Insights into Antibiotic Resistance Through Metagenomic Approaches

Robert Schmieder; Robert Edwards


Future Microbiol. 2012;7(1):73-89. 

In This Article

Antibiotic Resistance Associated With Wastewater Treatment Plants

Wastewater treatment plants are interfaces between different environments and, therefore, provide an opportunity for mobile elements (including resistance) to mix between pathogens, opportunistic pathogens, and environmental bacteria.[68] The presence of antibiotics in sewage selects for resistance markers that are able to spread through the microbial community and as a result, antibiotic-resistant bacteria can potentially disseminate their resistance genes widely among members of the endogenous microbial community (Figure 6). The sludge products of urban and rural wastewater treatment plants are increasingly used to fertilize agricultural crops, dispersing unknown amounts of resistance genes and antibiotics that withstand standard sewage treatment.

Figure 6.

Potential antibiotic resistance gene dissemination. The arrows indicate possible points of dissemination among different environments. Supporting metagenomic studies are marked as follows: (A),82 (B) 71 and (C).48,52

The level of antibiotic resistance in activated sludge is not known, and the few studies to date have been inconclusive. The activated sludge process may promote cellular interactions among all the diverse microorganisms in the sewage, but it is also a highly competitive environment where the fraction of pathogens decreases due to competition with other microbes or through predation. A function- and sequence-based metagenomic approach was used to identify antibiotic resistance determinants carried on bacterial chromosomes, plasmids or viruses within activated sludge (Table 1).[69] Functional screening of the viral metagenomic library did not yield any antibiotic resistant clones, and therefore, a sequence-based approach was employed that identified six clone inserts with homology to known resistance genes. In contrast to some of the studies we have discussed, the degree of similarity between the plasmid- or phage-derived antibiotic resistance determinants and the reference sequences was greater than that for other genes that were tested. However, none of the sequenced clones conferred their predicted antibiotic resistance in E. coli. There are a number of reasons that the genes may not confer resistance to E. coli, including the incorrect expression in that strain, or the incomplete cloning of the sequence. In another study, activated sludge used to treat industrial wastewater polluted with phenolic compounds, was screened for bleomycin resistance genes using a metagenomics approach and two novel genes were identified.[25]

A sequence-based metagenomic approach of wastewater using Roche/454 pyrosequencing showed a high diversity of plasmids and resistance genes in that sample.[70] The metagenomic sequences representing resistance genes, especially from β-lactamase protein families, were identified by searches against reference databases with known antibiotic resistance genes and by screening for particular motifs in the protein sequences. These motifs and sequences were similar to enzymes that were previously identified in pathogenic bacteria isolated from hospital patients with diverse infections, but were not tested for activity.

High levels of antibiotic resistance genes have also been found in bacteria that live in river sediments downstream from a wastewater treatment plant using sequence-based metagenomics.[71] The resistance genes made up almost 2% of the DNA samples taken. Clearly, the survival of antibiotics and antibiotic resistance genes through the sewage treatment process and in the aquatic environment merits further study, perhaps with comparisons between areas where different antibiotics are routinely used in the clinical setting.