CRISPR Phagemid for Selective Bacterial Killing
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Solution Overview
Problem
Traditional antimicrobials lack specificity in targeting bacteria, leading to unintended consequences such as antibiotic resistance and negative effects on human health, highlighting the need for tools to selectively control complex microbial populations.
Innovation Solution
Development of pharmaceutical compositions and methods utilizing a CRISPR system packaged in phagemids, which include a Cas enzyme and targeting RNA, to selectively reduce antibiotic-resistant and virulent bacteria by targeting unique DNA sequences specific to these bacteria.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If traditional antimicrobials are used to kill bacteria, then bacterial population is reduced, but antibiotic resistance emerges and non-targeted bacteria are also affected
Solution Approach 1:
The patent uses CRISPR-Cas systems as intermediaries to achieve selective bacterial killing. The system employs guide RNAs that specifically recognize and bind to target bacterial DNA sequences, directing the Cas nuclease to cleave only those sequences. This intermediary mechanism enables precise discrimination between target and non-target bacteria, resolving the selectivity problem of traditional antimicrobials
Solution Approach 2:
The invention applies local quality by designing CRISPR target sequences that are specific to particular bacterial species or strains. By targeting unique genomic regions rather than universal bacterial components, the system achieves localized specificity - affecting only the intended target while leaving other bacteria unaffected. This is accomplished through careful selection of spacer sequences that match only the desired target organism
2Object-affected harmful factors
If broad-spectrum antimicrobials are used to eliminate pathogenic bacteria, then virulent bacteria are killed, but beneficial bacteria are also harmed
Solution Approach 1:
The CRISPR-Cas system serves as a selective intermediary that distinguishes between pathogenic and beneficial bacteria through sequence-specific recognition. Guide RNAs are designed to target virulence factors or species-specific sequences of pathogenic bacteria, allowing the system to selectively eliminate harmful organisms while preserving beneficial members of the microbiome that lack the target sequences
3Reliability
If CRISPR systems are designed to target specific bacterial sequences, then selectivity is improved, but complexity of the system increases
Solution Approach 1:
The patent leverages the universal nature of the CRISPR-Cas mechanism, which can be programmed to target any DNA sequence by simply changing the guide RNA sequence. This multi-functional platform allows the same core Cas nuclease and CRISPR machinery to be adapted for targeting different bacterial species or strains, reducing overall system complexity while maintaining high selectivity through programmable RNA guides
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
The CRISPR system effectively reduces the population of targeted bacteria while sparing non-virulent and non-antibiotic-resistant bacteria, demonstrating sequence-specific killing and plasmid curing, with potential applications in therapeutic and prophylactic treatments.
Implementation Method 1
The compositions and methods involve targeting bacteria, wherein the targeted bacteria can be differentiated from other members of the population by at least one unique clustered regularly interspaced short palindromic repeats (CRISPR) targeted DNA sequence. The phagemid comprises a CRISPR system, wherein the CRISPR system comprises nucleotide sequences encoding i) a CRISPR-associated (Cas) enzyme; and ii) a targeting RNA
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.