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Transmission, infection, SIngle nucleotide polymorphism

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https://www.readbyqxmd.com/read/28267758/whole-genome-analysis-of-mycobacteria-from-birds-at-the-san-diego-zoo
#1
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
#2
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. Dinsinfectants 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 multi-drug resistant E. faecium bloodstream isolate, to perform a genome-wide screen to identify genetic determinants involved in tolerance to CHX...
February 27, 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
#3
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
#4
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 kilometres. Microsatellite genotypes were obtained for 203 clinical infection samples from eight locations, and Illumina paired-end sequences were obtained to yield high coverage genome-wide single nucleotide polymorphism (SNP) data for 65 clinical infection samples from four locations...
February 18, 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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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...
November 5, 2016: International Journal for Parasitology
https://www.readbyqxmd.com/read/27821902/rantes-gene-polymorphisms-associated-with-hiv-1-infections-in-kenyan-population
#13
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
https://www.readbyqxmd.com/read/27795724/host-genetic-variants-in-hla-loci-influence-risk-for-hepatitis-b-virus-infection-in-children
#14
Jie Fan, Xin Huang, Juan Chen, Yiling Cai, Lin Xiong, Lihong Mu, Li Zhou
BACKGROUND: Hepatitis B virus (HBV) infection is a serious public health problem in China and worldwide. Mother-to-child transmission is one of HBV's main transmission routes in highly endemic regions. Genome-wide association studies (GWAS) identify single nucleotide polymorphisms (SNPs) at HLA loci as associated with HBV infection. However, the mechanisms of HBV perinatal transmission and breakthrough in children have not yet been clearly defined. OBJECTIVES: We aimed to explore the association between SNPs at HLA loci and HBV infection and breakthrough in children...
August 2016: Hepatitis Monthly
https://www.readbyqxmd.com/read/27752322/emergence-and-spread-of-moxifloxacin-resistant-clostridium-difficile-ribotype-231-in-sweden-between-2006-and-2015
#15
H Harvala, E Alm, T Åkerlund, K Rizzardi
An aggregation of moxifloxacin-resistant Clostridium difficile ribotype 231 (RT231) isolates was first identified in the county of Stockholm in 2008, and by the end of 2015 isolates of RT231 had spread to 13 of 21 Swedish counties. We investigated the epidemiology of C. difficile RT231 in Sweden between 2006 and 2015 using whole genome sequencing (WGS) and evaluated whether its emergence could be associated with extended moxifloxacin use. We performed WGS and phylogenetic analysis of 51 C. difficile RT231 strains isolated in Sweden over a 10-year period...
November 2016: New Microbes and New Infections
https://www.readbyqxmd.com/read/27671066/whole-genome-sequencing-identifies-in-vivo-acquisition-of-a-blactx-m-27-carrying-incfii-transmissible-plasmid-as-the-cause-of-ceftriaxone-treatment-failure-for-an-invasive-salmonella-enterica-serovar-typhimurium-infection
#16
Bruce McCollister, Cassandra V Kotter, Daniel N Frank, Taylor Washburn, Michael G Jobling
We report a case of ceftriaxone treatment failure for bacteremia caused by Salmonella enterica subsp. enterica serovar Typhimurium, due to the in vivo acquisition of a blaCTX-M-27-encoding IncFII group transmissible plasmid. The original β-lactamase-susceptible isolate ST882S was replaced by the resistant isolate ST931R during ceftriaxone treatment. After relapse, treatment was changed to ciprofloxacin, and the patient recovered. Isolate ST931R could transfer resistance to Escherichia coli at 37°C. We used whole-genome sequencing of ST882S and ST931R, the E...
December 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27662900/multiple-major-disease-associated-clones-of-legionella-pneumophila-have-emerged-recently-and-independently
#17
Sophia David, Christophe Rusniok, Massimo Mentasti, Laura Gomez-Valero, Simon R Harris, Pierre Lechat, John Lees, Christophe Ginevra, Philippe Glaser, Laurence Ma, Christiane Bouchier, Anthony Underwood, Sophie Jarraud, Timothy G Harrison, Julian Parkhill, Carmen Buchrieser
Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires' disease. Just five sequence types (ST), from more than 2000 currently described, cause nearly half of disease cases in northwest Europe. Here, we report the sequence and analyses of 364 L. pneumophila genomes, including 337 from the five disease-associated STs and 27 representative of the species diversity. Phylogenetic analyses revealed that the five STs have independent origins within a highly diverse species. The number of de novo mutations is extremely low with maximum pairwise single-nucleotide polymorphisms (SNPs) ranging from 19 (ST47) to 127 (ST1), which suggests emergences within the last century...
November 2016: Genome Research
https://www.readbyqxmd.com/read/27613688/genomic-analysis-of-salmonella-enterica-serovar-typhimurium-from-wild-passerines-in-england-and-wales
#18
Alison E Mather, Becki Lawson, Elizabeth de Pinna, Paul Wigley, Julian Parkhill, Nicholas R Thomson, Andrew J Page, Mark A Holmes, Gavin K Paterson
Passerine salmonellosis is a well-recognized disease of birds in the order Passeriformes, which includes common songbirds such as finches and sparrows, caused by infection with Salmonella enterica serovar Typhimurium. Previous research has suggested that some subtypes of S Typhimurium-definitive phage types (DTs) 40, 56 variant, and 160-are host adapted to passerines and that these birds may represent a reservoir of infection for humans and other animals. Here, we have used the whole-genome sequences of 11 isolates from British passerines, five isolates of similar DTs from humans and a domestic cat, and previously published S Typhimurium genomes that include similar DTs from other hosts to investigate the phylogenetic relatedness of passerine salmonellae to other S Typhimurium isolates and investigate possible genetic features of the distinct disease pathogenesis of S Typhimurium in passerines...
November 15, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27567034/heat-shock-70-protein-genes-and-genetic-susceptibility-to-apical-periodontitis
#19
Kanwal Maheshwari, Renato M Silva, Leticia Guajardo-Morales, Gustavo P Garlet, Alexandre R Vieira, Ariadne Letra
INTRODUCTION: Heat shock proteins (HSPs) protect cells under adverse conditions such as infection, inflammation, and disease. The differential expression of HSPs in human periapical granulomas suggests a potential role for these proteins in periapical lesion development, which may contribute to different clinical outcomes. Therefore, we hypothesized that polymorphisms in HSP genes leading to perturbed gene expression and protein function may contribute to an individual's susceptibility to periapical lesion development...
October 2016: Journal of Endodontics
https://www.readbyqxmd.com/read/27499751/evolution-and-diversity-of-listeria-monocytogenes-from-clinical-and-food-samples-in-shanghai-china
#20
Jianmin Zhang, Guojie Cao, Xuebin Xu, Marc Allard, Peng Li, Eric Brown, Xiaowei Yang, Haijian Pan, Jianghong Meng
Listeria monocytogenes is a significant foodborne pathogen causing severe systemic infections in humans with high mortality rates. The objectives of this work were to establish a phylogenetic framework of L. monocytogenes from China and to investigate sequence diversity among different serotypes. We selected 17 L. monocytogenes strains recovered from patients and foods in China representing serotypes 1/2a, 1/2b, and 1/2c. Draft genome sequences were determined using Illumina MiSeq technique and associated protocols...
2016: Frontiers in Microbiology
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