The ocean as a global reservoir of antibiotic resistance genes

Abstract

Recent studies of natural environments have revealed vast genetic reservoirs of antibiotic resistance (AR) genes. Soil bacteria and human pathogens share AR genes, and AR genes have been discovered in a variety of habitats. However, there is little knowledge about the presence and diversity of AR genes in marine environments and which organisms host AR genes. To address this, we identified the diversity of genes conferring resistance to ampicillin, tetracycline, nitrofurantoin, and sulfadimethoxine in diverse marine environments using functional metagenomics (the cloning and screening of random DNA fragments). Marine environments were host to a diversity of AR-conferring genes. Antibiotic-resistant clones were found at all sites, with 28% of the genes identified as known AR genes (encoding beta-lactamases, bicyclomycin resistance pumps, etc.). However, the majority of AR genes were not previously classified as such but had products similar to proteins such as transport pumps, oxidoreductases, and hydrolases. Furthermore, 44% of the genes conferring antibiotic resistance were found in abundant marine taxa (e.g., Pelagibacter, Prochlorococcus, and Vibrio). Therefore, we uncovered a previously unknown diversity of genes that conferred an AR phenotype among marine environments, which makes the ocean a global reservoir of both clinically relevant and potentially novel AR genes.

FIG 1

Frequencies of antibiotic-resistant clones across samples and antibiotics. White squares represent low frequency, and darker squares represent higher frequency. Rows represent sample sites: Los Angeles Harbor (LA), San Pedro Channel (SP), Hawaii Ocean Time Series (HOT), Newport Bay (NB), and Agua Hedionda Lagoon (AH). Numbers next to sample sites represent replicate samples. Columns represent antibiotics on which clones were screened: sulfadimethoxine (Sul), tetracycline (Tet), nitrofurantoin (Nit), and ampicillin (Amp). “Unknown” taxa represent bacterial sequences that could not be assigned as marine or nonmarine because the taxonomic designation was too broad (e.g., Alphaproteobacteria).

FIG 2

Abundance and percent amino acid identity to known AR genes. (A) Abundance of known AR genes across sample sites. (B) Percent identity between AR genes from marine environments and the Antibiotic Resistance Gene Database or GenBank. Each symbol represents one sequence, and symbols represent the host organism the gene was in, identified using GenBank and EnvDB.

FIG 3

Relative abundances of marine and nonmarine bacterial taxa within all samples. “Other” represents groupings of taxa that had less than 2% relative abundance.

FIG 4

Frequency of antibiotic-resistant clones from the genomic libraries of E. coli and Synechococcus WH8102 on each of four antibiotics: ampicillin (Amp), nitrofurantoin (Nit), sulfadimethoxine (Sul), and tetracycline (Tet).