keyword
MENU ▼
Read by QxMD icon Read
search

whole genome sequence resistant

keyword
https://www.readbyqxmd.com/read/27909820/genomic-analysis-reveals-the-presence-of-a-class-d-beta-lactamase-with-broad-substrate-specificity-in-animal-bite-associated-capnocytophaga-species
#1
S Zangenah, A F Andersson, V Özenci, P Bergman
Capnocytophga canimorsus and Capnocytophga cynodegmi can be transmitted from cats and dogs to humans, and can cause a wide range of infections including wound infections, sepsis, or endocarditis. We and others recently discovered two new Capnocytophaga species, C. canis and C. stomatis, mainly associated with wound infections. The first-line treatment of animal bite related infections is penicillin, and in case of allergy, doxycycline and trimethoprim/sulfamethoxazole. However, there is a lack of antibiotic susceptibility patterns for animal bite associated Capnocytophaga species...
December 1, 2016: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/27909304/transmission-of-multiple-hiv-1-subtype-c-transmitted-founder-viruses-into-the-same-recipients-was-not-determined-by-modest-phenotypic-differences
#2
Hongshuo Song, Bhavna Hora, Elena E Giorgi, Amit Kumar, Fangping Cai, Tanmoy Bhattacharya, Alan S Perelson, Feng Gao
A severe bottleneck exists during HIV-1 mucosal transmission. However, viral properties that determine HIV-1 transmissibility are not fully elucidated. We identified multiple transmitted/founder (T/F) viruses in six HIV-1-infected subjects by analyzing whole genome sequences. Comparison of biological phenotypes of different T/F viruses from the same individual allowed us to more precisely identify critical determinants for viral transmissibility since they were transmitted under similar conditions. All T/F viruses used coreceptor CCR5, while no T/F viruses used CXCR4 or GPR15...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27905446/genomic-evolution-and-chemoresistance-in-germ-cell-tumours
#3
Amaro Taylor-Weiner, Travis Zack, Elizabeth O'Donnell, Jennifer L Guerriero, Brandon Bernard, Anita Reddy, G Celine Han, Saud AlDubayan, Ali Amin-Mansour, Steven E Schumacher, Kevin Litchfield, Clare Turnbull, Stacey Gabriel, Rameen Beroukhim, Gad Getz, Scott L Carter, Michelle S Hirsch, Anthony Letai, Christopher Sweeney, Eliezer M Van Allen
Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are nearly universal in GCTs, but specific somatic genomic features driving tumour initiation, chemosensitivity and progression are incompletely characterized. Here, using clinical whole-exome and transcriptome sequencing of precursor, primary (testicular and mediastinal) and chemoresistant metastatic human GCTs, we show that the primary somatic feature of GCTs is highly recurrent chromosome arm level amplifications and reciprocal deletions (reciprocal loss of heterozygosity), variations that are significantly enriched in GCTs compared to 19 other cancer types...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27903631/genomics-of-compensatory-adaptation-in-experimental-populations-of-aspergillus-nidulans
#4
Jeremy R Dettman, Nicolas Rodrigue, Sijmen E Schoustra, Rees Kassen
Knowledge of the number and nature of genetic changes responsible for adaptation is essential for understanding and predicting evolutionary trajectories. Here, we study the genomic basis of compensatory adaptation to the fitness cost of fungicide resistance in experimentally evolved strains of the filamentous fungus Aspergillus nidulans The original selection experiment tracked the fitness recovery of lines founded by an ancestral strain that was resistant to fludioxonil, but paid a fitness cost in the absence of the fungicide...
November 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27903602/whole-genome-sequencing-of-mycobacterium-tuberculosis-provides-insight-into-the-evolution-and-genetic-composition-of-drug-resistant-tuberculosis-in-belarus
#5
Kurt R Wollenberg, Christopher A Desjardins, Aksana Zalutskaya, Vervara Slodovnikova, Andrew J Oler, Mariam Quiñones, Thomas Abeel, Sinead B Chapman, Michael Tartakovsky, Andrei Gabrielian, Sven Hoffner, Aliaksandr Skrahin, Bruce W Birren, Alexander Rosenthal, Alena Skrahina, Ashlee M Earl
The emergence and spread of drug resistant Mycobacterium tuberculosis (DR-TB) is a critical global health issue. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M. tuberculosis isolates from 97 patients sampled between 2010 and 2013 in Minsk, Belarus. MDR and XDR-TB isolates were significantly more likely to belong to the Beijing lineage than to the Euro-American lineage, and known resistance-conferring loci accounted for the majority of phenotypic resistance to first- and second-line drugs in MDR and XDR-TB...
November 30, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27902899/endemic-variation-of-h9n2-avian-influenza-virus-in-china
#6
Yu-Fu Liu, Han-Zhang Lai, Lin Li, Yu-Peng Liu, Wen-Yan Zhang, Ren Gao, Wen-Ke Huang, Qin-Fang Luo, Yan Gao, Qiong Luo, Xiao-Yu Xie, Jia-Hua Xu, Rui-Ai Chen
Forty-two H9N2 subtype AIV strains were isolated from vaccinated commercial chickens in China from 2012 to 2015. Their HA genes had nucleotide sequence homology from 86.7% to 99.7%, and similarity to the classic vaccine strain was 88.6%-92.6%. A comparison was carried out with published HA genes (410 H9 strains) and whole genomes (306 strains) isolated in China during 2012-2015. Interestingly, 99.1% (448/452) of Chinese H9N2 AIV belonged to lineage h9.4.2, and 98.5% (445/452) of the viruses belonged to h9.4...
December 2016: Avian Diseases
https://www.readbyqxmd.com/read/27901104/development-and-evaluation-of-near-isogenic-lines-for-brown-planthopper-resistance-in-rice-cv-9311
#7
Cong Xiao, Jie Hu, Yi-Ting Ao, Ming-Xing Cheng, Guan-Jun Gao, Qing-Lu Zhang, Guang-Cun He, Yu-Qing He
Brown planthopper (BPH) is the most destructive pest of rice in Asia. To date 29 BPH resistance genes have been identified, but only a few genes are being used in breeding due to inefficient markers for marker-assisted selection (MAS) and little knowledge of the real effects of the genes. In this study we individually transferred 13 genes or QTLs (Bph14, QBph3, QBph4, Bph17, Bph15, Bph20, Bph24, Bph6, Bph3, Bph9, Bph10, Bph18 and Bph21) into cultivar 9311 by marker assisted backcross breeding (MABB). Through positive and negative selection we narrowed the segments from donors containing Bph14, Bph15, Bph6 and Bph9 to 100-400 kb...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899802/genomic-and-transcriptional-landscape-of-p2ry8-crlf2-positive-childhood-acute-lymphoblastic-leukemia
#8
C Vesely, C Frech, C Eckert, G Cario, A Mecklenbräuker, U Zur Stadt, K Nebral, F Kraler, S Fischer, A Attarbaschi, M Schuster, C Bock, H Cavé, A von Stackelberg, M Schrappe, M A Horstmann, G Mann, O A Haas, R Panzer-Grümayer
Children with P2RY8-CRLF2-positive ALL have an increased relapse risk. Their mutational and transcriptional landscape as well as the respective patterns at relapse remains largely elusive. We therefore performed an integrated analysis of whole-exome and RNA-sequencing in 41 major clone fusion-positive cases including 19 matched diagnosis/relapse pairs. We detected a variety of frequently subclonal and highly instable JAK/STAT but also RTK/Ras pathway activating mutations in 76% of cases at diagnosis and virtually all relapses...
November 30, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27899564/genbank
#9
Dennis A Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, David J Lipman, James Ostell, Eric W Sayers
GenBank(®) (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 370 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or the NCBI Submission Portal. GenBank staff assign accession numbers upon data receipt...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899115/characterizing-the-impact-of-sustained-sulfadoxine-pyrimethamine-use-upon-the-plasmodium-falciparum-population-in-malawi
#10
Matt Ravenhall, Ernest Diez Benavente, Mwapatsa Mipando, Anja T R Jensen, Colin J Sutherland, Cally Roper, Nuno Sepúlveda, Dominic P Kwiatkowski, Jacqui Montgomery, Kamija S Phiri, Anja Terlouw, Alister Craig, Susana Campino, Harold Ocholla, Taane G Clark
BACKGROUND: Malawi experienced prolonged use of sulfadoxine/pyrimethamine (SP) as the front-line anti-malarial drug, with early replacement of chloroquine and delayed introduction of artemisinin-based combination therapy. Extended use of SP, and its continued application in pregnancy is impacting the genomic variation of the Plasmodium falciparum population. METHODS: Whole genome sequence data of P. falciparum isolates covering 2 years of transmission within Malawi, alongside global datasets, were used...
November 29, 2016: Malaria Journal
https://www.readbyqxmd.com/read/27895808/mendelian-inheritance-of-trimodal-cpg-methylation-sites-suggests-distal-cis-acting-genetic-effects
#11
Shaza B Zaghlool, Mashael Al-Shafai, Wadha A Al Muftah, Pankaj Kumar, Christian Gieger, Melanie Waldenberger, Mario Falchi, Karsten Suhre
BACKGROUND: Environmentally influenced phenotypes, such as obesity and insulin resistance, can be transmitted over multiple generations. Epigenetic modifications, such as methylation of DNA cytosine-guanine (CpG) pairs, may be carriers of inherited information. At the population level, the methylation state of such "heritable" CpG sites is expected to follow a trimodal distribution, and their mode of inheritance should be Mendelian. METHODS: Using the Illumina Infinium 450 K DNA methylation array, we determined DNA CpG-methylation in blood cells from a family cohort 123 individuals of Arab ethnicity, including 18 elementary father-mother-child trios, we asked whether Mendelian inheritance of CpG methylation is observed, and most importantly, whether it is independent of any genetic signals...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895010/mutations-associated-with-decreased-susceptibility-to-seven-antimicrobial-families-in-field-and-laboratory-derived-mycoplasma-bovis-strains
#12
Kinga M Sulyok, Zsuzsa Kreizinger, Enikő Wehmann, Inna Lysnyansky, Krisztián Bányai, Szilvia Marton, Ákos Jerzsele, Zsuzsanna Rónai, Ibolya Turcsányi, László Makrai, Szilárd Jánosi, Sára Ágnes Nagy, Miklós Gyuranecz
The molecular mechanisms of resistance to fluoroquinolones, tetracyclines, an aminocyclitol, macrolides, a lincosamide, a phenicol and pleuromutilins were investigated in Mycoplasma bovis For the identification of mutations responsible for the high minimal inhibitory concentrations (MICs) to certain antibiotics, whole genome sequencing of 35 M. bovis field isolates and 36 laboratory-derived antibiotic resistant mutants was performed. In vitro resistant mutants were selected by serial passages of M. bovis in broth medium containing subinhibitory concentrations of the antibiotics...
November 28, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27893790/detection-of-a-cfr-b-variant-in-german-enterococcus-faecium-clinical-isolates-and-the-impact-on-linezolid-resistance-in-enterococcus-spp
#13
Jennifer K Bender, Carola Fleige, Ingo Klare, Stefan Fiedler, Alexander Mischnik, Nico T Mutters, Kate E Dingle, Guido Werner
The National Reference Centre for Staphylococci and Enterococci in Germany has received an increasing number of clinical linezolid-resistant E. faecium isolates in recent years. Five isolates harbored a cfr(B) variant gene locus the product of which is capable of conferring linezolid resistance. The cfr(B)-like methyltransferase gene was also detected in Clostridium difficile. Antimicrobial susceptibility was determined for cfr(B)-positive and linezolid-resistant E. faecium isolates and two isogenic C. difficile strains...
2016: PloS One
https://www.readbyqxmd.com/read/27890457/the-role-of-whole-genome-sequencing-wgs-in-antimicrobial-susceptibility-testing-of-bacteria-report-from-the-eucast-subcommittee
#14
REVIEW
Matthew J Ellington, Oskar Ekelund, Frank M Aarestrup, Rafael Canton, Michel Doumith, Christian Giske, Hajo Grundman, Henrik Hasman, Matthew Holden, Katie L Hopkins, Jon Iredell, Gunnar Kahlmeter, Claudio U Köser, Alasdair MacGowan, Dik Mevius, Mike Mulvey, Thierry Naas, Tim Peto, Jean-Marc Rolain, Ørjan Samuelsen, Neil Woodford
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion...
November 23, 2016: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/27889877/maldi-tof-ms-meets-wgs-in-a-vre-outbreak-investigation
#15
S Schlebusch, G R Price, R L Gallagher, V Horton-Szar, L D H Elbourne, P Griffin, D J Venter, S O Jensen, S J Van Hal
The use of MALDI-TOF MS (matrix-assisted laser desorption/ ionization-time of flight mass spectrometry) and WGS (whole genome sequencing) has been described for identification and strain relatedness determination. We describe the complementary use of MALDI-TOF MS and WGS in a VRE (vancomycin-resistant enterococci) outbreak investigation, and discuss some of the challenges with defining strain similarity across these two platforms. Although both assays indicated multiple clusters involved in the outbreak of vancomycin resistant Enterococcus faecium isolates from positive blood cultures of four haematology-oncology patients, the small cohort and discrepancies between findings indicate the limitations of MALDI-TOF MS and the cautious interpretation of MALDI-TOF MS dendrograms during outbreaks...
November 26, 2016: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/27889161/mrsa-and-multidrug-resistant-staphylococcus-aureus-in-u-s-retail-meats-2010-2011
#16
Beilei Ge, Sampa Mukherjee, Chih-Hao Hsu, Johnnie A Davis, Thu Thuy T Tran, Qianru Yang, Jason W Abbott, Sherry L Ayers, Shenia R Young, Emily T Crarey, Niketta A Womack, Shaohua Zhao, Patrick F McDermott
Methicillin-resistant Staphylococcus aureus (MRSA) has been detected in retail meats, although large-scale studies are scarce. We conducted a one-year survey in 2010-2011 within the framework of the National Antimicrobial Resistance Monitoring System. Among 3520 retail meats collected from eight U.S. states, 982 (27.9%) contained S. aureus and 66 (1.9%) were positive for MRSA. Approximately 10.4% (107/1032) of S. aureus isolates, including 37.2% (29/78) of MRSA, were multidrug-resistant (MDRSA). Turkey had the highest MRSA prevalence (3...
April 2017: Food Microbiology
https://www.readbyqxmd.com/read/27881973/livestock-associated-methicillin-resistant-staphylococcus-aureus-la-mrsa-clonal-complex-cc-398-isolated-from-uk-animals-belong-to-european-lineages
#17
Meenaxi Sharma, Javier Nunez-Garcia, Angela M Kearns, Michel Doumith, Patrick R Butaye, M Angeles Argudín, Angela Lahuerta-Marin, Bruno Pichon, Manal AbuOun, Jon Rogers, Richard J Ellis, Christopher Teale, Muna F Anjum
In recent years, there has been an increase in the number of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 recovered from S. aureus isolated animals in the UK. To determine possible origins of 12 LA-MRSA CC398 isolates collected after screening more than a thousand S. aureus animal isolates from the UK between 2013 and 2015, whole genome sequences (WGS) of CC398 European, including UK, and non-European isolates from diverse animal hosts were compared. Phylogenetic reconstruction applied to WGS data to assess genetic relatedness of all 89 isolates, clustered the 12 UK CC398 LA-MRSA within the European sub-lineages, although on different nodes; implicating multiple independent incursions into the UK, as opposed to a single introduction followed by clonal expansion...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27881539/coexistence-of-fosfomycin-and-colistin-resistance-in-klebsiella-pneumoniae-whole-genome-shotgun-sequencing
#18
Balaji Veeraraghavan, Susmitha K Perumalla, Naveen Kumar Devanga Ragupathi, Agila Kumari Pragasam, Dhiviya Prabaa Muthuirulandi Sethuvel, Sandhana Inian, Francis Yesurajan Inbanathan
Resistance to colistin is a major threat that limits therapeutic choices for treating carbapenem-resistant Klebsiella pneumoniae infections. Herein, we report the draft genome sequences of two colistin-resistant K. pneumoniae isolates (BA41763 and B6753). The sequence data indicate that BA41763 and B6753 contain genomes of ~5.9 and 5.7 Mb in size with several plasmids.
November 23, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27875980/comparative-genomics-of-european-avian-pathogenic-e-coli-apec
#19
Guido Cordoni, Martin J Woodward, Huihai Wu, Mishaal Alanazi, Tim Wallis, Roberto M La Ragione
BACKGROUND: Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were characterised using multiplex polymerase chain reactions (PCRs) targeting 22 equally weighted factors covering virulence genes, R-type and phylogroup. Following these analysis, 95 of the selected strains were further analysed using Whole Genome Sequencing (WGS)...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27872068/missense-mutations-in-the-unfoldase-clpc1-of-the-caseinolytic-protease-complex-are-associated-with-pyrazinamide-resistance-in-mycobacterium-tuberculosis
#20
Michelle Yee, Pooja Gopal, Thomas Dick
Previously we showed that mutations in Mycobacterium tuberculosis panD, involved in coenzyme A biosynthesis, cause resistance against pyrazinoic acid, the bioactive component of the prodrug pyrazinamide. To determine whether additional resistance mechanisms can be identified, we isolated mutants resistant against pyrazinoic acid and subjected panD wildtype strains to whole genome sequencing. 8 out of 9 resistant strains harbored missense mutations in the unfoldase ClpC1 associated with the caseinolytic protease complex...
November 21, 2016: Antimicrobial Agents and Chemotherapy
keyword
keyword
97999
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"