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https://www.readbyqxmd.com/read/28546829/vinasse-fertirrigation-alters-soil-resistome-dynamics-an-analysis-based-on-metagenomic-profiles
#1
Lucas P P Braga, Rafael F Alves, Marina T F Dellias, Acacio A Navarrete, Thiago O Basso, Siu M Tsai
Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management to fertilization for plant biomass production, and it is known as fertirrigation. Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. The metagenomes were annotated using the ResFam database...
2017: BioData Mining
https://www.readbyqxmd.com/read/28521338/klebsiella-pneumoniae-a-major-worldwide-source-and-shuttle-for-antibiotic-resistance
#2
Shiri Navon-Venezia, Kira Kondratyeva, Alessandra Carattoli
Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen affecting humans and a major source for hospital infections associated with high morbidity and mortality due to limited treatment options. We summarize the wide resistome of this pathogen, which encompasses plentiful chromosomal and plasmid-encoded antibiotic resistance genes (ARGs). Under antibiotic selective pressure, K. pneumoniae continuously accumulates ARGs, by de novo mutations, and via acquisition of plasmids and transferable genetic elements, leading to extremely drug resistant (XDR) strains harboring a 'super resistome'...
May 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28520993/effects-of-short-and-long-course-antibiotics-on-the-lower-intestinal-microbiome-as-they-relate-to-traveller-s-diarrhea
#3
Lawrence Clifford McDonald
BACKGROUND: Antibiotics have profound and lasting effects on the lower intestinal (gut) microbiome that can both promote resistance and increase susceptibility to colonization and infection; knowledge of these changes is important to the prevention and treatment of traveler's diarrhea. METHODS: Recent data from epidemiologic and modern metagenomics studies were reviewed in regard to how such findings could inform the prevention and treatment of traveler's diarrhea...
April 1, 2017: Journal of Travel Medicine
https://www.readbyqxmd.com/read/28515215/an-outbreak-of-ndm-1-producing-klebsiella-pneumoniae-in-a-dutch-hospital-with-interspecies-transfer-of-the-resistance-plasmid-and-unexpected-occurrence-in-unrelated-healthcare-centers
#4
Thijs Bosch, Suzanne P M Lutgens, Mirjam H A Hermans, Peter C Wever, Peter M Schneeberger, Nicole H M Renders, Alexander C A P Leenders, Jan A J W Kluytmans, Annelot Schoffelen, Daan Notermans, Sandra Witteveen, Erik Bathoorn, Leo M Schouls
Introduction. In the Netherlands, the number of cases with New Delhi metallo-beta-lactamase (NDM)-positive Enterobacteriaceae is low. Here, we report an outbreak of NDM-1 producing Klebsiella pneumoniae in a Dutch hospital with interspecies transfer of the resistance plasmid and unexpected occurrence in other unrelated healthcare centers (HCCs).Methods. Next-generation sequencing was performed on 250 carbapenemase-producing Enterobacteriaceae isolates including 42 NDM-positive isolates obtained from 29 persons at the outbreak site...
May 17, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28504647/identification-of-a-nucleoside-analog-active-against-adenosine-kinase-expressing-plasma-cell-malignancies
#5
Utthara Nayar, Jouliana Sadek, Jonathan Reichel, Denise Hernandez-Hopkins, Gunkut Akar, Peter J Barelli, Michelle A Sahai, Hufeng Zhou, Jennifer Totonchy, David Jayabalan, Ruben Niesvizky, Ilaria Guasparri, Duane Hassane, Yifang Liu, Shizuko Sei, Robert H Shoemaker, J David Warren, Olivier Elemento, Kenneth M Kaye, Ethel Cesarman
Primary effusion lymphoma (PEL) is a largely incurable malignancy of B cell origin with plasmacytic differentiation. Here, we report the identification of a highly effective inhibitor of PEL. This compound, 6-ethylthioinosine (6-ETI), is a nucleoside analog with toxicity to PEL in vitro and in vivo, but not to other lymphoma cell lines tested. We developed and performed resistome analysis, an unbiased approach based on RNA sequencing of resistant subclones, to discover the molecular mechanisms of sensitivity...
May 15, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28500429/the-antibiotic-resistome-gene-flow-in-environments-animals-and-human-beings
#6
REVIEW
Yongfei Hu, George F Gao, Baoli Zhu
The antibiotic resistance is natural in bacteria and predates the human use of antibiotics. Numerous antibiotic resistance genes (ARGs) have been discovered to confer resistance to a wide range of antibiotics. The ARGs in natural environments are highly integrated and tightly regulated in specific bacterial metabolic networks. However, the antibiotic selection pressure conferred by the use of antibiotics in both human medicine and agriculture practice leads to a significant increase of antibiotic resistance and a steady accumulation of ARGs in bacteria...
May 13, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/28461314/ndm-5-and-oxa-181-beta-lactamases-a-significant-threat-continues-to-spread-in-the-americas
#7
Laura J Rojas, Andrea M Hujer, Susan D Rudin, Meredith S Wright, T Nicholas Domitrovic, Steven H Marshall, Kristine M Hujer, Sandra S Richter, Eric Cober, Federico Perez, Mark D Adams, David van Duin, Robert A Bonomo
Among Gram-negative bacteria, carbapenem resistant (CR) infections pose a serious and life threatening challenge. Here, the CRACKLE network reports a sentinel detection and characterization of a CR Klebsiella pneumoniae ST147 isolate harboring blaNDM-5 and blaOXA-181, from a young man who underwent abdominal surgery in India. blaNDM-5 was located on an IncFII plasmid of ≈ 90Kb, while blaOXA-181 was chromosomally encoded. Resistome and genome analysis demonstrated multiple copies of the transposable element IS26 and a "hotspot region" in the IncFII plasmid...
May 1, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28453251/influence-of-manure-application-on-the-environmental-resistome-under-finnish-agricultural-practice-with-restricted-antibiotic-use
#8
Johanna Muurinen, Robert Stedtfeld, Antti Karkman, Katariina Pärnänen, James Tiedje, Marko Virta
The co-occurrence of antibiotic-resistance genes (ARGs) and mobile genetic elements (MGEs) in farm environments can potentially foster the development of antibiotic-resistant pathogens. We studied the resistome of Finnish dairy and swine farms where use of antibiotics is limited to treating bacterial infections and manure is only applied from April to September. The resistome of manure, soil, and tile drainage water from the ditch was investigated from the beginning of the growing season until forage harvest...
May 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28450856/toward-a-metagenomic-understanding-on-the-bacterial-composition-and-resistome-in-hong-kong-banknotes
#9
Yoshitaro Heshiki, Thrimendra Dissanayake, Tingting Zheng, Kang Kang, Ni Yueqiong, Zeling Xu, Chinmoy Sarkar, Patrick C Y Woo, Billy K C Chow, David Baker, Aixin Yan, Christopher J Webster, Gianni Panagiotou, Jun Li
Currency is possibly one of the main media transmitting pathogens and drug resistance due to its wide circulation in daily life. In this study, we made a comprehensive characterization of the bacterial community present on banknotes collected from different geographical regions of Hong Kong (HK) by performing in vitro characterization of the bacterial presence and resistome profile, as well as metagenomic analysis including microbial diversity, the prevalence of potential pathogens, the dissemination potential of antibiotic-resistance genes (ARGs), among others...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28450142/pan-genome-analysis-of-clostridium-botulinum-reveals-unique-targets-for-drug-development
#10
Tulika Bhardwaj, Pallavi Somvanshi
Clostridium botulinum, a formidable pathogen is responsible for the emerging cause of food poisoning cases on the global canvas. The endemicity of bacterium Clostridium botulinum is reflected by the sudden hospital outbreaks and increased resistance towards multiple drugs. Therefore, a combined approach of in-silico comparative genomic analysis with statistical analysis was applied to overcome the limitation of bench-top technologies. Owing to the paucity of genomic data available by the advent of third generation sequencing technologies, several 'omics' technologies were applied to understand the underlying evolutionary pattern and lifestyle of the bacterial pathogen using phylogenomics...
April 24, 2017: Gene
https://www.readbyqxmd.com/read/28448616/abundance-profiling-of-specific-gene-groups-using-precomputed-gut-metagenomes-yields-novel-biological-hypotheses
#11
Konstantin Yarygin, Alexander Tyakht, Andrey Larin, Elena Kostryukova, Sergei Kolchenko, Vilgelm Bitner, Dmitry Alexeev
The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions...
2017: PloS One
https://www.readbyqxmd.com/read/28395597/genome-sequencing-and-comparative-analysis-of-an-ndm-1-producing-klebsiella-pneumoniae-st15-isolated-from-a-refugee-patient
#12
Tamara Salloum, Harout Arabaghian, Sahar Alousi, Edmond Abboud, Sima Tokajian
The escalating problem of antibiotic resistance, specifically cabarpenemase and extended-spectrum β-lacatamase (ESBL) producing K. pneumoniae strains, is directly correlated with increased patient morbidity and mortality and prolonged hospitalization and costs. In this study, a comprehensive genomic analysis encompassing the resistomics, virulence repertoire and mobile genetic elements of an NDM-1 positive ESBL-producing K. pneumoniae EA-MEH ST15 isolated from a urine sample collected from a Syrian refugee was conducted...
April 11, 2017: Pathogens and Global Health
https://www.readbyqxmd.com/read/28392565/next-generation-approaches-to-understand-and-combat-the-antibiotic-resistome
#13
REVIEW
Terence S Crofts, Andrew J Gasparrini, Gautam Dantas
Antibiotic resistance is a natural feature of diverse microbial ecosystems. Although recent studies of the antibiotic resistome have highlighted barriers to the horizontal transfer of antibiotic resistance genes between habitats, the rapid global spread of genes that confer resistance to carbapenem, colistin and quinolone antibiotics illustrates the dire clinical and societal consequences of such events. Over time, the study of antibiotic resistance has grown from focusing on single pathogenic organisms in axenic culture to studying antibiotic resistance in pathogenic, commensal and environmental bacteria at the level of microbial communities...
April 10, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28389536/whole-genome-sequencing-of-drug-resistant-salmonella-enterica-isolated-from-dairy-cattle-and-humans-in-new-york-and-washington-states-reveals-source-and-geographic-associations
#14
Laura M Carroll, Martin Wiedmann, Henk den Bakker, Julie Siler, Steven Warchocki, David Kent, Svetlana Lyalina, Margaret Davis, William Sischo, Thomas Besser, Lorin D Warnick, Richard V Pereira
Multidrug-resistant (MDR) Salmonella enterica can be spread from cattle to humans through direct contact with animals shedding Salmonella, as well as through the food chain, making MDR Salmonella a serious threat to human health. The objective of this study was to use whole-genome sequencing to compare antimicrobial-resistant (AMR) S. Typhimurium, Newport, and Dublin isolated from dairy cattle and humans in Washington state and New York state at a genotypic and phenotypic level. A total of 90 isolates were selected for the study (37 Typhimurium, 32 Newport, 21 Dublin)...
April 7, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28383665/a-pan-genomic-approach-to-understand-the-basis-of-host-adaptation-in-achromobacter
#15
J Jeukens, L Freschi, A T Vincent, J G Emond-Rheault, I Kukavica-Ibrulj, S J Charette, R C Levesque
Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis (CF) lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the CF lung, not to mention other host environments...
April 5, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28334267/resistomap-online-visualization-of-human-gut-microbiota-antibiotic-resistome
#16
Konstantin S Yarygin, Boris A Kovarsky, Tatyana S Bibikova, Damir S Melnikov, Alexander V Tyakht, Dmitry G Alexeev
Summary: We created ResistoMap - a Web-based interactive visualization of the presence of genetic determinants conferring resistance to antibiotics, biocides and heavy metals in human gut microbiota. ResistoMap displays the data on more than 1500 published gut metagenomes of world populations including both healthy subjects and patients. Multiparameter display filters allow visual assessment of the associations between the meta-data and proportions of resistome. The geographic map navigation layer allows to state hypotheses regarding the global trends of antibiotic resistance and correlate the gut resistome variations with the national clinical guidelines on antibiotics application...
March 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28294141/gear-a-database-of-genomic-elements-associated-with-drug-resistance
#17
Yin-Ying Wang, Wei-Hua Chen, Pei-Pei Xiao, Wen-Bin Xie, Qibin Luo, Peer Bork, Xing-Ming Zhao
Drug resistance is becoming a serious problem that leads to the failure of standard treatments, which is generally developed because of genetic mutations of certain molecules. Here, we present GEAR (A database of Genomic Elements Associated with drug Resistance) that aims to provide comprehensive information about genomic elements (including genes, single-nucleotide polymorphisms and microRNAs) that are responsible for drug resistance. Right now, GEAR contains 1631 associations between 201 human drugs and 758 genes, 106 associations between 29 human drugs and 66 miRNAs, and 44 associations between 17 human drugs and 22 SNPs...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198411/the-secondary-resistome-of-multidrug-resistant-klebsiella-pneumoniae
#18
Bimal Jana, Amy K Cain, William T Doerrler, Christine J Boinett, Maria C Fookes, Julian Parkhill, Luca Guardabassi
Klebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258)...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198087/meta-analysis-of-the-human-gut-microbiome-from-urbanized-and-pre-agricultural-populations
#19
REVIEW
Leonardo Mancabelli, Christian Milani, Gabriele Andrea Lugli, Francesca Turroni, Chiara Ferrario, Douwe van Sinderen, Marco Ventura
Metagenomic studies of the human gut microbiome have only recently begun to explore the differences in taxonomic composition between subjects from diverse geographical origins. Here, we compared taxonomy, resistome and functional metabolic properties of publicly available shotgun datasets of human fecal samples collected from different geographical regions (Europe, North America, Asia and Oceania). Such datasets encompassed gut microbiota information corresponding to 13 developed/industrialized societies, as well as two traditional hunter-gatherer, pre-agricultural communities (Tanzanian and Peruvian individuals)...
February 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28165472/comprehensive-resistome-analysis-reveals-the-prevalence-of-ndm-and-mcr-1-in-chinese-poultry-production
#20
Yang Wang, Rongmin Zhang, Jiyun Li, Zuowei Wu, Wenjuan Yin, Stefan Schwarz, Jonathan M Tyrrell, Yongjun Zheng, Shaolin Wang, Zhangqi Shen, Zhihai Liu, Jianye Liu, Lei Lei, Mei Li, Qidi Zhang, Congming Wu, Qijing Zhang, Yongning Wu, Timothy R Walsh, Jianzhong Shen
By 2030, the global population will be 8.5 billion, placing pressure on international poultry production, of which China is a key producer(1). From April 2017, China will implement the withdrawal of colistin as a growth promoter, removing over 8,000 tonnes per year from the Chinese farming sector(2). To understand the impact of banning colistin and the epidemiology of multi-drug-resistant (MDR) Escherichia coli (using blaNDM and mcr-1 as marker genes), we sampled poultry, dogs, sewage, wild birds and flies...
February 6, 2017: Nature Microbiology
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