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Development of CRSIPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria

By Kotaro Kiga, Xin-Ee Tan, Rodrigo Ibarra-Chávez, Shinya Watanabe, Yoshifumi Aiba, Yusuke Sato’o, Feng-Yu Li, Teppei Sasahara, Bintao Cui, Moriyuki Kawauchi, Tanit Boonsiri, Kanate Thitiananpakorn, Yusuke Taki, Aa Haeruman Azam, Masato Suzuki, José R Penadés, Longzhu Cui

Posted 17 Oct 2019
bioRxiv DOI: 10.1101/808741

Emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. We established a series of CRISPR-Cas13a-based antibacterial nucleocapsid, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus through promiscuous RNA cleavage after recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs were generated by packaging CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibited strong bacterial killing activities upon recognizing target genes regardless of their location. The antimicrobials’ treatment efficacy was confirmed using a Galleria mellonella larvae model. Further, we demonstrated that the CapsidCas13a(s) can assist in bacterial gene detection without employing nucleic acid amplification and optical devices.

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