The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens
From Farm to Clinic? Soil organisms have long been assumed to be an important source of antibiotic resistance genes, in part because of antibiotic-treated livestock and in part because of the natural ecology of antibiotic production in the soil. Forsberg et al. (p. 1107) developed a metagenomic protocol to assemble short-read sequence data after antibiotic selection experiments, using 12 different drugs in all antibiotic classes, and compared antibiotic resistance gene sequences between soil bacteria and clinically occurring pathogens. Sixteen sequences, representing seven gene products, were discovered in farmland soil bacteria within long stretches of perfect nucleotide identity with pathogenic proteobacteria. Perfect identity between antibiotic resistance genes in farmland soil bacteria and human pathogens suggests direct transfer. Soil microbiota represent one of the ancient evolutionary origins of antibiotic resistance and have been proposed as a reservoir of resistance genes available for exchange with clinical pathogens. Using a high-throughput functional metagenomic approach in conjunction with a pipeline for the de novo assembly of short-read sequence data from functional selections (termed PARFuMS), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pathogens. We describe multidrug-resistant soil bacteria containing resistance cassettes against five classes of antibiotics (β-lactams, aminoglycosides, amphenicols, sulfonamides, and tetracyclines) that have perfect nucleotide identity to genes from diverse human pathogens. This identity encompasses noncoding regions as well as multiple mobilization sequences, offering not only evidence of lateral exchange but also a mechanism by which antibiotic resistance disseminates.
Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste.
Antibiotics are used in animal livestock production for therapeutic treatment of disease and at subtherapeutic levels for growth promotion and improvement of feed efficiency. It is estimated that approximately 75% of antibiotics are not absorbed by animals and are excreted in waste. Antibiotic resistance selection occurs among gastrointestinal bacteria, which are also excreted in manure and stored in waste holding systems. Land application of animal waste is a common disposal method used in the United States and is a means for environmental entry of both antibiotics and genetic resistance determinants. Concerns for bacterial resistance gene selection and dissemination of resistance genes have prompted interest about the concentrations and biological activity of drug residues and break-down metabolites, and their fate and transport. Fecal bacteria can survive for weeks to months in the environment, depending on species and temperature, however, genetic elements can persist regardless of cell viability. Phylogenetic analyses indicate antibiotic resistance genes have evolved, although some genes have been maintained in bacteria before the modern antibiotic era. Quantitative measurements of drug residues and levels of resistance genes are needed, in addition to understanding the environmental mechanisms of genetic selection, gene acquisition, and the spatiotemporal dynamics of these resistance genes and their bacterial hosts. This review article discusses an accumulation of findings that address aspects of the fate, transport, and persistence of antibiotics and antibiotic resistance genes in natural environments, with emphasis on mechanisms pertaining to soil environments following land application of animal waste effluent.
cloud computing social network regression model gene expression sample size confidence interval logistic regression social science systematic review linear regression model cloud datum xml document immune system carbon dioxide amino acid logistic regression model keyword search mental model process analysi background and objective encrypted datum quantitative assessment plant growth escherichia coli sequence analysi discourse analysi scientific publication channel condition immune response choice behavior programming paradigm natural selection organic matter odds ratio social structure microbial community signal transduction membrane protein encrypted cloud datum encrypted cloud lactic acid plant root oral cavity quorum sensing gene transfer antibiotic resistance cardiac surgery critical discourse analysi dental cary cell count marine ecosystem recombinant dna oxidative stres critical discourse aquatic ecosystem horizontal gene transfer bibliographic reference ribosomal rna horizontal gene lactic acid bacterium plasma membrane acute kidney acute kidney injury resistance gene cell survival genetic selection acid bacterium physiological aspect gram-negative bacterium social characteristic social inequality ranked keyword search ranked keyword abbott laboratory dental plaque oligonucleotide probe base pairing resistant bacterium antibiotic resistance gene lactobacillus acidophilu gram-positive bacterium genetic heterogeneity biofilm development nitrogen cycle microbial biofilm transcription, genetic interface device component metabolic process, cellular national origin biological adaptation to stress clone cell ethanol 0.62 ml/ml topical gel clinical act of insertion genetic translation proces hereditary disease greater than cognition disorder phobia, social nucleic acid hybridization gel electrophoresis (lab technique) stimulation (motivation) meta analysis (statistical procedure) the superficial genome, bacterial amino acid metabolism, inborn error denial (psychology) immunoglobulin lambda-chain fifty nine reservoir device component document completion status - documented gastrointestinal tract structure genus (mathematics) domain of discourse phylum (taxon) intestinal microbiome microbiota (plant) genus mycobacterium antibiotic resistance, microbial ammonia measurement ammonia oxidation models, mental anabolic steroid actinobacteria clas fecal microbiota transplantation kidney failure, acute gene transfer, horizontal ferrosoferric oxide dennis fairclough ruth teitelbaum shoshana wodak excretory function entity name part qualifier - adopted cessation of life anatomical layer biopolymer sequencing ephrin type-b receptor 1, human one thousand copy (object) review [publication type] promotion (action) pathogenic organism