Uncultured soil bacteria are a reservoir of new antibiotic resistance genes

Abstract

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.

Antibiotic-resistant soil bacteria in transgenic plant fields

“…Furthermore, strains characterized by intermediate mutation frequencies have significantly higher levels of antibiotic resistance than strains with low and high mutation frequencies (19). Correlation between point mutation and polymorphism could explain why uncultured soil bacteria are a reservoir of antibiotic resistance genes (20).…”

Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China

“…Soil has been regarded as a rich source of ARGs, deriving from both natural and anthropogenic processes. Although high frequency of antibiotic resistance was revealed in soils by culture-dependent approaches, it represents only a fraction of soildwelling bacteria (D'Costa et al, 2006), and uncultured soil bacteria represent a reservoir of new ARGs, which can be transferred to clinical pathogens via mobile genetic elements (Riesenfeld et al, 2004).…”

An introduction to and a reflection on the “ecogenomics promise”

“…(Pettit 2004;Riesenfeld et al 2004;Langer et al 2006;Schmeisser et al 2007;Demain and Adrio 2008;Oh et al 2009;Barke et al 2010;Kakirde et al 2010). Sixty per cent of the drugs that became commercially available over the past 20 years originate from existing natural compounds, and not directly from the chemical industry (Lefevre et al 2008).…”