Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil

Abstract

Despite the threat posed by antibiotic resistance in infectious bacteria, little is known about the diversity, distribution and origins of resistance genes, particularly among the as yet unculturable environmental bacteria. One potentially rich but largely unstudied environmental reservoir is soil. The complexity of its microbial community coupled with its high density of antibiotic-producing bacteria makes the soil a likely origin for diverse antibiotic resistance determinants. To investigate antibiotic resistance genes among uncultured bacteria in an undisturbed soil environment, we undertook a functional metagenomic analysis of a remote Alaskan soil. We report that this soil is a reservoir for b-lactamases that function in Escherichia coli, including divergent b-lactamases and the first bifunctional b-lactamase. Our findings suggest that even in the absence of selective pressure imposed by anthropogenic activity, the soil microbial community in an unpolluted site harbors unique and ancient b-lactam resistance determinants. Moreover, despite their evolutionary distance from previously known genes, the Alaskan b-lactamases confer resistance on E. coli without manipulating its gene expression machinery, demonstrating the potential for soil resistance genes to compromise human health, if transferred to pathogens.

High Throughput Profiling of Antibiotic Resistance Genes in Urban Park Soils with Reclaimed Water Irrigation

“…13 In the present study, a high-throughput qPCR with 295 validated primer sets (including 285 ARGs, 9 transposase genes, and 16S rRNA gene) has been used to investigate the impact of RWI on ARGs in public park soils of representative Chinese cities. Since ARGs can be present naturally, 24,25 the background level needs to be considered. So, soil samples without using reclaimed water were also collected as control for each RWI park soil.…”

Impact of reclaimed water irrigation on antibiotic resistance in public parks, Beijing, China

“…Therefore, soil samples from six public parks using reclaimed water irrigation were collected. Since antibiotic resistance is ancient (Allen et al, 2009;D'Costa et al, 2011), four pristine soil samples from Natural Scenic Resort of Ling Mountain not using reclaimed water were collected as control. The objective of this study was to evaluate whether the soil in public parks receiving reclaimed water acts as a reservoir of ARGs and has the potential for transferring ARGs to human pathogens.…”

Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure

“…2b). In fact, previous studies have recognized soil as a reservoir for a broad spectrum of β-lactamases, irrespective of human activities (Demaneche et al 2008;Allen et al 2009). The β-lactamases are among the most abundant ARGs commonly found in soils (Forsberg et al 2014) and clinical settings (Jacoby and Munoz-Price 2005), and seem to be ancient, being present in soil long time before the antibiotic era (Hall, Salipante and Barlow 2004).…”

“…The β-lactamases are among the most abundant ARGs commonly found in soils (Forsberg et al 2014) and clinical settings (Jacoby and Munoz-Price 2005), and seem to be ancient, being present in soil long time before the antibiotic era (Hall, Salipante and Barlow 2004). The β-lactam class of antibiotics, such as penicillins, and cephalosporins, are frequently prescribed antibiotics for humans and livestock (Allen et al 2009). In this study, none of these β-lactamases were found to be enriched in the manure samples; however, several β-lactamases (the Per-1, Per-2, IMP-2 and IMP-5 groups in the arable soil, whereas Per-1, SFO-1, IMP-2 and IMP-5 groups in the pasture soil), which are common in clinical isolates (e.g.…”

“…Furthermore, the transfer of ARGs from environmental bacteria to human-associated pathogens could be facilitated through mobility elements such as integrons, plasmids and transposons (Gogartion and Townsend 2005;Binh et al 2008). Despite the clinical importance of antibiotic resistance (Levy 1997), however, environmental reservoirs of ARGs and their potential contribution to clinical resistance remains less understood (Allen et al 2009). Therefore, it is essential to identify the sources and behaviors of ARGs in the environment enabling the design of appropriate strategies to reduce the dissemination of ARGs.…”