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https://www.readbyqxmd.com/read/29127051/genomic-analysis-of-in-vivo-acquired-resistance-to-colistin-and-rifampin-in-acinetobacter-baumannii
#1
Nadia Jaidane, Thierry Naas, Wejdene Mansour, Bechir Ben Radhia, Sofiene Jerbi, Noureddine Boujaafar, Olfa Bouallegue, Rémy A Bonnin
Acinetobacter baumannii is an opportunistic pathogen in health-care facilities responsible for nosocomial infections mostly in immune-compromised patients. Colistin resistance is increasingly reported worldwide in that species. We describe here in vivo selection of colistin and rifampin resistance in a carbapenem-resistant A. baumannii (Ab). Antimicrobial susceptibility testing, plasmid analysis, and Whole Genome Sequencing (WGS) were performed to fully characterize the resistome of AbS1 and AbS2 clinical isolates...
November 7, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29123512/alternative-growth-promoters-modulate-broiler-gut-microbiome-and-enhance-body-weight-gain
#2
Serajus Salaheen, Seon-Woo Kim, Bradd J Haley, Jo Ann S Van Kessel, Debabrata Biswas
Antibiotic growth promoters (AGPs) are frequently used to enhance weight-gain in poultry production. However, there has been increasing concern over the impact of AGP on the emergence of antibiotic resistance in zoonotic bacterial pathogens in the microbial community of the poultry gut. In this study, we adopted mass-spectrophotometric, phylogenetic, and shotgun-metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry (Vaccinium corymbosum) and blackberry (Rubus fruticosus) pomaces as AGP alternatives in broilers...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29112136/gut-microbiome-and-putative-resistome-of-inca-and-italian-nobility-mummies
#3
Tasha M Santiago-Rodriguez, Gino Fornaciari, Stefania Luciani, Gary A Toranzos, Isolina Marota, Valentina Giuffra, Raul J Cano
Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA) gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes...
November 7, 2017: Genes
https://www.readbyqxmd.com/read/29111480/draft-genome-sequences-of-two-fluoroquinolone-resistant-ctx-m-15-producing-escherichia-coli-st90-st23-complex-isolated-from-a-calf-and-a-dairy-cow-in-south-america
#4
Luciana Sartori, Miriam R Fernandes, Susan Ienne, Tiago A de Souza, Lilian Gregory, Louise Cerdeira, Nilton Lincopan
OBJECTIVES: Farm animals have been recognised as important carriers and reservoirs of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. The aim of this study was to report the draft genome sequences of two multidrug-resistant (MDR) CTX-M-15-producing E. coli strains (47VL and 13B) isolated from different bovine hosts (a calf and a dairy cow), housed separately in a commercial dairy farm in Brazil. METHODS: Total genomic DNA of the E. coli isolates was sequenced using an Illumina MiSeq paired-end 300-bp sequencing platform...
October 31, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29091848/fate-of-antibiotic-resistance-genes-and-metal-resistance-genes-during-thermophilic-aerobic-digestion-of-sewage-sludge
#5
Hyun Min Jang, Jangwoo Lee, Young Beom Kim, Jong Hun Jeon, Jingyeong Shin, Mee-Rye Park, Young Mo Kim
This study examines the fate of twenty-three representative antibiotic resistance genes (ARGs) encoding tetracyclines, sulfonamides, quinolones, β-lactam antibiotics, macrolides, florfenicol and multidrug resistance during thermophilic aerobic digestion (TAD) of sewage sludge. The bacterial community, class 1 integrons (intI1) and four metal resistance genes (MRGs) were also quantified to determine the key drivers of changes in ARGs during TAD. At the end of digestion, significant decreases in the quantities of ARGs, MRGs and intI1 as well as 16S rRNA genes were observed...
October 20, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29068237/insights-into-the-evolution-of-the-mutational-resistome-of-pseudomonas-aeruginosa-in-cystic-fibrosis
#6
Carla López-Causapé, Antonio Oliver
No abstract text is available yet for this article.
October 25, 2017: Future Microbiology
https://www.readbyqxmd.com/read/29066550/comparative-genomic-analysis-of-globally-dominant-st131-clone-with-other-epidemiologically-successful-extraintestinal-pathogenic-escherichia-coli-expec-lineages
#7
Sabiha Shaik, Amit Ranjan, Sumeet K Tiwari, Arif Hussain, Nishant Nandanwar, Narender Kumar, Savita Jadhav, Torsten Semmler, Ramani Baddam, Mohammed Aminul Islam, Munirul Alam, Lothar H Wieler, Haruo Watanabe, Niyaz Ahmed
Escherichia coli sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E...
October 24, 2017: MBio
https://www.readbyqxmd.com/read/29063140/biocide-selective-tolc-independent-efflux-pumps-in-enterobacteriaceae
#8
Carmine J Slipski, George G Zhanel, Denice C Bay
Bacterial resistance to biocides used as antiseptics, dyes, and disinfectants is a growing concern in food preparation, agricultural, consumer manufacturing, and health care industries, particularly among Gram-negative Enterobacteriaceae, some of the most common community and healthcare-acquired bacterial pathogens. Biocide resistance is frequently associated with antimicrobial cross-resistance leading to reduced activity and efficacy of both antimicrobials and antiseptics. Multidrug resistant efflux pumps represent an important biocide resistance mechanism in Enterobacteriaceae...
October 23, 2017: Journal of Membrane Biology
https://www.readbyqxmd.com/read/29054657/feed-additives-shift-gut-microbiota-and-enrich-antibiotic-resistance-in-swine-gut
#9
Yi Zhao, Jian-Qiang Su, Xin-Li An, Fu-Yi Huang, Christopher Rensing, Kristian Koefoed Brandt, Yong-Guan Zhu
Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Antibiotics and metals are widely used as feed additives and could consequently affect ARGs in swine gut. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) based ARG chip and next-generation 16S rRNA gene amplicon sequencing data were analyzed using multiple statistical approaches to profile the antibiotic resistome and investigate its linkages to antibiotics and metals used as feed additives and to the microbial community composition in freshly collected swine manure samples from three large-scale Chinese pig farms...
October 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29041965/enrichment-allows-identification-of-diverse-rare-elements-in-metagenomic-resistome-virulome-sequencing
#10
Noelle R Noyes, Maggie E Weinroth, Jennifer K Parker, Chris J Dean, Steven M Lakin, Robert A Raymond, Pablo Rovira, Enrique Doster, Zaid Abdo, Jennifer N Martin, Kenneth L Jones, Jaime Ruiz, Christina A Boucher, Keith E Belk, Paul S Morley
BACKGROUND: Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements...
October 17, 2017: Microbiome
https://www.readbyqxmd.com/read/29038283/ctx-m-15-producing-shewanella-sp-clinical-isolate-expressing-oxa-535-a-chromosome-encoded-oxa-48-variant-putative-progenitor-of-the-plasmid-encoded-oxa-436
#11
Agnès B Jousset, Laura Dabos, Rémy A Bonnin, Delphine Girlich, Anaïs Potron, Nicolas Cabanel, Laurent Dortet, Philippe Glaser, Thierry Naas
Shewanella spp. constitute a reservoir of antibiotic resistance determinants. In a bile sample, we have identified three Extended Spectrum β-lactamase (ESBL)-producing bacteria (Escherichia coli, Klebsiella pneumoniae and Shewanella sp. JAB-1) isolated from a child suffering from cholangitis. Our objectives were to characterize the genome and the resistome of the first ESBL-producing isolate of the genus Shewanella and determine whether plasmidic exchange occurred between the three-bacterial species. Bacterial isolates were characterized using MALDI-TOF, standard biochemical tools and antimicrobial susceptibility testing...
October 16, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29033338/antibiotic-resistance-genes-in-waste-water
#12
REVIEW
Antti Karkman, Thi Thuy Do, Fiona Walsh, Marko P J Virta
Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of antibiotic resistance. They have also been proposed to be hotspots for horizontal gene transfer, enabling the spread of antibiotic resistance genes between different bacterial species. Waste water contains antibiotics, disinfectants, and metals which can form a selection pressure for antibiotic resistance, even in low concentrations. Our knowledge of antibiotic resistance in waste water has increased tremendously in the past few years with advances in the molecular methods available...
October 12, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/29028006/polymorphism-of-antibiotic-inactivating-enzyme-driven-by-ecology-expands-the-environmental-resistome
#13
Dae-Wi Kim, Cung Nawl Thawng, Jung-Hye Choi, Kihyun Lee, Chang-Jun Cha
The environmental resistome has been recognized as the origin and reservoir of antibiotic resistance genes and considered to be dynamic and ever expanding. In this study, a targeted gene sequencing approach revealed that the polymorphic diversity of the aminoglycoside-inactivating enzyme AAC(6')-Ib was ecological niche-specific. AAC(6')-Ib-cr, previously known as a clinical variant, was prevalent in various soils and the intestines of chickens and humans, suggesting that this variant might not have arisen from adaptive mutations in the clinic but instead originated from the environment...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29017452/whole-genome-sequencing-for-the-molecular-characterization-of-carbapenem-resistant-klebsiella-pneumoniae-strains-isolated-at-the-italian-asst-fatebenefratelli-sacco-hospital-2012-2014
#14
Sara Giordana Rimoldi, Bernardina Gentile, Cristina Pagani, Annamaria Di Gregorio, Anna Anselmo, Anna Maria Palozzi, Antonella Fortunato, Valentina Pittiglio, Anna Lisa Ridolfo, Maria Rita Gismondo, Giuliano Rizzardini, Florigio Lista
BACKGROUND: The emergence of carbapenem-resistant Klebsiella pneumoniae strains is threatening antimicrobial treatment. METHODS: Sixty-eight carbapenemase-producing K. pneumoniae strains isolated at Luigi Sacco University Hospital-ASST Fatebenefratelli Sacco (Milan, Italy) between 2012 and 2014 were characterised microbiologically and molecularly. They were tested for drug susceptibility and carbapenemase phenotypes, investigated by means of repetitive extra-genic palindromic polymerase chain reaction (REP-PCR), and fully sequenced by means of next-generation sequencing for the in silico analysis of multi-locus sequence typing (MLST), their resistome, virulome and plasmid content, and their core single nucleotide polymorphism (SNP) genotypes...
October 10, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29017328/the-tolerome-a-database-of-transcriptome-level-contributions-to-diverse-escherichia-coli-resistance-and-tolerance-phenotypes
#15
Keesha E Erickson, James D Winkler, Danh Nyugen, Ryan T Gill, Anushree Chatterjee
Tolerance and resistance are complex biological phenotypes that are desirable bioengineering goals for those seeking to design industrial strains or prevent the spread of antibiotic resistance. Over decades of research, a wealth of information has been generated to attempt to decode a molecular basis for tolerance, but to fully achieve the goal of engineering tolerance, researchers must be able to easily learn from a variety of data sources. To this end, we here describe a resource designed to enable scrutiny of diverse tolerance phenotypes...
October 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28988290/early-microbiota-antibiotics-and-health
#16
REVIEW
Alicja M Nogacka, Nuria Salazar, Silvia Arboleya, Marta Suárez, Nuria Fernández, Gonzalo Solís, Clara G de Los Reyes-Gavilán, Miguel Gueimonde
The colonization of the neonatal digestive tract provides a microbial stimulus required for an adequate maturation towards the physiological homeostasis of the host. This colonization, which is affected by several factors, begins with facultative anaerobes and continues with anaerobic genera. Accumulating evidence underlines the key role of the early neonatal period for this microbiota-induced maturation, being a key determinant factor for later health. Therefore, understanding the factors that determine the establishment of the microbiota in the infant is of critical importance...
October 7, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28964602/temporal-succession-of-soil-antibiotic-resistance-genes-following-application-of-swine-cattle-and-poultry-manures-spiked-with-or-without-antibiotics
#17
Yu-Jing Zhang, Hang-Wei Hu, Min Gou, Jun-Tao Wang, Deli Chen, Ji-Zheng He
Land application of animal manure is a common agricultural practice potentially leading to dispersal and propagation of antibiotic resistance genes (ARGs) in environmental settings. However, the fate of resistome in agro-ecosystems over time following application of different manure sources has never been compared systematically. Here, soil microcosm incubation was conducted to compare effects of poultry, cattle and swine manures spiked with or without the antibiotic tylosin on the temporal changes of soil ARGs...
December 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28947833/metagenomic-characterization-of-the-effect-of-feed-additives-on-the-gut-microbiome-and-antibiotic-resistome-of-feedlot-cattle
#18
Milton Thomas, Megan Webb, Sudeep Ghimire, Amanda Blair, Kenneth Olson, Gavin John Fenske, Alex Thomas Fonder, Jane Christopher-Hennings, Derek Brake, Joy Scaria
In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals...
September 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#19
J Jeukens, I Kukavica-Ibrulj, J G Emond-Rheault, L Freschi, R C Levesque
Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28898936/aerobic-composting-reduces-antibiotic-resistance-genes-in-cattle-manure-and-the-resistome-dissemination-in-agricultural-soils
#20
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...
January 15, 2018: Science of the Total Environment
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