Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence
Bacterial persistence is a phenomenon in which a small fraction of isogenic bacterial cells survives a lethal dose of antibiotics. Although the refractoriness of persistent cell populations has classically been attributed to growth-inactive cells generated before drug exposure, evidence is accumulat...
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eLife Sciences Publications Ltd
2025-05-01
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| Online Access: | https://elifesciences.org/articles/79517 |
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| author | Miki Umetani Miho Fujisawa Reiko Okura Takashi Nozoe Shoichi Suenaga Hidenori Nakaoka Edo Kussell Yuichi Wakamoto |
| author_facet | Miki Umetani Miho Fujisawa Reiko Okura Takashi Nozoe Shoichi Suenaga Hidenori Nakaoka Edo Kussell Yuichi Wakamoto |
| author_sort | Miki Umetani |
| collection | DOAJ |
| description | Bacterial persistence is a phenomenon in which a small fraction of isogenic bacterial cells survives a lethal dose of antibiotics. Although the refractoriness of persistent cell populations has classically been attributed to growth-inactive cells generated before drug exposure, evidence is accumulating that actively growing cell fractions can also generate persister cells. However, single-cell characterization of persister cell history remains limited due to the extremely low frequencies of persisters. Here, we visualize the responses of over one million individual cells of wildtype Escherichia coli to lethal doses of antibiotics, sampling cells from different growth phases and culture media into a microfluidic device. We show that when cells sampled from exponentially growing populations were treated with ampicillin or ciprofloxacin, most persisters were growing before antibiotic treatment. Growing persisters exhibited heterogeneous survival dynamics, including continuous growth and fission with L-form-like morphologies, responsive growth arrest, or post-exposure filamentation. Incubating cells under stationary phase conditions increased both the frequency and the probability of survival of non-growing cells to ampicillin. Under ciprofloxacin, however, all persisters identified were growing before the antibiotic treatment, including samples from post-stationary phase culture. These results reveal diverse persister cell dynamics that depend on antibiotic types and pre-exposure history. |
| format | Article |
| id | doaj-art-9ed914852fc14835aaaf971a4aa24644 |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-05-01 |
| publisher | eLife Sciences Publications Ltd |
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| spelling | doaj-art-9ed914852fc14835aaaf971a4aa246442025-08-20T01:51:23ZengeLife Sciences Publications LtdeLife2050-084X2025-05-011410.7554/eLife.79517Observation of persister cell histories reveals diverse modes of survival in antibiotic persistenceMiki Umetani0https://orcid.org/0000-0002-3171-4327Miho Fujisawa1Reiko Okura2Takashi Nozoe3https://orcid.org/0000-0003-2556-6484Shoichi Suenaga4https://orcid.org/0000-0002-9097-1286Hidenori Nakaoka5https://orcid.org/0000-0001-8465-5853Edo Kussell6https://orcid.org/0000-0003-0590-4036Yuichi Wakamoto7https://orcid.org/0000-0002-6233-0844Research Center for Complex Systems Biology, The University of Tokyo, Tokyo, Japan; Universal Biology Institute, The University of Tokyo, Tokyo, Japan; Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, JapanDepartment of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, JapanDepartment of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, JapanResearch Center for Complex Systems Biology, The University of Tokyo, Tokyo, Japan; Universal Biology Institute, The University of Tokyo, Tokyo, Japan; Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, JapanDepartment of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, JapanDepartment of Optical Imaging, Advanced Research Promotion Center, Tokushima University, Tokushima, JapanDepartment of Biology, New York University, New York, United States; Department of Physics, New York University, New York, United StatesResearch Center for Complex Systems Biology, The University of Tokyo, Tokyo, Japan; Universal Biology Institute, The University of Tokyo, Tokyo, Japan; Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, JapanBacterial persistence is a phenomenon in which a small fraction of isogenic bacterial cells survives a lethal dose of antibiotics. Although the refractoriness of persistent cell populations has classically been attributed to growth-inactive cells generated before drug exposure, evidence is accumulating that actively growing cell fractions can also generate persister cells. However, single-cell characterization of persister cell history remains limited due to the extremely low frequencies of persisters. Here, we visualize the responses of over one million individual cells of wildtype Escherichia coli to lethal doses of antibiotics, sampling cells from different growth phases and culture media into a microfluidic device. We show that when cells sampled from exponentially growing populations were treated with ampicillin or ciprofloxacin, most persisters were growing before antibiotic treatment. Growing persisters exhibited heterogeneous survival dynamics, including continuous growth and fission with L-form-like morphologies, responsive growth arrest, or post-exposure filamentation. Incubating cells under stationary phase conditions increased both the frequency and the probability of survival of non-growing cells to ampicillin. Under ciprofloxacin, however, all persisters identified were growing before the antibiotic treatment, including samples from post-stationary phase culture. These results reveal diverse persister cell dynamics that depend on antibiotic types and pre-exposure history.https://elifesciences.org/articles/79517antibiotic persistencesingle-cell analysismicrofluidicsstationary phasephenotypic heterogeneity |
| spellingShingle | Miki Umetani Miho Fujisawa Reiko Okura Takashi Nozoe Shoichi Suenaga Hidenori Nakaoka Edo Kussell Yuichi Wakamoto Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence eLife antibiotic persistence single-cell analysis microfluidics stationary phase phenotypic heterogeneity |
| title | Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence |
| title_full | Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence |
| title_fullStr | Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence |
| title_full_unstemmed | Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence |
| title_short | Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence |
| title_sort | observation of persister cell histories reveals diverse modes of survival in antibiotic persistence |
| topic | antibiotic persistence single-cell analysis microfluidics stationary phase phenotypic heterogeneity |
| url | https://elifesciences.org/articles/79517 |
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