Identifying and linking antimicrobial resistance genes in metagenomes with new DNA sequencing technologies

The transfer of antimicrobial resistance genes (ARG) to pathogenic microbes is a major concern in modern medicine. Antibiotic therapies are often rendered ineffective by horizontal acquisition of these genes by previously susceptible microbes; however, the vectors of ARGs in the environment are difficult to identify. We have characterized the mechanisms for how mobile DNA that contains ARGs can enter other potential host bacterial cells, but we still have difficulty in identifying all of the potential hosts for these genomic islands in the surrounding environment. Using the cattle rumen microbiome as a model, I will show how improvements in DNA sequencing and chromatin conformation capture (Hi-C) technologies can be used to identify candidate host bacteria for viral and plasmid DNA that could carry ARGs to new bacterial hosts. Use of long-read DNA sequence data uncovered 10-fold more ARG alleles than discovered by short-read sequencing, suggesting that the true number and diversity of alleles were underestimated previously. Application of Hi-C links enabled the detection of living microbes likely to carry these ARG alleles in the community and would therefore serve as vectors for their transmission to other species or strains. This methodology and network analysis algorithm has been released to the community, and has already been used in a similar study looking at ARG allele distribution in human gut microbes. As we apply new technologies and methods to metagenomics data, we are slowly uncovering the true extent to which ARGs are transferred between microbial species in the same environments. These findings impact future considerations for antibiotic usage in clinical medicine and agriculture.

Learning Objectives:

1. Define several different classes of mobile DNA

2. Identify the challenges in identifying antimicrobial resistance genes in the microbiome

3. Discuss the implications of horizontal transfer of resistance genes for antibiotic use.