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mobile genetic elements

Yusuke Inoue, Tomonori Saga, Takumi Aikawa, Masahiko Kumagai, Atsuko Shimada, Yasushi Kawaguchi, Kiyoshi Naruse, Shinichi Morishita, Akihiko Koga, Hiroyuki Takeda
Mobile genetic elements (e.g., transposable elements and viruses) display significant diversity with various life cycles, but how novel elements emerge remains obscure. Here, we report a giant (180-kb long) transposon, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn belongs to the piggyBac superfamily and retains the transposition activity. Remarkably, Teratorn is largely derived from a herpesvirus of the Alloherpesviridae family that could infect fish and amphibians. Genomic survey of Teratorn-like elements reveals that some of them exist as a fused form between piggyBac transposon and herpesvirus genome in teleosts, implying the generality of transposon-herpesvirus fusion...
September 15, 2017: Nature Communications
Jean Cury, Marie Touchon, Eduardo P C Rocha
Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species' pan-genome...
September 6, 2017: Nucleic Acids Research
Camille Kolenda, Céline Dupieux, Jean-Winoc Decousser, Anders Rhod Larsen, Bruno Pichon, Mark Holmes, Michèle Bès, Christopher Teale, Elizabeth Dickson, Robert Hill, Robert Skov, Angela Kearns, Frédéric Laurent
Methicillin-resistance in Staphylococcus aureus is classically mediated by the mecA gene carried on a mobile genetic element, called staphylococcal cassette chromosome mec (SCCmec).….
September 13, 2017: Journal of Clinical Microbiology
Min Gou, Hang-Wei Hu, Yu-Jing Zhang, Jun-Tao Wang, Helen Hayden, Yue-Qin Tang, Ji-Zheng He
Composting has been suggested as a potential strategy to eliminate antibiotic residues and pathogens in livestock manure before its application as an organic fertilizer in agro-ecosystems. However, the impacts of composting on antibiotic resistance genes (ARGs) in livestock manure and their temporal succession following the application of compost to land are not well understood. We examined how aerobic composting affected the resistome profiles of cattle manure, and by constructing laboratory microcosms we compared the effects of manure and compost application to agricultural soils on the temporal succession of a wide spectrum of ARGs...
September 8, 2017: Science of the Total Environment
Peng Liu, Shuyu Jia, Xiwei He, Xuxiang Zhang, Lin Ye
Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash...
September 4, 2017: Chemosphere
Michael J Bottery, A Jamie Wood, Michael A Brockhurst
Bacteria gain antibiotic resistance genes by horizontal acquisition of mobile genetic elements (MGE) from other lineages. Newly acquired MGEs are often poorly adapted causing intragenomic conflicts, resolved by compensatory adaptation of the chromosome, the MGE or reciprocal coadaptation. The footprints of such intragenomic coevolution are present in bacterial genomes, suggesting an important role promoting genomic integration of horizontally acquired genes, but direct experimental evidence of the process is limited...
September 2017: Nature ecology & evolution
Sabrina Festa, Bibiana Marina Coppotelli, Laura Madueño, Claudia Lorena Loviso, Marianela Macchi, Ricardo Martin Neme Tauil, María Pía Valacco, Irma Susana Morelli
The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite...
2017: PloS One
Peiling Geng, Shen Tian, Zhiming Yuan, Xiaomin Hu
Cereulide-producing Bacillus cereus isolates can cause serious emetic (vomiting) syndrome and even acute lethality. As mobile genetic elements, the exploration of prophages derived from emetic B. cereus isolates will help in our understanding of the genetic diversity and evolution of these pathogens. In this study, five temperate phages derived from cereulide-producing B. cereus strains were induced, with four of them undergoing genomic sequencing. Sequencing revealed that they all belong to the Siphoviridae family, but presented in different forms in their hosts...
2017: PloS One
Charlotte Hedenstierna-Jonson, Anna Kjellström, Torun Zachrisson, Maja Krzewińska, Veronica Sobrado, Neil Price, Torsten Günther, Mattias Jakobsson, Anders Götherström, Jan Storå
OBJECTIVES: The objective of this study has been to confirm the sex and the affinity of an individual buried in a well-furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context...
September 8, 2017: American Journal of Physical Anthropology
Luis F Espinosa-Camacho, Gabriela Delgado, Gloria Soberón-Chávez, Luis D Alcaraz, Jorge Castañon, Rosario Morales-Espinosa
Four extensively drug-resistant Pseudomonas aeruginosa strains, isolated from patients with pneumonia, were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. Genome sequence analysis identified great variability among mobile genetic elements, as well as some previously undescribed genomic islands and new variants of class 1 integrons (In1402, In1403, In1404, and In1408).
September 7, 2017: Genome Announcements
Lina Amlinger, Mirthe Hoekzema, E Gerhart H Wagner, Sanna Koskiniemi, Magnus Lundgren
CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I...
September 4, 2017: Scientific Reports
Dorota Jamrozy, Francesc Coll, Alison E Mather, Simon R Harris, Ewan M Harrison, Alasdair MacGowan, Andreas Karas, Tony Elston, M Estée Török, Julian Parkhill, Sharon J Peacock
BACKGROUND: Horizontal transfer of mobile genetic elements (MGEs) that carry virulence and antimicrobial resistance genes mediates the evolution of methicillin-resistant Staphylococcus aureus, and the emergence of new MRSA clones. Most MRSA lineages show an association with specific MGEs and the evolution of MGE composition following clonal expansion has not been widely studied. RESULTS: We investigated the genomes of 1193 S. aureus bloodstream isolates, 1169 of which were MRSA, collected in the UK and the Republic of Ireland between 2001 and 2010...
September 4, 2017: BMC Genomics
M Sassi, B Felden, M Revest, P Tattevin, Y Augagneur, P-Y Donnio
Intravenous drug users are at increased risk of Staphylococcus aureus infections. Most cases are related to clones prevalent in the community. We report an outbreak of community-acquired methicillin-resistant Staphylococcus aureus infections that occurred from 2007 to 2009 in intravenous drug users and their close contacts in Northwestern France. Clinical and molecular investigations suggested that the clones were more similar than those usually isolated in the American continent although none of the patients traveled abroad or had contact with individuals who had traveled to the Americas...
September 2, 2017: European Journal of Clinical Microbiology & Infectious Diseases
Soo Sum Lean, Chew Chieng Yeo
Acinetobacter baumannii is a Gram-negative nosocomial pathogen that has become a serious healthcare concern within a span of two decades due to its ability to rapidly acquire resistance to all classes of antimicrobial compounds. One of the key features of the A. baumannii genome is an open pan genome with a plethora of plasmids, transposons, integrons, and genomic islands, all of which play important roles in the evolution and success of this clinical pathogen, particularly in the acquisition of multidrug resistance determinants...
2017: Frontiers in Microbiology
Ciro C Rossi, Thaysa Souza-Silva, Amanda V Araújo-Alves, Marcia Giambiagi-deMarval
The claimed role of gene reservoir of coagulase-negative staphylococci (CoNS) could be contradicted by estimates that CRISPR/Cas systems are found in the genomes of 40-50% of bacteria, as these systems interfere with plasmid uptake in staphylococci. To further correlate this role with presence of CRISPR, we analyzed, by computational methods, 122 genomes from 15 species of CoNS. Only 15% of them harbored CRISPR/Cas systems, and this proportion was much lower for S. epidermidis and S. haemolyticus, the CoNS most frequently associated with opportunistic infections in humans...
2017: Frontiers in Microbiology
Sayaka Tsuchida, Fumito Maruyama, Yoshitoshi Ogura, Atsushi Toyoda, Tetsuya Hayashi, Moriya Okuma, Kazunari Ushida
Genomic analysis was performed on seven strains of Bifidobacterium thermacidophilum, a Sus-associated Bifidobacterium. Three strains from the feces of domestic pigs (Sus scrofa domesticus) and four strains from the rectal feces of free-range Japanese wild boars (S. s. scrofa) were compared. The phylogenetic position of these isolates suggested by genomic analyses were not concordant with that suggested by 16S rRNA sequence. There was biased distribution of genes for virulence, phage, metabolism of aromatic compounds, iron acquisition, cell division, and DNA metabolism...
2017: Frontiers in Microbiology
Luis F Espinosa-Camacho, Gabriela Delgado, Guadalupe Miranda-Novales, Gloria Soberón-Chávez, Luis D Alcaraz, Rosario Morales-Espinosa
Two Pseudomonas aeruginosa strains isolated from children with bacteremia in Mexico City were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. The strains consist of a 7.0- to 7.4-Mb chromosome, with a high content of mobile elements, and variation in the genetic content of class 1 integron In1409.
August 31, 2017: Genome Announcements
Alexander Dyomin, Valeria Volodkina, Elena Koshel, Svetlana Galkina, Alsu Saifitdinova, Elena Gaginskaya
Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown...
August 30, 2017: Molecular Phylogenetics and Evolution
Eugene J Gardner, Vincent K Lam, Daniel N Harris, Nelson T Chuang, Emma C Scott, William S Pittard, Ryan E Mills, Scott E Devine
Mobile element insertions (MEIs) represent ~25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases, and clinical genomics. Here, we describe the Mobile Element Locator Tool (MELT), which was developed as part of the 1000 Genomes Project to perform MEI discovery on a population scale...
August 30, 2017: Genome Research
Ying Han, Jing Wang, Zelong Zhao, Jingwen Chen, Hong Lu, Guangfei Liu
Antibiotic resistance genes (ARGs) are globally prevalent in mariculture sediment, and their presence is an issue of concern in the context of antibiotic use. Although large amounts of fishmeal have been released into the sediment, the role of fishmeal in ARG dissemination remains unclear. In this study, high-throughput ARG profiles in representative fishmeal products and the impact of fishmeal on the sediment resistome were investigated. A total of 132 unique ARGs and 4 mobile genetic elements (MGEs) were detected in five fishmeal products...
August 30, 2017: Environmental Science & Technology
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