The shared antibiotic resistome of soil bacteria and human pathogens
By Kevin J. Forsberg, Alejandro Reyes, Bin Wang, Elizabeth M. Selleck, Morten O. A. Sommer, Gautam Dantas. Science, 2012
1,079 citations recorded by the source corpus.
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.
View Paper: https://www.semanticscholar.org/paper/30c4d3c6642f533cde270e4e8d5aaed5c6282cc8
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Citations in the corpus
- The evolutionary origins of pesticide resistance (2018, background): “HGT is most common in bacteria, to the extent that for plasmid-borne antibiotic resistance the source population for standing variation is a multi-species ‘resistome’ (Forsberg et al., 2012).”
- Antimicrobial peptides: Application informed by evolution (2020, background): “Becausemany antibiotics were originally evolved by bacteria and fungi formicrobe-microbe warfare, soil bacterial communities harbor a rich antibiotic resistome (88).”
- Diverse and abundant antibiotic resistance genes in Chinese swine farms (2013, neutral): “Proc Natl Acad Sci USA 109(5):1691–1696.”
- Antibiotics in the Soil Environment—Degradation and Their Impact on Microbial Activity and Diversity (2019, background): “This can be attributed to differences in treatment processes, such as nature of influent, treatment plant capacity, and the type of technology used (Forsberg et al., 2012; Wu et al., 2014).”
- Antibiotic resistome in the livestock and aquaculture industries: Status and solutions (2020, background): “Furthermore, the strong association between antibiotic resistome in soil environments and human clinical pathogens has been demonstrated showing that MGE-mediated HGT assembles tandem arrays of distinct ARGs into integrons, transposons and plasmids and then makes them mobile (Forsberg et al., 2012).”
- Antimicrobial resistance in humans, livestock and the wider environment (2015, positive): “For example, one recent metagenomics study found multiple examples of resistance genes in the soil that had 100% homology to those found in clinical isolates, across all major classes of antibiotics [9].”