1
|
Shuai Y, Li N, Zhang Y, Bao Q, Wei T, Yang T, Cheng Q, Wang W, Hu B, Mao C, Yang M. Aptamer-free upconversion nanoparticle/silk biosensor system for low-cost and highly sensitive detection of antibiotic residues. Biosens Bioelectron 2024; 258:116335. [PMID: 38710144 DOI: 10.1016/j.bios.2024.116335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The detection of antibiotics is crucial for safeguarding the environment, ensuring food safety, and promoting human health. However, developing a rapid, convenient, low-cost, and sensitive method for antibiotic detection presents significant challenges. Herein, an aptamer-free biosensor was successfully constructed using upconversion nanoparticles (UCNPs) coated with silk fibroin (SF), based on Förster resonance energy transfer (FRET) and the charge-transfer effect, for detecting roxithromycin (RXM). A synergistic FRET efficiency was achieved by utilizing alizarin red and RXM complexes as energy acceptors, with UCNP as the energy donor, and immobilizing an ultrathin SF protein corona within 10 nm. The biosensor detects RXM in deionized water with high sensitivity primarily through monolayer adsorption, with a detection range of 1.0 nM-141.6 nM and a detection limit as low as 0.68 nM. The performance of this biosensor was compared with the ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) method for detecting antibiotics in river water separately and a strong correlation between the two methods was observed. The biosensor exhibited long-term stability in aqueous solutions (up to 60 d) with no attenuation of fluorescence intensity. Furthermore, the biosensor's applicability extended to the highly sensitive detection of other antibiotics, such as azithromycin. This study introduces a low-cost, eco-friendly, and highly sensitive method for antibiotic detection, with broad potential for future applications in environmental, healthcare, and food-related fields.
Collapse
Affiliation(s)
- Yajun Shuai
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Institute of Applied Bioresource Research, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Na Li
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Institute of Applied Bioresource Research, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Ying Zhang
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Institute of Applied Bioresource Research, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, PR China
| | - Tiancheng Wei
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Institute of Applied Bioresource Research, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, PR China
| | - Qichao Cheng
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Institute of Applied Bioresource Research, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Wei Wang
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Baolan Hu
- Department of Environmental Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Chuanbin Mao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, PR China; Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, PR China
| | - Mingying Yang
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Institute of Applied Bioresource Research, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China.
| |
Collapse
|
2
|
Kollerová S, Jouvet L, Smelková J, Zunk-Parras S, Rodríguez-Rojas A, Steiner UK. Phenotypic resistant single-cell characteristics under recurring ampicillin antibiotic exposure in Escherichia coli. mSystems 2024:e0025624. [PMID: 38920373 DOI: 10.1128/msystems.00256-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Non-heritable, phenotypic drug resistance toward antibiotics challenges antibiotic therapies. Characteristics of such phenotypic resistance have implications for the evolution of heritable resistance. Diverse forms of phenotypic resistance have been described, but phenotypic resistance characteristics remain less explored than genetic resistance. Here, we add novel combinations of single-cell characteristics of phenotypic resistant E. coli cells and compare those to characteristics of susceptible cells of the parental population by exposure to different levels of recurrent ampicillin antibiotic. Contrasting expectations, we did not find commonly described characteristics of phenotypic resistant cells that arrest growth or near growth. We find that under ampicillin exposure, phenotypic resistant cells reduced their growth rate by about 50% compared to growth rates prior to antibiotic exposure. The growth reduction is a delayed alteration to antibiotic exposure, suggesting an induced response and not a stochastic switch or caused by a predetermined state as frequently described. Phenotypic resistant cells exhibiting constant slowed growth survived best under ampicillin exposure and, contrary to expectations, not only fast-growing cells suffered high mortality triggered by ampicillin but also growth-arrested cells. Our findings support diverse modes of phenotypic resistance, and we revealed resistant cell characteristics that have been associated with enhanced genetically fixed resistance evolution, which supports claims of an underappreciated role of phenotypic resistant cells toward genetic resistance evolution. A better understanding of phenotypic resistance will benefit combatting genetic resistance by developing and engulfing effective anti-phenotypic resistance strategies. IMPORTANCE Antibiotic resistance is a major challenge for modern medicine. Aside from genetic resistance to antibiotics, phenotypic resistance that is not heritable might play a crucial role for the evolution of antibiotic resistance. Using a highly controlled microfluidic system, we characterize single cells under recurrent exposure to antibiotics. Fluctuating antibiotic exposure is likely experienced under common antibiotic therapies. These phenotypic resistant cell characteristics differ from previously described phenotypic resistance, highlighting the diversity of modes of resistance. The phenotypic characteristics of resistant cells we identify also imply that such cells might provide a stepping stone toward genetic resistance, thereby causing treatment failure.
Collapse
Affiliation(s)
- Silvia Kollerová
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Lionel Jouvet
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Julia Smelková
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | | | - Ulrich K Steiner
- Department of Biology, University of Southern Denmark, Odense, Denmark
- Biological Institute, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
3
|
Rolon ML, Voloshchuk O, Bartlett KV, LaBorde LF, Kovac J. Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride. Biofilm 2024; 7:100177. [PMID: 38304489 PMCID: PMC10832383 DOI: 10.1016/j.bioflm.2024.100177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Listeria monocytogenes may survive and persist in food processing environments due to formation of complex multi-species biofilms of environmental microbiota that co-exists in these environments. This study aimed to determine the effect of selected environmental microbiota on biofilm formation and tolerance of L. monocytogenes to benzalkonium chloride in formed biofilms. The studied microbiota included bacterial families previously shown to co-occur with L. monocytogenes in tree fruit packing facilities, including Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae. Biofilm formation ability and the effect of formed biofilms on the tolerance of L. monocytogenes to benzalkonium chloride was measured in single- and multi-family assemblages. Biofilms were grown statically on polystyrene pegs submerged in a R2A broth. Biofilm formation was quantified using a crystal violet assay, spread-plating, confocal laser scanning microscopy, and its composition was assessed using amplicon sequencing. The concentration of L. monocytogenes in biofilms was determined using the most probable number method. Biofilms were exposed to the sanitizer benzalkonium chloride, and the death kinetics of L. monocytogenes were quantified using a most probable number method. A total of 8, 8, 6, and 3 strains of Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae, respectively, were isolated from the environmental microbiota of tree fruit packing facilities and were used in this study. Biofilms formed by Pseudomonadaceae, Xanthomonadaceae, and all multi-family assemblages had significantly higher concentration of bacteria, as well as L. monocytogenes, compared to biofilms formed by L. monocytogenes alone. Furthermore, multi-family assemblage biofilms increased the tolerance of L. monocytogenes to benzalkonium chloride compared to L. monocytogenes mono-species biofilms and planktonic multi-family assemblages. These findings suggest that L. monocytogenes control strategies should focus not only on assessing the efficacy of sanitizers against L. monocytogenes, but also against biofilm-forming microorganisms that reside in the food processing built environment, such as Pseudomonadaceae or Xanthomonadaceae.
Collapse
Affiliation(s)
- M. Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Olena Voloshchuk
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Katelyn V. Bartlett
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Luke F. LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
4
|
Krewing M, Mönch E, Bolten A, Niesalla H. Resistance or tolerance? Highlighting the need for precise terminology in the field of disinfection. J Hosp Infect 2024:S0195-6701(24)00176-2. [PMID: 38782058 DOI: 10.1016/j.jhin.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The terms resistance and tolerance are well defined in the context of antibiotic research. However, in the field of disinfection, these terms are often used synonymously, which creates ambiguity and can lead to misunderstandings and misconceptions. In addition, this inconsistency in terminology makes it difficult to assess the risk of a disinfectant resistance. This general review aims to discuss existing definitions of the terms adaptation, susceptibility, tolerance, persistence, and resistance in the light of disinfectants. The most ambiguity is found between tolerance and resistance. Whereas the former describes the not necessarily heritable survival of transient exposure to usually lethal concentrations, resistance is the strictly heritable ability to survive otherwise lethal concentrations of an antimicrobial agent, regardless of exposure time. A simple transfer of experience from antibiotic research is not recommended when assessing the risk of resistance to disinfectants, as there are important differences between antibiotics and disinfectants, although both are antimicrobials: (i) disinfectants are usually applied at concentrations that exceed the minimum inhibitory concentration by orders of magnitude, (ii) the exposure times of disinfectants are in the range of seconds, minutes, or a few hours, (iii) the mode of action of disinfectants is less specific, and (iv) disinfectants often contain more than one active agent with additive or synergistic effects. It is important to recognise that disinfectants, like other antimicrobial agents such as antibiotics, have a dualistic nature and should be used correctly and with caution.
Collapse
Affiliation(s)
- Marco Krewing
- HARTMANN SCIENCE CENTER, BODE Chemie GmbH - A company of the HARTMANN GROUP, Hamburg, Germany.
| | - Erika Mönch
- BODE Chemie GmbH - A company of the HARTMANN GROUP, Hamburg, Germany
| | - Astrid Bolten
- BODE Chemie GmbH - A company of the HARTMANN GROUP, Hamburg, Germany
| | - Heide Niesalla
- HARTMANN SCIENCE CENTER, BODE Chemie GmbH - A company of the HARTMANN GROUP, Hamburg, Germany
| |
Collapse
|
5
|
Dasilva MA, Andrada KFC, Torales MM, Hughes IM, Pez P, García-Martínez JC, Paraje MG. Synergistic activity of gold nanoparticles with amphotericin B on persister cells of Candida tropicalis biofilms. J Nanobiotechnology 2024; 22:254. [PMID: 38755625 PMCID: PMC11097580 DOI: 10.1186/s12951-024-02415-6] [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: 10/23/2023] [Accepted: 03/18/2024] [Indexed: 05/18/2024] Open
Abstract
AIM The antifungal activity was studied on sessile and persister cells (PCs) of Candida tropicalis biofilms of gold nanoparticles (AuNPs) stabilized with cetyltrimethylammonium bromide (CTAB-AuNPs) and those conjugated with cysteine, in combination with Amphotericin B (AmB). MATERIALS/METHODS The PC model was used and synergistic activity was tested by the checkerboard assay. Biofilms were studied by crystal violet and scanning electron microscopy. RESULTS/CONCLUSIONS After the combination of both AuNPs and AmB the biofilm biomass was reduced, with significant differences in architecture being observed with a reduced biofilm matrix. In addition, the CTAB-AuNPs-AmB combination significantly reduced PCs. Understanding how these AuNPs aid in the fight against biofilms and the development of new approaches to eradicate PCs has relevance for chronic infection treatment.
Collapse
Affiliation(s)
- M A Dasilva
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, X5000HUA, Argentina
| | - K F Crespo Andrada
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, X5000HUA, Argentina
| | - M Maldonado Torales
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, X5000HUA, Argentina
| | - I Manrrique Hughes
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, X5000HUA, Argentina
| | - P Pez
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, X5000HUA, Argentina
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - J C García-Martínez
- Facultad de Farmacia de Albacete, Centro Regional de Investigaciones Biomédicas, Universidad de Castilla-La Mancha, Ciudad Real, España
| | - María Gabriela Paraje
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina.
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, X5000HUA, Argentina.
| |
Collapse
|
6
|
Updegrove TB, Delerue T, Anantharaman V, Cho H, Chan C, Nipper T, Choo-Wosoba H, Jenkins LM, Zhang L, Su Y, Shroff H, Chen J, Bewley CA, Aravind L, Ramamurthi KS. Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587046. [PMID: 38903092 PMCID: PMC11188070 DOI: 10.1101/2024.03.27.587046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Starvation triggers bacterial spore formation, a committed differentiation program that transforms a vegetative cell into a dormant spore. Cells in a population enter sporulation non-uniformly to secure against the possibility that favorable growth conditions, which puts sporulation-committed cells at a disadvantage, may resume. This heterogeneous behavior is initiated by a passive mechanism: stochastic activation of a master transcriptional regulator. Here, we identify a cell-cell communication pathway that actively promotes phenotypic heterogeneity, wherein Bacillus subtilis cells that start sporulating early utilize a calcineurin-like phosphoesterase to release glycerol, which simultaneously acts as a signaling molecule and a nutrient to delay non-sporulating cells from entering sporulation. This produced a more diverse population that was better poised to exploit a sudden influx of nutrients compared to those generating heterogeneity via stochastic gene expression alone. Although conflict systems are prevalent among microbes, genetically encoded cooperative behavior in unicellular organisms can evidently also boost inclusive fitness.
Collapse
Affiliation(s)
- Taylor B. Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Delerue
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hyomoon Cho
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carissa Chan
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Nipper
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hyoyoung Choo-Wosoba
- Biostatistics and Data Management Support Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa M. Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Farm Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Janelia Farm Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kumaran S. Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
7
|
Wood WN, Rubio MA, Leiva LE, Phillips GJ, Ibba M. Methionyl-tRNA synthetase synthetic and proofreading activities are determinants of antibiotic persistence. Front Microbiol 2024; 15:1384552. [PMID: 38601944 PMCID: PMC11004401 DOI: 10.3389/fmicb.2024.1384552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
Bacterial antibiotic persistence is a phenomenon where bacteria are exposed to an antibiotic and the majority of the population dies while a small subset enters a low metabolic, persistent, state and are able to survive. Once the antibiotic is removed the persistent population can resuscitate and continue growing. Several different molecular mechanisms and pathways have been implicated in this phenomenon. A common mechanism that may underly bacterial antibiotic persistence is perturbations in protein synthesis. To investigate this mechanism, we characterized four distinct metG mutants for their ability to increase antibiotic persistence. Two metG mutants encode changes near the catalytic site of MetRS and the other two mutants changes near the anticodon binding domain. Mutations in metG are of particular interest because MetRS is responsible for aminoacylation both initiator tRNAMet and elongator tRNAMet indicating that these mutants could impact translation initiation and/or translation elongation. We observed that all the metG mutants increased the level of antibiotic persistence as did reduced transcription levels of wild type metG. Although, the MetRS variants did not have an impact on MetRS activity itself, they did reduce translation rates. It was also observed that the MetRS variants affected the proofreading mechanism for homocysteine and that these mutants' growth is hypersensitive to homocysteine. Taken together with previous findings, our data indicate that both reductions in cellular Met-tRNAMet synthetic capacity and reduced proofreading of homocysteine by MetRS variants are positive determinants for bacterial antibiotic persistence.
Collapse
Affiliation(s)
- Whitney N. Wood
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Miguel Angel Rubio
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Lorenzo Eugenio Leiva
- Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, IA, United States
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| |
Collapse
|
8
|
Frizzell JK, Taylor RL, Ryno LM. Constitutive Activation of RpoH and the Addition of L-arabinose Influence Antibiotic Sensitivity of PHL628 E. coli. Antibiotics (Basel) 2024; 13:143. [PMID: 38391529 PMCID: PMC10886279 DOI: 10.3390/antibiotics13020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Antibiotics are used to combat the ever-present threat of infectious diseases, but bacteria are continually evolving an assortment of defenses that enable their survival against even the most potent treatments. While the demand for novel antibiotic agents is high, the discovery of a new agent is exceedingly rare. We chose to focus on understanding how different signal transduction pathways in the gram-negative bacterium Escherichia coli (E. coli) influence the sensitivity of the organism to antibiotics from three different classes: tetracycline, chloramphenicol, and levofloxacin. Using the PHL628 strain of E. coli, we exogenously overexpressed two transcription factors, FliA and RpoH.I54N (a constitutively active mutant), to determine their influence on the minimum inhibitory concentration (MIC) and minimum duration of killing (MDK) concentration for each of the studied antibiotics. We hypothesized that activating these pathways, which upregulate genes that respond to specific stressors, could mitigate bacterial response to antibiotic treatment. We also compared the exogenous overexpression of the constitutively active RpoH mutant to thermal heat shock that has feedback loops maintained. While FliA overexpression had no impact on MIC or antibiotic tolerance, RpoH.I54N overexpression reduced the MIC for tetracycline and chloramphenicol but had no independent impact on antibiotic tolerance. Thermal heat shock alone also did not affect MIC or antibiotic tolerance. L-arabinose, the small molecule used to induce expression in our system, unexpectedly independently increased the MICs for tetracycline (>2-fold) and levofloxacin (3-fold). Additionally, the combination of thermal heat shock and arabinose provided a synergistic, 5-fold increase in MIC for chloramphenicol. Arabinose increased the tolerance, as assessed by MDK99, for chloramphenicol (2-fold) and levofloxacin (4-fold). These experiments highlight the potential of the RpoH pathway to modulate antibiotic sensitivity and the emerging implication of arabinose in enhanced MIC and antibiotic tolerance.
Collapse
Affiliation(s)
- Jenna K Frizzell
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA
| | - Ryan L Taylor
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA
| | - Lisa M Ryno
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA
| |
Collapse
|
9
|
Parsons JB, Sidders AE, Velez AZ, Hanson BM, Angeles-Solano M, Ruffin F, Rowe SE, Arias CA, Fowler VG, Thaden JT, Conlon BP. In-patient evolution of a high-persister Escherichia coli strain with reduced in vivo antibiotic susceptibility. Proc Natl Acad Sci U S A 2024; 121:e2314514121. [PMID: 38190524 PMCID: PMC10801923 DOI: 10.1073/pnas.2314514121] [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: 08/23/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024] Open
Abstract
Gram-negative bacterial bloodstream infections (GNB-BSI) are common and frequently lethal. Despite appropriate antibiotic treatment, relapse of GNB-BSI with the same bacterial strain is common and associated with poor clinical outcomes and high healthcare costs. The role of persister cells, which are sub-populations of bacteria that survive for prolonged periods in the presence of bactericidal antibiotics, in relapse of GNB-BSI is unclear. Using a cohort of patients with relapsed GNB-BSI, we aimed to determine how the pathogen evolves within the patient between the initial and subsequent episodes of GNB-BSI and how these changes impact persistence. Using Escherichia coli clinical bloodstream isolate pairs (initial and relapse isolates) from patients with relapsed GNB-BSI, we found that 4/11 (36%) of the relapse isolates displayed a significant increase in persisters cells relative to the initial bloodstream infection isolate. In the relapsed E. coli strain with the greatest increase in persisters (100-fold relative to initial isolate), we determined that the increase was due to a loss-of-function mutation in the ptsI gene encoding Enzyme I of the phosphoenolpyruvate phosphotransferase system. The ptsI mutant was equally virulent in a murine bacteremia infection model but exhibited 10-fold increased survival to antibiotic treatment. This work addresses the controversy regarding the clinical relevance of persister formation by providing compelling data that not only do high-persister mutations arise during bloodstream infection in humans but also that these mutants display increased survival to antibiotic challenge in vivo.
Collapse
Affiliation(s)
- Joshua B. Parsons
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC27710
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC27559
| | - Ashelyn E. Sidders
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC27559
| | - Amanda Z. Velez
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC27559
| | | | - Michelle Angeles-Solano
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC27559
| | - Felicia Ruffin
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC27710
| | - Sarah E. Rowe
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC27559
| | - Cesar A. Arias
- Division of Infectious Diseases, Houston Methodist Hospital and Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX77030
- Department of Medicine, Weill Cornell Medical College, New York, NY10065
| | - Vance G. Fowler
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC27710
| | - Joshua T. Thaden
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC27710
| | - Brian P. Conlon
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC27559
| |
Collapse
|
10
|
Windels EM, Cool L, Persy E, Swinnen J, Matthay P, Van den Bergh B, Wenseleers T, Michiels J. Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence. THE ISME JOURNAL 2024; 18:wrae070. [PMID: 38691440 PMCID: PMC11102087 DOI: 10.1093/ismejo/wrae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Effective treatment of bacterial infections proves increasingly challenging due to the emergence of bacterial variants that endure antibiotic exposure. Antibiotic resistance and persistence have been identified as two major bacterial survival mechanisms, and several studies have shown a rapid and strong selection of resistance or persistence mutants under repeated drug treatment. Yet, little is known about the impact of the environmental conditions on resistance and persistence evolution and the potential interplay between both phenotypes. Based on the distinct growth and survival characteristics of resistance and persistence mutants, we hypothesized that the antibiotic dose and availability of nutrients during treatment might play a key role in the evolutionary adaptation to antibiotic stress. To test this hypothesis, we combined high-throughput experimental evolution with a mathematical model of bacterial evolution under intermittent antibiotic exposure. We show that high nutrient levels during antibiotic treatment promote selection of high-level resistance, but that resistance mainly emerges independently of persistence when the antibiotic concentration is sufficiently low. At higher doses, resistance evolution is facilitated by the preceding or concurrent selection of persistence mutants, which ensures survival of populations in harsh conditions. Collectively, our experimental data and mathematical model elucidate the evolutionary routes toward increased bacterial survival under different antibiotic treatment schedules, which is key to designing effective antibiotic therapies.
Collapse
Affiliation(s)
- Etthel M Windels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- Department of Biosystems Science and Engineering, ETH Zürich, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lloyd Cool
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- Laboratory of Socioecology and Social Evolution, KU Leuven, 3000 Leuven, Belgium
| | - Eline Persy
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Janne Swinnen
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Paul Matthay
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, KU Leuven, 3000 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| |
Collapse
|
11
|
Charron R, Lemée P, Huguet A, Minlong O, Boulanger M, Houée P, Soumet C, Briandet R, Bridier A. Polyhexamethylene biguanide promotes adaptive cross-resistance to gentamicin in Escherichia coli biofilms. Front Cell Infect Microbiol 2023; 13:1324991. [PMID: 38149014 PMCID: PMC10750414 DOI: 10.3389/fcimb.2023.1324991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 12/28/2023] Open
Abstract
Antimicrobial resistance is a critical public health issue that requires a thorough understanding of the factors that influence the selection and spread of antibiotic-resistant bacteria. Biocides, which are widely used in cleaning and disinfection procedures in a variety of settings, may contribute to this resistance by inducing similar defense mechanisms in bacteria against both biocides and antibiotics. However, the strategies used by bacteria to adapt and develop cross-resistance remain poorly understood, particularly within biofilms -a widespread bacterial habitat that significantly influences bacterial tolerance and adaptive strategies. Using a combination of adaptive laboratory evolution experiments, genomic and RT-qPCR analyses, and biofilm structural characterization using confocal microscopy, we investigated in this study how Escherichia coli biofilms adapted after 28 days of exposure to three biocidal active substances and the effects on cross-resistance to antibiotics. Interestingly, polyhexamethylene biguanide (PHMB) exposure led to an increase of gentamicin resistance (GenR) phenotypes in biofilms formed by most of the seven E. coli strains tested. Nevertheless, most variants that emerged under biocidal conditions did not retain the GenR phenotype after removal of antimicrobial stress, suggesting a transient adaptation (adaptive resistance). The whole genome sequencing of variants with stable GenR phenotypes revealed recurrent mutations in genes associated with cellular respiration, including cytochrome oxidase (cydA, cyoC) and ATP synthase (atpG). RT-qPCR analysis revealed an induction of gene expression associated with biofilm matrix production (especially curli synthesis), stress responses, active and passive transport and cell respiration during PHMB exposure, providing insight into potential physiological responses associated with adaptive crossresistance. In addition, confocal laser scanning microscopy (CLSM) observations demonstrated a global effect of PHMB on biofilm architectures and compositions formed by most E. coli strains, with the appearance of dense cellular clusters after a 24h-exposure. In conclusion, our results showed that the PHMB exposure stimulated the emergence of an adaptive cross-resistance to gentamicin in biofilms, likely induced through the activation of physiological responses and biofilm structural modulations altering gradients and microenvironmental conditions in the biological edifice.
Collapse
Affiliation(s)
- Raphaël Charron
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
- Université Paris-Saclay, National Research Institute for Agriculture, Food and the Environment (INRAE), AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Lemée
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Antoine Huguet
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Ornella Minlong
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Marine Boulanger
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Paméla Houée
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Christophe Soumet
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| | - Romain Briandet
- Université Paris-Saclay, National Research Institute for Agriculture, Food and the Environment (INRAE), AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères, France
| |
Collapse
|
12
|
Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023; 24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We discuss how the control system learns and processes information about the target system by sensing or measuring, through adaptive evolution or computational prediction of future trajectories. This information flow distinguishes pre-emptive control strategies by humans from feedback control in biotic systems. We establish a cost-benefit calculus to gauge and optimize control protocols, highlighting the fundamental link between predictability of evolution and efficacy of pre-emptive control.
Collapse
Affiliation(s)
- Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| |
Collapse
|
13
|
Thompson NT, Kitzenberg DA, Kao DJ. Persister-mediated emergence of antimicrobial resistance in agriculture due to antibiotic growth promoters. AIMS Microbiol 2023; 9:738-756. [PMID: 38173975 PMCID: PMC10758577 DOI: 10.3934/microbiol.2023038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/16/2023] [Accepted: 11/02/2023] [Indexed: 01/05/2024] Open
Abstract
The creation and continued development of antibiotics have revolutionized human health and disease for the past century. The emergence of antimicrobial resistance represents a major threat to human health, and practices that contribute to the development of this threat need to be addressed. Since the 1950s, antibiotics have been used in low doses to increase growth and decrease the feed requirement of animal-derived food sources. A consequence of this practice is the accelerated emergence of antimicrobial resistance that can influence human health through its distribution via animal food products. In the laboratory setting, sublethal doses of antibiotics promote the expansion of bacterial persister populations, a low energy, low metabolism phenotype characterized broadly by antibiotic tolerance. Furthermore, the induction of persister bacteria has been positively correlated with an increased emergence of antibiotic-resistant strains. This body of evidence suggests that the use of antibiotics in agriculture at subtherapeutic levels is actively catalyzing the emergence of antimicrobial-resistant bacteria through the expansion of bacterial persister populations, which is potentially leading to increased infections in humans and decreased antibiotic potency. There is an urgent need to address this debilitating effect on antibiotics and its influence on human health. In this review, we summarize the recent literature on the topic of emerging antimicrobial resistance and its association with bacterial persister populations.
Collapse
Affiliation(s)
- Noah T Thompson
- Department of Medicine and Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - David A Kitzenberg
- Department of Medicine and Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Daniel J Kao
- Department of Medicine and Mucosal Inflammation Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| |
Collapse
|
14
|
Grucela PK, Zhang YE. Basal level of ppGpp coordinates Escherichia coli cell heterogeneity and ampicillin resistance and persistence. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:248-260. [PMID: 37933276 PMCID: PMC10625690 DOI: 10.15698/mic2023.11.808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/20/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
The universal stringent response alarmone ppGpp (guanosine penta and tetra phosphates) plays a crucial role in various aspects of fundamental cell physiology (e.g., cell growth rate, cell size) and thus bacterial tolerance to and survival of external stresses, including antibiotics. Besides transient antibiotic tolerance (persistence), ppGpp was recently found to contribute to E. coli resistance to ampicillin. How ppGpp regulates both the persistence and resistance to antibiotics remains incompletely understood. In this study, we first clarified that the absence of ppGpp in E. coli (ppGpp0 strain) resulted in a decreased minimal inhibition concentration (MIC) value of ampicillin but, surprisingly, a higher persistence level to ampicillin during exponential growth in MOPS rich medium. High basal ppGpp levels, thus lower growth rate, did not produce high ampicillin persistence. Importantly, we found that the high ampicillin persistence of the ppGpp0 strain is not due to dormant overnight carry-over cells. Instead, the absence of ppGpp produced higher cell heterogeneity, propagating during the regrowth and the killing phases, leading to higher ampicillin persistence. Consistently, we isolated a suppressor mutation of the ppGpp0 strain that restored the standard MIC value of ampicillin and reduced its cell heterogeneity and the ampicillin persistence level concomitantly. Altogether, we discussed the fundamental role of basal level of ppGpp in regulating cell homogeneity and ampicillin persistence.
Collapse
Affiliation(s)
| | - Yong Everett Zhang
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| |
Collapse
|
15
|
Yang S, Li X, Cang W, Mu D, Ji S, An Y, Wu R, Wu J. Biofilm tolerance, resistance and infections increasing threat of public health. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:233-247. [PMID: 37933277 PMCID: PMC10625689 DOI: 10.15698/mic2023.11.807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 11/08/2023]
Abstract
Microbial biofilms can cause chronic infection. In the clinical setting, the biofilm-related infections usually persist and reoccur; the main reason is the increased antibiotic resistance of biofilms. Traditional antibiotic therapy is not effective and might increase the threat of antibiotic resistance to public health. Therefore, it is urgent to study the tolerance and resistance mechanism of biofilms to antibiotics and find effective therapies for biofilm-related infections. The tolerance mechanism and host reaction of biofilm to antibiotics are reviewed, and bacterial biofilm related diseases formed by human pathogens are discussed thoroughly. The review also explored the role of biofilms in the development of bacterial resistance mechanisms and proposed therapeutic intervention strategies for biofilm related diseases.
Collapse
Affiliation(s)
- Shanshan Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Xinfei Li
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
| | - Weihe Cang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
| | - Delun Mu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Shuaiqi Ji
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Yuejia An
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| | - Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, P.R. China
- Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang 110866, P.R. China
- Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang 110866, P.R. China
| |
Collapse
|
16
|
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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564761. [PMID: 37961139 PMCID: PMC10634941 DOI: 10.1101/2023.10.30.564761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Traditionally, bacteriostatic antibiotics are agents able to arrest bacterial growth. Despite being 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, Georgia, 30322, USA
| | - Brandon A. Berryhill
- Department of Biology, Emory University; Atlanta, Georgia, 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, Georgia, 30322, USA
| | - Andrew P. Smith
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Ingrid C. McCall
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| | - Fernando Baquero
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, and Centro de Investigación Médica en Red, Epidemiologíy Salud Pública (CIBERESP) Madrid, Spain
| | - Bruce R. Levin
- Department of Biology, Emory University; Atlanta, Georgia, 30322, USA
| |
Collapse
|
17
|
Xu T, Fang D, Li F, Wang Z, Liu Y. A Dietary Source of High Level of Fluoroquinolone Tolerance in mcr-Carrying Gram-Negative Bacteria. RESEARCH (WASHINGTON, D.C.) 2023; 6:0245. [PMID: 37808177 PMCID: PMC10557118 DOI: 10.34133/research.0245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023]
Abstract
The emergence of antibiotic tolerance, characterized by the prolonged survival of bacteria following antibiotic exposure, in natural bacterial populations, especially in pathogens carrying antibiotic resistance genes, has been an increasing threat to public health. However, the major causes contributing to the formation of antibiotic tolerance and underlying molecular mechanisms are yet poorly understood. Herein, we show that potassium sorbate (PS), a widely used food additive, triggers a high level of fluoroquinolone tolerance in bacteria carrying mobile colistin resistance gene mcr. Mechanistic studies demonstrate that PS treatment results in the accumulation of intracellular fumarate, which activates bacterial two-component system and decreases the expression level of outer membrane protein OmpF, thereby reducing the uptake of ciprofloxacin. In addition, the supplementation of PS inhibits aerobic respiration, reduces reactive oxygen species production and alleviates DNA damage caused by bactericidal antibiotics. Furthermore, we demonstrate that succinate, an intermediate product of the tricarboxylic acid cycle, overcomes PS-mediated ciprofloxacin tolerance. In multiple animal models, ciprofloxacin treatment displays failure outcomes in PS preadministrated animals, including comparable survival and bacterial loads with the vehicle group. Taken together, our works offer novel mechanistic insights into the development of antibiotic tolerance and uncover potential risks associated with PS use.
Collapse
Affiliation(s)
- Tianqi Xu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
| | - Dan Fang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
| | - Fulei Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China,
Yangzhou University, Yangzhou 225009, China
| | - Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine,
Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China,
Yangzhou University, Yangzhou 225009, China
- Institute of Comparative Medicine,
Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
18
|
Wang C, Jin L. Microbial persisters and host: recent advances and future perspectives. Crit Rev Microbiol 2023; 49:658-670. [PMID: 36165023 DOI: 10.1080/1040841x.2022.2125286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022]
Abstract
Microbial persisters are defined as the tiny sub-population of microorganisms that develop intrinsic strategies for survival with high tolerance to various antimicrobials. Currently, persister research remains in its infancy, and it is indeed a great challenge to precisely distinguish persister cells from other drug tolerant ones. Notably, the existence of persisters crucially contributes to prolonged antibiotic exposure time and treatment failure, yet there is the formation of antibiotic-resistant mutants. Further understanding on persisters is of profound importance for effective prevention and control of chronic infections/inflammation. The past two decades have witnessed rapid advances on the science, technologies and methodologies for persister investigations, along with deep knowledge about persisters and numerous anti-persister approaches developed. Whereas, various critical issues remain unsolved, such as what are the potential interaction profiles of persisters and host cells, and how to apply what we know about persisters to translational studies and clinical practice. Importantly, it is highly essential to better understand the multifaceted and complex cross-talk of microbial persisters with the host to develop novel tackling strategies for precision healthcare in the near future.
Collapse
Affiliation(s)
- Chuan Wang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | | |
Collapse
|
19
|
Zhang C, Kong Y, Xiang Q, Ma Y, Guo Q. Bacterial memory in antibiotic resistance evolution and nanotechnology in evolutionary biology. iScience 2023; 26:107433. [PMID: 37575196 PMCID: PMC10415926 DOI: 10.1016/j.isci.2023.107433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Bacterial memory refers to the phenomenon in which past experiences influence current behaviors in response to changing environments. It serves as a crucial process that enables adaptation and evolution. We first summarize the state-of-art approaches regarding history-dependent behaviors that impact growth dynamics and underlying mechanisms. Then, the phenotypic and genotypic origins of memory and how encoded memory modulates drug tolerance/resistance are reviewed. We also provide a summary of possible memory effects induced by antimicrobial nanoparticles. The regulatory networks and genetic underpinnings responsible for memory building partially overlap with nanoparticle and drug exposures, which may raise concerns about the impact of nanotechnology on adaptation. Finally, we provide a perspective on the use of nanotechnology to harness bacterial memory based on its unique mode of actions on information processing and transmission in bacteria. Exploring bacterial memory mechanisms provides valuable insights into acclimation, evolution, and the potential applications of nanotechnology in harnessing memory.
Collapse
Affiliation(s)
- Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yan Kong
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qingxin Xiang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yayun Ma
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Quanyi Guo
- School of Environment, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
20
|
Ganesan N, Mishra B, Felix L, Mylonakis E. Antimicrobial Peptides and Small Molecules Targeting the Cell Membrane of Staphylococcus aureus. Microbiol Mol Biol Rev 2023; 87:e0003722. [PMID: 37129495 PMCID: PMC10304793 DOI: 10.1128/mmbr.00037-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Clinical management of Staphylococcus aureus infections presents a challenge due to the high incidence, considerable virulence, and emergence of drug resistance mechanisms. The treatment of drug-resistant strains, such as methicillin-resistant S. aureus (MRSA), is further complicated by the development of tolerance and persistence to antimicrobial agents in clinical use. To address these challenges, membrane disruptors, that are not generally considered during drug discovery for agents against S. aureus, should be explored. The cell membrane protects S. aureus from external stresses and antimicrobial agents, but membrane-targeting antimicrobial agents are probably less likely to promote bacterial resistance. Nontypical linear cationic antimicrobial peptides (AMPs), highly modified AMPs such as daptomycin (lipopeptide), bacitracin (cyclic peptide), and gramicidin S (cyclic peptide), are currently in clinical use. Recent studies have demonstrated that AMPs and small molecules can penetrate the cell membrane of S. aureus, inhibit phospholipid biosynthesis, or block the passage of solutes between the periplasm and the exterior of the cell. In addition to their primary mechanism of action (MOA) that targets the bacterial membrane, AMPs and small molecules may also impact bacteria through secondary mechanisms such as targeting the biofilm, and downregulating virulence genes of S. aureus. In this review, we discuss the current state of research into cell membrane-targeting AMPs and small molecules and their potential mechanisms of action against drug-resistant physiological forms of S. aureus, including persister cells and biofilms.
Collapse
Affiliation(s)
- Narchonai Ganesan
- Infectious Diseases Division, Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Biswajit Mishra
- Infectious Diseases Division, Alpert Medical School, Brown University, Providence, Rhode Island, USA
- Department of Medicine, The Miriam Hospital, Providence, Rhode Island, USA
| | - LewisOscar Felix
- Infectious Diseases Division, Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Eleftherios Mylonakis
- Infectious Diseases Division, Alpert Medical School, Brown University, Providence, Rhode Island, USA
- Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
| |
Collapse
|
21
|
Li X, Song Y, Chen X, Yin J, Wang P, Huang H, Yin H. Single-cell microfluidics enabled dynamic evaluation of drug combinations on antibiotic resistance bacteria. Talanta 2023; 265:124814. [PMID: 37343360 DOI: 10.1016/j.talanta.2023.124814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/23/2023]
Abstract
The rapid spread of antibiotic resistance has become a significant threat to global health, yet the development of new antibiotics is outpaced by emerging new resistance. To treat multidrug-resistant bacteria and prolong the lifetime of existing antibiotics, a productive strategy is to use combinations of antibiotics and/or adjuvants. However, evaluating drug combinations is primarily based on end-point checkerboard measurements, which provide limited information to study the mechanism of action and the discrepancies in the clinical outcomes. Here, single-cell microfluidics is used for rapid evaluation of the efficacy and mode of action of antibiotic combinations within 3 h. Focusing on multidrug-resistant Acinetobacter baumannii, the combination between berberine hydrochloride (BBH, as an adjuvant) and carbapenems (meropenem, MEM) or β-lactam antibiotic is evaluated. Real-time tracking of individual cells to programmable delivered antibiotics reveals multiple phenotypes (i.e., susceptible, resistant, and persistent cells) with fidelity. Our study discovers that BBH facilitates the accumulation of antibiotics within cells, indicating synergistic effects (FICI = 0.5). For example, the combination of 256 mg/L BBH and 16 mg/L MEM has a similar killing effect (i.e., the inhibition rates >90%) as the MIC of MEM (64 mg/L). Importantly, the synergistic effect of a combination can diminish if the bacteria are pre-stressed with any single drug. Such information is vital for understanding the underlying mechanisms of combinational treatments. Overall, our platform provides a promising approach to evaluate the dynamic and heterogenous response of a bacterial population to antibiotics, which will facilitate new drug discovery and reduce emerging antibiotic resistance.
Collapse
Affiliation(s)
- Xiaobo Li
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, China; James Watt School of Engineering, University of Glasgow, G12 8LT, UK
| | - Yanqing Song
- James Watt School of Engineering, University of Glasgow, G12 8LT, UK
| | - Xiuzhao Chen
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Jianan Yin
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, China
| | - Ping Wang
- Tianjin Modern Innovative TCM Technology Co. Ltd., 300392, China
| | - He Huang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, China.
| | - Huabing Yin
- James Watt School of Engineering, University of Glasgow, G12 8LT, UK.
| |
Collapse
|
22
|
Martínez-Fructuoso L, Arends SJR, Freire VF, Evans JR, DeVries S, Peyser BD, Akee RK, Thornburg CC, Kumar R, Ensel S, Morgan GM, McConachie GD, Veeder N, Duncan LR, Grkovic T, O’Keefe BR. Screen for New Antimicrobial Natural Products from the NCI Program for Natural Product Discovery Prefractionated Extract Library. ACS Infect Dis 2023; 9:1245-1256. [PMID: 37163243 PMCID: PMC10262198 DOI: 10.1021/acsinfecdis.3c00067] [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: 02/08/2023] [Indexed: 05/11/2023]
Abstract
The continuing emergence of antibiotic-resistant microbes highlights the need for the identification of new chemotypes with antimicrobial activity. One of the most prolific sources of antimicrobial molecules has been the systematic screening of natural product samples. The National Institute of Allergy and Infectious Diseases and the National Cancer Institute here report a large screen of 326,656 partially purified natural product fractions against a panel of four microbial pathogens, resulting in the identification of >3000 fractions with antifungal and/or antibacterial activity. A small sample of these active fractions was further purified and the chemical structures responsible for the antimicrobial activity were elucidated. The proof-of-concept study identified many different chemotypes, several of which have not previously been reported to have antimicrobial activity. The results show that there remain many unidentified antibiotic compounds from nature.
Collapse
Affiliation(s)
- Lucero Martínez-Fructuoso
- Natural
Products Branch, Developmental Therapeutic Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | | | - Vitor F. Freire
- Natural
Products Branch, Developmental Therapeutic Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - Jason R. Evans
- Natural
Products Branch, Developmental Therapeutic Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - Sean DeVries
- JMI
Laboratories, North Liberty, Iowa 52317, United States
| | - Brian D. Peyser
- Natural
Products Branch, Developmental Therapeutic Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
| | - Rhone K. Akee
- Natural
Products Support Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United
States
| | - Christopher C. Thornburg
- Natural
Products Support Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United
States
| | - Rohitesh Kumar
- Natural
Products Support Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United
States
| | - Susan Ensel
- Natural
Products Support Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United
States
- Department
of Chemistry and Physics, Hood College, Frederick, Maryland 21701-8599, United
States
| | - Gina M. Morgan
- JMI
Laboratories, North Liberty, Iowa 52317, United States
| | - Grant D. McConachie
- Natural
Products Support Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United
States
| | - Nathan Veeder
- JMI
Laboratories, North Liberty, Iowa 52317, United States
| | | | - Tanja Grkovic
- Natural
Products Branch, Developmental Therapeutic Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Barry R. O’Keefe
- Natural
Products Branch, Developmental Therapeutic Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702-1201, United States
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| |
Collapse
|
23
|
Khan ZA, Warden AR, Jiang H, Abdullah A, Ahmad M, Jiang L, Ding X. Time-lapse proteomics unveil constant high exposure of non-antibiotic drug induces synthetic susceptibility towards regular antibiotics. Microbiol Res 2023; 269:127320. [PMID: 36764262 DOI: 10.1016/j.micres.2023.127320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/10/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Antibiotic resistance is a significant threat to the human race, as regular consumption of antibiotics may lead to antibiotic-resistant bacterial strains. Non-antibiotic drugs also have an extensive impact on bacterial strains, where persistent uptake alters the survival mechanisms of bacteria that could lead to cross-resistance towards other antibiotics. Here, we use time-lapse proteomics shift assays to examine Gram-negative (E. coli. O157:H7 and P. aeruginosa) and Gram-positive (E. faecalis and S. aureus) strains of bacteria for short and continuous exposure to the non-antibiotic drug Hydroxychloroquine (HCQ). Proteomic transitions from wild type to HCQ-exposed strains revealed bacterial transitions and their survival adaptabilities, which were different across all strains. In addition to their structural differences, some shared pathways were enriched among Gram-negative and positive strains. We also validated the cross-resistance and sensitivity towards 24 regularly prescribed antibiotics, indicating that long-term exposure to non-antibiotic drugs may induce general proteomics alterations in the bacterial strains, promoting antibiotic resistance. We validated that HCQ exposure renders Gram-negative strains resistant to Β-lactam and susceptible to macrolides and folic acid. In contrast, Gram-positive strains become susceptible to Β-lactam and resistant to aminoglycosides. Exposure to non-antibiotic drugs causes resistance or susceptibility toward other antibiotics, providing clinicians a reason to overcome antibiotic resistance.
Collapse
Affiliation(s)
- Zara Ahmad Khan
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Antony R Warden
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Jiang
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Aynur Abdullah
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mashaal Ahmad
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
24
|
Usui M, Yoshii Y, Thiriet-Rupert S, Ghigo JM, Beloin C. Intermittent antibiotic treatment of bacterial biofilms favors the rapid evolution of resistance. Commun Biol 2023; 6:275. [PMID: 36928386 PMCID: PMC10020551 DOI: 10.1038/s42003-023-04601-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial antibiotic resistance is a global health concern of increasing importance and intensive study. Although biofilms are a common source of infections in clinical settings, little is known about the development of antibiotic resistance within biofilms. Here, we use experimental evolution to compare selection of resistance mutations in planktonic and biofilm Escherichia coli populations exposed to clinically relevant cycles of lethal treatment with the aminoglycoside amikacin. Consistently, mutations in sbmA, encoding an inner membrane peptide transporter, and fusA, encoding the essential elongation factor G, are rapidly selected in biofilms, but not in planktonic cells. This is due to a combination of enhanced mutation rate, increased adhesion capacity and protective biofilm-associated tolerance. These results show that the biofilm environment favors rapid evolution of resistance and provide new insights into the dynamic evolution of antibiotic resistance in biofilms.
Collapse
Affiliation(s)
- Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan.
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
| | - Yutaka Yoshii
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Stanislas Thiriet-Rupert
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France
| | - Christophe Beloin
- Institut Pasteur, Université de Paris Cité, UMR CNRS 6047, Genetics of Biofilms Laboratory, 75015, Paris, France.
| |
Collapse
|
25
|
Scott J, Valero C, Mato-López Á, Donaldson IJ, Roldán A, Chown H, Van Rhijn N, Lobo-Vega R, Gago S, Furukawa T, Morogovsky A, Ben Ami R, Bowyer P, Osherov N, Fontaine T, Goldman GH, Mellado E, Bromley M, Amich J. Aspergillus fumigatus Can Display Persistence to the Fungicidal Drug Voriconazole. Microbiol Spectr 2023; 11:e0477022. [PMID: 36912663 PMCID: PMC10100717 DOI: 10.1128/spectrum.04770-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/12/2023] [Indexed: 03/14/2023] Open
Abstract
Aspergillus fumigatus is a filamentous fungus that can infect the lungs of patients with immunosuppression and/or underlying lung diseases. The mortality associated with chronic and invasive aspergillosis infections remain very high, despite availability of antifungal treatments. In the last decade, there has been a worrisome emergence and spread of resistance to the first-line antifungals, the azoles. The mortality caused by resistant isolates is even higher, and patient management is complicated as the therapeutic options are reduced. Nevertheless, treatment failure is also common in patients infected with azole-susceptible isolates, which can be due to several non-mutually exclusive reasons, such as poor drug absorption. In addition, the phenomena of tolerance or persistence, where susceptible pathogens can survive the action of an antimicrobial for extended periods, have been associated with treatment failure in bacterial infections, and their occurrence in fungal infections already proposed. Here, we demonstrate that some isolates of A. fumigatus display persistence to voriconazole. A subpopulation of the persister isolates can survive for extended periods and even grow at low rates in the presence of supra-MIC of voriconazole and seemingly other azoles. Persistence cannot be eradicated with adjuvant drugs or antifungal combinations and seemed to reduce the efficacy of treatment for certain individuals in a Galleria mellonella model of infection. Furthermore, persistence implies a distinct transcriptional profile, demonstrating that it is an active response. We propose that azole persistence might be a relevant and underestimated factor that could influence the outcome of infection in human aspergillosis. IMPORTANCE The phenomena of antibacterial tolerance and persistence, where pathogenic microbes can survive for extended periods in the presence of cidal drug concentrations, have received significant attention in the last decade. Several mechanisms of action have been elucidated, and their relevance for treatment failure in bacterial infections demonstrated. In contrast, our knowledge of antifungal tolerance and, in particular, persistence is still very limited. In this study, we have characterized the response of the prominent fungal pathogen Aspergillus fumigatus to the first-line therapy antifungal voriconazole. We comprehensively show that some isolates display persistence to this fungicidal antifungal and propose various potential mechanisms of action. In addition, using an alternative model of infection, we provide initial evidence to suggest that persistence may cause treatment failure in some individuals. Therefore, we propose that azole persistence is an important factor to consider and further investigate in A. fumigatus.
Collapse
Affiliation(s)
- Jennifer Scott
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Clara Valero
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Álvaro Mato-López
- Mycology Reference Laboratory (Laboratorio de Referencia e Investigación en Micología [LRIM]), National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Ian J. Donaldson
- Bioinformatics Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Alejandra Roldán
- Mycology Reference Laboratory (Laboratorio de Referencia e Investigación en Micología [LRIM]), National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Harry Chown
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Norman Van Rhijn
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Rebeca Lobo-Vega
- Mycology Reference Laboratory (Laboratorio de Referencia e Investigación en Micología [LRIM]), National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Sara Gago
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Takanori Furukawa
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Alma Morogovsky
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronen Ben Ami
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paul Bowyer
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Thierry Fontaine
- Institut Pasteur, Université de Paris, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Emilia Mellado
- Mycology Reference Laboratory (Laboratorio de Referencia e Investigación en Micología [LRIM]), National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
- CiberInfec ISCIII, CIBER en Enfermedades Infecciosas, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael Bromley
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jorge Amich
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Mycology Reference Laboratory (Laboratorio de Referencia e Investigación en Micología [LRIM]), National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| |
Collapse
|
26
|
Manoharan-Basil SS, Balduck M, Abdellati S, Gestels Z, de Block T, Kenyon C. Enolase Is Implicated in the Emergence of Gonococcal Tolerance to Ceftriaxone. Antibiotics (Basel) 2023; 12:antibiotics12030534. [PMID: 36978401 PMCID: PMC10044683 DOI: 10.3390/antibiotics12030534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Antibiotic tolerance is associated with antibiotic treatment failure, and molecular mechanisms underlying tolerance are poorly understood. We recently succeeded in inducing tolerance to ceftriaxone (CRO) in an N. gonorrhoeae reference isolate. In a prior in vitro study, six biological replicates of WHO P strains were exposed to CRO (10× the MIC) followed by overnight growth, and tolerance was assessed using a modified Tolerance Disc (T.D.) test. In the current study, we characterized the mutation profile of these CRO-tolerant phenotypes. The whole genome was sequenced from isolates from different replicates and time points. We identified mutations in four genes that may contribute to ceftriaxone tolerance in N. gonorrhoeae, including a mutation in the enolase (eno) gene that arose independently in three lineages.
Collapse
Affiliation(s)
| | - Margaux Balduck
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | - Saïd Abdellati
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Zina Gestels
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
| | - Tessa de Block
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Chris Kenyon
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium
- Department of Medicine, University of Cape Town, Cape Town 7700, South Africa
| |
Collapse
|
27
|
Community interactions drive the evolution of antibiotic tolerance in bacteria. Proc Natl Acad Sci U S A 2023; 120:e2209043119. [PMID: 36634144 PMCID: PMC9934204 DOI: 10.1073/pnas.2209043119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The emergence of antibiotic tolerance (prolonged survival against exposure) in natural bacterial populations is a major concern. Since it has been studied primarily in isogenic populations, we do not yet understand how ecological interactions in a diverse community impact the evolution of tolerance. To address this, we studied the evolutionary dynamics of a synthetic bacterial community composed of two interacting strains. In this community, an antibiotic-resistant strain protected the other, susceptible strain by degrading the antibiotic ampicillin in the medium. Surprisingly, we found that in the presence of antibiotics, the susceptible strain evolved tolerance. Tolerance was typified by an increase in survival as well as an accompanying decrease in the growth rate, highlighting a trade-off between the two. A simple mathematical model explained that the observed decrease in the death rate, even when coupled with a decreased growth rate, is beneficial in a community with weak protective interactions. In the presence of strong interactions, the model predicted that the trade-off would instead be detrimental, and tolerance would not emerge, which we experimentally verified. By whole genome sequencing the evolved tolerant isolates, we identified two genetic hot spots which accumulated mutations in parallel lines, suggesting their association with tolerance. Our work highlights that ecological interactions can promote antibiotic tolerance in bacterial communities, which has remained understudied.
Collapse
|
28
|
Abstract
The rise of antibiotic-resistant bacterial infections poses a global threat. Antibiotic resistance development is generally studied in batch cultures which conceals the heterogeneity in cellular responses. Using single-cell imaging, we studied the growth response of Escherichia coli to sub-inhibitory and inhibitory concentrations of nine antibiotics. We found that the heterogeneity in growth increases more than what is expected from growth rate reduction for three out of the nine antibiotics tested. For two antibiotics (rifampicin and nitrofurantoin), we found that sub-populations were able to maintain growth at lethal antibiotic concentrations for up to 10 generations. This perseverance of growth increased the population size and led to an up to 40-fold increase in the frequency of antibiotic resistance mutations in gram-negative and gram-positive species. We conclude that antibiotic perseverance is a common phenomenon that has the potential to impact antibiotic resistance development across pathogenic bacteria.
Collapse
|
29
|
Geerts N, De Vooght L, Passaris I, Delputte P, Van den Bergh B, Cos P. Antibiotic Tolerance Indicative of Persistence Is Pervasive among Clinical Streptococcus pneumoniae Isolates and Shows Strong Condition Dependence. Microbiol Spectr 2022; 10:e0270122. [PMID: 36374111 PMCID: PMC9769776 DOI: 10.1128/spectrum.02701-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Streptococcus pneumoniae is an important human pathogen, being one of the most common causes of community-acquired pneumonia and otitis media. Antibiotic resistance in S. pneumoniae is an emerging problem, as it depletes our arsenal of effective drugs. In addition, persistence also contributes to the antibiotic crisis in many other pathogens, yet for S. pneumoniae, little is known about antibiotic-tolerant persisters and robust experimental means are lacking. Persister cells are phenotypic variants that exist as a subpopulation within a clonal culture. Being tolerant to lethal antibiotics, they underly the chronic nature of a variety of infections and even help in acquiring genetic resistance. In this study, we set out to identify and characterize persistence in S. pneumoniae. Specifically, we followed different strategies to overcome the self-limiting nature of S. pneumoniae as a confounding factor in the prolonged monitoring of antibiotic survival needed to study persistence. Under optimized conditions, we identified genuine persisters in various growth phases and for four relevant antibiotics through biphasic survival dynamics and heritability assays. Finally, we detected a high variety in antibiotic survival levels across a diverse collection of S. pneumoniae clinical isolates, which assumes that a high natural diversity in persistence is widely present in S. pneumoniae. Collectively, this proof of concept significantly progresses the understanding of the importance of antibiotic persistence in S. pneumoniae infections, which will set the stage for characterizing its relevance to clinical outcomes and advocates for increased attention to the phenotype in both fundamental and clinical research. IMPORTANCE S. pneumoniae is considered a serious threat by the Centers for Disease Control and Prevention because of rising antibiotic resistance. In addition to resistance, bacteria can also survive lethal antibiotic treatment by developing antibiotic tolerance, more specifically, antibiotic tolerance through persistence. This phenotypic variation seems omnipresent among bacterial life, is linked to therapy failure, and acts as a catalyst for resistance development. This study gives the first proof of the presence of persister cells in S. pneumoniae and shows a high variety in persistence levels among diverse strains, suggesting that persistence is a general trait in S. pneumoniae cultures. Our work advocates for higher interest for persistence in S. pneumoniae as a contributing factor for therapy failure and resistance development.
Collapse
Affiliation(s)
- Nele Geerts
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | - Linda De Vooght
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | | | - Peter Delputte
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven, Leuven, Belgium
- Center for Microbiology, Flanders Institute for Biotechnology, VIB, Leuven, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Wilrijk, Belgium
| |
Collapse
|
30
|
Molecular Characterization of Clinical Rel Mutations and Consequences for Resistance Expression and Fitness in Staphylococcus aureus. Antimicrob Agents Chemother 2022; 66:e0093822. [PMID: 36346240 PMCID: PMC9764984 DOI: 10.1128/aac.00938-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The stringent response (SR) is a universal stress response that acts as a global regulator of bacterial physiology and virulence, and is a contributor to antibiotic tolerance and resistance. In most bacteria, the SR is controlled by a bifunctional enzyme, Rel, which both synthesizes and hydrolyzes the alarmone (p)ppGpp via two distinct catalytic domains. The balance between these antagonistic activities is fine-tuned to the needs of the cell and, in a "relaxed" state, the hydrolase activity of Rel dominates. We have previously shown that two single amino acid substitutions in Rel (that were identified in clinical isolates from persistent infections) confer elevated basal concentrations of (p)ppGpp and consequent multidrug tolerance in Staphylococcus aureus. Here, we explore the molecular details of how these mutations bring about this increase in cellular (p)ppGpp and investigate the wider cellular consequences in terms of resistance expression, resistance development, and bacterial fitness. Using enzyme assays, we show that both these mutations drastically reduce the hydrolase activity of Rel, thereby shifting the balance of Rel activity in favor of (p)ppGpp synthesis. We also demonstrate that these mutations induce high-level, homogeneous expression of β-lactam resistance and confer a significant fitness advantage in the presence of bactericidal antibiotics (but a fitness cost in the absence of antibiotic). In contrast, these mutations do not appear to accelerate the emergence of endogenous resistance mutations in vitro. Overall, our findings reveal the complex nature of Rel regulation and the multifaceted implications of clinical Rel mutations in terms of antibiotic efficacy and bacteria survival.
Collapse
|
31
|
Newson JP, Gaissmaier MS, McHugh SC, Hardt WD. Studying antibiotic persistence in vivo using the model organism Salmonella Typhimurium. Curr Opin Microbiol 2022; 70:102224. [PMID: 36335713 DOI: 10.1016/j.mib.2022.102224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/22/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
Abstract
Antibiotic persistence permits a subpopulation of susceptible bacteria to survive lethal concentrations of bactericidal antibiotics. This prolongs antibiotic therapy, promotes the evolution of antibiotic-resistant pathogen strains and can select for pathogen virulence within infected hosts. Here, we review the literature exploring antibiotic persistence in vivo, and describe the consequences of recalcitrant subpopulations, with a focus on studies using the model pathogen Salmonella Typhimurium. In vitro studies have established a concise set of features distinguishing true persisters from other forms of bacterial recalcitrance to bactericidal antibiotics. We discuss how animal infection models are useful for exploring these features in vivo, and describe how technical challenges can sometimes prevent the conclusive identification of true antibiotic persistence within infected hosts. We propose using two complementary working definitions for studying antibiotic persistence in vivo: the strict definition for studying the mechanisms of persister formation, and an operative definition for functional studies assessing the links between invasive virulence and persistence as well as the consequences for horizontal gene transfer, or the emergence of antibiotic-resistant mutants. This operative definition will enable further study of how antibiotic persisters arise in vivo, and of how surviving populations contribute to diverse downstream effects such as pathogen transmission, horizontal gene transfer and the evolution of virulence and antibiotic resistance. Ultimately, such studies will help to improve therapeutic control of antibiotic- recalcitrant populations.
Collapse
Affiliation(s)
- Joshua Pm Newson
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Marla S Gaissmaier
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Sarah C McHugh
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
32
|
Kundar R, Gokarn K. CRISPR-Cas System: A Tool to Eliminate Drug-Resistant Gram-Negative Bacteria. Pharmaceuticals (Basel) 2022; 15:ph15121498. [PMID: 36558949 PMCID: PMC9781512 DOI: 10.3390/ph15121498] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
Rapidly emerging drug-resistant superbugs, especially Gram-negative bacteria, pose a serious threat to healthcare systems all over the globe. Newer strategies are being developed to detect and overcome the arsenal of weapons that these bacteria possess. The development of antibiotics is time-consuming and may not provide full proof of action on evolving drug-resistant pathogens. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are promising in curbing drug-resistant bacteria. This review focuses on the pathogenesis of Gram-negative bacteria, emergence of antimicrobial drug resistance, and their treatment failures. It also draws attention to the present status of the CRISPR-Cas system in diagnosisand treatment of Gram-negative bacterial infections.
Collapse
Affiliation(s)
- Rajeshwari Kundar
- Department of Microbiology, Sir H.N. Medical Research Society, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai 400004, Maharashtra, India
| | - Karuna Gokarn
- Department of Microbiology, Sir H.N. Medical Research Society, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai 400004, Maharashtra, India
- Department of Microbiology, St. Xavier’s College, 5- Mahapalika Marg, Mumbai 400001, Maharashtra, India
- Correspondence: or
| |
Collapse
|
33
|
Microfluidic dose-response platform to track the dynamics of drug response in single mycobacterial cells. Sci Rep 2022; 12:19578. [PMID: 36379978 PMCID: PMC9666435 DOI: 10.1038/s41598-022-24175-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Preclinical analysis of drug efficacy is critical for drug development. However, conventional bulk-cell assays statically assess the mean population behavior, lacking resolution on drug-escaping cells. Inaccurate estimation of efficacy can lead to overestimation of compounds, whose efficacy will not be confirmed in the clinic, or lead to rejection of valuable candidates. Time-lapse microfluidic microscopy is a powerful approach to characterize drugs at high spatiotemporal resolution, but hard to apply on a large scale. Here we report the development of a microfluidic platform based on a pneumatic operating principle, which is scalable and compatible with long-term live-cell imaging and with simultaneous analysis of different drug concentrations. We tested the platform with mycobacterial cells, including the tubercular pathogen, providing the first proof of concept of a single-cell dose-response assay. This dynamic in-vitro model will prove useful to probe the fate of drug-stressed cells, providing improved predictions of drug efficacy in the clinic.
Collapse
|
34
|
Witzany C, Regoes RR, Igler C. Assessing the relative importance of bacterial resistance, persistence and hyper-mutation for antibiotic treatment failure. Proc Biol Sci 2022; 289:20221300. [PMID: 36350213 PMCID: PMC9653239 DOI: 10.1098/rspb.2022.1300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/18/2022] [Indexed: 08/01/2023] Open
Abstract
To curb the rising threat of antimicrobial resistance, we need to understand the routes to antimicrobial treatment failure. Bacteria can survive treatment by using both genetic and phenotypic mechanisms to diminish the effect of antimicrobials. We assemble empirical data showing that, for example, Pseudomonas aeruginosa infections frequently contain persisters, transiently non-growing cells unaffected by antibiotics (AB) and hyper-mutators, mutants with elevated mutation rates, and thus higher probability of genetic resistance emergence. Resistance, persistence and hyper-mutation dynamics are difficult to disentangle experimentally. Hence, we use stochastic population modelling and deterministic fitness calculations to investigate the relative importance of genetic and phenotypic mechanisms for immediate treatment failure and establishment of prolonged, chronic infections. We find that persistence causes 'hidden' treatment failure with very low cell numbers if antimicrobial concentrations prevent growth of genetically resistant cells. Persister cells can regrow after treatment is discontinued and allow for resistance evolution in the absence of AB. This leads to different mutational routes during treatment and relapse of an infection. By contrast, hyper-mutation facilitates resistance evolution during treatment, but rarely contributes to treatment failure. Our findings highlight the time and concentration dependence of different bacterial mechanisms to escape AB killing, which should be considered when designing 'failure-proof' treatments.
Collapse
Affiliation(s)
| | - Roland R. Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Claudia Igler
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
35
|
González-Villarreal JA, González-Lozano KJ, Aréchiga-Carvajal ET, Morlett-Chávez JA, Luévanos-Escareño MP, Balagurusamy N, Salinas-Santander MA. Molecular mechanisms of multidrug resistance in clinically relevant enteropathogenic bacteria (Review). Exp Ther Med 2022; 24:753. [PMID: 36561977 PMCID: PMC9748766 DOI: 10.3892/etm.2022.11689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 11/11/2022] Open
Abstract
Multidrug resistant (MDR) enteropathogenic bacteria are a growing problem within the clinical environment due to their acquired tolerance to a wide range of antibiotics, thus causing severe illnesses and a tremendous economic impact in the healthcare sector. Due to its difficult treatment, knowledge and understanding of the molecular mechanisms that confer this resistance are needed. The aim of the present review is to describe the mechanisms of antibiotic resistance from a genomic perspective observed in bacteria, including naturally acquired resistance. The present review also discusses common pharmacological and alternative treatments used in cases of infection caused by MDR bacteria, thus covering necessary information for the development of novel antimicrobials and adjuvant molecules inhibiting bacterial proliferation.
Collapse
Affiliation(s)
| | - Katia Jamileth González-Lozano
- Microbiology Department, Phytopathology and Mycology Laboratory, Faculty of Biological Sciences, Genetic Manipulation Unit, Autonomous University of Nuevo Leon, Monterrey, Nuevo León 66459, Mexico
| | - Elva Teresa Aréchiga-Carvajal
- Microbiology Department, Phytopathology and Mycology Laboratory, Faculty of Biological Sciences, Genetic Manipulation Unit, Autonomous University of Nuevo Leon, Monterrey, Nuevo León 66459, Mexico
| | - Jesús Antonio Morlett-Chávez
- Research Department, Faculty of Medicine Saltillo Unit, Autonomous University of Coahuila, Saltillo, Coahuila 25000, Mexico
| | | | - Nagamani Balagurusamy
- Bioremediation Laboratory, Faculty of Biological Sciences, Autonomous University of Coahuila, Torreón, Coahuila 27275, Mexico
| | - Mauricio Andrés Salinas-Santander
- Research Department, Faculty of Medicine Saltillo Unit, Autonomous University of Coahuila, Saltillo, Coahuila 25000, Mexico,Correspondence to: Dr Mauricio Andrés Salinas-Santander, Research Department, Faculty of Medicine Saltillo Unit, Autonomous University of Coahuila, Calle Francisco Murguía Sur 205, Zona Centro, Saltillo, Coahuila 25000, Mexico
| |
Collapse
|
36
|
Balduck M, Laumen JGE, Abdellati S, De Baetselier I, de Block T, Manoharan-Basil SS, Kenyon C. Tolerance to Ceftriaxone in Neisseria gonorrhoeae: Rapid Induction in WHO P Reference Strain and Detection in Clinical Isolates. Antibiotics (Basel) 2022; 11:1480. [PMID: 36358135 PMCID: PMC9686967 DOI: 10.3390/antibiotics11111480] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 09/16/2023] Open
Abstract
In addition to antimicrobial resistance, bacteria contain other mechanisms to survive antibiotic exposure such as tolerance, defined as the ability to slow metabolism by the extension of the lag phase without altering antimicrobial susceptibility. In a number of bacterial species, tolerance has been associated with treatment failure and infection chronicity and is found to precede and facilitate antimicrobial resistance. It is unknown if tolerance can be induced in Neisseria gonorrhoeae. In this study, we determined if tolerance to ceftriaxone (CRO) can be induced in N. gonorrhoeae and detected in clinical isolates. To induce tolerance, WHO P N. gonorrhoeae reference strain samples were grown under daily 3 h intermittent CRO exposure (10× the MIC), partitioned by overnight growth in GC broth. This cyclic exposure was performed for 7 consecutive days in sextuplicate, with two control cultures to which GC medium without antibiotics was added. To detect tolerance and assess CRO susceptibility, modified Tolerance Disc (TD) and Epsilometer tests were performed on isolates after each CRO exposure cycle. Additionally, this experiment was carried out on 18 clinical N. gonorrhoeae isolates. Tolerance was first detected after two CRO exposure cycles in five out of six samples. The phenotype differed per cycle with no clear pattern. No tolerance was found in control samples but was detected in 10 out of 18 clinical isolates. The present study is the first to demonstrate the induction of tolerance to CRO in N. gonorrhoeae through antibiotic exposure. In addition, tolerance to CRO was found in clinical samples.
Collapse
Affiliation(s)
- Margaux Balduck
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Jolein Gyonne Elise Laumen
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
- Laboratory of Medical Microbiology, University of Antwerp, 2610 Wilrijk, Belgium
| | - Saïd Abdellati
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Irith De Baetselier
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Tessa de Block
- Clinical Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | | | - Chris Kenyon
- HIV/STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Anzio Road, Observatory 7700, South Africa
| |
Collapse
|
37
|
Jones RM, Adams KN, Eldesouky HE, Sherman DR. The evolving biology of Mycobacterium tuberculosis drug resistance. Front Cell Infect Microbiol 2022; 12:1027394. [PMID: 36275024 PMCID: PMC9579286 DOI: 10.3389/fcimb.2022.1027394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 01/13/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (Mtb) is an ancient disease that has remained a leading cause of infectious death. Mtb has evolved drug resistance to every antibiotic regimen ever introduced, greatly complicating treatment, lowering rates of cure and menacing TB control in parts of the world. As technology has advanced, our understanding of antimicrobial resistance has improved, and our models of the phenomenon have evolved. In this review, we focus on recent research progress that supports an updated model for the evolution of drug resistance in Mtb. We highlight the contribution of drug tolerance on the path to resistance, and the influence of heterogeneity on tolerance. Resistance is likely to remain an issue for as long as drugs are needed to treat TB. However, with technology driving new insights and careful management of newly developed resources, antimicrobial resistance need not continue to threaten global progress against TB, as it has done for decades.
Collapse
Affiliation(s)
| | | | | | - David R. Sherman
- Department of Microbiology, University of Washington, Seattle, WA, United States
| |
Collapse
|
38
|
Ciofu O, Moser C, Jensen PØ, Høiby N. Tolerance and resistance of microbial biofilms. Nat Rev Microbiol 2022; 20:621-635. [PMID: 35115704 DOI: 10.1038/s41579-022-00682-4] [Citation(s) in RCA: 276] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 02/07/2023]
Abstract
Chronic infections caused by microbial biofilms represent an important clinical challenge. The recalcitrance of microbial biofilms to antimicrobials and to the immune system is a major cause of persistence and clinical recurrence of these infections. In this Review, we present the extent of the clinical problem, and the mechanisms underlying the tolerance of biofilms to antibiotics and to host responses. We also explore the role of biofilms in the development of antimicrobial resistance mechanisms.
Collapse
Affiliation(s)
- Oana Ciofu
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Claus Moser
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Peter Østrup Jensen
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Niels Høiby
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
39
|
Mohiuddin SG, Ghosh S, Kavousi P, Orman MA. Proton Motive Force Inhibitors Are Detrimental to Methicillin-Resistant Staphylococcus aureus Strains. Microbiol Spectr 2022; 10:e0202422. [PMID: 35943153 PMCID: PMC9430991 DOI: 10.1128/spectrum.02024-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/08/2022] [Indexed: 11/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) strains are tolerant of conventional antibiotics, making them extremely dangerous. Previous studies have shown the effectiveness of proton motive force (PMF) inhibitors at killing bacterial cells; however, whether these agents can launch a new treatment strategy to eliminate antibiotic-tolerant cells mandates further investigation. Here, using known PMF inhibitors and two different MRSA isolates, we showed that the bactericidal potency of PMF inhibitors seemed to correlate with their ability to disrupt PMF and permeabilize cell membranes. By screening a small chemical library to verify this correlation, we identified a subset of chemicals (including nordihydroguaiaretic acid, gossypol, trifluoperazine, and amitriptyline) that strongly disrupted PMF in MRSA cells by dissipating either the transmembrane electric potential (ΔΨ) or the proton gradient (ΔpH). These drugs robustly permeabilized cell membranes and reduced MRSA cell levels below the limit of detection. Overall, our study further highlights the importance of cellular PMF as a target for designing new bactericidal therapeutics for pathogens. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) emerged as a major hypervirulent pathogen that causes severe health care-acquired infections. These pathogens can be multidrug-tolerant cells, which can facilitate the recurrence of chronic infections and the emergence of diverse antibiotic-resistant mutants. In this study, we aimed to investigate whether proton motive force (PMF) inhibitors can launch a new treatment strategy to eliminate MRSA cells. Our in-depth analysis showed that PMF inhibitors that strongly dissipate either the transmembrane electric potential or the proton gradient can robustly permeabilize cell membranes and reduce MRSA cell levels below the limit of detection.
Collapse
Affiliation(s)
- Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Sreyashi Ghosh
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Pouria Kavousi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| |
Collapse
|
40
|
Sulaiman JE, Long L, Qian PY, Lam H. Proteome profiling of evolved methicillin-resistant Staphylococcus aureus strains with distinct daptomycin tolerance and resistance phenotypes. Front Microbiol 2022; 13:970146. [PMID: 35992709 PMCID: PMC9386379 DOI: 10.3389/fmicb.2022.970146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a highly dangerous pathogen, and daptomycin has been increasingly used to treat its infections in clinics. Recently, several groups have shown that tolerance and resistance of microbes can evolve rapidly under cyclic antibiotic exposure. We have previously shown that the same tolerance and resistance development occurs in MRSA treated with daptomycin in an adaptive laboratory evolution (ALE) experiment. In the present study, we performed proteomic analysis to compare six daptomycin-tolerant and resistant MRSA strains that were evolved from the same ancestral strain. The strain with a higher tolerance level than the others had the most different proteome and response to antibiotic treatment, resembling those observed in persister cells, which are small subpopulations of bacteria that survive lethal antibiotics treatment. By comparing the proteome changes across strains with similar phenotypes, we identified the key proteins that play important roles in daptomycin tolerance and resistance in MRSA. We selected two candidates to be confirmed by gene overexpression analysis. Overexpression of EcsA1 and FabG, which were up-regulated in all of the tolerant evolved strains, led to increased daptomycin tolerance in wild-type MRSA. The proteomics data also suggested that cell wall modulations were implicated in both resistance and tolerance, but in different ways. While the resistant strains had peptidoglycan changes and a more positive surface charge to directly repel daptomycin, the tolerant strains possessed different cell wall changes that do not involve the peptidoglycan nor alterations of the surface charge. Overall, our study showed the differential proteome profiles among multiple tolerant and resistant strains, pinpointed the key proteins for the two phenotypes and revealed the differences in cell wall modulations between the daptomycin-tolerant/resistant strains.
Collapse
Affiliation(s)
- Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Lexin Long
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- *Correspondence: Henry Lam,
| |
Collapse
|
41
|
Mira P, Lozano‐Huntelman N, Johnson A, Savage VM, Yeh P. Evolution of antibiotic resistance impacts optimal temperature and growth rate in
Escherichia coli
and
Staphylococcus epidermidis. J Appl Microbiol 2022; 133:2655-2667. [DOI: 10.1111/jam.15736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Portia Mira
- Department of Ecology and Evolutionary Biology University of California Los Angeles U.S.A
| | | | - Adrienne Johnson
- Department of Ecology and Evolutionary Biology University of California Los Angeles U.S.A
| | - Van M. Savage
- Department of Ecology and Evolutionary Biology University of California Los Angeles U.S.A
- Department of Computational Medicine, David Geffen School of Medicine University of California Los Angeles U.S.A
- Santa Fe Institute Santa Fe New Mexico U.S.A
| | - Pamela Yeh
- Department of Ecology and Evolutionary Biology University of California Los Angeles U.S.A
- Santa Fe Institute Santa Fe New Mexico U.S.A
| |
Collapse
|
42
|
Oh S, Kim Y, Choi D, Park JW, Noh JH, Chung SY, Maeng SK, Cha CJ. Effects of biochar addition on the fate of ciprofloxacin and its associated antibiotic tolerance in an activated sludge microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119407. [PMID: 35526648 DOI: 10.1016/j.envpol.2022.119407] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/31/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
This study investigated the effects of adding biochar (BC) on the fate of ciprofloxacin (CIP) and its related antibiotic tolerance (AT) in activated sludge. Three activated sludge reactors were established with different types of BC, derived from apple, pear, and mulberry tree, respectively, and one reactor with no BC. All reactors were exposed to an environmentally relevant level of CIP that acted as a definitive selective pressure significantly promoting AT to four representative antibiotics (CIP, ampicillin, tetracycline, and polymyxin B) by up to two orders of magnitude. While CIP removal was negligible in the reactor without BC, the BC-dosed reactors effectively removed CIP (70-95% removals) through primarily adsorption by BC and biodegradation/biosorption by biomass. The AT in the BC-added reactors was suppressed by 10-99%, compared to that without BC. The BC addition played a key role in sequestering CIP, thereby decreasing the selective pressure that enabled the proactive prevention of AT increase. 16S rRNA gene sequencing analysis showed that the BC addition alleviated the CIP-mediated toxicity to community diversity and organisms related to phosphorous removal. Machine learning modeling with random forest and support vector models using AS microbiome data collectively pinpointed Achromobacter selected by CIP and strongly associated with the AT increase in activated sludge. The identification of Achromobacter as an important AT bacteria revealed by the machine learning modeling with multiple models was also validated with a linear Pearson's correlation analysis. Overall, our study highlighted Achromobacter as a potential useful sentinel for monitoring AT occurring in the environment and suggested BC as a promising additive in wastewater treatment to improve micropollutant removal, mitigate potential AT propagation, and maintain community diversity against toxic antibiotic loadings.
Collapse
Affiliation(s)
- Seungdae Oh
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Yongin-si, Gyeonggi-do, 17104, Republic of Korea.
| | - Youngjun Kim
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Yongin-si, Gyeonggi-do, 17104, Republic of Korea
| | - Donggeon Choi
- Department of Civil Engineering, Kyung Hee University, 1732 Deogyeong-daero, Yongin-si, Gyeonggi-do, 17104, Republic of Korea
| | - Ji Won Park
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Jin Hyung Noh
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Sang-Yeop Chung
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Sung Kyu Maeng
- Department of Civil and Environmental Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, 4726 Seodong-daero, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| |
Collapse
|
43
|
Mutation in the Two-Component System Regulator YycH Leads to Daptomycin Tolerance in Methicillin-Resistant Staphylococcus aureus upon Evolution with a Population Bottleneck. Microbiol Spectr 2022; 10:e0168722. [PMID: 35913149 PMCID: PMC9431245 DOI: 10.1128/spectrum.01687-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptive laboratory evolution (ALE) is a useful tool to study the evolution of antibiotic tolerance in bacterial populations under diverse environmental conditions. The role of population bottlenecks in the evolution of tolerance has been investigated in Escherichia coli, but not in a more clinically relevant pathogen, methicillin-resistant Staphylococcus aureus (MRSA). In this study, we used ALE to evolve MRSA under repetitive daptomycin treatment and incorporated population bottlenecks following antibiotic exposure. We observed that the populations finally attained a tolerance mutation in the yycH gene after 2 weeks of evolution with population bottlenecks, and additional mutations in yycI and several other genes further increased the tolerance level. The tolerant populations also became resistant to another glycopeptide antibiotic, vancomycin. Through proteomics, we showed that yycH and yycI mutations led to the loss of function of the proteins and downregulated the WalKR two-component system and the downstream players, including the autolysin Atl and amidase Sle1, which are important for cell wall metabolism. Overall, our study offers new insights into the evolution of daptomycin tolerance under population bottlenecking conditions, which are commonly faced by pathogens during infection; the study also identified new mutations conferring daptomycin tolerance and revealed the proteome alterations in the evolved tolerant populations. IMPORTANCE Although population bottlenecks are known to influence the evolutionary dynamics of microbial populations, how such bottlenecks affect the evolution of tolerance to antibiotics in a clinically relevant methicillin-resistant S. aureus (MRSA) pathogen are still unclear. Here, we performed in vitro evolution of MRSA under cyclic daptomycin treatment and applied population bottlenecks following the treatment. We showed that under these experimental conditions, MRSA populations finally attained mutations in yycH, yycI, and several other genes that led to daptomycin tolerance. The discovered yycH and yycI mutations caused early termination of the genes and loss of function of the proteins, and they subsequently downregulated the expression of proteins controlled by the WalKR two-component system, such as Atl and Sle1. In addition, we compared our proteomics data with multiple studies on distinct daptomycin-tolerant MRSA mutants to identify proteins with a consistent expression pattern that could serve as biological markers for daptomycin tolerance in MRSA.
Collapse
|
44
|
Johnson MS, Desai MM. Mutational robustness changes during long-term adaptation in laboratory budding yeast populations. eLife 2022; 11:76491. [PMID: 35880743 PMCID: PMC9355567 DOI: 10.7554/elife.76491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
As an adapting population traverses the fitness landscape, its local neighborhood (i.e., the collection of fitness effects of single-step mutations) can change shape because of interactions with mutations acquired during evolution. These changes to the distribution of fitness effects can affect both the rate of adaptation and the accumulation of deleterious mutations. However, while numerous models of fitness landscapes have been proposed in the literature, empirical data on how this distribution changes during evolution remains limited. In this study, we directly measure how the fitness landscape neighborhood changes during laboratory adaptation. Using a barcode-based mutagenesis system, we measure the fitness effects of 91 specific gene disruption mutations in genetic backgrounds spanning 8000–10,000 generations of evolution in two constant environments. We find that the mean of the distribution of fitness effects decreases in one environment, indicating a reduction in mutational robustness, but does not change in the other. We show that these distribution-level patterns result from differences in the relative frequency of certain patterns of epistasis at the level of individual mutations, including fitness-correlated and idiosyncratic epistasis.
Collapse
Affiliation(s)
- Milo S Johnson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| |
Collapse
|
45
|
Eisenreich W, Rudel T, Heesemann J, Goebel W. Link Between Antibiotic Persistence and Antibiotic Resistance in Bacterial Pathogens. Front Cell Infect Microbiol 2022; 12:900848. [PMID: 35928205 PMCID: PMC9343593 DOI: 10.3389/fcimb.2022.900848] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022] Open
Abstract
Both, antibiotic persistence and antibiotic resistance characterize phenotypes of survival in which a bacterial cell becomes insensitive to one (or even) more antibiotic(s). However, the molecular basis for these two antibiotic-tolerant phenotypes is fundamentally different. Whereas antibiotic resistance is genetically determined and hence represents a rather stable phenotype, antibiotic persistence marks a transient physiological state triggered by various stress-inducing conditions that switches back to the original antibiotic sensitive state once the environmental situation improves. The molecular basics of antibiotic resistance are in principle well understood. This is not the case for antibiotic persistence. Under all culture conditions, there is a stochastically formed, subpopulation of persister cells in bacterial populations, the size of which depends on the culture conditions. The proportion of persisters in a bacterial population increases under different stress conditions, including treatment with bactericidal antibiotics (BCAs). Various models have been proposed to explain the formation of persistence in bacteria. We recently hypothesized that all physiological culture conditions leading to persistence converge in the inability of the bacteria to re-initiate a new round of DNA replication caused by an insufficient level of the initiator complex ATP-DnaA and hence by the lack of formation of a functional orisome. Here, we extend this hypothesis by proposing that in this persistence state the bacteria become more susceptible to mutation-based antibiotic resistance provided they are equipped with error-prone DNA repair functions. This is - in our opinion - in particular the case when such bacterial populations are exposed to BCAs.
Collapse
Affiliation(s)
- Wolfgang Eisenreich
- Bavarian NMR Center – Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
- *Correspondence: Wolfgang Eisenreich,
| | - Thomas Rudel
- Chair of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jürgen Heesemann
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| | - Werner Goebel
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, München, Germany
| |
Collapse
|
46
|
Oguadinma IC, Mishra A, Juneja VK, Dev Kumar G. Antibiotic Resistance Influences Growth Rates and Cross-Tolerance to Lactic Acid in Escherichia coli O157:H7 H1730. Foodborne Pathog Dis 2022; 19:622-629. [PMID: 35856661 DOI: 10.1089/fpd.2022.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli O157:H7-contaminated beef has been implicated in numerous foodborne outbreaks. Contamination occurs despite the use of antimicrobial interventions such as lactic acid (LA). In addition, resistance to antibiotics such as ampicillin and streptomycin among isolates has been frequently reported. The influence of antibiotic resistance (ABR) on growth rates and cross-tolerance of lettuce isolate E. coli O157:H7 H1730 to LA was evaluated. Antibiotic-resistant strain variants were generated by conferring resistance to either ampicillin (ampC) or streptomycin (strepC) or both ampicillin and streptomycin (ampC strepC) through incremental exposure to the antibiotics. Ampicillin resistance was also conferred by plasmid transformation to generate the ampP and ampP strepC strains. The minimum inhibitory concentration of LA on all the strains evaluated was 0.375% v/v. The lag phase duration of all strains except E. coli O157:H7 ampP strepC increased with increasing concentration of LA. The ampP strepC and ampC strains were most tolerant to 5% LA with declines in the cell population of 2.86 and 2.56 log CFU/mL, respectively (p < 0.05). The ampP strepC strain was the most tolerant when evaluated by the live/dead viability assay. The addition of the efflux pump inhibitor, carbonyl cyanide m-chlorophenylhydrazone, with 2.5% LA resulted in a significant increase in sensitivity in the no resistance (NR) wild-type and ampC strains, resulting in 6.62 and 6.65 log CFU/mL reduction, respectively, while the highly tolerant ampP strepC strain had a 2.90 log CFU/mL decrease. Tolerance to LA was significantly influenced by both the ABR profile of the strain and LA concentration. The results from this study indicate that E. coli O157:H7 strains with certain ABR profiles might be more tolerant to LA.
Collapse
Affiliation(s)
- Ikechukwu Chukwuma Oguadinma
- Center for Food Safety, College of Agriculture and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| | - Abhinav Mishra
- Department of Food Science & Technology, University of Georgia, Athens, Georgia, USA
| | - Vijay K Juneja
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Govindaraj Dev Kumar
- Center for Food Safety, College of Agriculture and Environmental Sciences, University of Georgia, Griffin, Georgia, USA
| |
Collapse
|
47
|
Microwave-assisted green synthesis of AM-ZnO NP from Atalantia monophylla leaf extract, opto-structural property characterization and biomedical applications. APPLIED NANOSCIENCE 2022. [DOI: 10.1007/s13204-022-02549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
48
|
Ojha D, Jaszczur MM, Sikand A, McDonald JP, Robinson A, van Oijen AM, Mak CH, Pinaud F, Cox MM, Woodgate R, Goodman MF. Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase. Nucleic Acids Res 2022; 50:6854-6869. [PMID: 35736210 PMCID: PMC9262582 DOI: 10.1093/nar/gkac515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 12/24/2022] Open
Abstract
Homologs of the mutagenic Escherichia coli DNA polymerase V (pol V) are encoded by numerous pathogens and mobile elements. We have used Rum pol (RumA'2B), from the integrative conjugative element (ICE), R391, as a model mobile element-encoded polymerase (MEPol). The highly mutagenic Rum pol is transferred horizontally into a variety of recipient cells, including many pathogens. Moving between species, it is unclear if Rum pol can function on its own or requires activation by host factors. Here, we show that Rum pol biochemical activity requires the formation of a physical mutasomal complex, Rum Mut, containing RumA'2B-RecA-ATP, with RecA being donated by each recipient bacteria. For R391, Rum Mut specific activities in vitro and mutagenesis rates in vivo depend on the phylogenetic distance of host-cell RecA from E. coli RecA. Rum pol is a highly conserved and effective mobile catalyst of rapid evolution, with the potential to generate a broad mutational landscape that could serve to ensure bacterial adaptation in antibiotic-rich environments leading to the establishment of antibiotic resistance.
Collapse
Affiliation(s)
- Debika Ojha
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Malgorzata M Jaszczur
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Adhirath Sikand
- Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew Robinson
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons Institute and School of Chemistry and Biomolecular Science, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Chi H Mak
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA.,Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Fabien Pinaud
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA.,Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 Wisconsin, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| |
Collapse
|
49
|
Chen Q, Dharmaraj T, Cai PC, Burgener EB, Haddock NL, Spakowitz AJ, Bollyky PL. Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics. Pharmaceutics 2022; 14:1425. [PMID: 35890320 PMCID: PMC9318951 DOI: 10.3390/pharmaceutics14071425] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages, viruses that infect and replicate within bacteria, impact bacterial responses to antibiotics in complex ways. Recent studies using lytic bacteriophages to treat bacterial infections (phage therapy) demonstrate that phages can promote susceptibility to chemical antibiotics and that phage/antibiotic synergy is possible. However, both lytic and lysogenic bacteriophages can contribute to antimicrobial resistance. In particular, some phages mediate the horizontal transfer of antibiotic resistance genes between bacteria via transduction and other mechanisms. In addition, chronic infection filamentous phages can promote antimicrobial tolerance, the ability of bacteria to persist in the face of antibiotics. In particular, filamentous phages serve as structural elements in bacterial biofilms and prevent the penetration of antibiotics. Over time, these contributions to antibiotic tolerance favor the selection of resistance clones. Here, we review recent insights into bacteriophage contributions to antibiotic susceptibility, resistance, and tolerance. We discuss the mechanisms involved in these effects and address their impact on bacterial fitness.
Collapse
Affiliation(s)
- Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Tejas Dharmaraj
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Pamela C. Cai
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA;
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; (E.B.B.); (A.J.S.)
| | - Naomi L. Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Andy J. Spakowitz
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; (E.B.B.); (A.J.S.)
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| |
Collapse
|
50
|
Peptidoglycan Recycling Promotes Outer Membrane Integrity and Carbapenem Tolerance in Acinetobacter baumannii. mBio 2022; 13:e0100122. [PMID: 35638738 PMCID: PMC9239154 DOI: 10.1128/mbio.01001-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
β-Lactam antibiotics exploit the essentiality of the bacterial cell envelope by perturbing the peptidoglycan layer, typically resulting in rapid lysis and death. Many Gram-negative bacteria do not lyse but instead exhibit "tolerance," the ability to sustain viability in the presence of bactericidal antibiotics for extended periods. Antibiotic tolerance has been implicated in treatment failure and is a stepping-stone in the acquisition of true resistance, and the molecular factors that promote intrinsic tolerance are not well understood. Acinetobacter baumannii is a critical-threat nosocomial pathogen notorious for its ability to rapidly develop multidrug resistance. Carbapenem β-lactam antibiotics (i.e., meropenem) are first-line prescriptions to treat A. baumannii infections, but treatment failure is increasingly prevalent. Meropenem tolerance in Gram-negative pathogens is characterized by morphologically distinct populations of spheroplasts, but the impact of spheroplast formation is not fully understood. Here, we show that susceptible A. baumannii clinical isolates demonstrate tolerance to high-level meropenem treatment, form spheroplasts upon exposure to the antibiotic, and revert to normal growth after antibiotic removal. Using transcriptomics and genetic screens, we show that several genes associated with outer membrane integrity maintenance and efflux promote tolerance, likely by limiting entry into the periplasm. Genes associated with peptidoglycan homeostasis in the periplasm and cytoplasm also answered our screen, and their disruption compromised cell envelope barrier function. Finally, we defined the enzymatic activity of the tolerance determinants penicillin-binding protein 7 (PBP7) and ElsL (a cytoplasmic ld-carboxypeptidase). These data show that outer membrane integrity and peptidoglycan recycling are tightly linked in their contribution to A. baumannii meropenem tolerance. IMPORTANCE Carbapenem treatment failure associated with "superbug" infections has rapidly increased in prevalence, highlighting the urgent need to develop new therapeutic strategies. Antibiotic tolerance can directly lead to treatment failure but has also been shown to promote the acquisition of true resistance within a population. While some studies have addressed mechanisms that promote tolerance, factors that underlie Gram-negative bacterial survival during carbapenem treatment are not well understood. Here, we characterized the role of peptidoglycan recycling in outer membrane integrity maintenance and meropenem tolerance in A. baumannii. These studies suggest that the pathogen limits antibiotic concentrations in the periplasm and highlight physiological processes that could be targeted to improve antimicrobial treatment.
Collapse
|