FLC MidWest Regional Technology Transfer Award

Authors: Bickhart, Derek; Panke-Buisse, Kevin; Smith, Timothy - Tim; KOREN, SERGEY - National Institutes Of Health (NIH); WATSON, MICK - Roslin Institute; HEINER, CHERYL - Pacific Biosciences Inc; CERSOSIMO, LAURA - Orise Fellow; PRESS, MAXIMILLIAN - Phase Genomics, Inc; SULLIVAN, SHAWN - Phase Genomics, Inc; LIACHKO, IVAN - Phase Genomics, Inc; PHILLIPPY, ADAM - National Institutes Of Health (NIH)

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/28/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The exchange of antimicrobial resistance genes (AMR) among bacteria is thought to be a key process leading to the emergence of antibiotic resistance in human pathogens (multidrug resistance, MDR). Study of the mechanism by which AMR transfer occurs in a natural setting have been hampered by an inability to assign the MDR genes identified in metagenomic sequencing studies, to the bacterial species carrying the mobile DNA on which MDR genes are typically carried. If there are detected differences in the transfer of AMR genes and differences in the range of potential host microbes to contain them, this has broader implications on several benign or beneficial microbial species in the environment that could serve as vectors for AMR transmission to pathogens. A partnership between the USDA ARS, NIH NHGRI, the Roslin Institute in Scotland, Pacific Biosciences Inc., and Phase Genomics Inc. was formed to develop a method to assign mobile DNA and AMR to bacterial and archaeal hosts in metagenomic sequence. The method incorporates long read sequencing technology from Pacific Biosciences, “Hi-C” (or modified chromatin conformation capture) technology from Phase Genomics, and informatics expertise from ARS, NHGRI, and the Roslin Institute to associate mobile DNA elements with the bacterial species in which they are harbored, and simultaneously identifies MDR genes within them. A proof of principle survey was conducted on the cattle rumen, an important environment with respect to food safety due to the implications of MDR bacteria emerging from the use of cattle as food and cattle byproducts as fertilizer. The study successfully developed a method that connected mobile DNA and potential hosts for that mobile DNA, which led to unique biological insights previously poorly characterized or unknown in the rumen microbial environment. Our analysis uncovered 188 associations between viral mobile DNA and bacteria in one single experiment. These associations tracked candidate metabolic and antimicrobial resistance genes that were shuttled between hosts and could be used by strains of bacteria that would otherwise not display phenotypes related to metabolic activity or resistance, respectively. The approach was 20 times more sensitive in detecting tetracycline resistance genes being transferred among bacterial species compared to previous methods, along with being the first time that AMR genes in the rumen could be directly connected to specific host bacteria. This novel discovery can now be used to track persistence of AMR alleles in the rumen during the course of standard veterinary antibiotic treatment and help to address the question of whether antibiotic administration to cattle is affecting the frequency of antibiotic resistant infections in humans. The approach we developed can be used in other environments beyond the cattle rumen. The unique blend of technologies we recommend and the packaged software that our group designed supports identification of potential hosts for mobile DNA within nearly any microbial community. Since our methods rely on biological signal from Hi-C links, predicted associations of viral/plasmid/mobile DNA with host genomes is made at the cellular level. This means that we can identify that these DNA molecules existed within living cells, in contrast to purely computational association methods which infer host availability based on DNA sequence similarity. A new assessment of mobile DNA “vectors” in a microbial community can now be conducted using the methods we have pioneered.