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Mobile genetic element

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https://www.readbyqxmd.com/read/28107719/occurrence-and-elimination-of-antibiotic-resistance-genes-in-a-long-term-operation-integrated-surface-flow-constructed-wetland
#1
Hansun Fang, Qin Zhang, Xiangping Nie, Baowei Chen, Yuandong Xiao, Qiubai Zhou, Wei Liao, Ximei Liang
Wetland construction is a recommended domestic sewage treatment technique, owing to its simplicity and cost efficiency. Concentrations of 14 antibiotic resistance genes (ARGs) in an integrated surface flow constructed wetland (ICW) steadily operated over 10 years were investigated in the winter and summer. Domestic sewage was observed to be the primary source of ARGs in the ICW, and 77.8% and 59.5% removal rates of total targeted ARGs in the ICW were achieved in the winter and summer, respectively. Concentrations of five ARGs (sul1, tetA, tetC, tetE, and qnrS) in the winter and of six ARGs (sul1, sul3, tetA, tetC, tetE, and qnrS) in the summer were increased throughout the treatment process...
January 6, 2017: Chemosphere
https://www.readbyqxmd.com/read/28103802/proteomics-informed-by-transcriptomics-for-characterising-active-transposable-elements-and-genome-annotation-in-aedes-aegypti
#2
Kevin Maringer, Amjad Yousuf, Kate J Heesom, Jun Fan, David Lee, Ana Fernandez-Sesma, Conrad Bessant, David A Matthews, Andrew D Davidson
BACKGROUND: Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs...
January 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28103259/characterization-and-genetic-variation-of-vibrio-cholerae-isolated-from-clinical-and-environmental-sources-in-thailand
#3
Achiraya Siriphap, Pimlapas Leekitcharoenphon, Rolf S Kaas, Chonchanok Theethakaew, Frank M Aarestrup, Orasa Sutheinkul, Rene S Hendriksen
Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/28101896/adaptation-of-genetically-monomorphic-bacteria-evolution-of-copper-resistance-through-multiple-horizontal-gene-transfers-of-complex-and-versatile-mobile-genetic-elements
#4
D Richard, V Ravigné, A Rieux, B Facon, C Boyer, K Boyer, P Grygiel, S Javegny, M Terville, B I Canteros, I Robène, C Vernière, A Chabirand, O Pruvost, P Lefeuvre
Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons...
January 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28087584/emergence-of-klebsiella-variicola-positive-for-ndm-9-a-variant-of-new-delhi-metallo-%C3%AE-lactamase-in-an-urban-river-in-south-korea
#5
Doris Y W Di, Jeonghwan Jang, Tatsuya Unno, Hor-Gil Hur
OBJECTIVES: To examine the presence of pathogenic bacteria carrying New Delhi metallo-β-lactamase in the environment and to characterize the genome structures of these strains. METHODS: Phenotypic screening of antimicrobial susceptibility and WGS were conducted on three Klebsiella variicola strains possessing NDM-9 isolated from an urban river. RESULTS: Three carbapenem-resistant K. variicola isolated from Gwangju tributary were found to possess blaNDM-9 genes...
January 12, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28086793/methicillin-resistance-and-virulence-genes-in-invasive-and-nasal-staphylococcus-epidermidis-isolates-from-neonates
#6
Vivian Carolina Salgueiro, Natalia Lopes Pontes Iorio, Marcelle Cristina Ferreira, Raiane Cardoso Chamon, Kátia Regina Netto Dos Santos
BACKGROUND: Staphylococcus epidermidis is an opportunistic pathogen involved in hospital-acquired infections, particularly in those related to medical devices. This study characterized 50 genetically unrelated S. epidermidis isolates from bloodstream infections (BSIs, n = 31) and nares (n = 19) of neonates in relation to staphylococcal chromosomal cassette mec (SCCmec) type, biofilm production and associated genes, and the arginine catabolic mobile elements (ACME), in order to detect virulence factors that could discriminate a potential invasiveness isolate or predict an increasing pathogenicity...
January 13, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28077567/farme-db-a-functional-antibiotic-resistance-element-database
#7
James C Wallace, Jesse A Port, Marissa N Smith, Elaine M Faustman
Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077405/vrprofile-gene-cluster-detection-based-profiling-of-virulence-and-antibiotic-resistance-traits-encoded-within-genome-sequences-of-pathogenic-bacteria
#8
Jun Li, Cui Tai, Zixin Deng, Weihong Zhong, Yongqun He, Hong-Yu Ou
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28077029/the-behavior-of-mobile-genetic-elements-mges-in-different-environments
#9
Masaki Shintani
Mobile genetic elements (MGEs) including plasmids have an important role in the rapid evolution and adaptation of bacteria. Here, the behavior of MGEs in different environments is reviewed, in particular, behavior of the plasmid pCAR1, a carbazole-degradative plasmid isolated from Pseudomonas resinovorans CA10. pCAR1 belongs to incompatibility P-7 group and is self-transmissible among different bacteria. Comparisons of changes in the transcriptome of different host strains caused by carrying pCAR1 revealed common responses in the hosts and host-specific responses...
January 12, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28073961/genetic-characterization-of-mcr-1-bearing-plasmids-to-depict-molecular-mechanisms-underlying-dissemination-of-the-colistin-resistance-determinant
#10
Ruichao Li, Miaomiao Xie, Jinfei Zhang, Zhiqiang Yang, Lizhang Liu, Xiaobo Liu, Zhiwei Zheng, Edward Wai-Chi Chan, Sheng Chen
OBJECTIVES: To analyse and compare mcr-1-bearing plasmids from animal Escherichia coli isolates, and to investigate potential mechanisms underlying dissemination of mcr-1. METHODS: Ninety-seven ESBL-producing E. coli strains isolated from pig farms in China were screened for the mcr-1 gene. Fifteen mcr-1-positive strains were subjected to molecular characterization and bioinformatic analysis of the mcr-1-bearing plasmids that they harboured. RESULTS: Three major types of mcr-1-bearing plasmids were recovered: IncX4 (∼33 kb), IncI2 (∼60 kb) and IncHI2 (∼216-280 kb), among which the IncX4 and IncI2 plasmids were found to harbour the mcr-1 gene only, whereas multiple resistance elements including blaCTX-M, blaCMY, blaTEM, fosA, qnrS, floR and oqxAB were detected, in various combinations, alongside mcr-1 in the IncHI2 plasmids...
September 28, 2016: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28062463/ymc-2011-a-temperate-phage-of-streptococcus-salivarius-57-i
#11
Wen-Chun Chou, Szu-Chuan Huang, Cheng-Hsun Chiu, Yi-Ywan M Chen
: Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally with an estimated copy number of 3 to 4...
January 6, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28057823/genetic-conflicts-the-usual-suspects-and-beyond
#12
REVIEW
Richard N McLaughlin, Harmit S Malik
Selfishness is pervasive and manifests at all scales of biology, from societies, to individuals, to genetic elements within a genome. The relentless struggle to seek evolutionary advantages drives perpetual cycles of adaptation and counter-adaptation, commonly referred to as Red Queen interactions. In this review, we explore insights gleaned from molecular and genetic studies of such genetic conflicts, both extrinsic (between genomes) and intrinsic (within genomes or cells). We argue that many different characteristics of selfish genetic elements can be distilled into two types of advantages: an over-replication advantage (e...
January 1, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28057730/insertion-polymorphisms-of-mobile-genetic-elements-in-sexual-and-asexual-populations-of-daphnia-pulex
#13
Xiaoqian Jiang, Haixu Tang, Zhiqiang Ye, Michael Lynch
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28049704/the-nucleotide-excision-repair-pathway-limits-l1-retrotransposition
#14
Geraldine Servant, Vincent A Streva, Rebecca S Derbes, Madushani I Wijetunge, Marc Neeland, Travis B White, Victoria P Belancio, Astrid M Roy-Engel, Prescott L Deininger
Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a "copy-and-paste" mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3' DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best characterized in the nucleotide excision repair (NER) pathway...
January 2017: Genetics
https://www.readbyqxmd.com/read/28039271/novel-lnu-g-gene-conferring-resistance-to-lincomycin-by-nucleotidylation-located-on-tn6260-from-enterococcus-faecalis-e531
#15
Xiao-Qing Zhu, Xiao-Ming Wang, Hui Li, Yan-Hong Shang, Yu-Shan Pan, Cong-Ming Wu, Yang Wang, Xiang-Dang Du, Jian-Zhong Shen
OBJECTIVES: To identify a novel putative lincosamide resistance gene determinant in a swine Enterococcus faecalis E531 exhibiting a lincosamide resistance/macrolide susceptibility (L(R)M(S)) phenotype and to determine its location and genetic environment. METHODS: The whole genomic DNA of E. faecalis E531, which tested negative for the known lincosamide nucleotidyltransferase genes, was sequenced. A putative lincosamide resistance gene determinant was cloned into an Escherichia coli-E...
December 30, 2016: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28030622/effects-of-menthol-supplementation-in-feedlot-cattle-diets-on-the-fecal-prevalence-of-antimicrobial-resistant-escherichia-coli
#16
C C Aperce, R Amachawadi, C L Van Bibber-Krueger, T G Nagaraja, H M Scott, J Vinasco-Torre, J S Drouillard
The pool of antimicrobial resistance determinants in the environment and in the gut flora of cattle is a serious public health concern. In addition to being a source of human exposure, these bacteria can transfer antibiotic resistance determinants to pathogenic bacteria and endanger the future of antimicrobial therapy. The occurrence of antimicrobial resistance genes on mobile genetic elements, such as plasmids, facilitates spread of resistance. Recent work has shown in vitro anti-plasmid activity of menthol, a plant-based compound with the potential to be used as a feed additive to beneficially alter ruminal fermentation...
2016: PloS One
https://www.readbyqxmd.com/read/28018320/single-molecule-sequencing-pacbio-of-the-staphylococcus-capitis-nrcs-a-clone-reveals-the-basis-of-multidrug-resistance-and-adaptation-to-the-neonatal-intensive-care-unit-environment
#17
Patrícia Martins Simões, Hajar Lemriss, Yann Dumont, Sanâa Lemriss, Jean-Philippe Rasigade, Sophie Assant-Trouillet, Azeddine Ibrahimi, Saâd El Kabbaj, Marine Butin, Frédéric Laurent
The multi-resistant Staphylococcus capitis clone NRCS-A has recently been described as a major pathogen causing nosocomial, late-onset sepsis (LOS) in preterm neonates worldwide. NRCS-A representatives exhibit an atypical antibiotic resistance profile. Here, the complete closed genome (chromosomal and plasmid sequences) of NRCS-A prototype strain CR01 and the draft genomes of three other clinical NRCS-A strains from Australia, Belgium and the United Kingdom are annotated and compared to available non-NRCS-A S...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28008854/one-genome-s-junk-is-another-s-garbage
#18
Lydia J Bright, Douglas L Chalker
Experiments on a single-celled ciliate reveal how mobile genetic elements can shape a genome, even one which is not transcriptionally active.
December 23, 2016: ELife
https://www.readbyqxmd.com/read/28007890/multiple-transcriptional-and-post-transcriptional-pathways-collaborate-to-control-sense-and-antisense-rnas-of-tf2-retroelements-in-fission-yeast
#19
Pierre-Luc Mallet, Marc Larochelle, François Bachand
Retrotransposons are mobile genetic elements that colonize eukaryotic genomes by replicating through an RNA intermediate. As retrotransposons can move within the host genome, defense mechanisms have evolved to repress their potential mutagenic activities. In the fission yeast Schizosaccharomyces pombe, the mRNA of Tf2 long terminal repeat retrotransposons is targeted for degradation by the 3'-5' exonucleolytic activity of the exosome-associated protein Rrp6. Here, we show that the nuclear poly(A)-binding protein Pab2 functions with Rrp6 to negatively control Tf2 mRNA accumulation...
December 22, 2016: Genetics
https://www.readbyqxmd.com/read/28003200/genome-integration-and-excision-by-a-new-streptomyces-bacteriophage-%C3%AF-joe
#20
Paul C M Fogg, Joshua A Haley, W Marshall Stark, Margaret C M Smith
: Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In Streptomyces, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here we present the genome of a new Streptomyces phage, ϕJoe, and investigate the conditions for integration and excision of the φJoe genome...
December 21, 2016: Applied and Environmental Microbiology
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