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SMRT sequencing

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https://www.readbyqxmd.com/read/29229636/topical-antibiotic-use-co-selects-for-the-carriage-of-mobile-genetic-elements-conferring-resistance-to-unrelated-antimicrobials-in-staphylococcus-aureus
#1
Glen P Carter, Mark B Schultz, Sarah L Baines, Anders Goncalves da Silva, Helen Heffernan, Audrey Tiong, Peter H Pham, Ian R Monk, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Topical antibiotics such as mupirocin and fusidic acid are commonly used in the prevention and treatment of skin infections, particularly those caused by staphylococci. However, widespread use of these agents is associated with increased resistance to these agents, potentially limiting their efficacy. Of particular concern is the observation that resistance to topical antibiotics is often associated with multidrug resistance, suggesting that topical antibiotics may play a role in the emergence of multidrug-resistant (MDR) strains...
December 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29188195/comparative-genomic-analysis-of-two-clonally-related-multidrug-resistant-mycobacterium-tuberculosis-by-single-molecule-real-time-sequencing
#2
Kenneth Siu-Sing Leung, Gilman Kit-Hang Siu, Kingsley King-Gee Tam, Sabrina Wai-Chi To, Rahim Rajwani, Pak-Leung Ho, Samson Sai-Yin Wong, Wei W Zhao, Oliver Chiu-Kit Ma, Wing-Cheong Yam
Background: Multidrug-resistant tuberculosis (MDR-TB) is posing a major threat to global TB control. In this study, we focused on two consecutive MDR-TB isolated from the same patient before and after the initiation of anti-TB treatment. To better understand the genomic characteristics of MDR-TB, Single Molecule Real-Time (SMRT) Sequencing and comparative genomic analyses was performed to identify mutations that contributed to the stepwise development of drug resistance and growth fitness in MDR-TB under in vivo challenge of anti-TB drugs...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29186486/long-read-sequence-assembly-of-the-firefly-pyrocoelia-pectoralis-genome
#3
Xinhua Fu, Jingjing Li, Yu Tian, Weipeng Quan, Shu Zhang, Qian Liu, Fan Liang, Xinlei Zhu, Liangsheng Zhang, Depeng Wang, Jiang Hu
Findings: Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883) (Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8Gb long reads were generated and assembled into a 760.4Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect BUSCOs. The k-mer analysis showed this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3...
November 24, 2017: GigaScience
https://www.readbyqxmd.com/read/29184138/centromere-evolution-and-cpg-methylation-during-vertebrate-speciation
#4
Kazuki Ichikawa, Shingo Tomioka, Yuta Suzuki, Ryohei Nakamura, Koichiro Doi, Jun Yoshimura, Masahiko Kumagai, Yusuke Inoue, Yui Uchida, Naoki Irie, Hiroyuki Takeda, Shinich Morishita
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago...
November 28, 2017: Nature Communications
https://www.readbyqxmd.com/read/29178836/chromosome-level-assembly-and-secondary-metabolite-potential-of-the-parasitic-fungus-cordyceps-militaris
#5
Glenna J Kramer, Justin R Nodwell
BACKGROUND: Cordyceps militaris is an insect pathogenic fungus that is prized for its use in traditional medicine. This and other entomopathogenic fungi are understudied sources for the discovery of new bioactive molecules. In this study, PacBio SMRT long read sequencing technology was used to sequence the genome of C. militaris with a focus on the genetic potential for secondary metabolite production in the genome assembly of this fungus. RESULTS: This is first chromosome level assembly of a species in the Cordyceps genera...
November 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29171935/single-molecule-real-time-smrt%C3%A2-dna-sequencing-of-hla-genes-at-ultra-high-resolution-from-126-international-hla-and-immunogenetics-workshop-cell-lines
#6
T R Turner, J D Hayhurst, D R Hayward, W P Bultitude, D J Barker, J Robinson, J Alejandro Madrigal, N P Mayor, S G E Marsh
The hyperpolymorphic HLA genes play important roles in disease and transplantation and act as genetic markers of migration and evolution. A panel of 107 B-lymphoblastoid cell lines (B-LCLs) was established in 1987 at the 10(th) International Histocompatibility Workshop as a resource for the immunogenetics community. These B-LCLs are well characterised and represent diverse ethnicities and HLA haplotypes. Here we have applied Pacific Biosciences' Single Molecule Real-Time (SMRT) DNA sequencing to HLA type 126 B-LCL, including the 107 IHIW cells, to ultra-high resolution...
November 24, 2017: HLA
https://www.readbyqxmd.com/read/29167264/complete-genome-sequences-of-two-strains-of-the-meat-spoilage-bacterium-brochothrix-thermosphacta-isolated-from-ground-chicken
#7
George C Paoli, Chandi Wijey, Ly-Huong Nguyen, Chin-Yi Chen, Xianghe Yan, Peter L Irwin
Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT) technology and are the first complete genome sequences reported for B. thermosphacta.
November 22, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#8
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29134592/identification-of-dna-base-modifications-by-means-of-pacific-biosciences-rs-sequencing-technology
#9
Philip Kelleher, James Murphy, Jennifer Mahony, Douwe van Sinderen
Whole phage genomes can be sequenced readily using one or a combination of next generation sequencing (NGS) technologies. One of the most recently developed NGS platforms, the so-called Single-Molecule Real-Time (SMRT) sequencing approach provided by the PacBio RS platform, is particularly useful in providing complete (i.e., un-gapped) genome sequences, but differs from other technologies in that the platform also allows for downstream analysis to identify nucleotides that have been modified by DNA methylation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29109705/complete-genome-sequence-of-vibrio-campbellii-lmb-29-isolated-from-red-drum-with-four-native-megaplasmids
#10
Jinxin Liu, Zhe Zhao, Yiqing Deng, Yan Shi, Yupeng Liu, Chao Wu, Peng Luo, Chaoqun Hu
Vibrio spp. are the most common pathogens for animals reared in aquaculture. Vibrio campbellii, which is often involved in shrimp, fish and mollusks diseases, is widely distributed in the marine environment worldwide, but our knowledge about its pathogenesis and antimicrobial resistance is very limited. The existence of this knowledge gap is at least partially because that V. campbellii was originally classified as Vibrio harveyi, and the detailed information of its comparative genome analysis to other Vibrio spp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29102123/convergence-of-plasmid-architectures-drives-emergence-of-multi-drug-resistance-in-a-clonally-diverse-escherichia-coli-population-from-a-veterinary-clinical-care-setting
#11
Sam Wagner, Nadejda Lupolova, David L Gally, Sally A Argyle
The purpose of this study was to determine the plasmid architecture and context of resistance genes in multi-drug resistant (MDR) Escherichia coli strains isolated from urinary tract infections in dogs. Illumina and single-molecule real-time (SMRT) sequencing were applied to assemble the complete genomes of E. coli strains associated with clinical urinary tract infections, which were either phenotypically MDR or drug susceptible. This revealed that multiple distinct families of plasmids were associated with building an MDR phenotype...
November 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/29091199/monitoring-microevolution-of-oxa-48-producing-klebsiella-pneumoniae-st147-in-a-hospital-setting-by-smrt-sequencing
#12
Andreas E Zautner, Boyke Bunk, Yvonne Pfeifer, Cathrin Spröer, Utz Reichard, Helmut Eiffert, Simone Scheithauer, Uwe Groß, Jörg Overmann, Wolfgang Bohne
Objectives: Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for healthcare facilities worldwide. A continuous monitoring of ST distribution and its association with resistance and virulence genes is required for early detection of successful K. pneumoniae lineages. In this study, we used WGS to characterize MDR blaOXA-48-positive K. pneumoniae isolated from inpatients at the University Medical Center Göttingen, Germany, between March 2013 and August 2014. Methods: Closed genomes for 16 isolates of carbapenemase-producing K...
October 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29079625/bioinformatics-analysis-and-characterization-of-highly-efficient-polyvinyl-alcohol-pva-degrading-enzymes-from-the-novel-pva-degrader-stenotrophomonas-rhizophila-ql-p4
#13
Yahong Wei, Jing Fu, Jianying Wu, Xinmiao Jia, Yunheng Zhou, Cuidan Li, Mengxing Dong, Shanshan Wang, Ju Zhang, Fei Chen
Polyvinyl alcohol (PVA) is used widely in industry, and associated environmental pollution is a serious problem. Herein, we report a novel, efficient PVA degrader, Stenotrophomonas rhizophila QL-P4, isolated from fallen leaves from virgin forest in the Qinling Mountains. The complete genome was obtained using single-molecule real-time (SMRT) technology and corrected using Illumina sequencing. Bioinformatics analysis revealed eight PVA/OVA (vinyl alcohol oligomer)-degrading genes. Of these, seven genes were predicted to be involved in the classical intracellular PVA/OVA degradation pathway, and one (BAY15_3292) was identified as a novel PVA oxidase...
October 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29078745/single-virion-sequencing-of-lamivudine-treated-hbv-populations-reveal-population-evolution-dynamics-and-demographic-history
#14
Yuan O Zhu, Pauline P K Aw, Paola Florez de Sessions, Shuzhen Hong, Lee Xian See, Lewis Z Hong, Andreas Wilm, Chen Hao Li, Stephane Hue, Seng Gee Lim, Niranjan Nagarajan, William F Burkholder, Martin Hibberd
BACKGROUND: Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge...
October 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29046457/hiv-1-infection-of-primary-cd4-t-cells-regulates-the-expression-of-specific-herv-k-hml-2-elements
#15
George R Young, Sandra N Terry, Lara Manganaro, Alvaro Cuesta-Dominguez, Gintaras Deikus, Dabeiba Bernal-Rubio, Laura Campisi, Ana Fernandez-Sesma, Robert Sebra, Viviana Simon, Lubbertus C F Mulder
Endogenous retroviruses (ERVs) occupy extensive regions of the human genome. Although many of these retroviral elements have lost their ability to replicate, those whose insertion took place more recently, such as the HML-2 group of HERV-K elements, still retain intact open reading frames and the capacity to produce certain viral RNA and/or proteins. Transcription of these ERVs is, however, tightly regulated by dedicated epigenetic control mechanisms. Nonetheless, it has been reported that some pathologic states, such as viral infections and certain cancers, coincide with ERV expression suggesting transcriptional reawakening is possible...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29036602/n6-adenine-dna-methylation-is-associated-with-the-linker-dna-of-h2a-z-containing-well-positioned-nucleosomes-in-pol-ii-transcribed-genes-in-tetrahymena
#16
Yuanyuan Wang, Xiao Chen, Yalan Sheng, Yifan Liu, Shan Gao
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036429/genome-re-annotation-of-the-wild-strawberry-fragaria-vesca-using-extensive-illumina-and-smrt-based-rna-seq-datasets
#17
Yongping Li, Wei Wei, Jia Feng, Huifeng Luo, Mengting Pi, Zhongchi Liu, Chunying Kang
The genome of the wild diploid strawberry species Fragaria vesca, an ideal model system of cultivated strawberry (Fragaria × ananassa, octoploid) and other Rosaceae family crops, was first published in 2011 and followed by a new assembly (Fvb). However, the annotation for Fvb mainly relied on ab initio predictions and included only predicted coding sequences, therefore an improved annotation is highly desirable. Here, a new annotation version named v2.0.a2 was created for the Fvb genome by a pipeline utilizing one PacBio library, 90 Illumina RNA-seq libraries, and 9 small RNA-seq libraries...
September 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29019980/radically-truncated-mecp2-rescues-rett-syndrome-like-neurological-defects
#18
Rebekah Tillotson, Jim Selfridge, Martha V Koerner, Kamal K E Gadalla, Jacky Guy, Dina De Sousa, Ralph D Hector, Stuart R Cobb, Adrian Bird
Heterozygous mutations in the X-linked MECP2 gene cause the neurological disorder Rett syndrome. The methyl-CpG-binding protein 2 (MeCP2) protein is an epigenetic reader whose binding to chromatin primarily depends on 5-methylcytosine. Functionally, MeCP2 has been implicated in several cellular processes on the basis of its reported interaction with more than 40 binding partners, including transcriptional co-repressors (for example, the NCoR/SMRT complex), transcriptional activators, RNA, chromatin remodellers, microRNA-processing proteins and splicing factors...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29018412/a-novel-lactobacilli-based-teat-disinfectant-for-improving-bacterial-communities-in-the-milks-of-cow-teats-with-subclinical-mastitis
#19
Jie Yu, Yan Ren, XiaoXia Xi, Weiqiang Huang, Heping Zhang
Teat disinfection pre- and post-milking is important for the overall health and hygiene of dairy cows. The objective of this study was to evaluate the efficacy of a novel probiotic lactobacilli-based teat disinfectant based on changes in somatic cell count (SCC) and profiling of the bacterial community. A total of 69 raw milk samples were obtained from eleven Holstein-Friesian dairy cows over 12 days of teat dipping in China. Single molecule, real-time sequencing technology (SMRT) was employed to profile changes in the bacterial community during the cleaning protocol and to compare the efficacy of probiotic lactic acid bacteria (LAB) and commercial teat disinfectants...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29017889/complete-genome-sequence-of-acinetobacter-baumannii-a1296-st1469-with-a-small-plasmid-harbouring-the-tet-39-tetracycline-resistance-gene
#20
Xiaoting Hua, Chao Pan, Li Zhu, Zhicheng Liu, Qingye Xu, Hengliang Wang, Yunsong Yu
OBJECTIVES: Acinetobacter baumannii is considered an important nosocomial pathogen worldwide owing to its increasing antibiotic resistance. This study aimed to determine the complete genome sequence of A. baumannii strain A1296 and to perform a comparative analysis among A. baumannii. METHODS: The complete genome sequence of A. baumannii A1296 was sequenced on two SMRT cells using P6C4 chemistry on a PacBio Single Molecule, Real-Time (SMRT) RS II instrument. The A1296 genome sequence was annotated using Prokaryotic Genome Automatic Annotation Pipeline (PGAAP), and the sequence type and resistance genes of the strain were analysed...
October 7, 2017: Journal of Global Antimicrobial Resistance
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