Heavy metal pollution and co-selection for antibiotic resistance through analysis of sediment extracted from the floor of a pond in a heavily industrialised area.

Frequent and persistent heavy metal pollution has profound effects on the composition and activity of microbial communities. Heavy metals select for metal resistance but can also co-select for resistance to antibiotics, which is a global health concern. We here document metal concentration, metal resistance and antibiotic resistance along a sediment archive from a pond in the North West of the United Kingdom covering over a century of anthropogenic pollution. We specifically focus on zinc as it is a ubiquitous and toxic metal contaminant known to co-select for antibiotic resistance. This approach allows us to test whether antibiotic resistance predates the clinical use of antibiotics, instead arising through co-selection for metal resistance. Zinc concentration and bioavailability was found to vary over the core, likely reflecting increased industrialisation around the middle of the 20th century, and had a significant effect on bacterial community composition as revealed by a positive correlation between the level of zinc resistance in culturable bacteria and zinc concentration. The proportion of zinc resistant isolates positively correlated with resistance to three clinically relevant antibiotics (oxacillin, cefotaxime and trimethoprim). The abundance of the class 1 integron-integrase gene, intI1, marker for anthropogenic pollutants correlated with the prevalence of zinc- and cefotaxime resistance but not with oxacillin and trimethoprim resistance. Our microbial palaeontology approach reveals that metal-contaminated sediments from depths that pre-date the use of antibiotics were enriched in antibiotic resistant bacteria, demonstrating the pervasive effects of metal-antibiotic co-selection in the environment.