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Transmission, infection, SIngle nucleotide polymorphism

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https://www.readbyqxmd.com/read/29616014/routine-whole-genome-sequencing-for-outbreak-investigations-of-staphylococcus-aureus-in-a-national-reference-center
#1
Geraldine Durand, Fabien Javerliat, Michèle Bes, Jean-Baptiste Veyrieras, Ghislaine Guigon, Nathalie Mugnier, Stéphane Schicklin, Gaël Kaneko, Emmanuelle Santiago-Allexant, Coralie Bouchiat, Patrícia Martins-Simões, Frederic Laurent, Alex Van Belkum, François Vandenesch, Anne Tristan
The French National Reference Center for Staphylococci currently uses DNA arrays and spa typing for the initial epidemiological characterization of Staphylococcus aureus strains. We here describe the use of whole-genome sequencing (WGS) to investigate retrospectively four distinct and virulent S. aureus lineages [clonal complexes (CCs): CC1, CC5, CC8, CC30] involved in hospital and community outbreaks or sporadic infections in France. We used a WGS bioinformatics pipeline based on de novo assembly (reference-free approach), single nucleotide polymorphism analysis, and on the inclusion of epidemiological markers...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29577990/whole-genome-sequencing-in-the-investigation-of-recurrent-invasive-group-a-streptococcus-outbreaks-in-a-maternity-unit
#2
Harriet Dickinson, Mark Reacher, Bernadette Nazareth, Heidi Eagle, Deirdre Fowler, Anthony Underwood, Meera Chand, Victoria Chalker, Juliana Coelho, Roger Daniel, Georgia Kapatai, Ali Al-Shabib, Richard Puleston
BACKGROUND: The clinical manifestations of Group A streptococcus (GAS) - (Streptococcus pyogenes) are diverse, ranging from asymptomatic colonisation to devastating invasive disease. Maternity related clusters of invasive Group A streptococcus (iGAS) infection are complex to investigate and control, especially if recurrent. AIM: We report on the investigation into three episodes of emm 75 GAS/iGAS infection in maternity patients at one hospital site over a 4 year period, two with monophyletic ancestry...
March 22, 2018: Journal of Hospital Infection
https://www.readbyqxmd.com/read/29527064/population-structure-of-the-ash-dieback-pathogen-hymenoscyphus-fraxineus-in-relation-to-its-mode-of-arrival-in-the-uk
#3
E S Orton, C M Brasier, L J Bilham, A Bansal, J F Webber, J K M Brown
The ash dieback fungus, Hymenoscyphus fraxineus , a destructive, alien pathogen of common ash ( Fraxinus excelsior ), has spread across Europe over the past 25 years and was first observed in the UK in 2012. To investigate the relationship of the pathogen's population structure to its mode of arrival, isolates were obtained from locations in England and Wales, either where established natural populations of ash had been infected by wind-dispersed ascospores or where the fungus had been introduced on imported planting stock...
February 2018: Plant Pathology
https://www.readbyqxmd.com/read/29488865/farm-to-fork-investigation-of-an-outbreak-of-shiga-toxin-producing-escherichia-coli-o157
#4
Deborah Wilson, Gayle Dolan, Heather Aird, Shirley Sorrell, Timothy J Dallman, Claire Jenkins, Lucy Robertson, Russell Gorton
Fifteen cases of Shiga toxin-producing Escherichia coli (STEC) O157 infection were associated with the consumption of contaminated food from two related butchers' premises in the north-east of England. Ten cases were admitted to hospital and seven cases developed haemolytic uraemic syndrome. A case control study found a statistically significant association with the purchase of raw and/or ready-to-eat (RTE) food supplied by the implicated butchers' shops. Isolates of STEC O157 were detected in two raw lamb burgers taken from one of the butchers' premises...
February 28, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29482619/population-based-analysis-of-ocular-chlamydia-trachomatis-in-trachoma-endemic-west-african-communities-identifies-genomic-markers-of-disease-severity
#5
A R Last, H Pickering, C H Roberts, F Coll, J Phelan, S E Burr, E Cassama, M Nabicassa, H M B Seth-Smith, J Hadfield, L T Cutcliffe, I N Clarke, D C W Mabey, R L Bailey, T G Clark, N R Thomson, M J Holland
BACKGROUND: Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. METHODS: Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa...
February 26, 2018: Genome Medicine
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
#6
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
#7
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
#8
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
#9
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
#10
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...
April 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29259599/epidemiology-of-danish-aeromonas-salmonicida-subsp-salmonicida-in-fish-farms-using-whole-genome-sequencing
#11
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
#12
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...
March 2018: Sexually Transmitted Infections
https://www.readbyqxmd.com/read/29208056/importation-mitigation-and-genomic-epidemiology-of-candida-auris-at-a-large-teaching-hospital
#13
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...
January 2018: 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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