The Experts below are selected from a list of 50625 Experts worldwide ranked by ideXlab platform
Tom Slezak - One of the best experts on this subject based on the ideXlab platform.
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mvirdb a microbial database of protein toxins virulence factors and Antibiotic Resistance Genes for bio defence applications
Nucleic Acids Research, 2007Co-Authors: Carol Ecale L Zhou, Jason Smith, Adam Zemla, Matthew D Dyer, Tom SlezakAbstract:Knowledge of toxins, virulence factors and Antibiotic Resistance Genes is essential for bio-defense applications aimed at identifying ‘functional’ signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of Genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and Antibiotic Resistance Genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at http://mvirdb.llnl.gov/.
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mvirdb a microbial database of protein toxins virulence factors and Antibiotic Resistance Genes for bio defence applications
Nucleic Acids Research, 2007Co-Authors: Carol Ecale L Zhou, Jason Smith, Adam Zemla, Matthew D Dyer, Marisa Lam, Tom SlezakAbstract:Knowledge of toxins, virulence factors and Antibiotic Resistance Genes is essential for bio-defense applications aimed at identifying ‘functional’ signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of Genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and Antibiotic Resistance Genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at http://mvirdb.llnl.gov/.
Jo Handelsman - One of the best experts on this subject based on the ideXlab platform.
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diverse Antibiotic Resistance Genes in dairy cow manure
Mbio, 2014Co-Authors: Fabienne Wichmann, Nikolina Udikovickolic, S M Andrew, Jo HandelsmanAbstract:ABSTRACT Application of manure from Antibiotic-treated animals to crops facilitates the dissemination of Antibiotic Resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these Antibiotic Resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for Resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different Antibiotic Resistance Genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The Resistance Genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple Resistance Genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional Antibiotic Resistance Genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of Antibiotic Resistance Genes in agriculture and clinical settings. IMPORTANCE The increasing prevalence of Antibiotic Resistance among bacteria is one of the most intractable challenges in 21st-century public health. The origins of Resistance are complex, and a better understanding of the impacts of Antibiotics used on farms would produce a more robust platform for public policy. Microbiomes of farm animals are reservoirs of Antibiotic Resistance Genes, which may affect distribution of Antibiotic Resistance Genes in human pathogens. Previous studies have focused on Antibiotic Resistance Genes in manures of animals subjected to intensive Antibiotic use, such as pigs and chickens. Cow manure has received less attention, although it is commonly used in crop production. Here, we report the discovery of novel and diverse Antibiotic Resistance Genes in the cow microbiome, demonstrating that it is a significant reservoir of Antibiotic Resistance Genes. The genomic resource presented here lays the groundwork for understanding the dispersal of Antibiotic Resistance from the agroecosystem to other settings.
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uncultured soil bacteria are a reservoir of new Antibiotic Resistance Genes
Environmental Microbiology, 2004Co-Authors: Christian S Riesenfeld, Robert M Goodman, Jo HandelsmanAbstract:Antibiotic Resistance Genes are typically isolated by cloning from cultured bacteria or by polymerase chain reaction (PCR) amplification from environmental samples. These methods do not access the potential reservoir of undiscovered Antibiotic Resistance Genes harboured by soil bacteria because most soil bacteria are not cultured readily, and PCR detection of Antibiotic Resistance Genes depends on primers that are based on known Genes. To explore this reservoir, we isolated DNA directly from soil samples, cloned the DNA and selected for clones that expressed Antibiotic Resistance in Escherichia coli. We constructed four libraries that collectively contain 4.1 gigabases of cloned soil DNA. From these and two previously reported libraries, we identified nine clones expressing Resistance to aminoglycoside Antibiotics and one expressing tetracycline Resistance. Based on the predicted amino acid sequences of the Resistance Genes, the Resistance mechanisms include efflux of tetracycline and inactivation of aminoglycoside Antibiotics by phosphorylation and acetylation. With one exception, all the sequences are considerably different from previously reported sequences. The results indicate that soil bacteria are a reservoir of Antibiotic Resistance Genes with greater genetic diversity than previously accounted for, and that the diversity can be surveyed by a culture-independent method.
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uncultured soil bacteria are a reservoir of new Antibiotic Resistance Genes
Environmental Microbiology, 2004Co-Authors: Christian S Riesenfeld, Robert M Goodman, Jo HandelsmanAbstract:Antibiotic Resistance Genes are typically isolated by cloning from cultured bacteria or by polymerase chain reaction (PCR) amplification from environmental samples. These methods do not access the potential reservoir of undiscovered Antibiotic Resistance Genes harboured by soil bacteria because most soil bacteria are not cultured readily, and PCR detection of Antibiotic Resistance Genes depends on primers that are based on known Genes. To explore this reservoir, we isolated DNA directly from soil samples, cloned the DNA and selected for clones that expressed Antibiotic Resistance in Escherichia coli. We constructed four libraries that collectively contain 4.1 gigabases of cloned soil DNA. From these and two previously reported libraries, we identified nine clones expressing Resistance to aminoglycoside Antibiotics and one expressing tetracycline Resistance. Based on the predicted amino acid sequences of the Resistance Genes, the Resistance mechanisms include efflux of tetracycline and inactivation of aminoglycoside Antibiotics by phosphorylation and acetylation. With one exception, all the sequences are considerably different from previously reported sequences. The results indicate that soil bacteria are a reservoir of Antibiotic Resistance Genes with greater genetic diversity than previously accounted for, and that the diversity can be surveyed by a culture-independent method.
Jianhua Wang - One of the best experts on this subject based on the ideXlab platform.
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proliferation of Antibiotic Resistance Genes in coastal recirculating mariculture system
Environmental Pollution, 2019Co-Authors: Jianhua Wang, Yuxuan Zhang, Cui ZhangAbstract:Abstract The abuse of Antibiotics has caused the propagation of Antibiotic Resistance Genes (ARGs) in aquaculture systems. Although the recirculating systems have been considered as a promising approach for preventing the coastal water pollution of Antibiotics and ARG, rare information is available on the distribution and proliferation of ARGs in the recirculating mariculture system. This study firstly investigated the proliferation of ARGs in coastal recirculating mariculture systems. Ten subtypes of ARGs including tet (tetB, tetG, tetX), sul (sul1, sul2), qnr (qnrA, qnrB, qnrS), and erm (ermF, ermT) were detected. The absolute abundances of the ARGs detected in the mariculture farm were more than 1 × 104 copies/mL. The sulfonamide Resistance Genes (sul1 and sul2) were the most abundant ARGs with the abundance of 3.5 × 107–6.5 × 1010 copies/mL. No obvious correlation existed between the Antibiotics and ARGs. Some bacteria were positively correlated with two or more ARGs to indicate the occurrence of multidrug Resistance. The fluidized-bed biofilter for wastewater treatment in the recirculating system was the main breeding ground for ARGs while the UV sterilization process could reduce the ARGs. The highest flux of ARGs (6.5 × 1021 copies/d) indicated that the discharge of feces and residual baits was the main gateway for ARGs in the recirculating mariculture system to enter the environments.
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Proliferation of Antibiotic Resistance Genes in coastal recirculating mariculture system
'Elsevier BV', 2019Co-Authors: Jianhua Wang, Lu J(吕剑)Abstract:The abuse of Antibiotics has caused the propagation of Antibiotic Resistance Genes (ARGs) in aquaculture systems. Although the recirculating systems have been considered as a promising approach for preventing the coastal water pollution of Antibiotics and ARG, rare information is available on the distribution and proliferation of ARGs in the recirculating mariculture system. This study firstly investigated the proliferation of ARGs in coastal recirculating mariculture systems. Ten subtypes of ARGs including tet (tetB, tetG, tetX), sul (sul1, sul2), qnr (qnrA, qnrB, qnrS), and erm (ermF, ermT) were detected. The absolute abundances of the ARGs detected in the mariculture farm were more than 1 x 10(4) copies/mL. The sulfonamide Resistance Genes (sul1 and sul2) were the most abundant ARGs with the abundance of 3.5 x 10(7) -6.5 x 10(10) copies/mL. No obvious correlation existed between the Antibiotics and ARGs. Some bacteria were positively correlated with two or more ARGs to indicate the occurrence of multidrug Resistance. The fluidized-bed biofilter for wastewater treatment in the recirculating system was the main breeding ground for ARGs while the UV sterilization process could reduce the ARGs. The highest flux of ARGs (6.5 x 10(21) copies/d) indicated that the discharge of feces and residual baits was the main gateway for ARGs in the recirculating mariculture system to enter the environments. (C) 2019 Elsevier Ltd. All rights reserved
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metagenomic analysis of Antibiotic Resistance Genes in coastal industrial mariculture systems
Bioresource Technology, 2018Co-Authors: Jianhua Wang, Yuxuan Zhang, Yongming Luo, Hao LiuAbstract:Abstract The overuse of Antibiotics has posed a propagation of Antibiotic Resistance Genes (ARGs) in aquaculture systems. This study firstly explored the ARGs profiles of the typical mariculture farms including conventional and recirculating systems using metagenomics approach. Fifty ARGs subtypes belonging to 21 ARGs types were identified, showing the wide-spectrum profiles of ARGs in the coastal industrial mariculture systems. ARGs with multiple Antibiotics Resistance have emerged in the mariculure systems. The co-occurrence pattern between ARGs and microbial taxa showed that Proteobacteria and Bacteroidetes were potential dominant hosts of ARGs in the industrial mariculture systems. Typical nitrifying bacteria such as Nitrospinae in mariculture systems also carried with some Resistance Genes. Relative abundance of ARGs in fish ponds and wastewater treatment units was relatively high. The investigation showed that industrial mariculture systems were important ARGs reservoirs in coastal area, indicating the critical role of recirculating systems in the terms of ARGs pollution control.
Carol Ecale L Zhou - One of the best experts on this subject based on the ideXlab platform.
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mvirdb a microbial database of protein toxins virulence factors and Antibiotic Resistance Genes for bio defence applications
Nucleic Acids Research, 2007Co-Authors: Carol Ecale L Zhou, Jason Smith, Adam Zemla, Matthew D Dyer, Tom SlezakAbstract:Knowledge of toxins, virulence factors and Antibiotic Resistance Genes is essential for bio-defense applications aimed at identifying ‘functional’ signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of Genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and Antibiotic Resistance Genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at http://mvirdb.llnl.gov/.
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mvirdb a microbial database of protein toxins virulence factors and Antibiotic Resistance Genes for bio defence applications
Nucleic Acids Research, 2007Co-Authors: Carol Ecale L Zhou, Jason Smith, Adam Zemla, Matthew D Dyer, Marisa Lam, Tom SlezakAbstract:Knowledge of toxins, virulence factors and Antibiotic Resistance Genes is essential for bio-defense applications aimed at identifying ‘functional’ signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of Genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and Antibiotic Resistance Genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at http://mvirdb.llnl.gov/.
Cui Zhang - One of the best experts on this subject based on the ideXlab platform.
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proliferation of Antibiotic Resistance Genes in coastal recirculating mariculture system
Environmental Pollution, 2019Co-Authors: Jianhua Wang, Yuxuan Zhang, Cui ZhangAbstract:Abstract The abuse of Antibiotics has caused the propagation of Antibiotic Resistance Genes (ARGs) in aquaculture systems. Although the recirculating systems have been considered as a promising approach for preventing the coastal water pollution of Antibiotics and ARG, rare information is available on the distribution and proliferation of ARGs in the recirculating mariculture system. This study firstly investigated the proliferation of ARGs in coastal recirculating mariculture systems. Ten subtypes of ARGs including tet (tetB, tetG, tetX), sul (sul1, sul2), qnr (qnrA, qnrB, qnrS), and erm (ermF, ermT) were detected. The absolute abundances of the ARGs detected in the mariculture farm were more than 1 × 104 copies/mL. The sulfonamide Resistance Genes (sul1 and sul2) were the most abundant ARGs with the abundance of 3.5 × 107–6.5 × 1010 copies/mL. No obvious correlation existed between the Antibiotics and ARGs. Some bacteria were positively correlated with two or more ARGs to indicate the occurrence of multidrug Resistance. The fluidized-bed biofilter for wastewater treatment in the recirculating system was the main breeding ground for ARGs while the UV sterilization process could reduce the ARGs. The highest flux of ARGs (6.5 × 1021 copies/d) indicated that the discharge of feces and residual baits was the main gateway for ARGs in the recirculating mariculture system to enter the environments.