Marine Sediment Bacteria Harbour a Pool of Antibiotic Resistance Genes similar to Human Pathogens

Bacterial resistance to antibiotics is an increasing and serious problem for disease control, especially for public health since the common antibiotics are becoming less effective and only a few new drugs are under investigation. Due to the use of antibiotics in aquaculture, many compounds accumulate in the oceans and various bacterial species have developed resistance. The resistance genes are commonly associated with mobile plasmids within the bacteria and genetic exchange between bacteria via horizontal gene transfer (HGT) often involves these parts of genetic information. The total gene pool for antibiotic resistance of pathogenic and non-pathogenic bacteria is referred to as the resistome, which has not been well studied for marine bacteria.

This study aimed to investigate the bacterial resistome of marine fish farm sediment and further examined the relationship between the ocean resistome and the pathogenic resistome in order to establish its clinical importance. Marine sediment was sampled and plasmids were metagenomically analysed to identify the resistance genes. Results showed that the majority of collected plasmid DNA came from Proteobacteria hosts (82 %) of which 54 % belonged to the Gammaproteobacteria. 58 resistance genes with high homology (≥ 80 % identity) were found as well as numerous ones with an overlap of 40 – 80 % of resistance genes from the databank which suggests an occurrence of yet unknown genes from the marine sediment.

The 58 resistance genes with high identity were associated with 11 classes of antibiotics and the distribution of these genes is shown in the figure below and it becomes obvious that the marine sediment is a reservoir of a variety of antibiotic resistance genes.

                                      The diversity of antibiotics identified from the 58 highly homologous resistance genes.

In addition to this, around 10 % of all reads were linked to a gene which encodes an antibiotic resistance compound in the human pathogen Salmonella enterica that causes gastroenteritis. Altogether, six contigs (overlapping DNA segments/reads) with antibiotic resistance genes from human pathogens were found in the marine samples with more than 90 % identity. Among the six, contig891 shared 99 % overlap with several human pathogen species such as Yersinia ruckeri and has also been detected in the fish pathogenic bacterium Aeromonas salmonicida.

This study confirmed that plasmids are the key carriers of antibiotic resistance genes and added knowledge to the diversity of antibiotics present in the marine environment; so far only tetracycline and few others had been identified. Moreover it was uncovered that many marine bacteria in the sediment harbour antibiotic resistance genes highly similar to the ones found in human pathogens and it can be concluded that these bacteria acquired their resistance through HGT from the human pathogens that are continuously released into the oceans. Since many antibiotics are introduced into the ocean through aquaculture, many bacteria also had the opportunity to develop resistance. The fish farm sediment bacteria are in constant contact with the fish and thus, these bacteria can have a great impact on the global spread of antibiotic resistance genes.

 

Yang, et al. (2013) Marine Sediment Bacteria Harbour Antibiotic Resistance Genes Highly Similar To Those Found in Human Pathogens. Microbiology of Aquatic Systems