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Mobile genetic element

Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
P D Croughs, C H W Klaassen, J van Rosmalen, D M Maghdid, S A Boers, J P Hays, W H F Goessens
Pseudomonas aeruginosa is one of the most important causes of infection in the intensive care unit. It is intrinsically resistant to many antibiotics and easily acquires additional resistance genes via horizontal gene transfer of mobile genetic elements. In the present study, 1,528 P. aeruginosa isolates, obtained from a Dutch national surveillance program between the years 1998 and 2011, were analyzed for the presence of Extended Spectrum β-Lactamase (ESBL) genes blaCTX-M , blaSHV , blaTEM , blaBEL , blaPER , blaVEB , blaOXA-10 and metallo-β-Lactamase (MBL) genes blaIMP , blaVIM and blaNDM ...
May 14, 2018: International Journal of Antimicrobial Agents
Maryury Brown-Jaque, Lirain Rodriguez Oyarzun, Thais Cornejo-Sánchez, Maria T Martín-Gómez, Silvia Gartner, Javier de Gracia, Sandra Rovira, Antonio Alvarez, Joan Jofre, Juan J González-López, Maite Muniesa
Cystic fibrosis (CF) is a chronic disease in which the bacterial colonization of the lung is linked to an excessive inflammatory response that leads to respiratory failure. The microbiology of CF is complex. Staphylococcus aureus is the first bacterium to colonize the lungs in 30% of pediatric CF patients, and 80% of adult patients develop a chronic Pseudomonas aeruginosa infection, but other microorganisms can also be found. The use of antibiotics is essential to treat the disease, but antibiotic performance is compromised by resistance mechanisms...
2018: Frontiers in Microbiology
Ziyan Wei, Kai Feng, Shuzhen Li, Yu Zhang, Hongrui Chen, Huaqun Yin, Meiying Xu, Ye Deng
An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing...
May 9, 2018: Environment International
Xin-Li An, Jian-Qiang Su, Bing Li, Wei-Ying Ouyang, Yi Zhao, Qing-Lin Chen, Li Cui, Hong Chen, Michael R Gillings, Tong Zhang, Yong-Guan Zhu
Wastewater treatment plants (WWTPs) contain diverse antibiotic resistance genes (ARGs), and thus are considered as a major pathway for the dissemination of these genes into the environments. However, comprehensive evaluations of ARGs dynamic during wastewater treatment process lack extensive investigations on a broad spectrum of ARGs. Here, we investigated the dynamics of ARGs and bacterial community structures in 114 samples from eleven Chinese WWTPs using high-throughput quantitative PCR and 16S rRNA-based Illumina sequencing analysis...
May 8, 2018: Environment International
Kate S Baker, Timothy J Dallman, Nigel Field, Tristan Childs, Holly Mitchell, Martin Day, François-Xavier Weill, Sophie Lefèvre, Mathieu Tourdjman, Gwenda Hughes, Claire Jenkins, Nicholas Thomson
Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with traditional typing methods, and has identified sublineages associated with specific geographical regions or patient groups. Genomic analyses reveal temporal increases in Shigella antimicrobial resistance (AMR) gene content, which is frequently encoded on mobile genetic elements...
May 9, 2018: Scientific Reports
Niranjana Mahalingam, Bhavani Manivannan, Balaram Khamari, Shivakumara Siddaramappa, Sudeshna Adak, Eswarappa Pradeep Bulagonda
OBJECTIVES: The aim of this study was to analyze the prevalence of CTX-M, TEM, SHV, VIM, NDM and OXA genes in carbapenemase-producing E. coli and their transmissibility at a tertiary care hospital in south India. MATERIALS AND METHODS: Twenty-one carbapenem-resistant E. coli (CRE) were collected from Sri Sathya Sai Institute of Higher Medical Sciences, Prasanthigram, India. Resistance to antibiotics was analyzed by Vitek-2, and identity of the isolates was confirmed by 16S rDNA sequencing...
May 8, 2018: Medical Principles and Practice: International Journal of the Kuwait University, Health Science Centre
A V Olina, A V Kulbachinskiy, A A Aravin, D M Esyunina
Noncoding RNAs play essential roles in genetic regulation in all organisms. In eukaryotic cells, many small noncoding RNAs act in complex with Argonaute proteins and regulate gene expression by recognizing complementary RNA targets. The complexes of Argonaute proteins with small RNAs also play a key role in silencing of mobile genetic elements and, in some cases, viruses. These processes are collectively called RNA interference. RNA interference is a powerful tool for specific gene silencing in both basic research and therapeutic applications...
May 2018: Biochemistry. Biokhimii︠a︡
Yunyan Guo, Min Liu, Lemian Liu, Xuan Liu, Huihuang Chen, Jun Yang
In freshwater systems, both antibiotic resistance genes (ARGs) and cyanobacterial blooms attract global public health concern. Cyanobacterial blooms can greatly impact bacterial taxonomic communities, but very little is known about the influence of the blooms on antibiotic resistance functional community. In this study, the ARGs in both free-living (FL) and particle-attached (PA) bacteria under bloom and non-bloom conditions were simultaneously investigated in a subtropical reservoir using high-throughput approaches...
May 4, 2018: Environment International
Xiaobin Li, Yingzhou Xie, Meng Liu, Cui Tai, Jingyong Sun, Zixin Deng, Hong-Yu Ou
oriTfinder is a web server that facilitates the rapid identification of the origin of transfer site (oriT) of a conjugative plasmid or chromosome-borne integrative and conjugative element. The utilized back-end database oriTDB was built upon more than one thousand known oriT regions of bacterial mobile genetic elements (MGEs) as well as the known MGE-encoding relaxases and type IV coupling proteins (T4CP). With a combination of similarity searches for the oriTDB-archived oriT nucleotide sequences and the co-localization of the flanking relaxase homologous genes, the oriTfinder can predict the oriT region with high accuracy in the DNA sequence of a bacterial plasmid or chromosome in minutes...
May 4, 2018: Nucleic Acids Research
Jiao Wu, Ye Huang, Dawei Rao, Yongkui Zhang, Kun Yang
The aquatic bird, egret, could carry antibiotic resistance (AR) from a contaminated waterway (Jin River, Chengdu, China) into the surrounding environment (Wangjianglou Park). A systematic study was carried out on the unique environmental dissemination mode of AR mediated by birds. The minimum inhibitory concentrations of various antibiotics against the environmental Escherichia coli isolates were used to evaluate the bacterial AR at the environmental locations where these isolates were recovered, i.e., the Jin River water, the egret feces, the park soil, and the campus soil...
2018: Frontiers in Microbiology
Mariel Fulham, Michelle Power, Rachael Gray
The dissemination of human-associated bacteria into the marine environment has the potential to expose wildlife populations to atypical microbes that can alter the composition of the gut microbiome or act as pathogens. The objective of the study was to determine whether endangered Australian sea lion (Neophoca cinerea) pups from two South Australian colonies, Seal Bay, Kangaroo Island and Dangerous Reef, Spencer Gulf, have been colonised by human-associated Escherichia coli. Faecal samples (n = 111) were collected to isolate E...
May 3, 2018: Infection, Genetics and Evolution
Gregory A Gambetta, Mark A Matthews, Michael Syvanen
BACKGROUND: Xylella fastidiosa (Xf) is a gram negative bacterium inhabiting the plant vascular system. In most species this bacterium lives as a benign symbiote, but in several agriculturally important plants (e.g. coffee, citrus, grapevine) Xf is pathogenic. Xf has four loci encoding homologues to hemolysin RTX proteins, virulence factors involved in a wide range of plant pathogen interactions. RESULTS: We show that all four genes are expressed during pathogenesis in grapevine...
May 4, 2018: BMC Genomics
Min Oh, Amy Pruden, Chaoqi Chen, Lenwood S Heath, Kang Xia, Liqing Zhang
The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by various environmental compartments is lacking. Here we introduce MetaCompare, a publicly-available tool for ranking 'resistome risk,' which we define as the potential for antibiotic resistance genes (ARGs) to be associated with mobile genetic elements (MGEs) and mobilize to pathogens based on metagenomic data...
April 26, 2018: FEMS Microbiology Ecology
Karthik Hullahalli, Marinelle Rodrigues, Uyen Thy Nguyen, Kelli Palmer
Antibiotic-resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Enterococcus faecalis , since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E...
May 1, 2018: MBio
Zhen Xu, Raju Misra, Dorota Jamrozy, Gavin K Paterson, Ronald R Cutler, Mark A Holmes, Saheer Gharbia, Hermine V Mkrtchyan
Staphylococcus epidermidis is a major opportunistic pathogen primarily recovered from device-associated healthcare associated infections (DA-HAIs). Although S. epidermidis and other coagulase-negative staphylococci (CoNS) are less virulent than Staphylococcus aureus , these bacteria are an important reservoir of antimicrobial resistance genes and resistance-associated mobile genetic elements that can be transferred between staphylococcal species. We report a whole genome sequence of a multidrug resistant S...
April 30, 2018: G3: Genes—Genomes—Genetics
Nisrine Chelkha, Philippe Colson, Anthony Levasseur, Bernard La Scola
Giant viruses infect protozoa, especially amoebae of the genus Acanthamoeba. These viruses possess genetic elements named Mobilome. So far, this mobilome comprises provirophages which are integrated into the genome of their hosts, transpovirons, and Maverick/Polintons. Virophages replicate inside virus factories within Acanthamoeba and can decrease the infectivity of giant viruses. The virophage infecting CroV was found to be integrated in the host of CroV, Cafeteria roenbergensis, thus protecting C. roenbergensis by reduction of CroV multiplication...
April 28, 2018: Virus Research
Mui-Choo Jong, Jian-Qiang Su, Joshua T Bunce, Colin R Harwood, Jason R Snape, Yong-Guan Zhu, David W Graham
Inadequate sanitation can lead to the spread of infectious diseases and antimicrobial resistance (AMR) via contaminated water. Unfortunately, wastewater treatment is not universal in many developing and emerging countries, especially in rural and peri-urban locations that are remote from central sewers. As such, small-scale, more sustainable treatment options are needed, such as aerobic-Denitrifying Downflow Hanging Sponge (DDHS) bioreactors. In this study, DDHS reactors were assessed for such applications, and achieved over 79% and 84% removal of Chemical Oxygen Demand and Ammonium, respectively, and up to 71% removal of Total Nitrogen (TN) from domestic wastes...
April 13, 2018: Science of the Total Environment
Stefan Spring, Boyke Bunk, Cathrin Spröer, Manfred Rohde, Hans-Peter Klenk
Anaerobic strains affiliated with a novel order-level lineage of the Phycisphaerae class were retrieved from the suboxic zone of a hypersaline cyanobacterial mat and anoxic sediments of solar salterns. Genome sequences of five isolates were obtained and compared with metagenome-assembled genomes representing related uncultured bacteria from various anoxic aquatic environments. Gene content surveys suggest a strictly fermentative saccharolytic metabolism for members of this lineage, which could be confirmed by the phenotypic characterization of isolates...
April 26, 2018: Environmental Microbiology
Paul A Rowley, Kurt Patterson, Suzanne B Sandmeyer, Sara L Sawyer
Yeasts serve as hosts to several types of genetic parasites. Few studies have addressed the evolutionary trajectory of yeast genes that control the stable co-existence of these parasites with their host cell. In Saccharomyces yeasts, the retrovirus-like Ty retrotransposons must access the nucleus. We show that several genes encoding components of the yeast nuclear pore complex have experienced natural selection for substitutions that change the encoded protein sequence. By replacing these S. cerevisiae genes with orthologs from other Saccharomyces species, we discovered that natural sequence changes have affected the mobility of Ty retrotransposons...
April 2018: PLoS Genetics
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