1
|
Gil-Gil T, Berryhill BA, Manuel JA, Smith AP, McCall IC, Baquero F, Levin BR. The evolution of heteroresistance via small colony variants in Escherichia coli following long term exposure to bacteriostatic antibiotics. Nat Commun 2024; 15:7936. [PMID: 39261449 PMCID: PMC11391013 DOI: 10.1038/s41467-024-52166-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 08/27/2024] [Indexed: 09/13/2024] Open
Abstract
Traditionally, bacteriostatic antibiotics are agents able to arrest bacterial growth. Despite being traditionally viewed as unable to kill bacterial cells, when they are used clinically the outcome of these drugs is frequently as effective as when a bactericidal drug is used. We explore the dynamics of Escherichia coli after exposure to two ribosome-targeting bacteriostatic antibiotics, chloramphenicol and azithromycin, for thirty days. The results of our experiments provide evidence that bacteria exposed to these drugs replicate, evolve, and generate a sub-population of small colony variants (SCVs) which are resistant to multiple drugs. These SCVs contribute to the evolution of heteroresistance and rapidly revert to a susceptible state once the antibiotic is removed. Stated another way, exposure to bacteriostatic drugs selects for the evolution of heteroresistance in populations previously lacking this trait. More generally, our results question the definition of bacteriostasis as populations exposed to bacteriostatic drugs are replicating despite the lack of net growth.
Collapse
Affiliation(s)
- Teresa Gil-Gil
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Brandon A Berryhill
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
- Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, 30322, USA
| | - Joshua A Manuel
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Andrew P Smith
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Ingrid C McCall
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Fernando Baquero
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, and Centro de Investigación Médica en Red, Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
| |
Collapse
|
2
|
Herencias C, Rivero-Buceta V, Salgado S, Hernández-Herreros N, Baquero F, Del Campo R, Nogales J, Prieto MA. Bdellovibrio's prey-independent lifestyle is fueled by amino acids as a carbon source. Appl Microbiol Biotechnol 2024; 108:422. [PMID: 39031211 PMCID: PMC11271337 DOI: 10.1007/s00253-024-13250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/22/2024]
Abstract
Identifying the nutritional requirements and growth conditions of microorganisms is crucial for determining their applicability in industry and understanding their role in clinical ecology. Predatory bacteria such as Bdellovibrio bacteriovorus have emerged as promising tools for combating infections by human bacterial pathogens due to their natural killing features. Bdellovibrio's lifecycle occurs inside prey cells, using the cytoplasm as a source of nutrients and energy. However, this lifecycle supposes a challenge when determining the specific uptake of metabolites from the prey to complete the growth inside cells, a process that has not been completely elucidated. Here, following a model-based approach, we illuminate the ability of B. bacteriovorus to replicate DNA, increase biomass, and generate adenosine triphosphate (ATP) in an amino acid-based rich media in the absence of prey, keeping intact its predatory capacity. In this culture, we determined the main carbon sources used and their preference, being glutamate, serine, aspartate, isoleucine, and threonine. This study offers new insights into the role of predatory bacteria in natural environments and establishes the basis for developing new Bdellovibrio applications using appropriate metabolic and physiological methodologies. KEY POINTS: • Amino acids support axenic lifestyle of Bdellovibrio bacteriovorus. • B. bacteriovorus preserves its predatory ability when growing in the absence of prey.
Collapse
Affiliation(s)
- Cristina Herencias
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Virginia Rivero-Buceta
- Polymer Biotechnology Laboratory, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - Sergio Salgado
- Polymer Biotechnology Laboratory, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - Natalia Hernández-Herreros
- Polymer Biotechnology Laboratory, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública-CIBERESP, Instituto Carlos III, Madrid, Spain
| | - Rosa Del Campo
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Nogales
- Systems Biotechnology GroupDepartment of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Laboratory, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain.
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain.
| |
Collapse
|
3
|
Herencias C, Álvaro-Llorente L, Ramiro-Martínez P, Fernández-Calvet A, Muñoz-Cazalla A, DelaFuente J, Graf FE, Jaraba-Soto L, Castillo-Polo JA, Cantón R, San Millán Á, Rodríguez-Beltrán J. β-lactamase expression induces collateral sensitivity in Escherichia coli. Nat Commun 2024; 15:4731. [PMID: 38830889 PMCID: PMC11148083 DOI: 10.1038/s41467-024-49122-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
Major antibiotic groups are losing effectiveness due to the uncontrollable spread of antimicrobial resistance (AMR) genes. Among these, β-lactam resistance genes -encoding β-lactamases- stand as the most common resistance mechanism in Enterobacterales due to their frequent association with mobile genetic elements. In this context, novel approaches that counter mobile AMR are urgently needed. Collateral sensitivity (CS) occurs when the acquisition of resistance to one antibiotic increases susceptibility to another antibiotic and can be exploited to eliminate AMR selectively. However, most CS networks described so far emerge as a consequence of chromosomal mutations and cannot be leveraged to tackle mobile AMR. Here, we dissect the CS response elicited by the acquisition of a prevalent antibiotic resistance plasmid to reveal that the expression of the β-lactamase gene blaOXA-48 induces CS to colistin and azithromycin. We next show that other clinically relevant mobile β-lactamases produce similar CS responses in multiple, phylogenetically unrelated E. coli strains. Finally, by combining experiments with surveillance data comprising thousands of antibiotic susceptibility tests, we show that β-lactamase-induced CS is pervasive within Enterobacterales. These results highlight that the physiological side-effects of β-lactamases can be leveraged therapeutically, paving the way for the rational design of specific therapies to block mobile AMR or at least counteract their effects.
Collapse
Affiliation(s)
- Cristina Herencias
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Laura Álvaro-Llorente
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Paula Ramiro-Martínez
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | - Ada Muñoz-Cazalla
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | | | - Fabrice E Graf
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Laura Jaraba-Soto
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Juan Antonio Castillo-Polo
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Álvaro San Millán
- Centro Nacional de Biotecnología-CSIC, Madrid, Spain.
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública-CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
4
|
Baquero F, Rodríguez-Beltrán J, Levin BR. Bacteriostatic cells instead of bacteriostatic antibiotics? mBio 2024; 15:e0268023. [PMID: 38126752 PMCID: PMC10865802 DOI: 10.1128/mbio.02680-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
This year we commemorate the centennial of the birth of the mature concept of bacteriostasis by John W. Churchman at Cornell University Medical School. The term bacteriostasis has primarily been applied to antibiotics (bacteriostatic antibiotics). In this Opinion paper, we are revisiting this concept by suggesting that bacteriostasis essentially reflects a distinct cellular status (or "cell variant") characterized by the inability to be killed as a consequence of an antibiotic-induced stress impacting on bacterial physiology/metabolism (growth). Note that the term "bacteriostasis" should not be associated only with antimicrobials but with many stressful conditions. In that respect, the drug promotion of bacteriostasis might resemble other types of stress-induced cellular differentiation, such as sporulation, in which spores can be considered "bacteriostatic cells" or perhaps as persister bacteria, which can become "normal cells" again when the stressful conditions have abated.IMPORTANCEThis year we commemorate the centennial of the birth of the mature concept of bacteriostasis by John W. Churchman at Cornell University Medical School. The term bacteriostasis has primarily been applied to antibiotics (bacteriostatic antibiotics). In this Opinion paper, we are revisiting this concept by suggesting that some antibiotics are drugs that induce bacteria to become bacteriostatic. Cells that are unable to multiply, thereby preventing the antibiotic from exerting major lethal effects on them, are a variant ("different") type of cells, bacteriostatic cells. Note that the term "bacteriostasis" should not be associated only with antimicrobials but with many stressful conditions. In that respect, the drug promotion of bacteriostasis might resemble other types of stress-induced cellular differentiation, such as sporulation, in which spores can be considered "bacteriostatic cells" or perhaps as persister bacteria, which can become "normal cells" again when the stressful conditions have abated.
Collapse
Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Public Health Networking Biomedical Research Centre in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Public Health Networking Biomedical Research Centre in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Bruce R. Levin
- Department of Biology, Emory University, Atlanta, Georgia, USA
| |
Collapse
|
5
|
Martínez JL, Baquero F. What are the missing pieces needed to stop antibiotic resistance? Microb Biotechnol 2023; 16:1900-1923. [PMID: 37417823 PMCID: PMC10527211 DOI: 10.1111/1751-7915.14310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 07/08/2023] Open
Abstract
As recognized by several international agencies, antibiotic resistance is nowadays one of the most relevant problems for human health. While this problem was alleviated with the introduction of new antibiotics into the market in the golden age of antimicrobial discovery, nowadays few antibiotics are in the pipeline. Under these circumstances, a deep understanding on the mechanisms of emergence, evolution and transmission of antibiotic resistance, as well as on the consequences for the bacterial physiology of acquiring resistance is needed to implement novel strategies, beyond the development of new antibiotics or the restriction in the use of current ones, to more efficiently treat infections. There are still several aspects in the field of antibiotic resistance that are not fully understood. In the current article, we make a non-exhaustive critical review of some of them that we consider of special relevance, in the aim of presenting a snapshot of the studies that still need to be done to tackle antibiotic resistance.
Collapse
Affiliation(s)
| | - Fernando Baquero
- Ramón y Cajal Institute for Health Research (IRYCIS), Department of MicrobiologyRamón y Cajal University Hospital, CIBER en Epidemiología y Salud Pública (CIBERESP)MadridSpain
| |
Collapse
|