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https://www.readbyqxmd.com/read/29330721/transcriptomic-analysis-and-discovery-of-genes-in-the-response-of-arachis-hypogaea-to-drought-stress
#1
Xiaobo Zhao, Chunjuan Li, Shubo Wan, Tingting Zhang, Caixia Yan, Shihua Shan
The peanut (Arachis hypogaea) is an important crop species that is threatened by drought stress. The genome sequences of peanut, which was officially released in 2016, may help explain the molecular mechanisms that underlie drought tolerance in this species. We report here a gene expression profiling of A. hypogaea to gain a global view of its drought resistance. Using whole-transcriptome sequencing, we analysed differential gene expression in response to drought stress in the drought-resistant peanut cultivar J11...
January 12, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29328655/identification-of-novel-coumestan-derivatives-as-polyketide-synthase-13-inhibitors-against-mycobacterium-tuberculosis
#2
Wei Zhang, Shichun Lun, Shu-Huan Wang, Xingwu Jiang, Fan Yang, Jie Tang, Abigail L Manson, Ashlee M Earl, Hendra Gunosewoyo, William R Bishai, Li-Fang Yu
Inhibition of the mycolic acid pathway has proven a viable strategy in antitubercular drug discovery. The AccA3/AccD4/FadD32/Pks13 complex of Mycobacterium tuberculosis constitutes an essential biosynthetic mechanism for mycolic acids. Small molecules targeting the thioesterase domain of Pks13 have been reported, including a benzofuran-based compound, whose X-ray co-crystal structure has been very recently solved. Its initial inactivity in a serum inhibition titration (SIT) assay led us to further probe other structurally-related benzofurans with the aim to improve their potency and bioavailability...
January 12, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29326221/genome-sequences-of-acholeplasma-laidlawii-strains-with-increased-resistance-to-tetracycline-and-melittin
#3
Natalia B Baranova, Tatyana Y Malygina, Elena S Medvedeva, Eugenia A Boulygina, Maria N Siniagina, Mohamed Amine Dramchini, Reshad Akbor Prottoy, Alexey A Mouzykantov, Marina N Davydova, Olga A Chernova, Vladislav M Chernov
Acholeplasma laidlawii is a well-suited model for studying the molecular basis for adapting mollicutes to environmental conditions. Here, we present the whole-genome sequences of two strains of A. laidlawii with increased resistance to tetracycline and melittin.
January 11, 2018: Genome Announcements
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
#4
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/29326010/genomics-of-corynebacterium-striatum-an-emerging-multi-drug-resistant-pathogen-of-immunocompromised-patients
#5
Kathleen Nudel, Xiaomin Zhao, Sankha Basu, Xiaoxi Dong, Maria Hoffmann, Michael Feldgarden, Marc Allard, Michael Klompas, Lynn Bry
OBJECTIVES: Corynebacterium striatum is an emerging multi-drug resistant (MDR) pathogen of immunocompromised and chronically ill patients. The objective of these studies was to provide a detailed genomic analysis of disease causing C. striatum and determine the genomic drivers of resistance and resistance-gene transmission. METHODS: A multi-institutional and prospective pathogen genomics program flagged seven MDR C. striatum infections occurring close in time, and specifically in immunocompromised patients with underlying respiratory diseases...
January 8, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29325523/fanconi-anemia-with-sun-sensitivity-caused-by-a-xeroderma-pigmentosum-associated-missense-mutation-in-xpf
#6
Isabell Popp, Maqsood Punekar, Nick Telford, Stavros Stivaros, Kate Chandler, Meenakshi Minnis, Anna Castleton, Claire Higham, Louise Hopewell, D Gareth Evans, Anja Raams, Arjan F Theil, Stefan Meyer, Detlev Schindler
BACKGROUND: Fanconi anemia (FA) is an inherited genomic instability disorder with congenital and developmental abnormalities, bone marrow failure and predisposition to cancer early in life, and cellular sensitivity to DNA interstrand crosslinks. CASE PRESENTATION: A fifty-one-year old female patient, initially diagnosed with FA in childhood on the basis of classic features and increased chromosomal breakage, and remarkable sun-sensitivity is described. She only ever had mild haematological abnormalities and no history of malignancy...
January 11, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29324814/comprehensive-molecular-profiling-of-advanced-metastatic-olfactory-neuroblastomas
#7
Jasmina Topcagic, Rebecca Feldman, Anatole Ghazalpour, Jeffrey Swensen, Zoran Gatalica, Semir Vranic
Olfactory neuroblastoma (ONB) is a rare, locally aggressive, malignant neoplasm originating in the olfactory epithelium in the nasal vault. The recurrence rate of ONB remains high and there are no specific treatment guidelines for recurrent/metastatic ONBs. This study retrospectively evaluated 23 ONB samples profiled at Caris Life Sciences (Phoenix, Arizona) using DNA sequencing (Sanger/NGS [Illumina], n = 15) and gene fusions (Archer FusionPlex, n = 6), whole genome RNA microarray (HumanHT-12 v4 beadChip, Illumina, n = 4), gene copy number assays (chromogenic and fluorescent in situ hybridization), and immunohistochemistry...
2018: PloS One
https://www.readbyqxmd.com/read/29323230/developing-an-in-silico-minimum-inhibitory-concentration-panel-test-for-klebsiella-pneumoniae
#8
Marcus Nguyen, Thomas Brettin, S Wesley Long, James M Musser, Randall J Olsen, Robert Olson, Maulik Shukla, Rick L Stevens, Fangfang Xia, Hyunseung Yoo, James J Davis
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of Klebsiella pneumoniae to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322462/methods-to-determine-mutational-trajectories-after-experimental-evolution-of-antibiotic-resistance
#9
Douglas L Huseby, Diarmaid Hughes
The evolution of bacterial resistance to antibiotics by mutation within the genome (as distinct from horizontal gene transfer of new material into a genome) could occur in a single step but is usually a multistep process. Resistance evolution can be studied in laboratory environments by serial passage of bacteria in liquid culture or on agar, with selection at constant, or varying, concentrations of drug. Whole genome sequencing can be used to make an initial analysis of the evolved mutants. The trajectory of evolution can be determined by sequence analysis of strains from intermediate steps in the evolution, complemented by phenotypic analysis of genetically reconstructed isogenic strains that recapitulate the intermediate steps in the evolution...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29321570/transfer-of-a-bla-ctx-m-1-carrying-plasmid-between-different-escherichia-coli-strains-within-the-human-gut-explored-by-whole-genome-sequencing-analyses
#10
Per Kristian Knudsen, Karianne Wiger Gammelsrud, Kristian Alfsnes, Martin Steinbakk, Tore G Abrahamsen, Fredrik Müller, Jon Bohlin
Horizontal transfer of antibiotic resistance determinants contributes to dissemination of antibiotic resistance. Such transfer of resistance genes within the human gut has been documented in some in vivo studies. The present study investigated seven bla CTX-M-1-carrying Escherichia coli isolates from three consecutive faecal samples collected from one cystic fibrosis patient in a nine-months period, by analysing whole genome sequencing data. The analyses showed that the seven E. coli isolates represented three genetically diverse strains...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321052/asgdb-a-specialised-genomic-resource-for-interpreting-anopheles-sinensis-insecticide%C3%A2-resistance
#11
Dan Zhou, Yang Xu, Cheng Zhang, Meng-Xue Hu, Yun Huang, Yan Sun, Lei Ma, Bo Shen, Chang-Liang Zhu
BACKGROUND: Anopheles sinensis is an important malaria vector in Southeast Asia. The widespread emergence of insecticide resistance in this mosquito species poses a serious threat to the efficacy of malaria control measures, particularly in China. Recently, the whole-genome sequencing and de novo assembly of An. sinensis (China strain) has been finished. A series of insecticide-resistant studies in An. sinensis have also been reported. There is a growing need to integrate these valuable data to provide a comprehensive database for further studies on insecticide-resistant management of An...
January 10, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29320720/simultaneous-emergence-and-rapid-spread-of-three-oxa-23-producing-acinetobacter-baumannii-st208-strains-in-intensive-care-units-confirmed-by-whole-genome-sequencing
#12
Qiong Chen, Jia-Wei Zhou, Jian-Zhong Fan, Sheng-Hai Wu, Li-Hui Xu, Yan Jiang, Zhi Ruan, Yun-Song Yu, Dao-Jun Yu, Xian-Jun Wang
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a common nosocomial bacterial pathogen with limited treatment options. CRAB outbreaks are disastrous for critically ill patients. This study investigated carbapenemase-produced A. baumannii outbreaks in a tertiary hospital. Although multiple outbreaks were suggested by pulse-field gel electrophoresis, the genetic lineages and evolution between these isolates were not clear. To investigate the genomic epidemiology of these outbreaks and to reveal possible transmission routes, whole genome sequences (WGS) were compared and analyzed...
January 8, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29315303/genome-wide-comparison-of-ethiopian-leishmania-donovani-strains-reveals-differences-potentially-related-to-parasite-survival
#13
Arie Zackay, James A Cotton, Mandy Sanders, Asrat Hailu, Abedelmajeed Nasereddin, Alon Warburg, Charles L Jaffe
Leishmania donovani is the main cause of visceral leishmaniasis (VL) in East Africa. Differences between northern Ethiopia/Sudan (NE) and southern Ethiopia (SE) in ecology, vectors, and patient sensitivity to drug treatment have been described, however the relationship between differences in parasite genotype between these two foci and phenotype is unknown. Whole genomic sequencing (WGS) was carried out for 41 L. donovani strains and clones from VL and VL/HIV co-infected patients in NE (n = 28) and SE (n = 13)...
January 9, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29314726/the-complete-genome-sequence-of-vibrio-aestuarianus-w-40-reveals-virulence-factor-genes
#14
Xiaojin Xu, Lixing Huang, Yongquan Su, Qingpi Yan
Vibrio aestuarianus is an opportunistic environmental pathogen that has been associated with epidemics in cultured shrimp Penaeus vannamei. Hepatopancreas microsporidian (HPM) and monodon slow growth syndrome (MSGS) have been reported in cultured P. vannamei. In this study, we sequenced and assembled the whole genome of V. aestuarianus strain W-40, a strain that was originally isolated from the intestines of an infected P. vannamei. The genome of V. aestuarianus strain W-40 contains two circular chromosomes of 483,7307 bp with a 46...
January 3, 2018: MicrobiologyOpen
https://www.readbyqxmd.com/read/29311090/investigation-of-multiple-resistance-mechanisms-in-voriconazole-resistant-aspergillus-flavus-clinical-isolates-from-a-chest-hospital-surveillance-in-delhi-india
#15
Cheshta Sharma, Rakesh Kumar, Nitin Kumar, Aradhana Masih, Dinesh Gupta, Anuradha Chowdhary
Invasive and allergic infections by Aspergillus flavus are more common in tropical and subtropical countries. The emergence of voriconazole (VRC) resistance in A. flavus impacts the management of aspergillosis as azoles are used as the first line and empiric therapy. We screened molecularly confirmed 120 A. flavus isolates obtained from respiratory and sino-nasal specimens in a chest hospital in Delhi for azole resistance using CLSI BMD method. Overall, 2.5% (n=3/120) of A. flavus isolates had VRC MICs above epidemiological cutoff values (>1μg/ml)...
January 8, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29311074/molecular-epidemiology-and-mechanism-of-sulbactam-resistance-in-acinetobacter-baumannii-isolates-with-diverse-genetic-background-in-china
#16
Yunxing Yang, Ying Fu, Peng Lan, Qingye Xu, Yan Jiang, Yan Chen, Zhi Ruan, Shujuan Ji, Xiaoting Hua, Yunsong Yu
Sulbactam is a plausible option for treating Acinetobacter infection because of its intrinsic antibacterial activity against the Acinetobacter genus, but the mechanisms of sulbactam resistance have not been studied fully in Acinetobacter baumannii In this study, a total of 2197 clinical A. baumannii isolates were collected from 27 provinces in China. Eighty-eight isolates with various minimal inhibitory concentrations (MICs) for sulbactam were selected based on their diverse clonality and underwent multilocus sequence typing, antimicrobial-susceptibility testing and resistance gene screening...
January 8, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29310751/multi-clonal-evolution-of-multi-drug-resistant-extensively-drug-resistant-mycobacterium-tuberculosis-in-a-high-prevalence-setting-of-papua-new-guinea-for-over-three-decades
#17
Arnold Bainomugisa, Evelyn Lavu, Stenard Hiashiri, Suman Majumdar, Alice Honjepari, Rendi Moke, Paison Dakulala, Grant A Hill-Cawthorne, Sushil Pandey, Ben J Marais, Chris Coulter, Lachlan Coin
An outbreak of multi-drug resistant (MDR) tuberculosis (TB) has been reported on Daru Island, Papua New Guinea. Mycobacterium tuberculosis strains driving this outbreak and the temporal accrual of drug resistance mutations have not been described. Whole genome sequencing of 100 of 165 clinical isolates referred from Daru General Hospital to the Supranational reference laboratory, Brisbane, during 2012-2015 revealed that 95 belonged to a single modern Beijing sub-lineage strain. Molecular dating suggested acquisition of streptomycin and isoniazid resistance in the 1960s, with potentially enhanced virulence mediated by an mycP1 mutation...
January 4, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29306352/porcine-commensal-escherichia-coli-a-reservoir-for-class-1-integrons-associated-with-is26
#18
Cameron J Reid, Ethan R Wyrsch, Piklu Roy Chowdhury, Tiziana Zingali, Michael Liu, Aaron E Darling, Toni A Chapman, Steven P Djordjevic
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia...
December 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29305957/isolation-of-an-incp-1-plasmid-with-mcr-1-from-a-chicken-isolate-of-citrobacter-braakii-in-china
#19
Jinxin Liu, Yanxian Yang, Yunxia Li, Dan Liu, Hongmei Tuo, Hongning Wang, Douglas R Call, Margaret Davis, Anyun Zhang
The plasmid-mediated colistin resistance gene mcr-1 has been found worldwide, but the diversity of organisms harboring this gene is unknown. In this study, twelve colistin-resistant Citrobacter spp. isolates were obtained from diseased or dead chickens in China, and PCR analysis indicated that five were positive for mcr-1. One Citrobacter braakii strain (SCC4) with a multidrug resistance phenotype was chosen for further analysis. SCC4 was resistant to ten tested antibiotics and the minimum inhibitory concentration (MIC) to colistin was >4 µg/mL...
January 3, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29305694/pervasiveness-of-uvc254-resistant-geobacillus-strains-in-extreme-environments
#20
Courtney Carlson, Nitin K Singh, Mohit Bibra, Rajesh K Sani, Kasthuri Venkateswaran
We have characterized a broad collection of extremophilic bacterial isolates from a deep subsurface mine, compost dumping sites, and several hot spring ecosystems. Spore-forming strains isolated from these environments comprised both obligate thermophiles/thermotolerant species (growing at > 55 °C; 240 strains) and mesophiles (growing at 15 to 40 °C; 12 strains). An overwhelming abundance of Geobacillus (81.3%) and Bacillus (18.3%) species was observed among the tested isolates. 16S rRNA sequence analysis documented the presence of 24 species among these isolates, but the 16S rRNA gene was shown to possess insufficient resolution to reliably discern Geobacillus phylogeny...
January 5, 2018: Applied Microbiology and Biotechnology
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