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Morales-Durán N, León-Buitimea A, Morones-Ramírez JR. Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions. Heliyon 2024; 10:e27984. [PMID: 38510041 PMCID: PMC10950705 DOI: 10.1016/j.heliyon.2024.e27984] [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: 08/10/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Antimicrobial resistance is a global health threat. Misuse and overuse of antimicrobials are the main drivers in developing drug-resistant bacteria. The emergence of the rapid global spread of multi-resistant bacteria requires urgent multisectoral action to generate novel treatment alternatives. Combination therapy offers the potential to exploit synergistic effects for enhanced antibacterial efficacy of drugs. Understanding the complex dynamics and kinetics of drug interactions in combination therapy is crucial. Therefore, this review outlines the current advances in antibiotic resistance's evolutionary and genetic dynamics in combination therapies-exposed bacteria. Moreover, we also discussed four pivotal future research areas to comprehend better the development of antibiotic resistance in bacteria treated with combination strategies.
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Affiliation(s)
- Nami Morales-Durán
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - José R. Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
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2
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Yi J, Ahn J. Heterogeneous Phenotypic Responses of Antibiotic-Resistant Salmonella Typhimurium to Food Preservative-Related Stresses. Antibiotics (Basel) 2023; 12:1702. [PMID: 38136736 PMCID: PMC10740406 DOI: 10.3390/antibiotics12121702] [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: 11/17/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
This study was designed to evaluate the response of antibiotic-resistant Salmonella Typhimurium to food preservative-related stresses, such as lactic acid and sodium chloride (NaCl). S. Typhimurium cells were exposed to 1 µg/mL of ciprofloxacin (CIP), 0.2% lactic acid (LA), 6% NaCl, CIP followed by LA (CIP-LA), and CIP followed by NaCl (CIP-NaCl). The untreated S. Typhimurium cells were the control (CON). All treatments were as follows: CON, CIP, LA, NaCl, CIP-LA, and CIP-NaCl. The phenotypic heterogeneity was evaluated by measuring the antimicrobial susceptibility, bacterial fluctuation, cell injury, persistence, and cross-resistance. The CIP, CIP-LA, and CIP-NaCl groups were highly resistant to ciprofloxacin, showing MIC values of 0.70, 0.59, and 0.54 µg/mL, respectively, compared to the CON group (0.014 µg/mL). The susceptibility to lactic acid was not changed after exposure to NaCl, while that to NaCl was decreased after exposure to NaCl. The Eagle phenomenon was observed in the CIP, CIP-LA, and CIP-NaCl groups, showing Eagle effect concentrations (EECs) of more than 8 µg/mL. No changes in the MBCs of lactic acid and NaCl were observed in the CIP, LA, and CIP-LA groups, and the EECs of lactic acid and NaCl were not detected in all treatments. The bacterial fluctuation rates of the CIP-LA and CIP-NaCl groups were considerably increased to 33% and 41%, respectively, corresponding to the injured cell proportions of 82% and 89%. CIP-NaCl induced persister cells as high as 2 log cfu/mL. The LA and NaCl treatments decreased the fitness cost. The CIP-NaCl treatment showed positive cross-resistance to erythromycin (ERY) and tetracycline (TET), while the LA and NaCl treatments were collaterally susceptible to chloramphenicol (CHL), ciprofloxacin (CIP), piperacillin (PIP), and TET. The results provide new insight into the fate of antibiotic-resistant S. Typhimurium during food processing and preservation.
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Affiliation(s)
- Jiseok Yi
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea;
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
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3
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Adams-Ward X, Chapalain A, Ginevra C, Jarraud S, Doublet P, Gilbert C. Bacterial persistence in Legionella pneumophila clinical isolates from patients with recurring legionellosis. Front Cell Infect Microbiol 2023; 13:1219233. [PMID: 37600942 PMCID: PMC10434508 DOI: 10.3389/fcimb.2023.1219233] [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: 05/08/2023] [Accepted: 06/29/2023] [Indexed: 08/22/2023] Open
Abstract
Bacterial persisters are a transient subpopulation of non-growing, antibiotic-tolerant cells. There is increasing evidence that bacterial persisters play an important role in treatment failure leading to recurring infections and promoting the development of antibiotic resistance. Current research reveals that recurring legionellosis is often the result of relapse rather than reinfection and suggests that the mechanism of bacterial persistence may play a role. The development of single-cell techniques such as the Timerbac system allows us to identify potential persister cells and investigate their physiology. Here, we tested the persister forming capacity of 7 pairs of Legionella pneumophila (Lp) clinical isolates, with isolate pairs corresponding to two episodes of legionellosis in the same patient. We distinguished non-growing subpopulations from their replicating counterparts during infection in an amoeba model. Imaging flow cytometry allowed us to identify single non-growing bacteria within amoeba cells 17 h post-infection, thus corresponding to this subpopulation of potential persister cells. Interestingly the magnitude of this subpopulation varies between the 7 pairs of Lp clinical isolates. Biphasic killing kinetics using ofloxacin stress confirmed the persister development capacity of ST1 clinical isolates, highlighting enhanced persister formation during the host cell infection. Thus, persister formation appears to be strain or ST (sequence type) dependent. Genome sequence analysis was carried out between ST1 clinical isolates and ST1 Paris. No genetic microevolution (SNP) linked to possible increase of persistence capacity was revealed among all the clones tested, even in clones issued from two persistence cycle experiments, confirming the transient reversible phenotypic status of persistence. Treatment failure in legionellosis is a serious issue as infections have a 5-10% mortality rate, and investigations into persistence in a clinical context and the mechanisms involved may allow us to combat this issue.
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Affiliation(s)
- Xanthe Adams-Ward
- Centre International De Recherche En Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, École normale supérieure (ENS) Lyon, Centre national de la recherche scientifique (CNRS) UMR5308, Université Lyon 1, Université De Lyon, Lyon, France
| | - Annelise Chapalain
- Centre International De Recherche En Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, École normale supérieure (ENS) Lyon, Centre national de la recherche scientifique (CNRS) UMR5308, Université Lyon 1, Université De Lyon, Lyon, France
| | - Christophe Ginevra
- Centre International De Recherche En Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, École normale supérieure (ENS) Lyon, Centre national de la recherche scientifique (CNRS) UMR5308, Université Lyon 1, Université De Lyon, Lyon, France
- Hospices Civils De Lyon, Institut Des Agents Infectieux, Centre National De Référence Des Légionelles, Lyon, France
| | - Sophie Jarraud
- Centre International De Recherche En Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, École normale supérieure (ENS) Lyon, Centre national de la recherche scientifique (CNRS) UMR5308, Université Lyon 1, Université De Lyon, Lyon, France
- Hospices Civils De Lyon, Institut Des Agents Infectieux, Centre National De Référence Des Légionelles, Lyon, France
| | - Patricia Doublet
- Centre International De Recherche En Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, École normale supérieure (ENS) Lyon, Centre national de la recherche scientifique (CNRS) UMR5308, Université Lyon 1, Université De Lyon, Lyon, France
| | - Christophe Gilbert
- Centre International De Recherche En Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, École normale supérieure (ENS) Lyon, Centre national de la recherche scientifique (CNRS) UMR5308, Université Lyon 1, Université De Lyon, Lyon, France
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4
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Dawan J, Ahn J. Variability in Adaptive Resistance of Salmonella Typhimurium to Sublethal Levels of Antibiotics. Antibiotics (Basel) 2022; 11:antibiotics11121725. [PMID: 36551382 PMCID: PMC9774383 DOI: 10.3390/antibiotics11121725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
This study was designed to evaluate the adaptive resistance of Salmonella Typhimurium under continuous sublethal selective pressure. Salmonella Typhimurium ATCC 19585 (STATCC) and S. Typhimurium CCARM 8009 (STCCARM) were sequentially cultured for 3 days at 37 °C in trypticase soy broth containing 1/2 × MICs of cefotaxime (CEF1/2), chloramphenicol (CHL1/2), gentamicin (GEN1/2), and polymyxin B (POL1/2). The STATCC and STCCARM exposed to CEF1/2, CHL1/2, GEN1/2, and POL1/2 were evaluated using antibiotic susceptibility, cross-resistance, and relative fitness. The susceptibilities of STATCC exposed to GEN1/2 and POL1/2 were increased by a 2-fold (gentamicin) and 8-fold (polymyxin B) increase in minimum inhibitory concentration (MIC) values, respectively. The MIC values of STCCARM exposed to CEF1/2, CHL1/2, GEN1/2, and POL1/2 were increased by 4-fold (cefotaxime), 2-fold (chloramphenicol), 2-fold (gentamicin), and 8-fold (polymyxin B). The highest heterogeneous fractions were observed for the STATCC exposed to CEF1/2 (38%) and POL1/2 (82%). The STCCARM exposed to GEN1/2 was cross-resistant to cefotaxime (p < 0.05), chloramphenicol (p < 0.01), and polymyxin B (p < 0.05). The highest relative fitness levels were 0.92 and 0.96, respectively, in STATCC exposed to CEF1/2 and STCCARM exposed to POL1/2. This study provides new insight into the fate of persistent cells and also guidance for antibiotic use.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Republic of Korea
- Correspondence: ; Tel.: +82-33-250-6564
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de Brito FAE, de Freitas APP, Nascimento MS. Multidrug-Resistant Biofilms (MDR): Main Mechanisms of Tolerance and Resistance in the Food Supply Chain. Pathogens 2022; 11:pathogens11121416. [PMID: 36558750 PMCID: PMC9784232 DOI: 10.3390/pathogens11121416] [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: 09/30/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
Biofilms are mono- or multispecies microbial communities enclosed in an extracellular matrix (EPS). They have high potential for dissemination and are difficult to remove. In addition, biofilms formed by multidrug-resistant strains (MDRs) are even more aggravated if we consider antimicrobial resistance (AMR) as an important public health issue. Quorum sensing (QS) and horizontal gene transfer (HGT) are mechanisms that significantly contribute to the recalcitrance (resistance and tolerance) of biofilms, making them more robust and resistant to conventional sanitation methods. These mechanisms coordinate different strategies involved in AMR, such as activation of a quiescent state of the cells, moderate increase in the expression of the efflux pump, decrease in the membrane potential, antimicrobial inactivation, and modification of the antimicrobial target and the architecture of the EPS matrix itself. There are few studies investigating the impact of the use of inhibitors on the mechanisms of recalcitrance and its impact on the microbiome. Therefore, more studies to elucidate the effect and applications of these methods in the food production chain and the possible combination with antimicrobials to establish new strategies to control MDR biofilms are needed.
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Hare PJ, Englander HE, Mok WWK. Probiotic Escherichia coli Nissle 1917 inhibits bacterial persisters that survive fluoroquinolone treatment. J Appl Microbiol 2022; 132:4020-4032. [PMID: 35332984 PMCID: PMC9468890 DOI: 10.1111/jam.15541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/22/2022] [Indexed: 12/01/2022]
Abstract
AIMS Bacterial persisters are rare phenotypic variants in clonal bacterial cultures that can endure antimicrobial therapy and potentially contribute to infection relapse. Here, we investigate the potential of leveraging microbial interactions to disrupt persisters as they resuscitate during the post-antibiotic treatment recovery period. METHODS AND RESULTS We treated stationary-phase E. coli MG1655 with a DNA-damaging fluoroquinolone and co-cultured the cells with probiotic E. coli Nissle following antibiotic removal. We found that E. coli Nissle reduced the survival of fluoroquinolone persisters and their progeny by over three orders of magnitude within 24 h. Using a bespoke H-diffusion cell apparatus that we developed, we showed that E. coli Nissle antagonized the fluoroquinolone-treated cells in a contact-dependent manner. We further demonstrated that the fluoroquinolone-treated cells can still activate the SOS response as they recover from antibiotic treatment in the presence of E. coli Nissle and that the persisters depend on TolC-associated efflux systems to defend themselves against the action of E. coli Nissle. CONCLUSION Our results demonstrate that probiotic bacteria, such as E. coli Nissle, have the potential to inhibit persisters as they resuscitate following antibiotic treatment. SIGNIFICANCE AND IMPACT OF THE STUDY Bacterial persisters are thought to underlie chronic infections and they can lead to an increase in antibiotic-resistant mutants in their progenies. Our data suggest that we can leverage the knowledge we gain on the interactions between microbial strains/species that interfere with persister resuscitation, such as those involving probiotic E. coli Nissle and E. coli MG1655 (a K-12 strain), to bolster the activity of our existing antibiotics.
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Affiliation(s)
- Patricia J. Hare
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, Connecticut, USA
- School of Dental Medicine, UCONN Health, Farmington, Connecticut, USA
| | - Hanna E. Englander
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, Connecticut, USA
- Department of Physiology & Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UCONN Health, Farmington, Connecticut, USA
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7
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Pamplona Pagnossa J, Rocchetti G, Bezerra JDP, Batiha GES, El-Masry EA, Mahmoud MH, Alsayegh AA, Mashraqi A, Cocconcelli PS, Santos C, Lucini L, Hilsdorf Piccoli R. Untargeted Metabolomics Approach of Cross-Adaptation in Salmonella Enterica Induced by Major Compounds of Essential Oils. Front Microbiol 2022; 13:769110. [PMID: 35694295 PMCID: PMC9174793 DOI: 10.3389/fmicb.2022.769110] [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: 09/09/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cross-adaptation phenomena in bacterial populations, induced by sublethal doses of antibacterial solutions, are a major problem in the field of food safety. In this regard, essential oils and their major compounds appear as an effective alternative to common sanitizers in food industry environments. The present study aimed to evaluate the untargeted metabolomics perturbations of Salmonella enterica serovar Enteritidis that has been previously exposed to the sublethal doses of the major components of essential oils: cinnamaldehyde, citral, and linalool (CIN, CIT, and LIN, respectively). Cinnamaldehyde appeared to be the most efficient compound in the assays evaluating the inhibitory effects [0.06% (v/v) as MBC]. Also, preliminary tests exhibited a phenotype of adaptation in planktonic and sessile cells of S. Enteritidis when exposed to sublethal doses of linalool, resulting in tolerance to previously lethal concentrations of citral. A metabolomics approach on S. Enteritidis provided an important insight into the phenomenon of cross-adaptation induced by sublethal doses of major compounds of some essential oils. In addition, according to the results obtained, when single molecules were used, many pathways may be involved in bacterial tolerance, which could be different from the findings revealed in previous studies regarding the use of phytocomplex of essential oils. Orthogonal projection to latent structures (OPLS) proved to be an interesting predictive model to demonstrate the adaptation events in pathogenic bacteria because of the global engagement to prevent and control foodborne outbreaks.
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Affiliation(s)
- Jorge Pamplona Pagnossa
- Health and Biological Sciences Institute, Pontifical Catholic University–PUC Minas, Poços de Caldas, Brazil
| | - Gabriele Rocchetti
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Jadson Diogo Pereira Bezerra
- Setor de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Eman A. El-Masry
- Microbiology and Immunology Unit, Department of Pathology, College of Medicine, Jouf University, Sakaka, Saudi Arabia
- Department of Medical Microbiology and Immunology, College of Medicine, Menoufia University, Shebeen El-Kom, Egypt
| | - Mohamed H. Mahmoud
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman A. Alsayegh
- Clinical Nutrition Department, Applied Medical Sciences College, Jazan University, Jazan, Saudi Arabia
| | - Abdullah Mashraqi
- Biology Department, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Pier Sandro Cocconcelli
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Cledir Santos
- Department of Chemical Science and Natural Resources, Universidad de La Frontera, Temuco, Chile
- *Correspondence: Cledir Santos,
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
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The polyamino-isoprenyl potentiator NV716 revives disused antibiotics against Gram-negative bacteria in broth, infected monocytes, or biofilms, by disturbing the barrier effect of their outer membrane. Eur J Med Chem 2022; 238:114496. [DOI: 10.1016/j.ejmech.2022.114496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022]
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Liu X, Tang R, Li H, Wang L, Wan C. The physiological and ecological properties of bacterial persisters discovered from municipal sewage sludge and the potential risk. ENVIRONMENTAL RESEARCH 2022; 205:112481. [PMID: 34871595 DOI: 10.1016/j.envres.2021.112481] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Bacterial persisters are a special microbial population and are considered to be the bacterial reservoir of antibiotic-resistant bacteria. They can survive antibiotic treatment even in high concentrations of antibiotics and revive in the appropriate conditions. However, the characteristics of bacterial persisters in the municipal sewage sludge and their potential environmental risks have not yet been paid much attention to. In this study, bacterial persisters were discovered from the sludge of wastewater treatment plants in four different regions (Jilin, Lhasa, Shenzhen, and Yili), and the metagenomic analysis confirmed that bacterial persisters were ubiquitous in all four municipal sewage sludge and positively related to the protobacterium populations. At the taxonomic genus level, a total of 57 genera of bacterial persisters were shared by the four sewage sludge, and the genera with abundance exceeding 2% were Acinetobacter, Lysinibacillus, Aeromonas, Brevundimonas, Pseudomonas, and Alcaligenes, among which Acinetobacter accounted for 57.24%. Genus Lysinibacillus and Aeromonas were significant in Jilin and Lhasa, respectively. The persistence mechanism of bacterial persisters derived from sludge was also clarified, among which, Aeromonas, Brevundimonas, and Alcaligenes rely on the hipBA toxin-antitoxin system, while Acinetobacter enters the persistence state mainly through the stringent response system based on (p)ppGpp. Moreover, it was found that a typical bacterial persister originated from Acinetobacter, named T9-9, could tolerate a variety of antibiotics, such as 1000 μg/mL of kanamycin, 160 μg/mL of tetracycline, and 30 μg/mL of ciprofloxacin. Even if the ultraviolet intensity was 6-36 times the usual dosage of ultraviolet disinfection in wastewater treatment plants, it could not completely kill T9-9, but the killing efficiency by chlorine disinfection technology could reach 100%. This study pointed out an environmental risk of bacterial persisters that existed in sewage sludge that had been neglected and strongly recommended to improve the disinfection process in the wastewater treatment plant.
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Affiliation(s)
- Xiang Liu
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200438, China.
| | - Rui Tang
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Huiqi Li
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Li Wang
- Center of Analysis and Measurement, Fudan University, Shanghai, 200438, China
| | - Chunli Wan
- Department of Environmental Science and Engineering, Fudan University, Shanghai, 200438, China.
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10
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Jo J, Price-Whelan A, Dietrich LEP. Gradients and consequences of heterogeneity in biofilms. Nat Rev Microbiol 2022; 20:593-607. [PMID: 35149841 DOI: 10.1038/s41579-022-00692-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/15/2022]
Abstract
Historically, appreciation for the roles of resource gradients in biology has fluctuated inversely to the popularity of genetic mechanisms. Nevertheless, in microbiology specifically, widespread recognition of the multicellular lifestyle has recently brought new emphasis to the importance of resource gradients. Most microorganisms grow in assemblages such as biofilms or spatially constrained communities with gradients that influence, and are influenced by, metabolism. In this Review, we discuss examples of gradient formation and physiological differentiation in microbial assemblages growing in diverse settings. We highlight consequences of physiological heterogeneity in microbial assemblages, including division of labour and increased resistance to stress. Our impressions of microbial behaviour in various ecosystems are not complete without complementary maps of the chemical and physical geographies that influence cellular activities. A holistic view, incorporating these geographies and the genetically encoded functions that operate within them, will be essential for understanding microbial assemblages in their many roles and potential applications.
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Affiliation(s)
- Jeanyoung Jo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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11
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Zhou BQ, Zhou YF, Apata CO, Jiang L, Pei QM. Effects of bidirectional phenotype switching on signal noise in a bacterial community. Phys Rev E 2021; 104:054116. [PMID: 34942774 DOI: 10.1103/physreve.104.054116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/29/2021] [Indexed: 11/07/2022]
Abstract
Cells can sense and process various signals. Noise is inevitable in the cell signaling system. In a bacterial community, the mutual conversion between normal cells and persistent cells forms a bidirectional phenotype switching cascade, in which either one can be used as an upstream signal and the other as a downstream signal. In order to quantitatively describe the relationship between noise and signal amplification of each phenotype, the gain-fluctuation relationship is obtained by using the linear noise approximation of the master equation. Through the simulation of these theoretical formulas, it is found that the bidirectional phenotype switching can directly generate interconversion noise which is usually very small and almost negligible. In particular, the bidirectional phenotype switching can provide a global fluctuating environment, which will not only affect the values of noise and covariance, but also generate additional intrinsic noise. The additional intrinsic noise in each phenotype is the main part of the total noise and can be transmitted to the other phenotype. The transmitted noise is also a powerful supplement to the total noise. Therefore, the indirect impact of bidirectional phenotype switching is far greater than its direct impact, which may be one of the reasons why chronic infections caused by persistent cells are refractory to treat.
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Affiliation(s)
- Bin-Qian Zhou
- School of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou 434023, China
| | - Yi-Fan Zhou
- School of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou 434023, China
| | - Charles Omotomide Apata
- School of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou 434023, China
| | - Long Jiang
- School of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou 434023, China
| | - Qi-Ming Pei
- School of Physics and Optoelectronic Engineering, Yangtze University, Jingzhou 434023, China
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12
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Peng S, Wang Y, Chen R, Lin X. Chicken Manure and Mushroom Residues Affect Soil Bacterial Community Structure but Not the Bacterial Resistome When Applied at the Same Rate of Nitrogen for 3 Years. Front Microbiol 2021; 12:618693. [PMID: 34093457 PMCID: PMC8177108 DOI: 10.3389/fmicb.2021.618693] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 04/19/2021] [Indexed: 01/17/2023] Open
Abstract
Animal manure is a reservoir of antibiotic resistance genes (ARGs), and direct application of the manure will lead to spread of ARGs in farmland. Here, we explored the impacts of chicken manure and heat-treated chicken manure on the patterns of soil resistome after 3 years’ application, with mushroom residues set as the plant-derived organic manure treatment. A total of 262 ARG subtypes were detected in chicken manure using high-throughput qPCR, and heat treatment can effectively remove 50 types of ARGs. Although ARG subtypes and abundance were both higher in chicken manure, there was no significant difference in the ARG profiles and total ARG abundance among three manure-treated soils. Soil bacteria community compositions were significantly different among manure-treated soils, but they were not significantly correlated with soil ARG profiles. Fast expectation–maximization microbial source tracking (FEAST) was used for quantifying the contributions of the potential sources to microbial taxa and ARGs in manure-fertilized soil. Results revealed that only 0.2% of the chicken manure-derived bacterial communities survived in soil, and intrinsic ARGs were the largest contributor of soil ARGs (95.8–99.7%); ARGs from chicken manure only contributed 0.4%. The total ARG abundance in the heat-treated chicken manure-amended soils was similar to that in the mushroom residue-treated soils, while it was 1.41 times higher in chicken manure-treated soils. Thus, heat treatment of chicken manure may efficiently reduce ARGs introduced into soil and decrease the risk of dissemination of ARGs.
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Affiliation(s)
- Shuang Peng
- College of Environment and Ecology, Jiangsu Open University, Nanjing, China.,State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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13
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Adikari S, Hong-Geller E, Micheva-Viteva S. Methods for Enrichment of Bacterial Persister Populations for Phenotypic Screens and Genomic Studies. Methods Mol Biol 2021; 2357:71-82. [PMID: 34590252 DOI: 10.1007/978-1-0716-1621-5_5] [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] [Indexed: 06/13/2023]
Abstract
Transient phenotypic adaptations in bacteria that enable survival at bactericidal antibiotic concentrations give rise to bacterial persistence. Naturally, the abundance of persister cells is very low (about 1 in 105 cells) in actively growing bacterial populations. Therefore, in order to study bacterial persistence mechanisms for therapeutics development, persister cells need to be enriched from a larger culture. Here, we describe three enrichment methods for obtaining Burkholderia thailandensis persisters: (1) flow sorting for persisters from exponentially dividing cultures by fluorescent staining of bacterial cells with a translational membrane depolarization-specific DiBAC4(3) dye, (2) antibiotic lysis of nonpersisters, and (3) culture aging to induce persister survival. We also describe herein the lysis of persister cells obtained by all three methods for downstream bacterial RNA extraction and transcriptomics analysis.
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Affiliation(s)
- Samantha Adikari
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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14
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Reva ON, Korotetskiy IS, Joubert M, Shilov SV, Jumagaziyeva AB, Suldina NA, Ilin AI. The Effect of Iodine-Containing Nano-Micelles, FS-1, on Antibiotic Resistance, Gene Expression and Epigenetic Modifications in the Genome of Multidrug Resistant MRSA Strain Staphylococcus aureus ATCC BAA-39. Front Microbiol 2020; 11:581660. [PMID: 33193215 PMCID: PMC7642360 DOI: 10.3389/fmicb.2020.581660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
Application of supplementary drugs which increase susceptibility of pathogenic bacteria to antibiotics is a promising yet unexplored approach to overcome the global problem of multidrug-resistant infections. The discovery of a new drug, an iodine-containing nano-molecular complex FS-1, which has proven to improve susceptibility to antibiotics in various pathogens, including MRSA strain Staphylococcus aureus ATCC BAA-39TM, allowed studying this phenomenon. Chromosomal DNA and total RNA samples extracted from the FS-1 treated strain (FS) and from the negative control (NC) cultures were sequenced by PacBio SMRT and Ion Torrent technologies, respectively. PacBio DNA reads were used to assemble chromosomal DNA of the NC and FS variants of S. aureus BAA-39 and to perform profiling of epigenetically modified nucleotides. Results of transcriptional profiling, variant calling and detection of epigenetic modifications in the FS variant were compared to the NC variant. Additionally, the genetic alterations caused by the treatment of S. aureus BAA-39 with FS-1 were compared to the results of a similar experiment conducted with another model organism, E. coli ATCC BAA-196. Several commonalities in responses of these phylogenetically distant microorganisms to the treatment with FS-1 were discovered, which included metabolic transition toward anaerobiosis and oxidative/osmotic stress response. S. aureus culture appeared to be more sensitive to FS-1 due to a higher penetrability of cells by iodine bound compounds, which caused carbonyl stress associated with nucleotide damaging by FS-1, abnormal epigenetic modifications and an increased rate of mutations. It was hypothesized that the disrupted pattern of adenine methylated loci within methicillin-resistance chromosome cassettes (SCCmec) may promote excision of this antibiotic resistance determinant from chromosomes while the altered pattern of cytosine methylation was behind the adaptive gene regulation in the culture FS. The selection against the antibiotic resistance in bacterial populations caused by abnormal epigenetic modifications exemplifies possible mechanisms of antibiotic resistance reversion induced by iodine-containing compounds. These finding will facilitate development of therapeutic agents against multidrug-resistant infections.
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Affiliation(s)
- Oleg N. Reva
- Centre for Bioinformatics and Computational Biology (CBCB), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Monique Joubert
- Centre for Bioinformatics and Computational Biology (CBCB), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Sergey V. Shilov
- Scientific Center for Anti-Infectious Drugs (SCAID), Almaty, Kazakhstan
| | | | | | - Alexandr I. Ilin
- Scientific Center for Anti-Infectious Drugs (SCAID), Almaty, Kazakhstan
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