Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases

By Robert J. Citorik, M. Mimee, Timothy K. Lu. Nature Biotechnology, 2014

724 citations recorded by the source corpus.

Current antibiotics tend to be broad spectrum, leading to indiscriminate killing of commensal bacteria and accelerated evolution of drug resistance. Here, we use CRISPR-Cas technology to create antimicrobials whose spectrum of activity is chosen by design. RNA-guided nucleases (RGNs) targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation. The DNA targets of RGNs can be undesirable genes or polymorphisms, including antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli. Delivery of RGNs significantly improves survival in a Galleria mellonella infection model. We also show that RGNs enable modulation of complex bacterial populations by selective knockdown of targeted strains based on genetic signatures. RGNs constitute a class of highly discriminatory, customizable antimicrobials that enact selective pressure at the DNA level to reduce the prevalence of undesired genes, minimize off-target effects and enable programmable remodeling of microbiota.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c491876426e29a10ab677c7734a7443cc019e68a

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In Ecology

1. S. Lemire
2. Hiroki Ando
3. Y. Taur
4. Rodolphe Barrangou
5. Eric G. Pamer
6. Gautam Dantas

In Molecular Biology

1. S. Lemire
2. Hiroki Ando
3. Y. Taur
4. Rodolphe Barrangou
5. Eric G. Pamer
6. Timothy K. Lu
7. Gautam Dantas
8. D. Pires

Citations in the corpus

• Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis (2019, background): “A resurging approach gaining significant interest is phage therapy, in which bacteriophages are used as antimicrobials (Bikard et al., 2014; Chen et al., 2014; Citorik et al., 2014; Devlin et al., 2016; Kutateladze and Adamia, 2010; Kutter et al., 2010, 2015; Lu and Collins, 2007, 2009; Maynard et a”
• Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing (2015, background): “Thus, CRISPR-Cas systems can help to overcome some challenges associated with engineering phage genomes in bacterial hosts for therapeutic applications (Bikard et al., 2014; Citorik et al., 2014; Goldberg et al., 2014; Kiro et al., 2014).”
• Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. (2016, background): “Finally, a strategy to eliminate selected bacterial targets exploiting the CRISPR/Cas9 system was recently proposed [127,128].”
• The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation (2016, background): “Recently, the natural transformation capacity of phages has been coupled with programmable nucleases to enable the generation of phages that specifically kill bacteria with undesirable genomic sequences, such as antibiotic resistance genes or virulence factors [164, 165].”
• Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins. (2019, background): “For example, several studies have demonstrated that targeted phage vectors can be utilized to re-sensitize or remove antibiotic-resistant bacteria frommixed populations (Bikard et al., 2014; Citorik et al., 2014; Edgar et al., 2012; Goren et al., 2017; Yosef et al., 2015).”
• Identifying and visualizing functional PAM diversity across CRISPR-Cas systems (2016, background): “The programmable and multiplexable nature of DNA/RNA targeting has led to a myriad of applications ranging from gene therapy to antimicrobials (Bikard et al., 2014; Citorik et al., 2014; Cong et al., 2013; Gomaa et al., 2014; Hilton et al., 2015; Mali et al., 2013).”