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https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#1
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
#2
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
https://www.readbyqxmd.com/read/28898777/different-impacts-of-manure-and-chemical-fertilizers-on-bacterial-community-structure-and-antibiotic-resistance-genes-in-arable-soils
#3
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
https://www.readbyqxmd.com/read/28874376/genomics-and-susceptibility-profiles-of-extensively-drug-resistant-xdr-pseudomonas-aeruginosa-from-spain
#4
Ester Del Barrio-Tofiño, Carla López-Causapé, Gabriel Cabot, Alba Rivera, Natividad Benito, Concepción Segura, María Milagro Montero, Luisa Sorlí, Fe Tubau, Silvia Gómez-Zorrilla, Nuria Tormo, Raquel Durá-Navarro, Esther Viedma, Elena Resino-Foz, Marta Fernández-Martínez, Claudia González-Rico, Izaskun Alejo-Cancho, Jose Antonio Martínez, Cristina Labayru-Echverria, Carlos Dueñas, Ignacio Ayestarán, Laura Zamorano, Luis Martinez-Martinez, Juan Pablo Horcajada, Antonio Oliver
This study assessed the molecular epidemiology, resistance mechanisms and susceptibility profiles of a collection of 150 XDR P. aeruginosa clinical isolates obtained from a 2015 Spanish multicenter study, with a particular focus on resistome analysis in relation to ceftolozane/tazobactam susceptibility. Broth microdilution MICs revealed that nearly all (>95%) of the isolates were nonsusceptible to piperacillin/tazobactam, ceftazidime, cefepime, aztreonam, imipenem, meropenem and ciprofloxacin. Most of them were also resistant to tobramycin (77%), whereas nonsusceptibility rates were lower for ceftolozane/tazobactam (31%), amikacin (7%) and colistin (2%)...
September 5, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28859442/emerging-multidrug-resistance-in-community-associated-staphylococcus-aureus-involved-in-skin-and-soft-tissue-infections-and-nasal-colonization
#5
Grace C Lee, Steven D Dallas, Yufeng Wang, Randall J Olsen, Kenneth A Lawson, James Wilson, Christopher R Frei
Background: Staphylococcus aureus is a major pathogen causing significant morbidity and mortality worldwide. The emergence of MDR S. aureus strains in the community setting has major implications in disease management. However, data regarding the occurrence and patterns of MDR community-associated S. aureus sub-clones is limited. Objectives: To use whole-genome sequences to describe the diversity and distribution of resistance mechanisms among community-associated S...
September 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28853291/fishmeal-application-induces-antibiotic-resistance-gene-propagation-in-mariculture-sediment
#6
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
https://www.readbyqxmd.com/read/28846900/antibiotic-resistome-promotion-in-drinking-water-during-biological-activated-carbon-treatment-is-it-influenced-by-quorum-sensing
#7
Ji Zheng, Tao Chen, Hong Chen
The contamination of antibiotic resistance genes (ARGs) in drinking water may pose a direct threat to human health. This study applied high-throughput qPCR and sequencing to investigate the dynamics of ARGs and bacterial communities during the advanced treatment of drinking water using biological activated carbon. The promotion of ARGs was observed, and the normalized copy number of ARGs increased significantly after BAC treatment, raising the number of detected ARGs from 84 to 159. Twenty-nine ARGs were identified as biofilm-influencing sources in the BAC, and they persisted after chlorination...
August 24, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28834351/preliminary-insights-into-the-occurrence-of-similar-clones-of-extended-spectrum-beta-lactamase-producing-bacteria-in-humans-animals-and-the-environment-in-tanzania-a-systematic-review-and-meta-analysis-between-2005-and-2016
#8
REVIEW
J Seni, N Moremi, M Matee, F van der Meer, R DeVinney, S E Mshana, J D D Pitout
The emergence and spread of extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-PE) are complex and of the public health concern across the globe. This review aimed at assessing the ESBL-PE clones circulating in humans, animals and the environment to provide evidence-based insights for combating ESBL-PE using One Health approach. Systematic search from Medline/PubMed, Google Scholar and African Journals Online was carried out and retrieved nine eligible articles (of 131) based on phenotypic and genotypic detection of ESBL-PE between 2005 and 2016 in Tanzania...
August 22, 2017: Zoonoses and Public Health
https://www.readbyqxmd.com/read/28827656/characterization-of-a-novel-class-a-carbapenemase-pad-1-from-paramesorhizobium-desertii-a-3-e-t-a-strain-highly-resistant-to-%C3%AE-lactam-antibiotics
#9
Ruichen Lv, Jingyu Guo, YanFeng Yan, Rong Chen, Lisheng Xiao, Min Wang, Nan Fang, Chengxiang Fang, Yujun Cui, Ruifu Yang, Yajun Song
Although clinical antibiotic-resistant bacteria have attracted tremendous attention in the microbiology community, the resistant bacteria that persist in natural environments have been overlooked for a longtime. We previously proposed a new species Paramesorhizobium desertii, isolated from the soil of the Taklimakan Desert in China that is highly resistant to most β-lactam antibiotics. To identify potential β-lactamase(s) in this bacteria, we first confirmed the carbapenemase activity in the freeze-thawed supernatant of a P...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#10
Cheng Wang, Da Dong, P J Strong, Weijing Zhu, Zhuang Ma, Yong Qin, Weixiang Wu
BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28811343/comparative-genomics-of-escherichia-coli-isolated-from-skin-and-soft-tissue-and-other-extraintestinal-infections
#11
Amit Ranjan, Sabiha Shaik, Nishant Nandanwar, Arif Hussain, Sumeet K Tiwari, Torsten Semmler, Savita Jadhav, Lothar H Wieler, Munirul Alam, Rita R Colwell, Niyaz Ahmed
Escherichia coli, an intestinal Gram-negative bacterium, has been shown to be associated with a variety of diseases in addition to intestinal infections, such as urinary tract infections (UTIs), meningitis in neonates, septicemia, skin and soft tissue infections (SSTIs), and colisepticemia. Thus, for nonintestinal infections, it is categorized as extraintestinal pathogenic E. coli (ExPEC). It is also an opportunistic pathogen, causing cross infections, notably as an agent of zoonotic diseases. However, comparative genomic data providing functional and genetic coordinates for ExPEC strains associated with these different types of infections have not proven conclusive...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28803549/comparative-gut-microbiota-and-resistome-profiling-of-intensive-care-patients-receiving-selective-digestive-tract-decontamination-and-healthy-subjects
#12
Elena Buelow, Teresita D J Bello González, Susana Fuentes, Wouter A A de Steenhuijsen Piters, Leo Lahti, Jumamurat R Bayjanov, Eline A M Majoor, Johanna C Braat, Maaike S M van Mourik, Evelien A N Oostdijk, Rob J L Willems, Marc J M Bonten, Mark W J van Passel, Hauke Smidt, Willem van Schaik
BACKGROUND: The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed "selective decontamination of the digestive tract" (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown...
August 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28792642/wastewater-pollution-differently-affects-the-antibiotic-resistance-gene-pool-and-biofilm-bacterial-communities-across-streambed-compartments
#13
Jèssica Subirats, Xavier Triadó-Margarit, Ladislav Mandaric, Vicenç Acuña, José Luis Balcázar, Sergi Sabater, Carles M Borrego
Wastewater discharges introduce antibiotic residues and antibiotic-resistant bacteria (ARB) into surface waters. Both inputs directly affect the streambed resistome, either by exerting a selective pressure that favor the proliferation of resistant phenotypes or by enriching the resident communities with wastewater-associated ARB. Here, we investigated the impact of raw and treated urban wastewater discharges on epilithic (growing on rocks) and epipsammic (growing on sandy substrata) streambed biofilms. The effects were assessed by comparing control and impact sites i) on the composition of bacterial communities; ii) on the abundance of twelve antibiotic resistance genes (ARGs) encoding resistance to β-lactams, fluoroquinolones, sulfonamides, tetracyclines, macrolides and vancomycin, as well as the class 1 integron-integrase gene (intI1); and iii) on the occurrence of wastewater-associated bacteria, including putative pathogens, and their potential linkage to target ARGs...
August 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28780361/untreated-urban-waste-contaminates-indian-river-sediments-with-resistance-genes-to-last-resort-antibiotics
#14
Nachiket P Marathe, Chandan Pal, Swapnil S Gaikwad, Viktor Jonsson, Erik Kristiansson, D G Joakim Larsson
Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-resistant bacteria. In many low and middle income countries, however, large proportions of sewage are still released untreated into receiving water bodies. In-depth knowledge of how such discharges of untreated urban waste influences the environmental resistome is largely lacking. Here, we highlight the impact of uncontrolled discharge of partially treated and/or untreated wastewater on the structure of bacterial communities and resistome of sediments collected from Mutha river flowing through Pune city in India...
July 25, 2017: Water Research
https://www.readbyqxmd.com/read/28763642/fate-of-antibiotic-resistance-genes-and-their-associations-with-bacterial-community-in-livestock-breeding-wastewater-and-its-receiving-river-water
#15
Shuyu Jia, Xu-Xiang Zhang, Yu Miao, Yanting Zhao, Lin Ye, Bing Li, Tong Zhang
Large amounts of antibiotics are currently used in livestock breeding, which is the main driving factor contributing to the occurrence, spread and proliferation of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment. In this study, high-throughput sequencing based metagenomic approaches were employed to characterize the tempo-spacial changes of antibiotic resistome, bacterial community and their correlations in pig farming wastewater and its receiving river. A total of 194 ARG subtypes within 14 ARG types were detectable in all the samples, and their total relative abundance increased in the river water after receiving wastewater discharge, while decreased in the downstream river water...
July 24, 2017: Water Research
https://www.readbyqxmd.com/read/28749938/the-mecillinam-resistome-reveals-a-role-for-peptidoglycan-endopeptidases-in-stimulating-cell-wall-synthesis-in-escherichia-coli
#16
Ghee Chuan Lai, Hongbaek Cho, Thomas G Bernhardt
Bacterial cells are typically surrounded by an net-like macromolecule called the cell wall constructed from the heteropolymer peptidoglycan (PG). Biogenesis of this matrix is the target of penicillin and related beta-lactams. These drugs inhibit the transpeptidase activity of PG synthases called penicillin-binding proteins (PBPs), preventing the crosslinking of nascent wall material into the existing network. The beta-lactam mecillinam specifically targets the PBP2 enzyme in the cell elongation machinery of Escherichia coli...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28724443/metagenomics-of-urban-sewage-identifies-an-extensively-shared-antibiotic-resistome-in-china
#17
Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael R Gillings, Hong Chen, Tong Zhang, Yong-Guan Zhu
BACKGROUND: Antibiotic-resistant pathogens are challenging treatment of infections worldwide. Urban sewage is potentially a major conduit for dissemination of antibiotic resistance genes into various environmental compartments. However, the diversity and abundance of such genes in wastewater are not well known. METHODS: Here, seasonal and geographical distributions of antibiotic resistance genes and their host bacterial communities from Chinese urban sewage were characterized, using metagenomic analyses and 16S rRNA gene-based Illumina sequencing, respectively...
July 19, 2017: Microbiome
https://www.readbyqxmd.com/read/28717172/evolution-of-the-pseudomonas-aeruginosa-mutational-resistome-in-an-international-cystic-fibrosis-clone
#18
Carla López-Causapé, Lea Mette Sommer, Gabriel Cabot, Rosa Rubio, Alain A Ocampo-Sosa, Helle Krogh Johansen, Joan Figuerola, Rafael Cantón, Timothy J Kidd, Soeren Molin, Antonio Oliver
Emergence of epidemic clones and antibiotic resistance development compromises the management of Pseudomonas aeruginosa cystic fibrosis (CF) chronic respiratory infections. Whole genome sequencing (WGS) was used to decipher the phylogeny, interpatient dissemination, WGS mutator genotypes (mutome) and resistome of a widespread clone (CC274), in isolates from two highly-distant countries, Australia and Spain, covering an 18-year period. The coexistence of two divergent CC274 clonal lineages was revealed, but without evident geographical barrier; phylogenetic reconstructions and mutational resistome demonstrated the interpatient transmission of mutators...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28711315/characterization-of-mobile-genetic-elements-carrying-vim-1-and-kpc-2-carbapenemases-in-citrobacter-freundii-isolates-in-madrid
#19
Jennifer Villa, David M Arana, Esther Viedma, Dafne Perez-Montarelo, Fernando Chaves
Carbapenemase producing Citrobacter freundii (CPCF) infections are still uncommon in European countries. Here we report a molecular study conducted in a tertiary care facility in southern Madrid, Spain, from 2009 to 2014 to investigate the epidemiology of CPCF. The blaIMP-1,blaIMP-2,blaKPC,blaNDM,blaOXA-48,blaVIM-1 and blaVIM-2 genes were screened by PCR. Molecular typing was carried out by Pulsed-field gel electrophoresis analysis (PFGE) and multilocus sequence typing (MLST). Whole genome sequencing (WGS) was performed to characterize the resistome and the mobile genetic elements associated with the carbapenems resistance of CPCF...
July 8, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28709370/sewers-as-potential-reservoirs-of-antibiotic-resistance
#20
Olga Auguet, Maite Pijuan, Carles M Borrego, Sara Rodriguez-Mozaz, Xavier Triadó-Margarit, Saulo Varela Della Giustina, Oriol Gutierrez
Wastewater transport along sewers favors the colonization of inner pipe surfaces by wastewater-derived microorganisms that grow forming biofilms. These biofilms are composed of rich and diverse microbial communities that are continuously exposed to antibiotic residues and antibiotic resistant bacteria (ARB) from urban wastewater. Sewer biofilms thus appear as an optimal habitat for the dispersal and accumulation of antibiotic resistance genes (ARGs). In this study, the concentration of antibiotics, integron (intI1) and antibiotic resistance genes (qnrS, sul1, sul2, blaTEM, blaKPC, ermB, tetM and tetW), and potential bacterial pathogens were analyzed in wastewater and biofilm samples collected at the inlet and outlet sections of a pressurized sewer pipe...
December 15, 2017: Science of the Total Environment
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