Academic Journal
Harnessing CRISPR interference to resensitize laboratory strains and clinical isolates to last resort antibiotics
| Title: | Harnessing CRISPR interference to resensitize laboratory strains and clinical isolates to last resort antibiotics |
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| Authors: | Angelica Frusteri Chiacchiera, Michela Casanova, Massimo Bellato, Aurora Piazza, Roberta Migliavacca, Gregory Batt, Paolo Magni, Lorenzo Pasotti |
| Source: | Scientific Reports, Vol 15, Iss 1, Pp 1-19 (2025) |
| Publisher Information: | Nature Portfolio, 2025. |
| Publication Year: | 2025 |
| Collection: | LCC:Medicine LCC:Science |
| Subject Terms: | Antimicrobial resistance, Antibiotic re-sensitization, CRISPR array, Escherichia coli clinical isolates, bla NDM-type, bla ctx−M-type, Medicine, Science |
| More Details: | Abstract The global race against antimicrobial resistance requires novel antimicrobials that are not only effective in killing specific bacteria, but also minimize the emergence of new resistances. Recently, CRISPR/Cas-based antimicrobials were proposed to address killing specificity with encouraging results. However, the emergence of target sequence mutations triggered by Cas-cleavage was identified as an escape strategy, posing the risk of generating new antibiotic-resistance gene (ARG) variants. Here, we evaluated an antibiotic re-sensitization strategy based on CRISPR interference (CRISPRi), which inhibits gene expression without damaging target DNA. The resistance to four antibiotics, including last resort drugs, was significantly reduced by individual and multi-gene targeting of ARGs in low- to high-copy numbers in recombinant E. coli. Escaper analysis confirmed the absence of mutations in target sequence, corroborating the harmless role of CRISPRi in the selection of new resistances. E. coli clinical isolates carrying ARGs of severe clinical concern were then used to assess the robustness of CRISPRi under different growth conditions. Meropenem, colistin and cefotaxime susceptibility was successfully increased in terms of MIC (up to > 4-fold) and growth delay (up to 11 h) in a medium-dependent fashion. ARG repression also worked in a pathogenic strain grown in human urine, as a demonstration of CRISPRi-mediated re-sensitization in host-mimicking media. This study laid the foundations for further leveraging CRISPRi as antimicrobial agent or research tool to selectively repress ARGs and investigate resistance mechanisms. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 2045-2322 |
| Relation: | https://doaj.org/toc/2045-2322 |
| DOI: | 10.1038/s41598-024-81989-5 |
| Access URL: | https://doaj.org/article/1c88d28c2cde4edeb8540db2f11fdafa |
| Accession Number: | edsdoj.1c88d28c2cde4edeb8540db2f11fdafa |
| Database: | Directory of Open Access Journals |
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| ISSN: | 20452322 |
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| DOI: | 10.1038/s41598-024-81989-5 |
| Published in: | Scientific Reports |
| Language: | English |