Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters
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Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.
KeywordsAcid mine drainage (AMD) Comparative genomics Extrusion pumps Genome evolution Horizontal gene transfer
We thank Abdelmalek ALIOUA for performing the Sanger sequencing experiments and Fabienne Battaglia-Brunet for providing the Tm. delicata DSM16361 strain.
O. C., D. L., J. F., K. C. F., S. F., and F. A.-P. performed research; O. C., K. C. F., V.B., and F.A.-P. wrote the paper.
This work was supported by the Université de Strasbourg (unistra), the Centre National de la Recherche Scientifique (CNRS) and the Region Alsace to J. F. This study was financed by the THIOFILM (ANR-12-ADAP-0013) projects. O. C., J. F., and K. C. F. were supported by the Agence Nationale de la Recherche, ANR THIOFILM (ANR-12-ADAP-0013).
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Conflict of interest
The authors declare that they have no conflict of interest.
- Battaglia-Brunet F, El Achbouni H, Quemeneur M et al (2011) Proposal that the arsenite-oxidizing organisms, Thiomonas cuprina and “Thiomonas arsenivorans” be reclassified as strains of Thiomonas delicata. Int J Syst Evol Microbiol 61:2816–2821. https://doi.org/10.1099/ijs.0.023408-0 CrossRefGoogle Scholar
- Coupland K, Battaglia-Brunet F, Hallberg KB et al (2004) Oxidation of iron, sulfur and arsenic in mine waters and mine wastes: an important role for novel Thiomonas spp. In: Tsezos M, Hatzikioseyian A, Remoudaki E (eds) Biohydrometallurgy: a sustainable technology in evolution. National Technical University of Athens, Zografou, pp 639–646Google Scholar
- Farias P, Espírito Santo C, Branco R et al (2015) Natural hot spots for gain of multiple resistances: arsenic and antibiotic resistances in heterotrophic, aerobic bacteria from marine hydrothermal vent fields. Appl Environ Microbiol 81:2534–2543. https://doi.org/10.1128/AEM.03240-14 CrossRefGoogle Scholar
- Milde K, Sand W, Wolff W, Bock E (1983) Thiobacilli of the corroded concrete walls of the Hamburg sewer system. J Gen Microbiol 129:1327–1333Google Scholar
- Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor, New YorkGoogle Scholar