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https://www.readbyqxmd.com/read/29346643/genetic-characterization-of-a-vang-type-vancomycin-resistant-enterococcus-faecium-clinical-isolate
#1
Mohamed Sassi, François Guérin, Léonie Lesec, Christophe Isnard, Marguerite Fines-Guyon, Vincent Cattoir, Jean-Christophe Giard
Objectives: To characterize, phenotypically and genotypically, the first Enterococcus faecium clinical isolate harbouring a vanG operon. Methods: The antibiotic resistance profile of E. faecium 16-346 was determined and its whole genome sequenced using PacBio technology. Attempts to transfer vancomycin resistance by filter mating were performed and the inducibility of expression of the vanG operon was studied by reverse-transcription quantitative PCR (RT-qPCR) in the presence or absence of subinhibitory concentrations of vancomycin...
January 16, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#2
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29342280/epigenetic-differentiation-of-natural-populations-of-lilium-bosniacum-associated-with-contrasting-habitat-conditions
#3
V Zoldoš, I Biruš, E Muratovic, Z Šatovic, A Vojta, O Robin, F Pustahija, F Bogunic, V Vicic Bockor, S Siljak-Yakovlev
Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses revealed that the three populations did not differentiate genetically, but were clearly separated in the three distinct clusters according to DNA methylation profiles...
January 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29339760/biochemical-and-genetic-characterization-of-a-novel-metallo-%C3%AE-lactamase-from-marine-bacterium-erythrobacter-litoralis-htcc-2594
#4
Xia-Wei Jiang, Hong Cheng, Ying-Yi Huo, Lin Xu, Yue-Hong Wu, Wen-Hong Liu, Fang-Fang Tao, Xin-Jie Cui, Bei-Wen Zheng
Metallo-β-lactamases (MBLs) are a group of enzymes that can inactivate most commonly used β-lactam-based antibiotics. Among MBLs, New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an urgent threat to public health as evidenced by its success in rapidly disseminating worldwide since its first discovery. Here we report the biochemical and genetic characteristics of a novel MBL, ElBla2, from the marine bacterium Erythrobacter litoralis HTCC 2594. This enzyme has a higher amino acid sequence similarity to NDM-1 (56%) than any previously reported MBL...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330182/fluorescence-recovery-allows-the-implementation-of-a-fluorescence-reporter-gene-platform-applicable-for-the-detection-and-quantification-of-horizontal-gene-transfer-in-anoxic-environments
#5
Rafael Pinilla, Leise Riber, Søren J Sørensen
The study of horizontal gene transfer (HGT) in microbial communities has been revolutionized by significant advances in cultivation-independent methods based on fluorescence reporter gene technologies. Recently, the combination of these novel approaches with flow cytometry has presented itself as one of the most powerful tools to study the spread of mobile genetic elements (MGEs) in the environment. However, the use of fluorescent markers like green fluorescent protein (GFP) and mCherry is limited by environmental constraints that affect the correct maturation of their fluorophores, such as oxygen availability and pH levels...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29324382/spatial-and-temporal-distribution-of-antibiotic-resistomes-in-a-peri-urban-area-is-associated-significantly-with-anthropogenic-activities
#6
Qian Xiang, Qing-Lin Chen, Dong Zhu, Xin-Li An, Xiao-Ru Yang, Jian-Qiang Su, Min Qiao, Yong-Guan Zhu
With the rapid development of urbanization and industrialization, the peri-urban areas are often the sites for waste dumps, which may exacerbate the occurrence and spread of antibiotic resistance from waste to soil bacteria. However, the profiles of antibiotic resistomes and the associated factors influencing their dissemination in peri-urban areas have not been fully explored. Here, we characterized the antibiotic resistance genes (ARGs) in peri-urban arable and pristine soils in four seasons at the watershed scale, by using high-throughput qPCR...
January 8, 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29322334/detection-of-%C3%AE-lactamase-encoding-genes-in-feces-soil-and-water-from-a-brazilian-pig-farm
#7
João Pedro Rueda Furlan, Eliana Guedes Stehling
β-lactam antibiotics are widely used for the treatment of different types of infections worldwide and the resistance to these antibiotics has grown sharply, which is of great concern. Resistance to β-lactams in gram-negative bacteria is mainly due to the production of β-lactamases, which are classified according to their functional activities. The aim of this study was to verify the presence of β-lactamases encoding genes in feces, soil, and water from a Brazilian pig farm. Different β-lactamases encoding genes were found, including blaCTX-M-Gp1, blaCTX-M-Gp9, blaSHV, blaOXA-1-like, blaGES, and blaVEB...
January 10, 2018: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/29287670/investigation-of-clostridium-botulinum-group-iii-s-mobilome-content
#8
Cédric Woudstra, Caroline Le Maréchal, Rozenn Souillard, Fabrizio Anniballi, Bruna Auricchio, Luca Bano, Marie-Hélène Bayon-Auboyer, Miriam Koene, Isabelle Mermoud, Roseane B Brito, Francisco C F Lobato, Rodrigo O S Silva, Martin B Dorner, Patrick Fach
Clostridium botulinum group III is mainly responsible for botulism in animals. It could lead to high animal mortality rates and, therefore, represents a major environmental and economic concern. Strains of this group harbor the botulinum toxin locus on an unstable bacteriophage. Since the release of the first complete C. botulinum group III genome sequence (strain BKT015925), strains have been found to contain others mobile elements encoding for toxin components. In this study, seven assays targeting toxin genes present on the genetic mobile elements of C...
December 26, 2017: Anaerobe
https://www.readbyqxmd.com/read/29281823/rna-independent-dna-cleavage-activities-of-cas9-and-cas12a
#9
Ramya Sundaresan, Hari Priya Parameshwaran, S D Yogesha, Mark Walter Keilbarth, Rakhi Rajan
CRISPR-Cas systems provide bacteria and archaea with sequence-specific protection against invading mobile genetic elements. In the presence of divalent metal ions, Cas9 and Cas12a (formerly Cpf1) proteins target and cleave DNA that is complementary to a cognate guide RNA. The recognition of a protospacer adjacent motif (PAM) sequence in the target DNA by Cas9 and Cas12a is essential for cleavage. This RNA-guided DNA targeting is widely used for gene-editing methods. Here, we show that Francisella tularensis novicida (Fno) Cas12a, FnoCas9, and Streptococcus pyogenes Cas9 (SpyCas9) cleave DNA without a guide RNA in the presence of Mn2+ ions...
December 26, 2017: Cell Reports
https://www.readbyqxmd.com/read/29278844/the-effects-of-bio-available-copper-on-macrolide-antibiotic-resistance-genes-and-mobile-elements-during-tylosin-fermentation-dregs-co-composting
#10
Bo Zhang, Meng Meng Wang, Bing Wang, Yanjun Xin, Jiaqi Gao, Huiling Liu
In this study, aerobic co-composting of tylosin fermentation dregs (TFDs) and sewage sludge with different adding concentrations of copper (Cu) was investigated to inspect the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Results showed that two concentrations of Cu did affect not only the abiotic factors but the relative abundances of resistance genes. High concentration of Cu inhibited the metabolic capacity of microbial community and the nitrogen-fixing process while had little effect on the degradation of TYL and TOC...
December 18, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29277877/comparative-genomics-in-drosophila
#11
Martin Oti, Attilio Pane, Michael Sammeth
Since the pioneering studies of Thomas Hunt Morgan and coworkers at the dawn of the twentieth century, Drosophila melanogaster and its sister species have tremendously contributed to unveil the rules underlying animal genetics, development, behavior, evolution, and human disease. Recent advances in DNA sequencing technologies launched Drosophila into the post-genomic era and paved the way for unprecedented comparative genomics investigations. The complete sequencing and systematic comparison of the genomes from 12 Drosophila species represents a milestone achievement in modern biology, which allowed a plethora of different studies ranging from the annotation of known and novel genomic features to the evolution of chromosomes and, ultimately, of entire genomes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29277867/a-practical-guide-for-comparative-genomics-of-mobile-genetic-elements-in-prokaryotic-genomes
#12
Danillo Oliveira Alvarenga, Leandro M Moreira, Mick Chandler, Alessandro M Varani
Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29273966/molecular-characterization-of-amic-a-positive-regulator-in-acetamidase-operon-of-mycobacterium-smegmatis
#13
Arunkumar Venkatesan, Kannan Palaniyandi, Sujatha Narayanan
Mycobacterium smegmatis, a rapidly growing non-pathogenic mycobacterium, is currently used as a model organism to study mycobacterial genetics. Acetamidase of M. smegmatis is the highly inducible enzyme of Mycobacteria, which utilizes several amide compounds as sole carbon and nitrogen sources. The acetamidase operon has a complex regulatory mechanism, which involves three regulatory proteins, four promoters, and three operator elements. In our previous study, we showed that over-expression of AmiA leads to a negative regulation of acetamidase by blocking the P2 promoter...
December 22, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/29259290/the-complex-resistomes-of-paenibacillaceae-reflect-diverse-antibiotic-chemical-ecologies
#14
Andrew C Pawlowski, Erin L Westman, Kalinka Koteva, Nicholas Waglechner, Gerard D Wright
The ecology of antibiotic resistance involves the interplay of a long natural history of antibiotic production in the environment, and the modern selection of resistance in pathogens through human use of these drugs. Important components of the resistome are intrinsic resistance genes of environmental bacteria, evolved and acquired over millennia, and their mobilization, which drives dissemination in pathogens. Understanding the dynamics and evolution of resistance across bacterial taxa is essential to address the current crisis in drug-resistant infections...
December 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/29258203/cleavage-and-structural-transitions-during-maturation-of-staphylococcus-aureus-bacteriophage-80%C3%AE-and-sapi1-capsids
#15
James L Kizziah, Keith A Manning, Altaira D Dearborn, Erin A Wall, Laura Klenow, Rosanne L L Hill, Michael S Spilman, Scott M Stagg, Gail E Christie, Terje Dokland
In the tailed bacteriophages, DNA is packaged into spherical procapsids, leading to expansion into angular, thin-walled mature capsids. In many cases, this maturation is accompanied by cleavage of the major capsid protein (CP) and other capsid-associated proteins, including the scaffolding protein (SP) that serves as a chaperone for the assembly process. Staphylococcus aureus bacteriophage 80α is capable of high frequency mobilization of mobile genetic elements called S. aureus pathogenicity islands (SaPIs), such as SaPI1...
December 16, 2017: Viruses
https://www.readbyqxmd.com/read/29250089/abiotic-stress-phenotypes-are-associated-with-conserved-genes-derived-from-transposable-elements
#16
Zoé Joly-Lopez, Ewa Forczek, Emilio Vello, Douglas R Hoen, Akiko Tomita, Thomas E Bureau
Plant phenomics offers unique opportunities to accelerate our understanding of gene function and plant response to different environments, and may be particularly useful for studying previously uncharacterized genes. One important type of poorly characterized genes is those derived from transposable elements (TEs), which have departed from a mobility-driven lifestyle to attain new adaptive roles for the host (exapted TEs). We used phenomics approaches, coupled with reverse genetics, to analyze T-DNA insertion mutants of both previously reported and novel protein-coding exapted TEs in the model plant Arabidopsis thaliana...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29250047/the-different-faces-of-rolling-circle-replication-and-its-multifunctional-initiator-proteins
#17
REVIEW
Paweł Wawrzyniak, Grażyna Płucienniczak, Dariusz Bartosik
Horizontal gene transfer (HGT) contributes greatly to the plasticity and evolution of prokaryotic and eukaryotic genomes. The main carriers of foreign DNA in HGT are mobile genetic elements (MGEs) that have extremely diverse genetic structures and properties. Various strategies are used for the maintenance and spread of MGEs, including (i) vegetative replication, (ii) transposition (and other types of recombination), and (iii) conjugal transfer. In many MGEs, all of these processes are dependent on rolling-circle replication (RCR)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29247056/genome-sequencing-links-persistent-outbreak-of-legionellosis-in-sydney-to-an-emerging-clone-of-legionella-pneumophila-st211
#18
Verlaine J Timms, Rebecca Rockett, Nathan L Bachmann, Elena Martinez, Qinning Wang, Sharon C-A Chen, Neisha Jeoffreys, Peter J Howard, Anna Smith, Sheena Adamson, Robin Gilmour, Vicky Sheppeard, Vitali Sintchenko
The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using SNP-based, core-genome MLST and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and Suburb 1...
December 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29237086/enterobacteriaceae-producing-oxa-48-like-carbapenemases-in-poland-2013-january-2017
#19
R Izdebski, A Baraniak, D Zabicka, M Machulska, P Urbanowicz, J Fiett, E Literacka, K Bojarska, A Kozinska, B Zieniuk, W Hryniewicz, M Gniadkowski
Objectives: To analyse OXA-48 (OXA-48/181)-type carbapenemase-producing Enterobacteriaceae reported in Poland from 2013 until January 2017. Methods: Bacterial isolates were typed by PFGE and MLST. Genes coding for OXA-48/181 types and other β-lactamases were amplified and sequenced. Mobile elements with blaOXA-48/181-like genes were PCR mapped. blaOXA-48/181-carrying plasmids were characterized by nuclease S1-hybridization profiling, transfer assays and PCR-based replicon typing, while the chromosomal location of the genes was confirmed by the I-CeuI analysis...
December 9, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29236574/genetic-diversity-of-kpc-producing-escherichia-coli-klebsiella-oxytoca-serratia-marcescens-and-citrobacter-freundii-isolates-from-argentina
#20
Denise De Belder, Celeste Lucero, Melina Rapoport, Adriana Rosato, Diego Faccone, Alejandro Petroni, Fernando Pasteran, Ezequiel Albornoz, Alejandra Corso, Sonia A Gomez
The predominance of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae was caused by the spread of ST258 clone. In Latin America, KPC was reported in 2006, with the isolation of genetically unrelated K. pneumoniae in Colombia. Since then, the expansion of blaKPC in either K. pneumoniae ST258 or other Enterobacteriaceae (ETB) species was increasingly reported. In this study, we characterized 89 KPC-producing Escherichia coli, Klebsiella oxytoca, Serratia marcescens, and Citrobacter freundii that were received between 2010 and 2014...
December 13, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
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