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.2011 Feb 16;6(2):e17038.
doi: 10.1371/journal.pone.0017038.

Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements

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Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements

Erik Kristiansson et al. PLoS One..

Abstract

The high and sometimes inappropriate use of antibiotics has accelerated the development of antibiotic resistance, creating a major challenge for the sustainable treatment of infections world-wide. Bacterial communities often respond to antibiotic selection pressure by acquiring resistance genes, i.e. mobile genetic elements that can be shared horizontally between species. Environmental microbial communities maintain diverse collections of resistance genes, which can be mobilized into pathogenic bacteria. Recently, exceptional environmental releases of antibiotics have been documented, but the effects on the promotion of resistance genes and the potential for horizontal gene transfer have yet received limited attention. In this study, we have used culture-independent shotgun metagenomics to investigate microbial communities in river sediments exposed to waste water from the production of antibiotics in India. Our analysis identified very high levels of several classes of resistance genes as well as elements for horizontal gene transfer, including integrons, transposons and plasmids. In addition, two abundant previously uncharacterized resistance plasmids were identified. The results suggest that antibiotic contamination plays a role in the promotion of resistance genes and their mobilization from environmental microbes to other species and eventually to human pathogens. The entire life-cycle of antibiotic substances, both before, under and after usage, should therefore be considered to fully evaluate their role in the promotion of resistance.

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Conflict of interest statement

Competing Interests:The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. High levels of ciprofloxacin were found in river sediments downstream from the Indian treatment plant.
The figure shows the amount of ciprofloxacin in relation to the total organic mass (µg/g) measured by liquid chromatography mass spectrometry. The levels were considerable even at the most distant sampling site (located 17.5 km downstream from the discharge site). No detectable levels were found at the Swedish treatment plant (marked with N.D.). The error bars describe the standard error of the mean based on the analysis of three separate samples taken in close vicinity.
Figure 2
Figure 2. Exposure to antibiotic-contaminated effluent promotes resistance genes in bacterial communities in river sediment.
The figure shows the relative abundance ofa)sul2,b)strA/B and c) genes with a pentapeptide structure, including knownqnr-genes, providing resistance against fluoroquinolones. The site in the immediate vicinity of the discharge had intermediate levels of bothsul2 andstrA/strB which are likely to reflect the continuous transport and deposition of surface sediment from the upstream area. The relative abundance was calculated in relation to the total number of identified bacterial genes.
Figure 3
Figure 3. Enzymes involved in horizontal transfer of resistance genes were highly enriched in the river sediment exposed to antibiotics.
The panel shows the relative abundance ofa) integrase of class 1 andb) insertion sequence common region transposase of class 2. The relative abundance was calculated in relation to the total number of identified bacterial genes.
Figure 4
Figure 4. The abundance of resistance-carrying plasmids in environmental bacterial communities exposed to antibiotics.
Four plasmids were detected at high levels, two already described (a–b) and two previously not characterized (c–d). Their relative abundance is given in relation to the total amount of sequenced DNA and the numbers above the bars show the estimated plasmid coverage in each metagenome.
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