Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential
Open Access
- 17 November 2015
- journal article
- research article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 16 (1), 1-14
- https://doi.org/10.1186/s12864-015-2153-5
Abstract
Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds. Despite numerous case studies, systematic and quantitative data on co-occurrence of such genes on plasmids and chromosomes is lacking, as is knowledge on environments and bacterial taxa that tend to carry resistance genes to such compounds. This effectively prevents identification of risk scenarios. Therefore, we aimed to identify general patterns for which biocide/metal resistance genes (BMRGs) and antibiotic resistance genes (ARGs) that tend to occur together. We also aimed to quantify co-occurrence of resistance genes in different environments and taxa, and investigate to what extent plasmids carrying both types of genes are conjugative and/or are carrying toxin-antitoxin systems. Co-occurrence patterns of resistance genes were derived from publicly available, fully sequenced bacterial genomes (n = 2522) and plasmids (n = 4582). The only BMRGs commonly co-occurring with ARGs on plasmids were mercury resistance genes and the qacE∆1 gene that provides low-level resistance to quaternary ammonium compounds. Novel connections between cadmium/zinc and macrolide/aminoglycoside resistance genes were also uncovered. Several clinically important bacterial taxa were particularly prone to carry both BMRGs and ARGs. Bacteria carrying BMRGs more often carried ARGs compared to bacteria without (p < 0.0001). BMRGs were found in 86 % of bacterial genomes, and co-occurred with ARGs in 17 % of the cases. In contrast, co-occurrences of BMRGs and ARGs were rare on plasmids from all external environments (p < 0.0001) and carry toxin-antitoxin systems (p < 0.0001) than plasmids without resistance genes. This is the first large-scale identification of compounds, taxa and environments of particular concern for co-selection of resistance against antibiotics, biocides and metals. Genetic co-occurrences suggest that plasmids provide limited opportunities for biocides and metals to promote horizontal transfer of antibiotic resistance through co-selection, whereas ample possibilities exist for indirect selection via chromosomal BMRGs. Taken together, the derived patterns improve our understanding of co-selection potential between biocides, metals and antibiotics, and thereby provide guidance for risk-reducing actions.Keywords
Funding Information
- Vetenskapsrådet (SE) (244314724)
- Svenska Forskningsrådet Formas (SE) (2012-86)
- Vetenskapsrådet (SE) (ᅟ)
This publication has 66 references indexed in Scilit:
- Roxarsone, Inorganic Arsenic, and Other Arsenic Species in Chicken: A U.S.-Based Market Basket SampleEnvironmental Health Perspectives, 2013
- PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic SpeciesInfection and Immunity, 2011
- Accelerated Profile HMM SearchesPLoS Computational Biology, 2011
- Selection of Fecal Enterococci Exhibiting tcrB -Mediated Copper Resistance in Pigs Fed Diets Supplemented with CopperApplied and Environmental Microbiology, 2011
- Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environmentThe ISME Journal, 2011
- Mobility of PlasmidsMicrobiology and Molecular Biology Reviews, 2010
- Search and clustering orders of magnitude faster than BLASTBioinformatics, 2010
- Complete Nucleotide Sequences of Plasmids pEK204, pEK499, and pEK516, Encoding CTX-M Enzymes in Three Major Escherichia coli Lineages from the United Kingdom, All Belonging to the International O25:H4-ST131 CloneAntimicrobial Agents and Chemotherapy, 2009
- Sequencing and Comparative Genomic Analysis of pK29, a 269-Kilobase Conjugative Plasmid Encoding CMY-8 and CTX-M-3 β-Lactamases in Klebsiella pneumoniaeAntimicrobial Agents and Chemotherapy, 2007
- Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksGenome Research, 2003