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https://www.readbyqxmd.com/read/28444372/quantifying-the-number-of-independent-organelle-dna-insertions-in-genome-evolution-and-human-health
#1
Einat Hazkani-Covo, William F Martin
Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy...
April 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28444231/whole-genome-sequencing-of-7-strains-of-staphylococcus-lugdunensis-allows-identification-of-mobile-genetic-elements
#2
Xavier Argemi, Véronique Martin, Valentin Loux, Sandrine Dahyot, Jérémie Lebeurre, Aurélien Guffroy, Mickael Martin, Aurélie Velay, Daniel Keller, Philippe Riegel, Yves Hansmann, Nicodème Paul, Gilles Prévost
Coagulase negative staphylococci are normal inhabitant of the human skin flora that account for an increasing number of infections, particularly hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most virulent species causing various infections with clinical characteristics close to what clinicians usually observe with Staphylococcus aureus and both bacteria share more than 70% of their genome. Virulence of S. aureus relies on a large repertoire of virulence factors, many of which are encoded on mobile genetic elements...
April 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28443223/detection-of-integrons-and-staphylococcal-cassette-chromosome-mec-types-in-clinical-methicillin-resistant-coagulase-negative-staphylococci-strains
#3
Fahimeh Hajiahmadi, Elham Salimi Ghale, Mohammad Yousef Alikhani, Alireza Mordadi, Mohammad Reza Arabestani
OBJECTIVES: Integrons are thought to play an important role in the spread of antibiotic resistance. This study investigates class 1 and 2 integron-positive methicillin-resistant coagulase-negative staphylococci strains isolated in Iran and characterizes their patterns of antimicrobial resistance. METHODS: Hundred clinical isolates of coagulase-negative staphylococci were characterized for integron content and staphylococcal cassette chromosome mec (SCCmec) type...
February 2017: Osong Public Health and Research Perspectives
https://www.readbyqxmd.com/read/28442219/virulence-potential-of-staphylococcus-aureus-isolates-from-buruli-ulcer-patients
#4
Nana Ama Amissah, Monika A Chlebowicz, Anthony Ablordey, Caitlin S Tetteh, Isaac Prah, Tjip S van der Werf, Alex W Friedrich, Jan Maarten van Dijl, Ymkje Stienstra, John W Rossen
Buruli ulcer (BU) is a necrotizing infection of the skin and subcutaneous tissue caused by Mycobacterium ulcerans. BU wounds may also be colonized with other microorganisms including Staphylococcus aureus. This study aimed to characterize the virulence factors of S. aureus isolated from BU patients. Previously sequenced genomes of 21 S. aureus isolates from BU patients were screened for the presence of virulence genes. The results show that all S. aureus isolates harbored on their core genomes genes for known virulence factors like α-hemolysin, and the α- and β-phenol soluble modulins...
April 19, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28439515/endogenous-retroviruses-with-us-and-against-us
#5
REVIEW
Thomas J Meyer, Jimi L Rosenkrantz, Lucia Carbone, Shawn L Chavez
Mammalian genomes are scattered with thousands of copies of endogenous retroviruses (ERVs), mobile genetic elements that are relics of ancient retroviral infections. After inserting copies into the germ line of a host, most ERVs accumulate mutations that prevent the normal assembly of infectious viral particles, becoming trapped in host genomes and unable to leave to infect other cells. While most copies of ERVs are inactive, some are transcribed and encode the proteins needed to generate new insertions at novel loci...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28439449/mobilizable-genomic-islands-different-strategies-for-the-dissemination-of-multidrug-resistance-and-other-adaptive-traits
#6
COMMENT
Nicolas Carraro, Nicolas Rivard, Vincent Burrus, Daniela Ceccarelli
Mobile genetic elements are near ubiquitous DNA segments that revealed a surprising variety of strategies for their propagation among prokaryotes and between eukaryotes. In bacteria, conjugative elements were shown to be key drivers of evolution and adaptation by efficiently disseminating genes involved in pathogenicity, symbiosis, metabolic pathways, and antibiotic resistance. Conjugative plasmids of the incompatibility groups A and C (A/C) are important vehicles for the dissemination of antibiotic resistance and the consequent global emergence and spread of multi-resistant pathogenic bacteria...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28436748/disruption-of-tetr-type-regulator-aden-by-mobile-genetic-element-confers-elevated-virulence-in-acinetobacter-baumannii
#7
Rajagopalan Saranathan, Sudhakar Pagal, Ajit R Sawant, Archana Tomar, M Madhangi, Suresh Sah, Annapurna Satti, K P Arunkumar, K Prashanth
Acinetobacter baumannii is an important human pathogen and considered as a major threat due to its extreme drug resistance. In this study, the genome of a hyper-virulent MDR strain PKAB07 of A. baumannii isolated from an Indian patient was sequenced and analysed to understand its mechanisms of virulence, resistance and evolution. Comparative genomics analysis of PKAB07 revealed virulence and resistance related genes scattered throughout the genome, instead of being organized as an island, indicating the highly mosaic nature of the genome...
April 24, 2017: Virulence
https://www.readbyqxmd.com/read/28434738/relationships-among-superantigen-toxin-gene-profiles-genotypes-and-pathogenic-characteristics-of-staphylococcus-aureus-isolates-from-bovine-mastitis
#8
Dong Wang, Limei Zhang, Changfu Yong, Mingliang Shen, Tariq Ali, Muhammad Shahid, Kun Han, Xuezhang Zhou, Bo Han
Staphylococcus aureus is one of the major etiological agents of bovine mastitis, harboring a wide variety of staphylococcal superantigen (SAg) toxin genes. The SAg toxin genes are reported to be closely associated with the pathogenicity of the Staph. aureus causing the bovine mastitis. This study was conducted to investigate SAg toxin gene profiles and to assess the relationships among SAg toxin genes, genotypes of Staph. aureus, and their pathogenic properties. A total of 327 quarter milk samples were collected from bovine mastitis cases for isolation and identification of pathogens...
April 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28432950/effects-of-chlortetracycline-and-copper-on-tetracyclines-and-copper-resistance-genes-and-microbial-community-during-swine-manure-anaerobic-digestion
#9
Rui Wang, Meixue Chen, Feng Feng, Junya Zhang, Qianwen Sui, Juan Tong, Yuansong Wei, Dongbin Wei
As antibiotic and heavy metals are over used in the livestock industry, animal manure is a reservoir of antibiotic resistance genes (ARGs). Anaerobic digestion has been reported to have the potential to reduce ARGs. However, few studies investigated whether reduction of ARGs would be affected by different external pressures including antibiotics and heavy metals during anaerobic digestion. The purpose of this study was thus to investigate effects of both chlortetracycline (CTC) and Cu on reduction of ARGs, heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) during the swine manure anaerobic digestion...
March 25, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28432093/diversity-of-integrative-and-conjugative-elements-of-streptococcus-salivarius-and-their-intra-and-interspecies-transfer
#10
Narimane Dahmane, Virginie Libante, Florence Charron-Bourgoin, Eric Guédon, Gérard Guédon, Nathalie Leblond-Bourget, Sophie Payot
Integrative and Conjugative Elements (ICEs) are widespread chromosomal mobile genetic elements, which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole genome sequencing. Sequence comparison highlighted ICE evolution by shuffling of 3 different integration/excision modules (for integration in the 3' end of fda, rpsI or rpmG genes) with the conjugation module of the ICESt3 subfamily...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28428775/genomics-reveals-a-unique-clone-of-burkholderia-cenocepacia-harboring-an-actively-excising-novel-genomic-island
#11
Prashant P Patil, Swapna Mali, Samriti Midha, Vikas Gautam, Lona Dash, Sunil Kumar, Jayanthi Shastri, Lipika Singhal, Prabhu B Patil
Burkholderia cenocepacia is a clinically dominant form among the other virulent species of Burkholderia cepacia complex (Bcc). In the present study, we sequenced and analyzed the genomes of seven nosocomial Bcc isolates, five of which were isolated from the bloodstream infections and two isolates were recovered from the hospital setting during the surveillance. Genome-based species identification of the Bcc isolates using a type strain explicitly identified the species as B. cenocepacia. Moreover, single nucleotide polymorphism analysis revealed that the six isolates were clonal and phylogenetically distinct from the other B...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28428290/draft-genome-sequence-of-acinetobacter-johnsonii-c6-an-environmental-isolate-engaging-in-interspecific-metabolic-interactions
#12
Rolf Sommer Kaas, Hanne Mordhorst, Pimlapas Leekitcharoenphon, Jacob Dyring Jensen, Janus A J Haagensen, Søren Molin, Sünje Johanna Pamp
Acinetobacter johnsonii C6 originates from creosote-polluted groundwater and performs ecological and evolutionary interactions with Pseudomonas putida in biofilms. The draft genome of A. johnsonii C6 is 3.7 Mbp and was shaped by mobile genetic elements. It reveals genes facilitating the biodegradation of aromatic hydrocarbons and resistance to antimicrobials and metals.
April 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28427330/pan-genome-and-crispr-analyses-of-the-bacterial-fish-pathogen-moritella-viscosa
#13
Christian Karlsen, Erik Hjerde, Terje Klemetsen, Nils Peder Willassen
BACKGROUND: Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28426231/the-prevalence-of-integrons-as-the-carrier-of-antibiotic-resistance-genes-in-natural-and-man-made-environments
#14
Liping Ma, An-Dong Li, Xiao-Le Yin, Tong Zhang
Class 1 integrase intI1 has been considered as a good proxy for anthropogenic pollution because of being linked to genes conferring resistance to antibiotics. The gene cassettes of class 1 integrons could carry diverse antibiotic resistance genes (ARGs) and conduct horizontal gene transfer among microorganisms. The present study applied high-throughput sequencing technique combined with an intI1 database and genome assembly to quantify the abundance of intI1 in 64 environmental samples from 8 ecosystems, and to investigate the diverse arrangements of ARG-carrying gene cassettes (ACGCs) carried by class 1 integrons...
April 20, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28426191/genome-wide-abolishment-of-mobile-genetic-elements-using-genome-shuffling-and-crispr-cas-assisted-mage-allows-the-efficient-stabilization-of-a-bacterial-chassis
#15
Kinga Umenhoffer, Gábor Draskovits, Ákos Nyerges, Ildikó Karcagi, Balázs Bogos, Edit Tímár, Bálint Csörgő, Róbert Herczeg, István Nagy, Tamás Fehér, Csaba Pál, György Pósfai
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, nonessential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization...
April 26, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28424761/sequencing-of-blaimp-carrying-incn2-plasmids-and-comparative-genomics-of-incn2-plasmids-harboring-class-1-integrons
#16
Xiaoyuan Jiang, Zhe Yin, Xiuyun Yin, Haihong Fang, Qiang Sun, Yigang Tong, Yuanhong Xu, Defu Zhang, Jiao Feng, Weijun Chen, Yajun Song, Jinglin Wang, Shuiping Chen, Dongsheng Zhou
This work presents the complete nucleotide sequences of p0801-IMP from Klebsiella pneumoniae, p7121-IMP from K. oxytoca, and p17285-IMP from Citrobacter freundii, which are recovered from three different cases of nosocomial infection. These three plasmids represent the first fully sequenced blaIMP-carrying IncN2 plasmids. Further comparative genomics analysis of all the five integron-carrying IncN2 plasmids p0801-IMP, p7121-IMP, p17285-IMP, pJIE137, and p34983-59.134kb indicates that they possess conserved IncN2 backbones with limited genetic variations with respect to gene content and organization...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28420154/mechanisms-of-ltr-retroelement-transposition-lessons-from-drosophila-melanogaster
#17
REVIEW
Lidia Nefedova, Alexander Kim
Long terminal repeat (LTR) retrotransposons occupy a special place among all mobile genetic element families. The structure of LTR retrotransposons that have three open reading frames is identical to DNA forms of retroviruses that are integrated into the host genome. Several lines of evidence suggest that LTR retrotransposons share a common ancestry with retroviruses and thus are highly relevant to understanding mechanisms of transposition. Drosophila melanogaster is an exceptionally convenient model for studying the mechanisms of retrotransposon movement because many such elements in its genome are transpositionally active...
April 16, 2017: Viruses
https://www.readbyqxmd.com/read/28419231/antibiotic-resistance-in-staphylococcus-aureus-current-status-and-future-prospects
#18
Timothy J Foster
The major targets for antibiotics in staphylococci are (i) the cell envelope, (ii) the ribosome and (iii) nucleic acids. Several novel targets emerged from recent targeted drug discovery programmes including the ClpP protease and FtsZ from the cell division machinery. Resistance can either develop by horizontal transfer of resistance determinants encoded by mobile genetic elements viz plasmids, transposons and the staphylococcal cassette chromosome or by mutations in chromosomal genes. Horizontally acquired resistance can occur by one of the following mechanisms: (i) enzymatic drug modification and inactivation, (ii) enzymatic modification of the drug binding site, (iii) drug efflux, (iv) bypass mechanisms involving acquisition of a novel drug-resistant target, (v) displacement of the drug to protect the target...
April 13, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28414318/initial-sites-of-hepadnavirus-integration-into-host-genome-in-human-hepatocytes-and-in-the-woodchuck-model-of-hepatitis-b-associated-hepatocellular-carcinoma
#19
R Chauhan, N D Churchill, P M Mulrooney-Cousins, T I Michalak
Hepatitis B virus (HBV) and the closely related woodchuck hepatitis virus (WHV) are potent carcinogens that trigger development of primary hepatocellular carcinoma (HCC). The initial sites of hepadnavirus-host genome integration, their diversity and kinetics of formation can be central to virus persistence and the initiation and progression of HCC. To recognize the nature of the very early virus-host interactions, we explored de novo infection of human hepatocyte-like HepaRG cells with authentic HBV and naive woodchucks with WHV...
April 17, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28409117/searching-for-active-mobile-genetic-elements-in-dsrna-fraction-of-pinus-sylvestris-having-witches-broom-abnormalities
#20
A A Pochtovyy, O Yu Baranov, I E Rubel', O A Razumova, V E Padutov, A V Khromov, A V Makhotenko, A P Tkachuk, V V Makarov, V A Gushchin
The most common type of coniferous mobile genetic elements are retrotransposons. Despite of their early positive impact on evolution of modern coniferous species they can have a significant negative impact for Forestry and breeding. Breaking genomic structural integrity mobile elements can cause phenotypic defects of plants. In this regard, the study of the diversity of coniferous mobile genetic elements is particularly interesting. In the present paper, we describe mobile genetic elements in dsRNA fraction of Pinus sylvestris having witches broom abnormalities...
June 2017: Genomics Data
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