Sequence-Specific CRISPR Antimicrobials for Selective Bacterial Killing
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Solution Overview
Problem
Existing antimicrobials lack specificity in targeting bacteria, leading to the emergence of antibiotic resistance and negative health effects, necessitating a need for tools to selectively control and manipulate complex microbial consortia.
Innovation Solution
Compositions and methods utilizing a CRISPR system delivered by recombinant phagemids to target specific bacteria through unique CRISPR DNA sequences, enabling selective reduction of antibiotic-resistant and virulent bacteria.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional antimicrobials are used to kill bacteria, then bacterial infection is reduced, but antibiotic resistance emerges and non-target bacteria are harmed
Solution Approach 1:
The antimicrobial activity is segmented into specific CRISPR-Cas systems that target only particular bacterial species or strains through unique DNA sequences, rather than affecting all bacteria indiscriminately. Each CRISPR system is designed with specific guide RNA sequences that recognize and bind to target bacterial genomes, enabling selective killing of pathogenic bacteria while preserving beneficial microbiota.
Solution Approach 2:
The patent applies local quality by designing CRISPR systems with customized target sequences that match specific pathogenic bacteria. The guide RNA sequences are tailored to recognize unique genomic regions of target bacteria, creating localized specificity in an otherwise broad antimicrobial approach. This allows the system to exert antimicrobial activity only where needed (against specific pathogens) while leaving other bacteria unaffected.
2Productivity
If broad-spectrum antibiotics are used to treat bacterial infections, then infection control is improved, but negative health effects and promotion of antibiotic resistance occur
Solution Approach 1:
The patent uses CRISPR-Cas systems as intermediary mechanisms that provide targeted antimicrobial activity. Instead of using traditional antibiotics that directly kill bacteria through enzymatic inhibition, the CRISPR system acts as an intermediary by introducing programmable RNA guides that direct Cas enzymes to specific bacterial DNA sequences, enabling precise pathogen elimination without the collateral damage of broad-spectrum antibiotics.
Solution Approach 2:
The patent changes the fundamental parameter of antimicrobial specificity from broad-spectrum to narrow-spectrum targeting. By modifying the guide RNA sequences in the CRISPR system, the target specificity can be precisely adjusted to match different pathogenic bacteria, allowing treatment of specific infections while preserving the broader microbiome and preventing resistance development.
3Measurement precision
If CRISPR systems are designed to target specific bacteria, then selective killing of pathogenic bacteria is achieved, but delivery into bacteria must be efficient
Solution Approach 1:
The patent transitions the CRISPR system from a purely genetic tool to a deliverable therapeutic by packaging it into viral vectors. This adds a new dimension (viral delivery capability) to the CRISPR system, enabling efficient introduction into target bacteria through natural viral infection mechanisms while maintaining the precise targeting capability of the original CRISPR design.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Achieves targeted killing of specific bacteria while preserving non-virulent strains, reducing antibiotic resistance and virulence factors, and eliminating plasmids carrying resistance genes, applicable in medical and non-medical settings.
Implementation Method 1
The CRISPR system comprises nucleotide sequences encoding i) a CRISPR-associated (Cas) enzyme; and ii) a targeting RNA
Implementation Method 2
contacting the bacterial population is such that at least some of the phagemids are introduced into at least some of the bacteria in the bacterial population
Data Source
AI summary
Provided are compositions and methods for selectively reducing the amount of antibiotic resistant and/or virulent bacteria in a mixed bacteria population, or for reducing any other type of unwanted bacteria in a mixed bacteria population. The compositions and methods involve targeting bacteria that are differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The compositions and methods can be readily adapted to target any bacteria or any bacteria plasmid, or both.