The clinic vs the farm: exploring prevalence and function of CRISPR-Cas in agriculturally relevant niches

Authors: UPRETI, CHAHAT - The University Of Texas At Dallas; KUMAR, PRANAV - The University Of Texas At Dallas; PAS, SAVANNAH - Texas A&M University; Durso, Lisa; PALMER, KELLI - The University Of Texas At Dallas

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2022
Publication Date: 11/10/2022
Citation: Upreti, C., Kumar, P., Pas, S., Durso, L.M., Palmer, K. 2022. The clinic vs the farm: exploring prevalence and function of CRISPR-Cas in agriculturally relevant niches. Meeting Abstract. Available: https://germomics.com/txasm/fall-2022-abstracts/.

Interpretive Summary: The development and use of antibiotics has transformed human health and livestock production. However, due to use and overuse of antibiotics, we are currently facing a global crisis of antibiotic resistance where bacteria have become resistant to the antibiotics we use against them. One of the major ways in which antibiotic resistance spreads is when bacteria exchange circular pieces of DNA called plasmids that contain antibiotic resistance genes. To protect themselves from foreign genetic elements, over the course of millions of years, bacteria have evolved several defense mechanisms. One important defense system that several bacterial species possess is called CRISPR-Cas. CRISPR-Cas has been shown to be effective at blocking the entry of plasmids in certain conditions. This makes CRISPR-Cas a promising tool to tackle the antibiotic resistance crisis. However, most studies in this field have exclusively looked at clinical strains. Since antibiotic use in agriculture is significant, it is crucial to explore the antibiotic resistance and CRISPR-Cas landscape in this niche. In this work, we have analyzed 1,984 genomes of the important zoonotic pathogen Enterococcus faecalis sourced from human and animal sources. We found significant differences in strains from the two groups in terms of genome size, sequence diversity, antibiotic resistance and CRISPR-Cas content. We then, gathered 130 agricultural E. faecalis samples from four farms across the country, sourced from several animals. We found that geography, the identity of the host animal and the presence of CRISPR-Cas were all important factors when considering genetic similarity across the samples. Finally, we experimentally tested if CRISPR-Cas is effective at blocking the transfer of plasmids in an agricultural niche (manure). If so, it would allow us to use the presence of CRISPR-Cas or a therapeutic based on it, in stemming antibiotic resistance spread. We found that CRISPR-Cas was indeed effective in manure, and it remained effective in manure longer than it did in standard lab conditions. Overall, our work explores the prevalence and function of CRISPR-Cas in agricultural strains of E. faecalis and in agricultural niches.

Technical Abstract: Global efforts to combat the spread of antibiotic resistance have highlighted the importance of a OneHealth approach that combines human, animal and environmental perspectives. A key driver of antibiotic resistance is horizontal gene transfer (HGT). As a native defense system against HGT in bacteria, CRISPR-Cas is a promising tool to address this crisis. Due to historical study biases favoring clinically-derived strains, we have a poor understanding of CRISPR-Cas prevalence and efficacy in agriculturally relevant strains. Here, we analyzed 1,984 genomes of the zoonotic pathogen, Enterococcus faecalis, from human and animal sources. We found that strains from humans had larger genomes and greater sequence diversity, whereas those from animals carried a higher proportion of multidrug resistant genomes and had more diverse sequence targets in their CRISPR systems. To further explore animal-origin strains, we obtained 130 agricultural E. faecalis isolated from farms across the USA. We found that apart from geography, the presence of a CRISPR-Cas system and host animal identity drove genetic similarity. Finally, to evaluate its therapeutic potential against the spread of resistance in agricultural environments, we tested the efficacy of CRISPR-Cas in this niche. For this, we determined the ability of CRISPR-Cas to block plasmid transfer in manure. We found that not only is CRISPR-Cas effective in manure, it maintains its efficacy longer than in solid agar or liquid BHI media. Together, our work shows for the first time a comprehensive picture of CRISPR-Cas prevalence and efficacy in agriculturally relevant niches for E. faecalis.