimpanzees (Pan troglodytes) and western gorillas (Gorilla gorilla). Binding of the parasite-encoded ligand RH5 to the host protein basigin is essential for erythrocyte invasion and has been implicated in host specificity. A recent study claimed to have found two amino acid changes in RH5 that "drove the host shift leading to the emergence of P...
January 23, 2018: MBio
https://www.readbyqxmd.com/read/29358725/fine-scale-landscape-genomics-helps-explain-the-slow-spatial-spread-of-wolbachia-through-the-aedes-aegypti-population-in-cairns-australia
#4
Thomas L Schmidt, Igor Filipović, Ary A Hoffmann, Gordana Rašić
The endosymbiotic bacterium Wolbachia suppresses the capacity for arbovirus transmission in the mosquito Aedes aegypti, and can spread spatially through wild mosquito populations following local introductions. Recent introductions in Cairns, Australia have demonstrated slower than expected spatial spread. Potential reasons for this include: (i) barriers to Ae. aegypti dispersal; (ii) higher incidence of long-range dispersal; and (iii) intergenerational loss of Wolbachia. We investigated these three potential factors using genome-wide single-nucleotide polymorphisms (SNPs) and an assay for the Wolbachia infection wMel in 161 Ae...
January 23, 2018: Heredity
https://www.readbyqxmd.com/read/29326013/a-cluster-of-multidrug-resistant-mycobacterium-tuberculosis-among-patients-arriving-in-europe-from-the-horn-of-africa-a-molecular-epidemiological-study
#5
Timothy M Walker, Matthias Merker, Astrid M Knoblauch, Peter Helbling, Otto D Schoch, Marieke J van der Werf, Katharina Kranzer, Lena Fiebig, Stefan Kröger, Walter Haas, Harald Hoffmann, Alexander Indra, Adrian Egli, Daniela M Cirillo, Jérôme Robert, Thomas R Rogers, Ramona Groenheit, Anne T Mengshoel, Vanessa Mathys, Marjo Haanperä, Dick van Soolingen, Stefan Niemann, Erik C Böttger, Peter M Keller
BACKGROUND: The risk of tuberculosis outbreaks among people fleeing hardship for refuge in Europe is heightened. We describe the cross-border European response to an outbreak of multidrug-resistant tuberculosis among patients from the Horn of Africa and Sudan. METHODS: On April 29 and May 30, 2016, the Swiss and German National Mycobacterial Reference Laboratories independently triggered an outbreak investigation after four patients were diagnosed with multidrug-resistant tuberculosis...
January 8, 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29259599/epidemiology-of-danish-aeromonas-salmonicida-subsp-salmonicida-in-fish-farms-using-whole-genome-sequencing
#6
Simona Bartkova, Pimlapas Leekitcharoenphon, Frank M Aarestrup, Inger Dalsgaard
Furunculosis, a serious infection caused by the bacterium Aeromonas salmonicida subsp. salmonicida is common in sea-reared rainbow trout production in Denmark. Developing an effective control strategy requires knowledge of the epidemiology, as well as the genomic and virulent variability of the Danish A. salmonicida subsp. salmonicida isolates. To obtain this, the genomes of 101 A. salmonicida subsp. salmonicida, including 99 Danish isolates, one Scottish strain and the type strain NCIMB 1102, were sequenced using the Illumina HiSeq platform...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29247013/whole-genome-sequencing-reveals-transmission-of-gonococcal-antibiotic-resistance-among-men-who-have-sex-with-men-an-observational-study
#7
Jason C Kwong, Eric P F Chow, Kerrie Stevens, Timothy P Stinear, Torsten Seemann, Christopher K Fairley, Marcus Y Chen, Benjamin P Howden
OBJECTIVES: Drug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N...
December 15, 2017: Sexually Transmitted Infections
https://www.readbyqxmd.com/read/29208056/importation-mitigation-and-genomic-epidemiology-of-candida-auris-at-a-large-teaching-hospital
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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