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Wei Y, Palacios Araya D, Palmer KL. Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics. Nat Rev Microbiol 2024; 22:705-721. [PMID: 38890478 DOI: 10.1038/s41579-024-01058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.
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Affiliation(s)
- Yahan Wei
- School of Podiatric Medicine, The University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA.
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2
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Leinberger FH, Cassidy L, Edelmann D, Schmid NE, Oberpaul M, Blumenkamp P, Schmidt S, Natriashvili A, Ulbrich MH, Tholey A, Koch HG, Berghoff BA. Protein aggregation is a consequence of the dormancy-inducing membrane toxin TisB in Escherichia coli. mSystems 2024:e0106024. [PMID: 39377584 DOI: 10.1128/msystems.01060-24] [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: 08/08/2024] [Accepted: 09/06/2024] [Indexed: 10/09/2024] Open
Abstract
Bacterial dormancy is a valuable strategy to survive stressful conditions. Toxins from chromosomal toxin-antitoxin systems have the potential to halt cell growth, induce dormancy, and eventually promote a stress-tolerant persister state. Due to their potential toxicity when overexpressed, sophisticated expression systems are needed when studying toxin genes. Here, we present a moderate expression system for toxin genes based on an artificial 5' untranslated region. We applied the system to induce expression of the toxin gene tisB from the chromosomal type I toxin-antitoxin system tisB/istR-1 in Escherichia coli. TisB is a small hydrophobic protein that targets the inner membrane, resulting in depolarization and ATP depletion. We analyzed TisB-producing cells by RNA-sequencing and revealed several genes with a role in recovery from TisB-induced dormancy, including the chaperone genes ibpAB and spy. The importance of chaperone genes suggested that TisB-producing cells are prone to protein aggregation, which was validated by an in vivo fluorescent reporter system. We moved on to show that TisB is an essential factor for protein aggregation upon DNA damage mediated by the fluoroquinolone antibiotic ciprofloxacin in E. coli wild-type cells. The occurrence of protein aggregates correlates with an extended dormancy duration, which underscores their importance for the life cycle of TisB-dependent persister cells. IMPORTANCE Protein aggregates occur in all living cells due to misfolding of proteins. In bacteria, protein aggregation is associated with cellular inactivity, which is related to dormancy and tolerance to stressful conditions, including exposure to antibiotics. In Escherichia coli, the membrane toxin TisB is an important factor for dormancy and antibiotic tolerance upon DNA damage mediated by the fluoroquinolone antibiotic ciprofloxacin. Here, we show that TisB provokes protein aggregation, which, in turn, promotes an extended state of cellular dormancy. Our study suggests that protein aggregation is a consequence of membrane toxins with the potential to affect the duration of dormancy and the outcome of antibiotic therapy.
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Affiliation(s)
- Florian H Leinberger
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Daniel Edelmann
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Nicole E Schmid
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Markus Oberpaul
- Branch for Bioresources of the Fraunhofer IME, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Giessen, Germany
- Department of Insect Biotechnology, Justus-Liebig-Universität, Giessen, Germany
| | - Patrick Blumenkamp
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Sebastian Schmidt
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Ana Natriashvili
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Maximilian H Ulbrich
- Internal Medicine IV, Department of Medicine, University Medical Center, and Faculty of Medicine, Albert-Ludwigs-Universität, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität, Freiburg, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
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3
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Liao H, Yan X, Wang C, Huang C, Zhang W, Xiao L, Jiang J, Bao Y, Huang T, Zhang H, Guo C, Zhang Y, Pu Y. Cyclic di-GMP as an antitoxin regulates bacterial genome stability and antibiotic persistence in biofilms. eLife 2024; 13:RP99194. [PMID: 39365286 PMCID: PMC11452175 DOI: 10.7554/elife.99194] [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] [Indexed: 10/05/2024] Open
Abstract
Biofilms are complex bacterial communities characterized by a high persister prevalence, which contributes to chronic and relapsing infections. Historically, persister formation in biofilms has been linked to constraints imposed by their dense structures. However, we observed an elevated persister frequency accompanying the stage of cell adhesion, marking the onset of biofilm development. Subsequent mechanistic studies uncovered a comparable type of toxin-antitoxin (TA) module (TA-like system) triggered by cell adhesion, which is responsible for this elevation. In this module, the toxin HipH acts as a genotoxic deoxyribonuclease, inducing DNA double strand breaks and genome instability. While the second messenger c-di-GMP functions as the antitoxin, exerting control over HipH expression and activity. The dynamic interplay between c-di-GMP and HipH levels emerges as a crucial determinant governing genome stability and persister generation within biofilms. These findings unveil a unique TA system, where small molecules act as the antitoxin, outlining a biofilm-specific molecular mechanism influencing genome stability and antibiotic persistence, with potential implications for treating biofilm infections.
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Affiliation(s)
- Hebin Liao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan UniversityWuhanChina
- Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
- Translational Medicine Research Center, North Sichuan Medical CollegeNanchongChina
| | - Xiaodan Yan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan UniversityWuhanChina
- Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Chenyi Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan UniversityWuhanChina
- Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Chun Huang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan UniversityWuhanChina
- Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Wei Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan UniversityWuhanChina
- Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Leyi Xiao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan UniversityWuhanChina
- Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
| | - Jun Jiang
- Center for Life Sciences, School of Life Sciences, Yunnan UniversityKunmingChina
| | - Yongjia Bao
- Center for Life Sciences, School of Life Sciences, Yunnan UniversityKunmingChina
| | - Tao Huang
- Center for Life Sciences, School of Life Sciences, Yunnan UniversityKunmingChina
| | - Hanbo Zhang
- Center for Life Sciences, School of Life Sciences, Yunnan UniversityKunmingChina
| | - Chunming Guo
- Center for Life Sciences, School of Life Sciences, Yunnan UniversityKunmingChina
| | - Yufeng Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan UniversityWuhanChina
- Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
- Taikang Center for Life and Medical Sciences, Wuhan UniversityWuhanChina
| | - Yingying Pu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan UniversityWuhanChina
- Frontier Science Center for Immunology and Metabolism, Wuhan UniversityWuhanChina
- Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, State Key Laboratory of Virology and Medical Research Institute, Wuhan University School of Basic Medical SciencesWuhanChina
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Carvalho F, Carreaux A, Sartori-Rupp A, Tachon S, Gazi AD, Courtin P, Nicolas P, Dubois-Brissonnet F, Barbotin A, Desgranges E, Bertrand M, Gloux K, Schouler C, Carballido-López R, Chapot-Chartier MP, Milohanic E, Bierne H, Pagliuso A. Aquatic environment drives the emergence of cell wall-deficient dormant forms in Listeria. Nat Commun 2024; 15:8499. [PMID: 39358320 PMCID: PMC11447242 DOI: 10.1038/s41467-024-52633-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
Stressed bacteria can enter a dormant viable but non-culturable (VBNC) state. VBNC pathogens pose an increased health risk as they are undetectable by growth-based techniques and can wake up back into a virulent state. Although widespread in bacteria, the mechanisms governing this phenotypic switch remain elusive. Here, we investigate the VBNC state transition in the human pathogen Listeria monocytogenes. We show that bacteria starved in mineral water become VBNC by converting into osmotically stable cell wall-deficient coccoid forms, a phenomenon that occurs in other Listeria species. We reveal the bacterial stress response regulator SigB and the autolysin NamA as major actors of VBNC state transition. We lastly show that VBNC Listeria revert to a walled and virulent state after passage in chicken embryos. Our study provides more detail on the VBNC state transition mechanisms, revealing wall-free bacteria naturally arising in aquatic environments as a potential survival strategy in hypoosmotic and oligotrophic conditions.
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Affiliation(s)
- Filipe Carvalho
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Alexis Carreaux
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | | | - Anastasia D Gazi
- Ultrastructural Bioimaging Facility, Institut Pasteur, Paris, France
| | - Pascal Courtin
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Nicolas
- INRAE, Université Paris-Saclay, MaIAGE, Jouy-en-Josas, France
| | | | - Aurélien Barbotin
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Emma Desgranges
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Matthieu Bertrand
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Karine Gloux
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Rut Carballido-López
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Eliane Milohanic
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Hélène Bierne
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Alessandro Pagliuso
- INRAE, Université Paris-Saclay, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
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Jiang Z, Wang Y, Bai S, Bai C, Tu Z, Li H, Guo P, Liao T, Qiu L. The viable but non-culturable (VBNC) status of Shewanella putrefaciens (S. putrefaciens) with thermosonication (TS) treatment. ULTRASONICS SONOCHEMISTRY 2024; 109:107008. [PMID: 39096846 PMCID: PMC11345692 DOI: 10.1016/j.ultsonch.2024.107008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
Although thermosonication (TS) treatment has been widely used in food sterilization, the viable but non-culturable (VBNC) of bacteria with TS treatment has still concerned potential food safety and public health. The molecular mechanism of VBNC status of bacteria with TS treatment is not clearly known. Therefore, in this study, we used Shewanella putrefaciens, which was a common putrefactive bacteria in aquatic products, to study the VBNC state of bacteria with TS treatment. Firstly, our results revealed that S. putrefaciens still could enter the VBNC state after TS treatments: 50 kHz, 300 W, 30 min ultrasonic treatment and 70 °C heating; Subsequently, we found the VBNC state of S. putrefaciens can resist the damage of TS treatment, such as cell wall break, DNA degradation, etc; Finally, four-dimensional data-independent acquisition-based proteomics showed that under VBNC state, S. putrefaciens upregulated functional proteins to resist TS treatment, such as: ribosomal proteins to accelerate the synthesis of stress proteins to counteract TS treatments, ornithine decarboxylase SpeF and MraY to repair TS treatment-induced damage, etc. Meanwhile, S. putrefaciens downregulates metabolic and transport functional proteins such as dehydrogenase to reduce the metabolism. Importantly, among those proteins, the ribosomal transcriptional regulatory protein family, such as rpsB, etc, may be the key proteins for S. putrefaciens entering VBNC state. This finding can provide some new strategies for preventing VBNC status of bacteria with TS treatment, such as: inhibition of key proteins, etc.
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Affiliation(s)
- Ziwei Jiang
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Engineering Research Center for Agro-Product Irradiation, Agro-product Processing Research Sub-center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan 430064, China; School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 4300731, China
| | - Yi Wang
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Engineering Research Center for Agro-Product Irradiation, Agro-product Processing Research Sub-center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan 430064, China
| | - Shunjie Bai
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Engineering Research Center for Agro-Product Irradiation, Agro-product Processing Research Sub-center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan 430064, China
| | - Chan Bai
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Engineering Research Center for Agro-Product Irradiation, Agro-product Processing Research Sub-center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan 430064, China
| | - Ziyi Tu
- HuBei Crawfish Industrial Tech Ltd., Qianjiang 433100, China
| | - Hailan Li
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Engineering Research Center for Agro-Product Irradiation, Agro-product Processing Research Sub-center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan 430064, China
| | - Peng Guo
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Engineering Research Center for Agro-Product Irradiation, Agro-product Processing Research Sub-center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan 430064, China
| | - Tao Liao
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Engineering Research Center for Agro-Product Irradiation, Agro-product Processing Research Sub-center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan 430064, China.
| | - Liang Qiu
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Engineering Research Center for Agro-Product Irradiation, Agro-product Processing Research Sub-center of Hubei Innovation Center of Agriculture Science and Technology, Wuhan 430064, China.
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Kungwani NA, Panda J, Mishra AK, Chavda N, Shukla S, Vikhe K, Sharma G, Mohanta YK, Sharifi-Rad M. Combating bacterial biofilms and related drug resistance: Role of phyto-derived adjuvant and nanomaterials. Microb Pathog 2024; 195:106874. [PMID: 39181190 DOI: 10.1016/j.micpath.2024.106874] [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: 05/09/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
The emergence of antimicrobial resistance (AMR) in clinical microbes has led to a search for novel antibiotics for combating bacterial infections. The treatment of bacterial infections becomes more challenging with the onset of biofilm formation. AMR is further accelerated by biofilm physiology and differential gene expression in bacteria with an inherent resistance to conventional antibiotics. In the search for innovative strategies to control the spread of AMR in clinical isolates, plant-derived therapeutic metabolites can be repurposed to control biofilm-associated drug resistance. Unlike antibiotics, designed to act on a single cellular process, phytochemicals can simultaneously target multiple cellular components. Furthermore, they can disrupt biofilm formation and inhibit quorum sensing, offering a comprehensive approach to combat bacterial infections. In bacterial biofilms, the first line of AMR is due to biofilms associated with the extracellular matrix, diffusion barriers, quorum sensing, and persister cells. These extracellular barriers can be overcome using phytochemical-based antibiotic adjuvants to increase the efficacy of antibiotic treatment and restrict the spread of AMR. Furthermore, phytochemicals can be used to target bacterial intracellular machinery such as DNA replication, protein synthesis, efflux pumps, and degrading enzymes. In parallel with pristine phytochemicals, phyto-derived nanomaterials have emerged as an effective means of fighting bacterial biofilms. These nanomaterials can be formulated to cross the biofilm barriers and function on cellular targets. This review focuses on the synergistic effects of phytochemicals and phyto-derived nanomaterials in controlling the progression of biofilm-related AMR. IT provides comprehensive insights into recent advancements and the underlying mechanisms of the use of phyto-derived adjuvants and nanomaterials.
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Affiliation(s)
- Neelam Amit Kungwani
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Gandhinagar, Gujarat, 382355, India.
| | - Jibanjyoti Panda
- Nano-biotechnology and Translational Knowledge Laboratory, Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya, Techno City, 9th Mile, Baridua, Ri-Bhoi, 793101, Meghalaya, India
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | | | - Sudhir Shukla
- Homi Bhabha National Institute, Biofouling and Biofilm Processes Section, WSCD, Chemistry Group, Bhabha Atomic Research Centre, Kalpakkam, Tamilnadu, 603102, India
| | - Kalyani Vikhe
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Gandhinagar, Gujarat, 382355, India
| | - Gunjan Sharma
- Department of Plant Biotechnology, Gujarat Biotechnology University, Gandhinagar, Gujarat, 382355, India
| | - Yugal Kishore Mohanta
- Nano-biotechnology and Translational Knowledge Laboratory, Department of Applied Biology, School of Biological Sciences, University of Science and Technology Meghalaya, Techno City, 9th Mile, Baridua, Ri-Bhoi, 793101, Meghalaya, India; Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India.
| | - Majid Sharifi-Rad
- Department of Range and Watershed Management, Faculty of Water and Soil, University of Zabol, Zabol, 98613-35856, Iran.
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To D, Blanco Massani M, Coraça-Huber DC, Seybold A, Ricci F, Zöller K, Bernkop-Schnürch A. Antibiotic-Polyphosphate Nanocomplexes: A Promising System for Effective Biofilm Eradication. Int J Nanomedicine 2024; 19:9707-9725. [PMID: 39309185 PMCID: PMC11416784 DOI: 10.2147/ijn.s473241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 09/25/2024] Open
Abstract
Purpose The eradication of bacterial biofilms poses an enormous challenge owing to the inherently low antibiotic susceptibility of the resident microbiota. The complexation of antibiotics with polyphosphate can substantially improve antimicrobial performance. Methods Nanoparticular complexes of the model drug colistin and polyphosphate (CP-NPs) were developed and characterized in terms of their particle size and morphology, polydispersity index (PDI), zeta potential, and cytotoxicity. Enzyme-triggered monophosphate and colistin release from the CP-NPs was evaluated in the presence of alkaline phosphatase (AP). Subsequently, antimicrobial efficacy was assessed by inhibition experiments on planktonic cultures, as well as time-kill assays on biofilms formed by the model organism Micrococcus luteus. Results The CP-NPs exhibited a spherical morphology with particle sizes <200 nm, PDI <0.25, and negative zeta potential. They showed reduced cytotoxicity toward two human cell lines and significantly decreased hemotoxicity compared with native colistin. Release experiments with AP verified the enzymatic cleavage of polyphosphate and subsequent release of monophosphate and colistin from CP-NPs. Although CP-NPs were ineffective against planktonic M. luteus cultures, they showed major activity against bacterial biofilms, outperforming native colistin treatment. Strongly elevated AP levels in the biofilm state were identified as a potential key factor for the observed findings. Conclusion Accordingly, polyphosphate-based nanocomplexes represent a promising tool to tackle bacterial biofilm.
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Affiliation(s)
- Dennis To
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Mariana Blanco Massani
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Débora C Coraça-Huber
- Research Laboratory for Implant Associated Infections (BIOFILM LAB), Experimental Orthopaedics, University Hospital for Orthopaedics and Traumatology, Medical University Innsbruck, Innsbruck, Austria
| | - Anna Seybold
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Fabrizio Ricci
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
- Thiomatrix Forschungs- und Beratungs GmbH, Innsbruck, Austria
| | - Katrin Zöller
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
| | - Andreas Bernkop-Schnürch
- Center for Chemistry and Biomedicine, Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innsbruck, Austria
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8
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Ikeda H, Maeda S. Characterization of Escherichia coli Persisters from Biofilm Culture: Multiple Dormancy Levels and Multigenerational Memory in Formation. Microorganisms 2024; 12:1888. [PMID: 39338564 PMCID: PMC11434456 DOI: 10.3390/microorganisms12091888] [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: 08/08/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 09/30/2024] Open
Abstract
Persister cells (PCs), a subpopulation occurring within normal cells, exhibit a transient tolerance to antibiotics because of their dormant state. PCs are categorized into two types: type I PCs, which emerge during the stationary phase, and type II PCs, which emerge during the logarithmic phase. Using the conventional colony-forming method, we previously demonstrated that type I PCs of Escherichia coli form more frequently in air-solid biofilm culture than in liquid culture. In the current study, we modified a cell filamentation method as a more efficient and rapid alternative for quantifying PCs. This modified method yielded results consistent with those of the conventional method with 103-104 times higher sensitivity and less detection time, within several hours, and further revealed the existence of multiple levels of type I PCs, including a substantial number of deeply dormant cells. This study also discovered a potential epigenetic memory mechanism, spanning several generations (four or six cell divisions), which influences type II PC formation based on prior biofilm experience in E. coli.
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Affiliation(s)
| | - Sumio Maeda
- Graduate School of Humanities and Sciences, Nara Women’s University, Kitauoya-nishimachi, Nara 630-8506, Japan
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9
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Dhaouadi Y, Hashemi MJ, Ren D. Persistence and Culturability of Escherichia coli under Induced Toxin Expression. Antibiotics (Basel) 2024; 13:863. [PMID: 39335036 PMCID: PMC11428644 DOI: 10.3390/antibiotics13090863] [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: 08/16/2024] [Revised: 09/05/2024] [Accepted: 09/07/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND/OBJECTIVES Bacteria are well known to enter dormancy under stress conditions. However, the mechanisms of different dormancy-related phenotypes are still under debate and many questions remain unanswered. This study aims to better understand the effects of toxin gene expression on the dormancy of Escherichia coli. METHODS The effects of toxin gene expression on growth, persistence, and culturability were characterized. Specifically, we detailed dose- and time-dependent dormancy of E. coli and its susceptibility to ofloxacin via arabinose-induced hipA toxin gene expression under the PBAD promoter. A new plot was developed to better describe the dynamic changes in culturability and persistence. The expression level of hipA was determined using qPCR and cellular activities were monitored using fluorescence imaging and flow cytometry. RESULTS High-level persister formation and strong tolerance to ofloxacin were observed after high-level hipA induction. The new plot reveals more information than the changes in persistence alone, e.g., reduced culturability of E. coli and thus deeper dormancy under high-level hipA induction. Consistently, controlled hipA induction led to decreased cellular activities at promoter PrrnBP1 and an increase in the non-culturable subpopulation. CONCLUSIONS Overall, this study provides new insights into dormancy induced by toxin gene expression and a more comprehensive view of persistence and culturability. The findings may help develop better control agents against dormant bacterial cells.
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Affiliation(s)
- Yousr Dhaouadi
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Mohamad Javad Hashemi
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
- Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244, USA
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
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10
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Xiao Y, Wang J, Sun P, Ding T, Li J, Deng Y. Formation and resuscitation of viable but non-culturable (VBNC) yeast in the food industry: A review. Int J Food Microbiol 2024; 426:110901. [PMID: 39243533 DOI: 10.1016/j.ijfoodmicro.2024.110901] [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: 04/23/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
The viable but non-culturable (VBNC) state is a survival strategy adopted by microorganisms in response to unfavorable conditions in the environment. VBNC cells are unable to form colonies but still maintain a low level of activity, posing a potential threat to food safety and public health. Therefore, the development of effective strategies to prevent the formation and resuscitation of VBNC cells of microorganisms is a key challenge in food science and microbiology research. However, current research on VBNC cells has primarily focused on bacteria, with relatively limited reports on fungi. This paper provides a comprehensive and systematic review of yeast in the VBNC state, discussing various factors that induce and facilitate resuscitation, along with detection methods and formation and recovery mechanisms. A comprehensive understanding of the induction and resuscitation of yeast in the VBNC state and exploration of its molecular mechanism hold significant implications for food safety and public health. It is imperative to enhance our comprehension of the underlying mechanisms and contributory factors pertaining to VBNC yeast, thereby facilitating the efficient management of the food fermentation process and ensuring the integrity of food quality and safety.
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Affiliation(s)
- Yang Xiao
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; School of Food Engineering, Qingdao Institute of Technology, Qingdao 266300, China
| | - Jiayang Wang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China; Shandong Technology Innovation Center of Special Food, Qingdao 266109, China
| | - Pengdong Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China; Shandong Technology Innovation Center of Special Food, Qingdao 266109, China; Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Ting Ding
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China; Shandong Technology Innovation Center of Special Food, Qingdao 266109, China; Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Jingyuan Li
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China; Shandong Technology Innovation Center of Special Food, Qingdao 266109, China; Qingdao Special Food Research Institute, Qingdao 266109, China
| | - Yang Deng
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; Key Laboratory of Special Food Processing (Co-construction by Ministry and Province), Ministry of Agriculture Rural Affairs, Qingdao Agricultural University, Qingdao 266109, China; Shandong Technology Innovation Center of Special Food, Qingdao 266109, China; Qingdao Special Food Research Institute, Qingdao 266109, China.
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11
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Mangiaterra G, Schiavoni V, Cedraro N, Citterio B, Vignaroli C, Gesuita R, Fabrizzi B, Biavasco F, Cirilli N. Clinical relevance of Pseudomonas aeruginosa viable but non-culturable forms in cystic fibrosis. Eur J Clin Microbiol Infect Dis 2024; 43:1865-1867. [PMID: 38976176 DOI: 10.1007/s10096-024-04890-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Affiliation(s)
| | - Valentina Schiavoni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Nicholas Cedraro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Barbara Citterio
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Rosaria Gesuita
- Center of Epidemiology, Biostatistics and Medical Information Technology, Polytechnic University of Marche, Ancona, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Centre, Department of Gastroenterology and Transplantation, University Hospital of Marche, Ancona, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Natalia Cirilli
- Cystic Fibrosis Centre, Department of Gastroenterology and Transplantation, University Hospital of Marche, Ancona, Italy
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12
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Li X, Ren Q, Sun Z, Wu Y, Pan H. Resuscitation Promotion Factor: A Pronounced Bacterial Cytokine in Propelling Bacterial Resuscitation. Microorganisms 2024; 12:1528. [PMID: 39203370 PMCID: PMC11356341 DOI: 10.3390/microorganisms12081528] [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: 07/06/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
While confronted with unfavorable growth conditions, bacteria may transform into the dormant state, such as viable but nonculturable (VBNC) state, which is a reversible state characterized by low metabolic activity and lack of division. These dormant cells can be reactivated through the influence of the resuscitation promoting factor (Rpf) family, which are classified as autocrine growth factors and possess peptidoglycan hydrolase activities. To date, with the significant resuscitation or growth promotion ability of Rpf, it has been extensively applied to increasing bacterial diversity and isolating functional microbial species. This review provides a comprehensive analysis of the distribution, mode of action, and functional mechanisms of Rpf proteins in various bacterial species. The aim is to create opportunities for decoding microbial communities and extracting microbial resources from real samples across different research fields.
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Affiliation(s)
| | | | | | | | - Hanxu Pan
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (X.L.); (Q.R.); (Z.S.); (Y.W.)
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13
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Hubert A, Tabuteau H, Farasin J, Loncar A, Dufresne A, Méheust Y, Le Borgne T. Fluid flow drives phenotypic heterogeneity in bacterial growth and adhesion on surfaces. Nat Commun 2024; 15:6161. [PMID: 39039040 PMCID: PMC11263347 DOI: 10.1038/s41467-024-49997-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 06/25/2024] [Indexed: 07/24/2024] Open
Abstract
Bacteria often thrive in surface-attached communities, where they can form biofilms affording them multiple advantages. In this sessile form, fluid flow is a key component of their environments, renewing nutrients and transporting metabolic products and signaling molecules. It also controls colonization patterns and growth rates on surfaces, through bacteria transport, attachment and detachment. However, the current understanding of bacterial growth on surfaces neglects the possibility that bacteria may modulate their division behavior as a response to flow. Here, we employed single-cell imaging in microfluidic experiments to demonstrate that attached Escherichia coli cells can enter a growth arrest state while simultaneously enhancing their adhesion underflow. Despite utilizing clonal populations, we observed a non-uniform response characterized by bistable dynamics, with co-existing subpopulations of non-dividing and actively dividing bacteria. As the proportion of non-dividing bacteria increased with the applied flow rate, it resulted in a reduction in the average growth rate of bacterial populations on flow-exposed surfaces. Dividing bacteria exhibited asymmetric attachment, whereas non-dividing counterparts adhered to the surface via both cell poles. Hence, this phenotypic diversity allows bacterial colonies to combine enhanced attachment with sustained growth, although at a reduced rate, which may be a significant advantage in fluctuating flow conditions.
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Affiliation(s)
- Antoine Hubert
- Géosciences Rennes, UMR 6118 University of Rennes and CNRS, Rennes, France
| | - Hervé Tabuteau
- Institut de Physique de Rennes, UMR 6251 University of Rennes and CNRS, Rennes, France.
| | - Julien Farasin
- Géosciences Rennes, UMR 6118 University of Rennes and CNRS, Rennes, France
| | - Aleksandar Loncar
- Géosciences Rennes, UMR 6118 University of Rennes and CNRS, Rennes, France
| | - Alexis Dufresne
- ECOBIO, UMR 6553 University of Rennes and CNRS, Rennes, France
| | - Yves Méheust
- Géosciences Rennes, UMR 6118 University of Rennes and CNRS, Rennes, France
| | - Tanguy Le Borgne
- Géosciences Rennes, UMR 6118 University of Rennes and CNRS, Rennes, France.
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14
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Niu H, Gu J, Zhang Y. Bacterial persisters: molecular mechanisms and therapeutic development. Signal Transduct Target Ther 2024; 9:174. [PMID: 39013893 PMCID: PMC11252167 DOI: 10.1038/s41392-024-01866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 07/18/2024] Open
Abstract
Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.
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Affiliation(s)
- Hongxia Niu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Jiaying Gu
- School of Basic Medical Science and Key Laboratory of Blood-stasis-toxin Syndrome of Zhejiang Province, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, 250022, Shandong, China.
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15
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Negi M, Kaushik N, Lamichhane P, Jaiswal A, Borkar SB, Patel P, Singh P, Choi EH, Kaushik NK. Biocompatible plasma-treated liquids: A sustainable approach for decontaminating gastrointestinal-infection causing pathogens. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134562. [PMID: 38743977 DOI: 10.1016/j.jhazmat.2024.134562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
Nosocomial infections are a serious threat and difficult to cure due to rising antibiotic resistance in pathogens and biofilms. Direct exposure to cold atmospheric plasma (CAP) has been widely employed in numerous biological research endeavors. Nonetheless, plasma-treated liquids (PTLs) formulated with physiological solutions may offer additional benefits such as enhanced portability, and biocompatibility. Additionally, CAP-infused long-lived reactive oxygen and nitrogen species (RONS) such as nitrite (NO2-), nitrate (NO3-), and hydrogen peroxide (H2O2) can synergistically induce their antibacterial activity. Herein, we investigated those argon-plasma jet-treated liquids, including Ringer's lactate (RL), phosphate-buffered saline (PBS), and physiological saline, have significant antibacterial activity against nosocomial/gastrointestinal-causing pathogens, which might be due to ROS-mediated lipid peroxidation. Combining the conventional culture-based method with propidium iodide monoazide quantitative PCR (PMAxx™-qPCR) indicated that PTLs induce a minimal viable but non-culturable (VBNC) state and moderately affect culturable counts. Specifically, the PTL exposure resulted in pathogenicity dysfunction via controlling T3SS-related effector genes of S. enterica. Overall, this study provides insights into the effectiveness of PTLs for inducing ROS-mediated damage, controlling the virulence of diarrheagenic bacteria, and modulating homeostatic genes.
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Affiliation(s)
- Manorma Negi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong 18323, South Korea.
| | - Prajwal Lamichhane
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Apurva Jaiswal
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Shweta B Borkar
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Paritosh Patel
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, Delhi, India
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, South Korea.
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16
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Ngo HG, Mohiuddin SG, Ananda A, Orman MA. UNRAVELING CRP/cAMP-MEDIATED METABOLIC REGULATION IN ESCHERICHIA COLI PERSISTER CELLS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598332. [PMID: 38915711 PMCID: PMC11195080 DOI: 10.1101/2024.06.10.598332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
A substantial gap persists in our comprehension of how bacterial metabolism undergoes rewiring during the transition to a persistent state. Also, it remains unclear which metabolic mechanisms become indispensable for persister cell survival. To address these questions, we directed our efforts towards persister cells in Escherichia coli that emerge during the late stationary phase. These cells have been recognized for their exceptional resilience and are commonly believed to be in a dormant state. Our results demonstrate that the global metabolic regulator Crp/cAMP redirects the metabolism of these antibiotic-tolerant cells from anabolism to oxidative phosphorylation. Although our data indicates that persisters exhibit a reduced metabolic rate compared to rapidly growing exponential-phase cells, their survival still relies on energy metabolism. Extensive genomic-level analyses of metabolomics, proteomics, and single-gene deletions consistently emphasize the critical role of energy metabolism, specifically the tricarboxylic acid (TCA) cycle, electron transport chain (ETC), and ATP synthase, in sustaining the viability of persisters. Altogether, this study provides much-needed clarification regarding the role of energy metabolism in antibiotic tolerance and highlights the importance of using a multipronged approach at the genomic level to obtain a broader picture of the metabolic state of persister cells.
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Affiliation(s)
- Han G. Ngo
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
| | - Sayed Golam Mohiuddin
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
| | - Aina Ananda
- Department of Biology, Monmouth University, NJ, 07764
| | - Mehmet A. Orman
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, 77204
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17
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Gunn NJ, Kidd SP, Solomon LB, Yang D, Roscioli E, Atkins GJ. Staphylococcus aureus persistence in osteocytes: weathering the storm of antibiotics and autophagy/xenophagy. Front Cell Infect Microbiol 2024; 14:1403289. [PMID: 38915921 PMCID: PMC11194354 DOI: 10.3389/fcimb.2024.1403289] [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: 03/19/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
Staphylococcus aureus is a major causative pathogen of osteomyelitis. Intracellular infections of resident bone cells including osteocytes can persist despite gold-standard clinical intervention. The mechanisms by which intracellular S. aureus evades antibiotic therapy are unknown. In this study, we utilised an in vitro S. aureus infection model of human osteocytes to investigate whether antibiotic-mediated dysregulation of autophagy contributes to this phenomenon. Infected or non-infected osteocyte-like cells were exposed to combinations of rifampicin, vancomycin, and modulators of autophagy. Intracellular bacterial growth characteristics were assessed using colony-forming unit (CFU) analysis, viable bacterial DNA abundance, and the rate of escape into antibiotic-free medium, together with measures of autophagic flux. Rifampicin, alone or in combination with vancomycin, caused a rapid decrease in the culturability of intracellular bacteria, concomitant with stable or increased absolute bacterial DNA levels. Both antibiotics significantly inhibited autophagic flux. However, modulation of autophagic flux did not affect viable bacterial DNA levels. In summary, autophagy was shown to be a factor in the host-pathogen relationship in this model, as its modulation affected the growth state of intracellular S. aureus with respect to both their culturability and propensity to escape the intracellular niche. While rifampicin and vancomycin treatments moderately suppressed autophagic flux acutely, this did not explain the paradoxical response of antibiotic treatment in decreasing S. aureus culturability whilst failing to clear bacterial DNA and hence intracellular bacterial load. Thus, off-target effects of rifampicin and vancomycin on autophagic flux in osteocyte-like cells could not explain the persistent S. aureus infection in these cells.
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Affiliation(s)
- Nicholas J. Gunn
- Biomedical Orthopaedic Research Group, Centre for Orthopaedic and Trauma Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Stephen P. Kidd
- Australian Centre for Antimicrobial Resistance Ecology, University of Adelaide, Adelaide, SA, Australia
- Research Centre for Infectious Disease, School of Biological Science, University of Adelaide, Adelaide, SA, Australia
| | - Lucian B. Solomon
- Biomedical Orthopaedic Research Group, Centre for Orthopaedic and Trauma Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Department of Orthopaedics and Trauma, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Dongqing Yang
- Biomedical Orthopaedic Research Group, Centre for Orthopaedic and Trauma Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Eugene Roscioli
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA, Australia
- Department of Medicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- Centre for Cancer Biology, South Australia (SA) Pathology and University of South Australia, Adelaide, SA, Australia
| | - Gerald J. Atkins
- Biomedical Orthopaedic Research Group, Centre for Orthopaedic and Trauma Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
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Guha M, Singh A, Butzin NC. Gram-positive bacteria are primed for surviving lethal doses of antibiotics and chemical stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596288. [PMID: 38895422 PMCID: PMC11185512 DOI: 10.1101/2024.05.28.596288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Antibiotic resistance kills millions worldwide yearly. However, a major contributor to recurrent infections lies in a small fraction of bacterial cells, known as persisters. These cells are not inherently antibiotic-resistant, yet they lead to increased antibiotic usage, raising the risk of developing resistant progenies. In a bacterial population, individual cells exhibit considerable fluctuations in their gene expression levels despite being cultivated under identical, stable conditions. This variability in cell-to-cell characteristics (phenotypic diversity) within an isogenic population enables persister cells to withstand antibiotic exposure by entering a non-dividing state. We recently showed the existence of "primed cells" in E. coli. Primed cells are dividing cells prepared for antibiotic stress before encountering it and are more prone to form persisters. They also pass their "prepared state" down for several generations through epigenetic memory. Here, we show that primed cells are common among distant bacterial lineages, allowing for survival against antibiotics and other chemical stress, and form in different growth phases. They are also responsible for increased persister levels in transition and stationary phases compared to the log phase. We tested and showed that the Gram-positive bacterium Bacillus megaterium, evolutionarily very distant from E. coli, forms primed cells and has a transient epigenetic memory that is maintained for 7 generations or more. We showed this using ciprofloxacin and the non-antibiotic chemical stress fluoride. It is well established that persister levels are higher in the stationary phase than in the log phase, and B. megaterium persisters levels are nearly identical from the early to late-log phase but are ~2-fold and ~4-fold higher in the transition and stationary phase, respectively. It was previously proposed that there are two distinct types of persisters: Type II forms in the log phase, while Type I forms in the stationary phase. However, we show that primed cells lead to increased persisters in the transition and stationary phase and found no evidence of Type I or II persisters with distant phenotypes. Overall, we have provided substantial evidence of the importance of primed cells and their transitory epigenetic memories to surviving stress.
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Affiliation(s)
- Manisha Guha
- Department of Biology and Microbiology; South Dakota State University; Brookings, SD, 57006; USA
| | - Abhyudai Singh
- Electrical & Computer Engineering; University of Delaware; Newark, DE 19716; USA
| | - Nicholas C. Butzin
- Department of Biology and Microbiology; South Dakota State University; Brookings, SD, 57006; USA
- Department of Chemistry and Biochemistry; South Dakota State University; Brookings, SD, 57006; USA
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Yang D, Wang W, Zhao L, Rao L, Liao X. Resuscitation of viable but nonculturable bacteria promoted by ATP-mediated NAD + synthesis. J Adv Res 2024; 60:27-39. [PMID: 37541583 PMCID: PMC11156606 DOI: 10.1016/j.jare.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/04/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023] Open
Abstract
INTRODUCTION Entry into the viable but nonculturable (VBNC) state is a survival strategy adopted by bacteria to survive harsh environment. Although VBNC cells still have metabolic activity, they lose the ability to form colonies on nonselective culture media. Thus, conventional bacterial detection methods, such as plate counting, are unable to detect the presence of VBNC cells. When the environmental conditions are appropriate, VBNC cells can initiate resuscitation, posing a great risk to the safety of public health. The study of the VBNC resuscitation mechanism could provide new insights into the prevention and control of VBNC resuscitation. OBJECTIVES Uncovering the molecular mechanism of VBNC cell resuscitation by investigating the role of O-antigen ligase (RfaL) in inhibiting the resuscitation of Escherichia coli O157:H7 in the VBNC state. METHODS RfaL was screened and verified as a resuscitation inhibitor of VBNC Escherichia coli O157:H7 by detecting resuscitation curve and time-lapse microscopy. The mechanism of RfaL impacts VBNC E. coli resuscitation was investigated by detecting the single cell ATP content, metabolomic changes, NAD(H) content and new protein biosynthesis of WT and ΔrfaL at different stage of resuscitation. RESULTS Mutation of rfaL, which encoded an O-antigen ligase, markedly shortened the resuscitating lag phase. Further studies indicated that ΔrfaL VBNC cells contained higher ATP levels, and ATP consumption during the resuscitating lag phase was highly correlated with resuscitation efficiency. Metabolomic analysis revealed that ATP was utilized to activate the Handler and salvage pathways to synthesize NAD+, balancing redox reactions to recover cell activity and promote cell resuscitation. CONCLUSION Our findings revealed a strategy employed by VBNC cells for revival, that is, using residual ATP to primarily recover metabolic activity, driving cells to exit dormancy. The synthesis pathway of lipopolysaccharide (LPS) in rfaL null mutant was inhibited and could supply more ATP to synthesis NAD+ and promote resuscitation.
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Affiliation(s)
- Dong Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit & Vegetable Processing, Beijing, China; Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Wenxin Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit & Vegetable Processing, Beijing, China; Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Liang Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit & Vegetable Processing, Beijing, China; Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Lei Rao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit & Vegetable Processing, Beijing, China; Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China.
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China; National Engineering Research Center for Fruit & Vegetable Processing, Beijing, China; Key Laboratory of Fruit & Vegetable Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China.
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İzgördü ÖK, Gurbanov R, Darcan C. Understanding the transition to viable but non-culturable state in Escherichia coli W3110: a comprehensive analysis of potential spectrochemical biomarkers. World J Microbiol Biotechnol 2024; 40:203. [PMID: 38753033 PMCID: PMC11098925 DOI: 10.1007/s11274-024-04019-6] [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: 03/01/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
The viable but non-culturable (VBNC) state is considered a survival strategy employed by bacteria to endure stressful conditions, allowing them to stay alive. Bacteria in this state remain unnoticed in live cell counts as they cannot proliferate in standard culture media. VBNC cells pose a significant health risk because they retain their virulence and can revive when conditions normalize. Hence, it is crucial to develop fast, reliable, and cost-effective methods to detect bacteria in the VBNC state, particularly in the context of public health, food safety, and microbial control assessments. This research examined the biomolecular changes in Escherichia coli W3110 induced into the VBNC state in artificial seawater under three different stress conditions (temperature, metal, and antibiotic). Initially, confirmation of VBNC cells under various stresses was done using fluorescence microscopy and plate counts. Subsequently, lipid peroxidation was assessed through the TBARS assay, revealing a notable increase in peroxidation end-products in VBNC cells compared to controls. ATR-FTIR spectroscopy and chemomometrics were employed to analyze biomolecular changes, uncovering significant spectral differences in RNA, protein, and nucleic acid concentrations in VBNC cells compared to controls. Notably, RNA levels increased, while protein and nucleic acid amounts decreased. ROC analyses identified the 995 cm- 1 RNA band as a consistent marker across all studied stress conditions, suggesting its potential as a robust biomarker for detecting cells induced into the VBNC state under various stressors.
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Affiliation(s)
- Özge Kaygusuz İzgördü
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, Bilecik, Turkey
- Department of Molecular Biology and Genetics, Institute of Graduate Education, Bilecik Şeyh Edebali University, Bilecik, Turkey
| | - Rafig Gurbanov
- Department of Bioengineering, Bilecik Şeyh Edebali University, Bilecik, Turkey.
- Central Research Laboratory, Bilecik Şeyh Edebali University, Bilecik, Turkey.
| | - Cihan Darcan
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, Bilecik, Turkey
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21
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Wahid SUH, Campbell BE, Moore RJ, Istivan T. Characterization of viable but nonculturable state of Campylobacter concisus. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240088. [PMID: 39076798 PMCID: PMC11285765 DOI: 10.1098/rsos.240088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 07/31/2024]
Abstract
Campylobacter concisus is an opportunistic bacterial pathogen linked with a range of human diseases. The objective of this study was to investigate the viable but nonculturable (VBNC) state of the bacterium. To induce the VBNC state, C. concisus cells were maintained in sterilized phosphate-buffered saline at 4°C for three weeks. The VBNC cells were monitored using quantitative analysis by propidium monoazide (PMAxx) coupled with quantitative real-time PCR (PMAxx-qPCR), targeting the DNA gyrase subunit B gene. The results demonstrated that C. concisus ATCC 51562 entered the VBNC state in 15 days, while ATCC 51561 entered the VBNC state in 9 days. The viable cell counts, assessed by PMAxx-qPCR, consistently remained close to the initial level of 107 CFU ml-1, indicating a substantial portion of the cell population had entered the VBNC state. Notably, morphological analysis revealed that the VBNC cells became coccoid and significantly smaller. The cells could be resuscitated through a temperature increase in the presence of a highly nutritious growth medium. In conclusion, under environmental stress, most C. concisus cells converted to the VBNC state. The VBNC state of C. concisus may be important for its environmental survival and spread, and the presence of VBNC forms should be considered in environmental and clinical monitoring.
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Affiliation(s)
| | | | - Robert J. Moore
- School of Science, RMIT University, Bundoora, Victoria, Australia
| | - Taghrid Istivan
- School of Science, RMIT University, Bundoora, Victoria, Australia
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22
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Aralar A, Goshia T, Ramchandar N, Lawrence SM, Karmakar A, Sharma A, Sinha M, Pride DT, Kuo P, Lecrone K, Chiu M, Mestan KK, Sajti E, Vanderpool M, Lazar S, Crabtree M, Tesfai Y, Fraley SI. Universal Digital High-Resolution Melt Analysis for the Diagnosis of Bacteremia. J Mol Diagn 2024; 26:349-363. [PMID: 38395408 PMCID: PMC11090205 DOI: 10.1016/j.jmoldx.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Fast and accurate diagnosis of bloodstream infection is necessary to inform treatment decisions for septic patients, who face hourly increases in mortality risk. Blood culture remains the gold standard test but typically requires approximately 15 hours to detect the presence of a pathogen. We, therefore, assessed the potential for universal digital high-resolution melt (U-dHRM) analysis to accomplish faster broad-based bacterial detection, load quantification, and species-level identification directly from whole blood. Analytical validation studies demonstrated strong agreement between U-dHRM load measurement and quantitative blood culture, indicating that U-dHRM detection is highly specific to intact organisms. In a pilot clinical study of 17 whole blood samples from pediatric patients undergoing simultaneous blood culture testing, U-dHRM achieved 100% concordance when compared with blood culture and 88% concordance when compared with clinical adjudication. Moreover, U-dHRM identified the causative pathogen to the species level in all cases where the organism was represented in the melt curve database. These results were achieved with a 1-mL sample input and sample-to-answer time of 6 hours. Overall, this pilot study suggests that U-dHRM may be a promising method to address the challenges of quickly and accurately diagnosing a bloodstream infection.
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Affiliation(s)
- April Aralar
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| | - Nanda Ramchandar
- Department of Pediatrics, Naval Medical Center San Diego, San Diego, California; Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Shelley M Lawrence
- Division of Neonatology, Department of Pediatrics, The University of Utah, Salt Lake City, Utah
| | | | | | | | - David T Pride
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Peiting Kuo
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Khrissa Lecrone
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Megan Chiu
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Karen K Mestan
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Eniko Sajti
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Michelle Vanderpool
- Department of Pathology and Laboratory Medicine, Rady Children's Hospital-San Diego, San Diego, California
| | - Sarah Lazar
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Melanie Crabtree
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Yordanos Tesfai
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, La Jolla, California.
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23
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Myung H, Joung YS. Contribution of Particulates to Airborne Disease Transmission and Severity: A Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6846-6867. [PMID: 38568611 DOI: 10.1021/acs.est.3c08835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/24/2024]
Abstract
The emergence of coronavirus disease 2019 (COVID-19) has catalyzed great interest in the spread of airborne pathogens. Airborne infectious diseases are classified into viral, bacterial, and fungal infections. Environmental factors can elevate their transmission and lethality. Air pollution has been reported as the leading environmental cause of disease and premature death worldwide. Notably, ambient particulates of various components and sizes are harmful pollutants. There are two prominent health effects of particles in the atmosphere: (1) particulate matter (PM) penetrates the respiratory tract and adversely affects health, such as heart and respiratory diseases; and (2) bioaerosols of particles act as a medium for the spread of pathogens in the air. Particulates contribute to the occurrence of infectious diseases by increasing vulnerability to infection through inhalation and spreading disease through interactions with airborne pathogens. Here, we focus on the synergistic effects of airborne particulates on infectious disease. We outline the concepts and characteristics of bioaerosols, from their generation to transformation and circulation on Earth. Considering that microorganisms coexist with other particulates as bioaerosols, we investigate studies examining respiratory infections associated with airborne PM. Furthermore, we discuss four factors (meteorological, biological, physical, and chemical) that may impact the influence of PM on the survival of contagious pathogens in the atmosphere. Our review highlights the significant role of particulates in supporting the transmission of infectious aerosols and emphasizes the need for further research in this area.
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Affiliation(s)
- Hyunji Myung
- Department of Mechanical Systems Engineering, Sookmyung Women's University, 100, Cheongpa-ro 47-gil, Yongsan-gu, Seoul 04310, Republic of Korea
| | - Young Soo Joung
- Department of Mechanical Systems Engineering, Sookmyung Women's University, 100, Cheongpa-ro 47-gil, Yongsan-gu, Seoul 04310, Republic of Korea
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24
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Lameira I, Pinto AS, Lima Â, Muzny CA, Cerca N. Optimized bacterial absolute quantification method by qPCR using an exogenous bacterial culture as a normalization strategy in triple-species BV-like biofilms. J Microbiol Methods 2024; 219:106895. [PMID: 38331102 PMCID: PMC11149788 DOI: 10.1016/j.mimet.2024.106895] [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: 10/20/2023] [Revised: 02/04/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Quantitative Polymerase Chain Reaction (qPCR) is a widely used method in molecular biology to quantify target DNA sequences. Despite its accuracy, there are important experimental controls that should be considered to avoid biased results. One of them is gDNA loss during extraction, which is higher among samples with lower bacterial concentrations. Improvement in qPCR quantification procedures is mandatory to obtain reproducible and accurate results. Herein, we report an improved qPCR method for bacterial quantification of Gardnerella vaginalis, Prevotella bivia, and Fannyhessea vaginae, three key-bacterial vaginosis (BV)-associated bacteria (BVAB) thought to play important roles in the pathogenesis of this common vaginal infection. The formation of a mature biofilm on vaginal epithelial cells is an unique feature of BV and, despite over 60 years of research, the exact etiology of BV remains unknown. Here, we optimized a qPCR method that accurately quantified triple-species biofilms containing these key BVAB, after the addition of an exogenous bacterial control containing a fixed concentration of Escherichia coli, prior to gDNA extraction. This improved method minimized and normalized the inherent losses associated with bacterial centrifugation, which allows better sensitivity at lower bacterial concentrations.
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Affiliation(s)
- Inês Lameira
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Ana S Pinto
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Ângela Lima
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nuno Cerca
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, Braga, Portugal; LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
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25
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Nalbone L, Forgia S, Ziino G, Sorrentino G, Giarratana F, Giuffrida A. A stochastic approach for modelling the in-vitro effect of osmotic stress on growth dynamics and persistent cell formation in Listeria monocytogenes. Int J Food Microbiol 2024; 413:110586. [PMID: 38262123 DOI: 10.1016/j.ijfoodmicro.2024.110586] [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: 09/29/2023] [Revised: 12/11/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Persistent bacteria (or persisters) can be defined as a microbial subpopulation that, exposed to bactericidal treatment, is killed more slowly than the rest of the population they are part of. They stochastically originate in response to environmental stressors or spontaneously without external signals. When transferred into a fresh medium, persisters can resume active replication although they spend more time adapting to the new conditions remaining in the lag phase longer. They were studied for decades for their ability to survive antibiotic treatments while studies on their formation in food and potential impact on their safety are lacking. The most common food preservation techniques may act as stressors that trigger the formation of persistent bacteria able to survive bactericidal treatments and grow later in foods during storage. This study aimed to investigate a possible relationship between exposure to different salt concentrations (osmotic stress) and the amount of persisters triggered in a strain of Listeria monocytogenes. Furthermore, we described this phenomenon from a mathematical perspective through predictive microbiology models commonly used in the food field. The lag time distribution of a L. monocytogenes ATCC 7644 strain grown in broth with additional 2 %, 4 % and 6 % NaCl was evaluated using the software ScanLag. It uses office scanners to automatically record the colony growth on agar plates and evaluate the frequency distribution of their appearance times (lag phase) by automated image analysis. The same broth cultures were diluted to equalize salt concentration and transferred into a fresh broth to evaluate how the previous salt exposure impacted their growth kinetics. The observed growth curves were reproduced using predictive models in which the mean duration of the lag phase of the whole population took into account the occurrence of persisters with a longer lag phase. The models were solved first using a deterministic approach and then a stochastic one introducing a stochastic term that mimics the variability of lag phase duration due to the persisters occurrence. Results showed that the growth of L. monocytogenes in broth with additional NaCl might trigger the formation of persistent cells whose number increased consistently with salt concentrations. The proposed predictive approach reproduced the observed real curves in strong agreement, especially through the stochastic resolution of the models. Persistence is currently a neglected bacterial defence strategy in the food sector but the persisters' formation during production cannot be excluded; therefore, further insights on the topic are certainly desirable.
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Affiliation(s)
- Luca Nalbone
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy
| | - Salvatore Forgia
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy
| | - Graziella Ziino
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; Riconnexia Srls, Spin-off of the University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy
| | - Giorgia Sorrentino
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; Riconnexia Srls, Spin-off of the University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy
| | - Filippo Giarratana
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; Riconnexia Srls, Spin-off of the University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy.
| | - Alessandro Giuffrida
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; Riconnexia Srls, Spin-off of the University of Messina, Polo Universitario dell'Annunziata, Viale Giovanni Palatucci SNC, 98168 Messina, Italy
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26
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Cirilli N, Schiavoni V, Tagliabracci V, Gesuita R, Tiano L, Fabrizzi B, D'Antuono A, Peruzzi A, Cedraro N, Carle F, Moretti M, Ferrante L, Vignaroli C, Biavasco F, Mangiaterra G. Role of viable but non culturable cells in patients with cystic fibrosis in the era of highly effective modulator therapy. J Cyst Fibros 2024:S1569-1993(24)00026-2. [PMID: 38423895 DOI: 10.1016/j.jcf.2024.02.013] [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: 11/21/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Lung infections antibiotic treatment in Cystic Fibrosis patients (pwCF) is often complicated by bacterial persisters, including the so-called Viable but Non Culturable (VBNC) forms, live cells undetected by the routine cultural microbiological methods. This study investigated the occurrence of VBNC cells of five CF bacterial pathogens in 94 pwCF over one year and the possible associations with the patients' clinical features. METHODS Sputum samples, recovered at routine visits and during exacerbation episodes, were analyzed for the presence of the five pathogens by both routine culture-based assays and species-specific qPCR. VBNC cells were estimated as the difference between molecular and cultural counts and their presence was matched with the clinical data in particular the therapeutic regimens. RESULTS All but ten pwCF showed the presence of VBNC cells at least once during the study. Pseudomonas aeruginosa and methicillin-susceptible Staphylococcus aureus were the species most frequently found in the VBNC state. Only the former showed a significant association between chronic infection and VBNC cells presence; VBNC-MSSA positive patients significantly increased overtime. The presence of non culturable bacteria was generally concurrent with poor lung functionality and more frequent pulmonary exacerbations. No significant association with modulator treatment was evidenced. CONCLUSIONS The obtained data demonstrated the overwhelming occurrence of bacterial VBNC cells in CF lung infections, warranting a constant monitoring of pwCF and underlining the need of implementing the routine culture-based assays with culture-independent techniques. This is pivotal to understand the CF bacterial population dynamics and to efficiently contrast the lung infection progression and worsening.
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Affiliation(s)
- Natalia Cirilli
- Cystic Fibrosis Centre, Department of Gastroenterology and Transplantation, University Hospital of Marche, Via Conca, 71, Ancona 60126, Italy.
| | - Valentina Schiavoni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Valentina Tagliabracci
- Cystic Fibrosis Centre, Department of Gastroenterology and Transplantation, University Hospital of Marche, Via Conca, 71, Ancona 60126, Italy
| | - Rosaria Gesuita
- Center of Epidemiology, Biostatistics e Medical Information Technology, Polytechnic University of Marche, Ancona, Italy
| | - Luca Tiano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Centre, Department of Gastroenterology and Transplantation, University Hospital of Marche, Via Conca, 71, Ancona 60126, Italy
| | - Anastasia D'Antuono
- Cystic Fibrosis Centre, Department of Gastroenterology and Transplantation, University Hospital of Marche, Via Conca, 71, Ancona 60126, Italy
| | - Arianna Peruzzi
- Cystic Fibrosis Centre, Department of Gastroenterology and Transplantation, University Hospital of Marche, Via Conca, 71, Ancona 60126, Italy
| | - Nicholas Cedraro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Flavia Carle
- Center of Epidemiology, Biostatistics e Medical Information Technology, Polytechnic University of Marche, Ancona, Italy
| | - Marco Moretti
- Clinical Laboratory, University Hospital of Marche, Ancona, Italy
| | - Luigi Ferrante
- Center of Epidemiology, Biostatistics e Medical Information Technology, Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Gianmarco Mangiaterra
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy; Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
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27
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Kim YJ, Choi HS, Park DH. Persistence and viable but non-culturable state induced by streptomycin in Erwinia amylovora. Front Microbiol 2024; 15:1346300. [PMID: 38450169 PMCID: PMC10914980 DOI: 10.3389/fmicb.2024.1346300] [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: 11/29/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
Persister cell and viable but non-culturable (VBNC) state of bacteria are survival strategies against antibiotics and various environmental stresses, respectively, but they tend to be ignored in agriculture fields, even though bacteria can regain their abilities to survive and produce disease once those stresses disappear. This study was carried out to determine whether persister cell and VBNC state in Erwinia amylovora are present after exposures to streptomycin, the length of their persistence, and the steps needed to decrease the inoculum. Persister cells were observed using biphasic killed growth curve for 4-8 h when the late stationary phase cells of E. amylovora were cultured in liquid medium containing streptomycin. This state was maintained for up to 12 h based on the colony forming units (CFUs) of the colonies that grew on the mannitol glutamate yeast extract (MGY) medium after streptomycin was removed. The CFUs on the MGY medium were lower than the total count determined using the LIVE/DEAD Kit, suggesting that persister cells and VBNC state might co-exist for up to 12 h after exposure to streptomycin. However, after 12 h, E. amylovora cells did not continue to grow on the medium for 9 days, suggesting that they entered a VBNC state at that time and remained in a persistent state. In addition, based on the Redox Sensor Green staining method, the presence of both states was confirmed for up to 12 h, and only then did the VBNC state became apparent. Furthermore, persister cells were observed for up to 24 h, and damaged cells reduced when E. amylovora cells were culture in distilled water with streptomycin, indicating that the uptake of lower nutrients in E. amylovora led to prolonged persister cells and VBNC state, which are more likely to survive after streptomycin treatments. The addition of sucrose and oxytetracycline to distilled water containing streptomycin reduced persister cells than other sources did. Thus, to inhibit the spread of fire blight, management techniques must consider the hazards of using streptomycin treatments that induce dormancy, such as persister cells and VBNC state, beyond the development of resistant strain.
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Affiliation(s)
- Yeon Ju Kim
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon-si, Republic of Korea
| | - Hyun Seo Choi
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon-si, Republic of Korea
| | - Duck Hwan Park
- Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon-si, Republic of Korea
- Plant Medicine Program, Division of Bioresource Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon-si, Republic of Korea
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28
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Li Y, Chen X, Zhang W, Fang K, Tian J, Li F, Han M, Huang J, Sun T, Bai F, Cheng M, Xu Y. The metabolic slowdown caused by the deletion of pspA accelerates protein aggregation during stationary phase facilitating antibiotic persistence. Antimicrob Agents Chemother 2024; 68:e0093723. [PMID: 38169282 PMCID: PMC10848772 DOI: 10.1128/aac.00937-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
Entering a dormant state is a prevailing mechanism used by bacterial cells to transiently evade antibiotic attacks and become persisters. The dynamic progression of bacterial dormancy depths driven by protein aggregation has been found to be critical for antibiotic persistence in recent years. However, our current understanding of the endogenous genes that affects dormancy depth remains limited. Here, we discovered a novel role of phage shock protein A (pspA) gene in modulating bacterial dormancy depth. Deletion of pspA of Escherichia coli resulted in increased bacterial dormancy depths and prolonged lag times for resuscitation during the stationary phase. ∆pspA exhibited a higher persister ratio compared to the wild type when challenged with various antibiotics. Microscopic images revealed that ∆pspA showed accelerated formation of protein aggresomes, which were collections of endogenous protein aggregates. Time-lapse imaging established the positive correlation between protein aggregation and antibiotic persistence of ∆pspA at the single-cell level. To investigate the molecular mechanism underlying accelerated protein aggregation, we performed transcriptome profiling and found the increased abundance of chaperons and a general metabolic slowdown in the absence of pspA. Consistent with the transcriptomic results, the ∆pspA strain showed a decreased cellular ATP level, which could be rescued by glucose supplementation. Then, we verified that replenishment of cellular ATP levels by adding glucose could inhibit protein aggregation and reduce persister formation in ∆pspA. This study highlights the novel role of pspA in maintaining proteostasis, regulating dormancy depth, and affecting antibiotic persistence during stationary phase.
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Affiliation(s)
- Yingxing Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Biomedical Engineering Facility of National Infrastructures for Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Chen
- Biomedical Pioneering Innovation Centre (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Weili Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Kefan Fang
- Biomedical Pioneering Innovation Centre (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Jingjing Tian
- Biomedical Engineering Facility of National Infrastructures for Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangyuan Li
- Clinical Biobank, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingfei Han
- National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, China
| | - Jingjing Huang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Clinical Laboratory, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Tianshu Sun
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Biobank, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Bai
- Biomedical Pioneering Innovation Centre (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Mei Cheng
- Department of Clinical Laboratory, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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29
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Rahman KMT, Butzin NC. Counter-on-chip for bacterial cell quantification, growth, and live-dead estimations. Sci Rep 2024; 14:782. [PMID: 38191788 PMCID: PMC10774380 DOI: 10.1038/s41598-023-51014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024] Open
Abstract
Quantifying bacterial cell numbers is crucial for experimental assessment and reproducibility, but the current technologies have limitations. The commonly used colony forming units (CFU) method causes a time delay in determining the actual numbers. Manual microscope counts are often error-prone for submicron bacteria. Automated systems are costly, require specialized knowledge, and are erroneous when counting smaller bacteria. In this study, we took a different approach by constructing three sequential generations (G1, G2, and G3) of counter-on-chip that accurately and timely count small particles and/or bacterial cells. We employed 2-photon polymerization (2PP) fabrication technology; and optimized the printing and molding process to produce high-quality, reproducible, accurate, and efficient counters. Our straightforward and refined methodology has shown itself to be highly effective in fabricating structures, allowing for the rapid construction of polydimethylsiloxane (PDMS)-based microfluidic devices. The G1 comprises three counting chambers with a depth of 20 µm, which showed accurate counting of 1 µm and 5 µm microbeads. G2 and G3 have eight counting chambers with depths of 20 µm and 5 µm, respectively, and can quickly and precisely count Escherichia coli cells. These systems are reusable, accurate, and easy to use (compared to CFU/ml). The G3 device can give (1) accurate bacterial counts, (2) serve as a growth chamber for bacteria, and (3) allow for live/dead bacterial cell estimates using staining kits or growth assay activities (live imaging, cell tracking, and counting). We made these devices out of necessity; we know no device on the market that encompasses all these features.
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Affiliation(s)
- K M Taufiqur Rahman
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA
| | - Nicholas C Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA.
- Department of Chemistry, Biochemistry and Physics, South Dakota State University, Brookings, SD, 57006, USA.
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Borkar SB, Negi M, Jaiswal A, Raj Acharya T, Kaushik N, Choi EH, Kaushik NK. Plasma-generated nitric oxide water: A promising strategy to combat bacterial dormancy (VBNC state) in environmental contaminant Micrococcus luteus. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132634. [PMID: 37793251 DOI: 10.1016/j.jhazmat.2023.132634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/08/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
The viable but non-culturable (VBNC) is an inactive state, and certain bacteria can enter under adverse conditions. The VBNC state challenges the environment, food safety, and public health since VBNCs may resuscitate and pose a risk to human health. The aim of this study was to investigate the effect of plasma-generated nitric oxide water (PG-NOW) on airborne contaminant Micrococcus luteus (M. luteus) and examine its potential to induce the VBNC state. The essential conditions for bacteria to enter VBNC state are low metabolic activity and rare or no culturable counts. The results indicated that PG-NOW effectively eliminates M. luteus, and the remaining bacteria are in culturable condition. Moreover, the conventional cultured-based method combined with a propidium iodide monoazide quantitative PCR (PMAxxTM-qPCR) showed no significant VBNC induction and moderate culturable counts. Results from the qPCR revealed that gene levels in PG-NOW treated bacteria related to resuscitation-promoting factors, amino acid biosynthesis, and fatty acid metabolism were notably upregulated. PG-NOW inactivated M. luteus showed negligible VBNC formation and alleviated infection ability in lung cells. This study provides new insights into the potential use of PG-NOW reactive species for the prevention and control of the VBNC state of M. luteus.
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Affiliation(s)
- Shweta B Borkar
- Department of Electrical and Biological Physics/Plasma Bioscience Research Center, Kwangwoon University, Seoul 01897, South Korea
| | - Manorma Negi
- Department of Electrical and Biological Physics/Plasma Bioscience Research Center, Kwangwoon University, Seoul 01897, South Korea
| | - Apurva Jaiswal
- Department of Electrical and Biological Physics/Plasma Bioscience Research Center, Kwangwoon University, Seoul 01897, South Korea
| | - Tirtha Raj Acharya
- Department of Electrical and Biological Physics/Plasma Bioscience Research Center, Kwangwoon University, Seoul 01897, South Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong 18323, South Korea.
| | - Eun Ha Choi
- Department of Electrical and Biological Physics/Plasma Bioscience Research Center, Kwangwoon University, Seoul 01897, South Korea.
| | - Nagendra Kumar Kaushik
- Department of Electrical and Biological Physics/Plasma Bioscience Research Center, Kwangwoon University, Seoul 01897, South Korea.
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Bao Q, Ma X, Bo X, Pang J, Dai L, Wang H, Chen Y, Kwok LY. Transcriptomic analysis of Lacticaseibacillus paracasei Zhang in transition to the viable but non-culturable state by RNA sequencing. Front Microbiol 2023; 14:1280350. [PMID: 38188563 PMCID: PMC10768001 DOI: 10.3389/fmicb.2023.1280350] [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: 08/20/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Background Some bacteria enter the viable but non-culturable (VBNC) state to survive harsh environmental conditions and external stresses. This alters cell physiology and has implications for the food industry as some bacteria, such as lactobacilli, undergo similar changes during food processing. Methods This study aimed to investigate the transcriptomic changes of a probiotic strain, Lacticaseibacillus paracasei Zhang (L. paracasei Zhang), upon transition to the VBNC state using high throughput RNA sequencing (RNA-seq). Results Bacteria were inoculated into the de Man, Rogosa, and Sharpe medium and maintained at low temperature and pH to induce cell transition to the VBNC state. Cells were harvested for analysis at five stages of VBNC induction: 0, 3, 30, and 180 days after induction and 210 days when the cells entered the VBNC state. Our results showed that the expression of 2,617, 2,642, 2,577, 2,829, and 2,840 genes was altered at these five different stages. The function of differentially expressed genes (DEGs, compared to healthy cells collected at day 0) and their encoded pathways were analyzed by the Gene Ontology Consortium and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. A total of 10 DEGs were identified in cells that entered the VBNC state: five continuously upregulated (LCAZH_0621, LCAZH_1986, LCAZH_2038, LCAZH_2040, and LCAZH_2174) and five continuously downregulated (LCAZH_0024, LCAZH_0210, LCAZH_0339, LCAZH_0621, and LCAZH_0754). Conclusions This study proposes a molecular model of the VBNC mechanism in L. paracasei Zhang, highlighting that changes in cell metabolism improve substrate utilization efficiency, thereby enhancing bacterial survival under adverse conditions. These data may be useful for improving the survival of probiotics in industrial food processing.
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Affiliation(s)
- Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xuebo Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoyu Bo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Pang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lixia Dai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Huiying Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongfu Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
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Hauser S, Lazarevic V, Tournoud M, Ruppé E, Santiago Allexant E, Guigon G, Schicklin S, Lanet V, Girard M, Mirande C, Gervasi G, Schrenzel J. A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia. Microbiol Spectr 2023; 11:e0129423. [PMID: 37889000 PMCID: PMC10715005 DOI: 10.1128/spectrum.01294-23] [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: 05/09/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.
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Affiliation(s)
| | - V. Lazarevic
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | - E. Ruppé
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | | | | | - V. Lanet
- bioMérieux, Marcy-l'Étoile, France
| | - M. Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - C. Mirande
- bioMérieux, La Balme-les-Grottes, France
| | | | - J. Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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Mulyukin AL, Recchia D, Kostrikina NA, Artyukhina MV, Martini BA, Stamilla A, Degiacomi G, Salina EG. Distinct Effects of Moxifloxacin and Bedaquiline on Growing and 'Non-Culturable' Mycobacterium abscessus. Microorganisms 2023; 11:2690. [PMID: 38004702 PMCID: PMC10673116 DOI: 10.3390/microorganisms11112690] [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: 09/29/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Mycobacterium abscessus has recently emerged as the cause of an increasing number of human infections worldwide. Unfortunately, it is highly resistant to existing drugs, and new specific agents to combat M. abscessus have not yet been found. The discovery of antibiotics that are effective not only against replicating but also against dormant and often recalcitrant cells is a daunting challenge. In this study, we developed a model of non-replicating M. abscessus, which represents a valuable screening tool for antibacterial agents. Thus, we demonstrated that, under a deficiency of potassium ions in the growth media and prolonged incubation, M. abscessus entered a 'non-culturable' state with a significant loss of colony-forming ability, but it retained viability, as confirmed using the most-probable-number (MPN) assay. The 'non-culturable' mycobacteria possessed decelerated cellular metabolism and noticeable differences in cell morphology from actively growing mycobacteria. 'Non-culturable' cells were used in a comprehensive screening of the efficacy of antibiotics, along with actively growing cells. Both CFU and MPN tests confirmed the prominent bactericidal effect of moxifloxacin on actively growing and 'non-culturable' M. abscessus, as proven by less than 0.01% of cells surviving after antibiotic treatment and prolonged storage. Bedaquiline exhibited a comparable bactericidal effect only on metabolically inactive non-culturable cells aged for 44 days. There were reductions ranging from 1000 to 10,000-fold in CFU and MPN, but it was not so efficient with respect to active cells, resulting in a bacteriostatic effect. The demonstrated specificity of bedaquiline in relation to inert non-replicating M. abscessus offers a new and unexpected result. Based on the findings of this research, moxifloxacin and bedaquiline can be regarded as potential treatments for infections caused by M. abscessus. In addition, a key outcome is the proposal to include the combination of viability assays for comprehensive testing of drug candidates. Relying on CFU-based assays alone resulted in overestimates of antibacterial efficacy, as demonstrated in our experiments.
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Affiliation(s)
- Andrey L. Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia (N.A.K.)
| | - Deborah Recchia
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy (A.S.)
| | - Nadezhda A. Kostrikina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia (N.A.K.)
| | - Maria V. Artyukhina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.V.A.)
| | - Billy A. Martini
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.V.A.)
| | - Alessandro Stamilla
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy (A.S.)
| | - Giulia Degiacomi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy (A.S.)
| | - Elena G. Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.V.A.)
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de Castro RJA, Marina CL, Sturny-Leclère A, Hoffmann C, Bürgel PH, Wong SSW, Aimanianda V, Varet H, Agrawal R, Bocca AL, Alanio A. Kicking sleepers out of bed: Macrophages promote reactivation of dormant Cryptococcus neoformans by extracellular vesicle release and non-lytic exocytosis. PLoS Pathog 2023; 19:e1011841. [PMID: 38033163 PMCID: PMC10715671 DOI: 10.1371/journal.ppat.1011841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/12/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023] Open
Abstract
Macrophages play a key role in disseminated cryptococcosis, a deadly fungal disease caused by Cryptococcus neoformans. This opportunistic infection can arise following the reactivation of a poorly characterized latent infection attributed to dormant C. neoformans. Here, we investigated the mechanisms underlying reactivation of dormant C. neoformans using an in vitro co-culture model of viable but non-culturable (VBNC; equivalent of dormant) yeast cells with bone marrow-derived murine macrophages (BMDMs). Comparative transcriptome analysis of BMDMs incubated with log, stationary phase or VBNC cells of C. neoformans showed that VBNC cells elicited a reduced transcriptional modification of the macrophage but retaining the ability to regulate genes important for immune response, such as NLRP3 inflammasome-related genes. We further confirmed the maintenance of the low immunostimulatory capacity of VBNC cells using multiplex cytokine profiling, and analysis of cell wall composition and dectin-1 ligands exposure. In addition, we evaluated the effects of classic (M1) or alternative (M2) macrophage polarization on VBNC cells. We observed that intracellular residence sustained dormancy, regardless of the polarization state of macrophages and despite indirect detection of pantothenic acid (or its derivatives), a known reactivator for VBNC cells, in the C. neoformans-containing phagolysosome. Notably, M0 and M2, but not M1 macrophages, induced extracellular reactivation of VBNC cells by the secretion of extracellular vesicles and non-lytic exocytosis. Our results indicate that VBNC cells retain the low immunostimulatory profile required for persistence of C. neoformans in the host. We also describe a pro-pathogen role of macrophage-derived extracellular vesicles in C. neoformans infection and reinforce the impact of non-lytic exocytosis and the macrophage profile on the pathophysiology of cryptococcosis.
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Affiliation(s)
- Raffael Júnio Araújo de Castro
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Clara Luna Marina
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Aude Sturny-Leclère
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
| | - Christian Hoffmann
- Food Research Center, Department of Food Sciences and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Pedro Henrique Bürgel
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Sarah Sze Wah Wong
- Immunobiology of Aspergillus, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vishukumar Aimanianda
- Immunobiology of Aspergillus, Institut Pasteur, Université Paris Cité, Paris, France
| | - Hugo Varet
- Plate-forme Technologique Biomics, Institut Pasteur, Université Paris Cité, Paris, France
| | - Ruchi Agrawal
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anamélia Lorenzetti Bocca
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Alexandre Alanio
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
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Koutsoumanis K, Ordóñez AA, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Banach J, Ottoson J, Zhou B, da Silva Felício MT, Jacxsens L, Martins JL, Messens W, Allende A. Microbiological hazards associated with the use of water in the post-harvest handling and processing operations of fresh and frozen fruits, vegetables and herbs (ffFVHs). Part 1 (outbreak data analysis, literature review and stakeholder questionnaire). EFSA J 2023; 21:e08332. [PMID: 37928944 PMCID: PMC10623241 DOI: 10.2903/j.efsa.2023.8332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
The contamination of water used in post-harvest handling and processing operations of fresh and frozen fruit, vegetables and herbs (ffFVHs) is a global concern. The most relevant microbial hazards associated with this water are: Listeria monocytogenes, Salmonella spp., human pathogenic Escherichia coli and enteric viruses, which have been linked to multiple outbreaks associated with ffFVHs in the European Union (EU). Contamination (i.e. the accumulation of microbiological hazards) of the process water during post-harvest handling and processing operations is affected by several factors including: the type and contamination of the FVHs being processed, duration of the operation and transfer of microorganisms from the product to the water and vice versa, etc. For food business operators (FBOp), it is important to maintain the microbiological quality of the process water to assure the safety of ffFVHs. Good manufacturing practices (GMP) and good hygienic practices (GHP) related to a water management plan and the implementation of a water management system are critical to maintain the microbiological quality of the process water. Identified hygienic practices include technical maintenance of infrastructure, training of staff and cooling of post-harvest process water. Intervention strategies (e.g. use of water disinfection treatments and water replenishment) have been suggested to maintain the microbiological quality of process water. Chlorine-based disinfectants and peroxyacetic acid have been reported as common water disinfection treatments. However, given current practices in the EU, evidence of their efficacy under industrial conditions is only available for chlorine-based disinfectants. The use of water disinfection treatments must be undertaken following an appropriate water management strategy including validation, operational monitoring and verification. During operational monitoring, real-time information on process parameters related to the process and product, as well as the water and water disinfection treatment(s) are necessary. More specific guidance for FBOp on the validation, operational monitoring and verification is needed.
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Ding N, Liu K, Jiang L, Liu H. The temperature-dependent kinetics and bacteria regrowth by performic acid and sodium hypochlorite disinfection. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:2233-2245. [PMID: 37966179 PMCID: wst_2023_351 DOI: 10.2166/wst.2023.351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Sodium hypochlorite (NaOCl) has been widely used as a disinfectant in water and wastewater treatment, because of its high efficiency and low cost, whereas the bio-toxicity of its disinfection byproducts (DBPs) raised great concern. Performic acid (PFA) produces less DBPs and shows strong oxidation abilities. In this study, the effect of temperature on NaOCl and PFA disinfection as well as bacteria regrowth were evaluated. First, the inactivation of Escherichia coli, Staphylococcus aureus, and Bacillus subtilis by NaOCl and PFA at 4 and 20 °C, detected by cell cultured-based plate counting were fitted to kinetic models, and the predicted CTs were calculated. The results showed that NaOCl was more effective than PFA for E. coli and S. aureus inactivation, and the temperature was positively correlated to disinfection. Second, bacteria regrowth was evaluated at different temperatures (4 and 20 °C) of disinfection and storage. The results showed that the bacteria inactivated by NaOCl regrew prominently, especially for those inactivated at 4 and stored at 4 °C, probably through the mechanism of reactivation of viable but non-culturable (VBNC) bacteria. PFA was superior in suppressing bacteria regrowth, and it may be used as an alternate disinfectant in water treatment in cold environment.
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Affiliation(s)
- Ning Ding
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, China; State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, China; Key Laboratory of Cleaner Production and Comprehensive Utilization of Resources, China National Light Industry, Beijing Technology and Business University, Beijing, China E-mail:
| | - Kun Liu
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, China
| | - Lin Jiang
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, China
| | - Hong Liu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Jiangsu Province, China
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Myckatyn TM, Duran Ramirez JM, Walker JN, Hanson BM. Management of Biofilm with Breast Implant Surgery. Plast Reconstr Surg 2023; 152:919e-942e. [PMID: 37871028 DOI: 10.1097/prs.0000000000010791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
LEARNING OBJECTIVES After studying this article, the participant should be able to: 1. Understand how bacteria negatively impact aesthetic and reconstructive breast implants. 2. Understand how bacteria infect breast implants. 3. Understand the evidence associated with common implant infection-prevention strategies, and their limitations. 4. Understand why implementation of bacteria-mitigation strategies such as antibiotic administration or "no-touch" techniques may not indefinitely prevent breast implant infection. SUMMARY Bacterial infection of aesthetic and reconstructive breast implants is a common and expensive problem. Subacute infections or chronic capsular contractures leading to device explantation are the most commonly documented sequelae. Although bench and translational research underscores the complexities of implant-associated infection, high-quality studies with adequate power, control groups, and duration of follow-up are lacking. Common strategies to minimize infections use antibiotics-administered systemically, in the breast implant pocket, or by directly bathing the implant before insertion-to limit bacterial contamination. Limiting contact between the implant and skin or breast parenchyma represents an additional common strategy. The clinical prevention of breast implant infection is challenged by the clean-contaminated nature of breast parenchyma, and the variable behavior of not only specific bacterial species but also their strains. These factors impact bacterial virulence and antibiotic resistance.
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Affiliation(s)
- Terence M Myckatyn
- From the Division of Plastic and Reconstructive Surgery, Washington University in St. Louis School of Medicine
| | | | - Jennifer N Walker
- Department of Microbiology and Molecular Genetics
- Center for Infectious Diseases, Department of Epidemiology, School of Public Health, University of Texas Health Science Center at Houston
| | - Blake M Hanson
- Center for Antimicrobial Resistance and Microbial Genomics, McGovern Medical School
- Center for Infectious Diseases, Department of Epidemiology, School of Public Health, University of Texas Health Science Center at Houston
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König P, Wilhelm A, Schaudinn C, Poehlein A, Daniel R, Widera M, Averhoff B, Müller V. The VBNC state: a fundamental survival strategy of Acinetobacter baumannii. mBio 2023; 14:e0213923. [PMID: 37768061 PMCID: PMC10653857 DOI: 10.1128/mbio.02139-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Currently, the viable but non-culturable (VBNC) state is an underappreciated niche for pathogenic bacteria which provides a continuous source for recurrent infections and transmission. We propose the VBNC state to be a global persistence mechanism used by various A. baumannii strains to cope with many stresses it is confronted with in the clinical environment and in the host. This requires a novel strategy to detect viable cells of this pathogen that is not only based on plating assays.
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Affiliation(s)
- Patricia König
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University, Frankfurt am Main, Germany
| | - Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Christoph Schaudinn
- Advanced Light and Electron Microscopy ZBS4, Robert-Koch-Institute, Berlin, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University, Frankfurt am Main, Germany
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Waidner LA, Potdukhe TV. Tools to Enumerate and Predict Distribution Patterns of Environmental Vibrio vulnificus and Vibrio parahaemolyticus. Microorganisms 2023; 11:2502. [PMID: 37894160 PMCID: PMC10609196 DOI: 10.3390/microorganisms11102502] [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: 09/07/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Vibrio vulnificus (Vv) and Vibrio parahaemolyticus (Vp) are water- and foodborne bacteria that can cause several distinct human diseases, collectively called vibriosis. The success of oyster aquaculture is negatively impacted by high Vibrio abundances. Myriad environmental factors affect the distribution of pathogenic Vibrio, including temperature, salinity, eutrophication, extreme weather events, and plankton loads, including harmful algal blooms. In this paper, we synthesize the current understanding of ecological drivers of Vv and Vp and provide a summary of various tools used to enumerate Vv and Vp in a variety of environments and environmental samples. We also highlight the limitations and benefits of each of the measurement tools and propose example alternative tools for more specific enumeration of pathogenic Vv and Vp. Improvement of molecular methods can tighten better predictive models that are potentially important for mitigation in more controlled environments such as aquaculture.
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Affiliation(s)
- Lisa A. Waidner
- Hal Marcus College of Science and Engineering, University of West Florida, 11000 University Pkwy, Building 58, Room 108, Pensacola, FL 32514, USA
| | - Trupti V. Potdukhe
- GEMS Program, College of Medicine, University of Illinois Chicago, 1853 W. Polk St., Chicago, IL 60612, USA;
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Liu J, Yang L, Kjellerup BV, Xu Z. Viable but nonculturable (VBNC) state, an underestimated and controversial microbial survival strategy. Trends Microbiol 2023; 31:1013-1023. [PMID: 37225640 DOI: 10.1016/j.tim.2023.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023]
Abstract
As a unique microbial response to adverse circumstances, the viable but nonculturable (VBNC) state is characterized by the loss of culturability of microbial cells on/in nutrient media that normally support their growth, while maintaining metabolic activity. These cells can resuscitate to a culturable state under suitable conditions. Given the intrinsic importance of the VBNC state and recent debates surrounding it, there is a need to redefine and standardize the term, and to address essential questions such as 'How to differentiate VBNC from other similar terms?' and 'How can VBNC cells be standardly and accurately determined?'. This opinion piece aims at contributing to an improved understanding of the VBNC state and promoting its proper handling as an underestimated and controversial microbial survival strategy.
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Affiliation(s)
- Junyan Liu
- College of Light Industry and Food Science, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Ministry of Agriculture, Guangzhou 510225, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Birthe Veno Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20742, USA
| | - Zhenbo Xu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou 510640, China; Department of Laboratory Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou, China.
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Wang H, Zhang Y, Dai L, Bo X, Liu X, Zhao X, Yu J, Kwok LY, Bao Q. Metabolomic Differences between Viable but Nonculturable and Recovered Lacticaseibacillus paracasei Zhang. Foods 2023; 12:3472. [PMID: 37761181 PMCID: PMC10527867 DOI: 10.3390/foods12183472] [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: 08/10/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
The fermentation process can be affected when the starter culture enters the viable but nonculturable (VBNC) state. Therefore, it is of interest to investigate how VBNC cells change physiologically. Lacticaseibacillus (L.) paracasei Zhang is both a probiotic and a starter strain. This study aimed to investigate the metabolomic differences between VBNC and recovered L. paracasei Zhang cells. First, L. paracasei Zhang was induced to enter the VBNC state by keeping the cells in a liquid de Man-Rogosa-Sharpe (MRS) medium at 4 °C for 220 days. Flow cytometry was used to sort the induced VBNC cells, and three different types of culture media (MRS medium, skim milk with 1% yeast extract, and skim milk) were used for cell resuscitation. Cell growth responses in the three types of recovery media suggested that the liquid MRS medium was the most effective in reversing the VBNC state in L. paracasei Zhang. Metabolomics analysis revealed 25 differential metabolites from five main metabolite classes (amino acid, carbohydrate, lipid, vitamin, and purine and pyrimidine). The levels of L-cysteine, L-alanine, L-lysine, and L-arginine notably increased in the revived cells, while cellulose, alginose, and guanine significantly decreased. This study confirmed that VBNC cells had an altered physiology.
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Affiliation(s)
- Huiying Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yuhong Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lixia Dai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiaoyu Bo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiangyun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xin Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
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Hossain T, Singh A, Butzin NC. Escherichia coli cells are primed for survival before lethal antibiotic stress. Microbiol Spectr 2023; 11:e0121923. [PMID: 37698413 PMCID: PMC10581089 DOI: 10.1128/spectrum.01219-23] [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: 03/20/2023] [Accepted: 07/16/2023] [Indexed: 09/13/2023] Open
Abstract
Non-genetic factors can cause significant fluctuations in gene expression levels. Regardless of growing in a stable environment, this fluctuation leads to cell-to-cell variability in an isogenic population. This phenotypic heterogeneity allows a tiny subset of bacterial cells in a population called persister cells to tolerate long-term lethal antibiotic effects by entering into a non-dividing, metabolically repressed state. We occasionally noticed a high variation in persister levels, and to explore this, we tested clonal populations starting from a single cell using a modified Luria-Delbrück fluctuation test. Although we kept the conditions same, the diversity in persistence level among clones was relatively consistent: varying from ~60- to 100- and ~40- to 70-fold for ampicillin and apramycin, respectively. Then, we divided and diluted each clone to observe whether the same clone had comparable persister levels for more than one generation. Replicates had similar persister levels even when clones were divided, diluted by 1:20, and allowed to grow for approximately five generations. This result explicitly shows a cellular memory passed on for generations and eventually lost when cells are diluted to 1:100 and regrown (>seven generations). Our result demonstrates (1) the existence of a small population prepared for stress ("primed cells") resulting in higher persister numbers; (2) the primed memory state is reproducible and transient, passed down for generations but eventually lost; and (3) a heterogeneous persister population is a result of a transiently primed reversible cell state and not due to a pre-existing genetic mutation. IMPORTANCE Antibiotics have been highly effective in treating lethal infectious diseases for almost a century. However, the increasing threat of antibiotic resistance is again causing these diseases to become life-threatening. The longer a bacteria can survive antibiotics, the more likely it is to develop resistance. Complicating matters is that non-genetic factors can allow bacterial cells with identical DNA to gain transient resistance (also known as persistence). Here, we show that a small fraction of the bacterial population called primed cells can pass down non-genetic information ("memory") to their offspring, enabling them to survive lethal antibiotics for a long time. However, this memory is eventually lost. These results demonstrate how bacteria can leverage differences among genetically identical cells formed through non-genetic factors to form primed cells with a selective advantage to survive antibiotics.
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Affiliation(s)
- Tahmina Hossain
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Abhyudai Singh
- Electrical & Computer Engineering, University of Delaware, Newark, Delaware, USA
| | - Nicholas C. Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA
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Aralar A, Goshia T, Ramchandar N, Lawrence SM, Karmakar A, Sharma A, Sinha M, Pride DT, Kuo P, Lecrone K, Chiu M, Mestan K, Sajti E, Vanderpool M, Lazar S, Crabtree M, Tesfai Y, Fraley SI. Universal digital high resolution melt analysis for the diagnosis of bacteremia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.07.23295215. [PMID: 37732245 PMCID: PMC10508820 DOI: 10.1101/2023.09.07.23295215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Fast and accurate diagnosis of bloodstream infection is necessary to inform treatment decisions for septic patients, who face hourly increases in mortality risk. Blood culture remains the gold standard test but typically requires ∼15 hours to detect the presence of a pathogen. Here, we assess the potential for universal digital high-resolution melt (U-dHRM) analysis to accomplish faster broad-based bacterial detection, load quantification, and species-level identification directly from whole blood. Analytical validation studies demonstrated strong agreement between U-dHRM load measurement and quantitative blood culture, indicating that U-dHRM detection is highly specific to intact organisms. In a pilot clinical study of 21 whole blood samples from pediatric patients undergoing simultaneous blood culture testing, U-dHRM achieved 100% concordance when compared with blood culture and 90.5% concordance when compared with clinical adjudication. Moreover, U-dHRM identified the causative pathogen to the species level in all cases where the organism was represented in the melt curve database. These results were achieved with a 1 mL sample input and sample-to-answer time of 6 hrs. Overall, this pilot study suggests that U-dHRM may be a promising method to address the challenges of quickly and accurately diagnosing a bloodstream infection. Universal digital high resolution melt analysis for the diagnosis of bacteremia April Aralar, Tyler Goshia, Nanda Ramchandar, Shelley M. Lawrence, Aparajita Karmakar, Ankit Sharma, Mridu Sinha, David Pride, Peiting Kuo, Khrissa Lecrone, Megan Chiu, Karen Mestan, Eniko Sajti, Michelle Vanderpool, Sarah Lazar, Melanie Crabtree, Yordanos Tesfai, Stephanie I. Fraley.
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44
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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.
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Affiliation(s)
- Chuan Wang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
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45
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Oldham RC, Held MA. Methods for detection and identification of beer-spoilage microbes. Front Microbiol 2023; 14:1217704. [PMID: 37637116 PMCID: PMC10448528 DOI: 10.3389/fmicb.2023.1217704] [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: 05/05/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
It is critical that breweries of all sizes routinely monitor the microbiome of their process to limit financial losses due to microbial contamination. Contamination by beer-spoiling microbes (BSMs) at any point during the brewing process may lead to significant losses for breweries if gone undetected and allowed to spread. Testing and detection of BSMs must be routine and rapid, and because even small breweries need the capability of BSM detection and identification, the method also needs to be affordable. Lactic acid bacteria (LAB) are responsible for most spoilage incidents, many of which have been shown to enter the viable but nonculturable (VBNC) state under conditions present in beer such as cold or oxidative stress. These bacteria are invisible to traditional methods of detection using selective media. This article describes several methods of BSM detection and identification that may be useful in the majority of craft breweries. While there are several genomic methods that meet some or many qualifications of being useful in craft breweries, real-time quantitative polymerase chain reaction (qPCR) currently best meets the desired method characteristics and holds the most utility in this industry, specifically SYBR Green qPCR. qPCR is a targeted method of detection and identification of microbes that is affordable, rapid, specific, sensitive, quantitative, and reliable, and when paired with valid DNA extraction techniques can be used to detect BSMs, including those in the VBNC state.
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Affiliation(s)
- Ryanne C. Oldham
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
- Quality Assurance and Quality Control Laboratory, Jackie O’s Brewery, Athens, OH, United States
| | - Michael A. Held
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
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Mangiaterra G, Cedraro N, Vaiasicca S, Citterio B, Frangipani E, Biavasco F, Vignaroli C. Involvement of Acquired Tobramycin Resistance in the Shift to the Viable but Non-Culturable State in Pseudomonas aeruginosa. Int J Mol Sci 2023; 24:11618. [PMID: 37511375 PMCID: PMC10380639 DOI: 10.3390/ijms241411618] [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: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Persistent and viable but non-culturable (VBNC) Pseudomonas aeruginosa cells are mainly responsible for the recurrence and non-responsiveness to antibiotics of cystic fibrosis (CF) lung infections. The sub-inhibitory antibiotic concentrations found in the CF lung in between successive therapeutic cycles can trigger the entry into the VBNC state, albeit with a strain-specific pattern. Here, we analyzed the VBNC cell induction in the biofilms of two CF P. aeruginosa isolates, exposed to starvation with/without antibiotics, and investigated the putative genetic determinants involved. Total viable bacterial cells were quantified by the validated ecfX-targeting qPCR protocol and the VBNC cells were estimated as the difference between qPCR and cultural counts. The isolates were both subjected to whole genome sequencing, with attention focused on their carriage of aminoglycoside resistance genes and on identifying mutated toxin-antitoxin and quorum sensing systems. The obtained results suggest the variable contribution of different antibiotic resistance mechanisms to VBNC cell abundance, identifying a major contribution from tobramycin efflux, mediated by MexXY efflux pump overexpression. The genome analysis evidenced putative mutation hotspots, which deserve further investigation. Therefore, drug efflux could represent a crucial mechanism through which the VBNC state is entered and a potential target for anti-persistence strategies.
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Affiliation(s)
- Gianmarco Mangiaterra
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via S. Chiara 27, 61029 Urbino, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Nicholas Cedraro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Salvatore Vaiasicca
- Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Via Tronto 10/a, 60020 Ancona, Italy
| | - Barbara Citterio
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via S. Chiara 27, 61029 Urbino, Italy
| | - Emanuela Frangipani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via S. Chiara 27, 61029 Urbino, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Wang J, Hao S, Ren Q. Uncultured Microorganisms and Their Functions in the Fermentation Systems of Traditional Chinese Fermented Foods. Foods 2023; 12:2691. [PMID: 37509783 PMCID: PMC10378637 DOI: 10.3390/foods12142691] [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: 06/04/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Traditional Chinese fermented foods are diverse and loved by people for their rich nutrition and unique flavors. In the fermentation processes of these foods, the microorganisms in the fermentation systems play a crucial role in determining the flavor and quality. Currently, some microorganisms in the fermentation systems of traditional Chinese fermented foods are in a state of being unculturable or difficult to culture, which hinders the comprehensive analysis and resource development of the microbial communities in the fermentation systems. This article provides an overview of the uncultured microorganisms in the natural environment, in the fermentation systems of traditional Chinese fermented foods, and the research methods for studying such microorganisms. It also discusses the prospects of utilizing the uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods. The aim is to gain a comprehensive understanding of the microbial diversity and uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods in order to better exploit and utilize these microorganisms and promote the development of traditional Chinese fermented foods.
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Affiliation(s)
- Jiaxuan Wang
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
| | - Shuyue Hao
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
| | - Qing Ren
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
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48
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Urbaniec J, Sanderson-Smith M, McFadden J, Hai FI, Hingley-Wilson SM. Dysregulated NAD(H) homeostasis associated with ciprofloxacin tolerance in Escherichia coli investigated on a single-cell level with the Peredox [NADH:NAD+] biosensor. Front Microbiol 2023; 14:1191968. [PMID: 37415820 PMCID: PMC10321300 DOI: 10.3389/fmicb.2023.1191968] [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: 03/22/2023] [Accepted: 05/11/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction Antibiotic persistence (subpopulation tolerance) occurs when a subpopulation of antibiotic sensitive cells survives prolonged exposure to a bactericidal concentration of an antibiotic, and is capable of regrowth once the antibiotic is removed. This phenomenon has been shown to contribute to prolonged treatment duration, infection recurrence, and accelerated development of genetic resistance. Currently, there are no biomarkers which would allow for segregation of these antibiotic-tolerant cells from the bulk population prior to antibiotic exposure, limiting research on this phenomenon to retrograde analyses. However, it has been previously shown that persisters often have a dysregulated intracellular redox homeostasis, warranting its investigation as a potential marker for antibiotic tolerance. Furthermore, it is currently unknown whether another antibiotic tolerant subpopulation - viable but non-culturable cells (VBNCs), are simply persisters with extreme lag phase, or are formed through separate pathways. VBNCs similarly to persisters remain viable following antibiotic exposure, however, are not capable of regrowth in standard conditions. Methods In this article we employed an NADH:NAD+ biosensor (Peredox) to investigate NADH homeostasis of ciprofloxacin-tolerant E. coli cells on a single-cell level. [NADH:NAD+] was used as a proxy for measuring intracellular redox homeostasis and respiration rate. Results and Discussion First, we demonstrated that ciprofloxacin exposure results in a high number of VBNCs, several orders of magnitude higher than persisters. However, we found no correlation in the frequencies of persister and VBNC subpopulations. Ciprofloxacin-tolerant cells (persisters & VBNCs) were actively undergoing respiration, although at a significantly lower rate on average when compared to the bulk population. We also noted significant heterogeneity on a single-cell level within the subpopulations, however were unable to segregate persisters from VBNCs based on these observations alone. Finally, we showed that in the highly-persistent strain of E. coli, E. coli HipQ, ciprofloxacin-tolerant cells have a significantly lower [NADH:NAD+] ratio than tolerant cells of its parental strain, providing further link between disturbed NADH homeostasis and antibiotic tolerance.
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Affiliation(s)
- Joanna Urbaniec
- Department of Microbial Sciences, University of Surrey, Guildford, United Kingdom
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Martina Sanderson-Smith
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Johnjoe McFadden
- Department of Microbial Sciences, University of Surrey, Guildford, United Kingdom
| | - Faisal I. Hai
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, Australia
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49
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Loiko N, Tereshkina K, Kovalenko V, Moiseenko A, Tereshkin E, Sokolova OS, Krupyanskii Y. DNA-Binding Protein Dps Protects Escherichia coli Cells against Multiple Stresses during Desiccation. BIOLOGY 2023; 12:853. [PMID: 37372138 DOI: 10.3390/biology12060853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Gradual dehydration is one of the frequent lethal yet poorly understood stresses that bacterial cells constantly face in the environment when their micro ecotopes dry out, as well as in industrial processes. Bacteria successfully survive extreme desiccation through complex rearrangements at the structural, physiological, and molecular levels, in which proteins are involved. The DNA-binding protein Dps has previously been shown to protect bacterial cells from many adverse effects. In our work, using engineered genetic models of E. coli to produce bacterial cells with overproduction of Dps protein, the protective function of Dps protein under multiple desiccation stresses was demonstrated for the first time. It was shown that the titer of viable cells after rehydration in the experimental variants with Dps protein overexpression was 1.5-8.5 times higher. Scanning electron microscopy was used to show a change in cell morphology upon rehydration. It was also proved that immobilization in the extracellular matrix, which is greater when the Dps protein is overexpressed, helps the cells survive. Transmission electron microscopy revealed disruption of the crystal structure of DNA-Dps crystals in E. coli cells that underwent desiccation stress and subsequent watering. Coarse-grained molecular dynamics simulations showed the protective function of Dps in DNA-Dps co-crystals during desiccation. The data obtained are important for improving biotechnological processes in which bacterial cells undergo desiccation.
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Affiliation(s)
- Nataliya Loiko
- Winogradsky Institute of Microbiology, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, 117312 Moscow, Russia
| | - Ksenia Tereshkina
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladislav Kovalenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Andrey Moiseenko
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Eduard Tereshkin
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Yurii Krupyanskii
- Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
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Stojowska-Swędrzyńska K, Kuczyńska-Wiśnik D, Laskowska E. New Strategies to Kill Metabolically-Dormant Cells Directly Bypassing the Need for Active Cellular Processes. Antibiotics (Basel) 2023; 12:1044. [PMID: 37370363 DOI: 10.3390/antibiotics12061044] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Antibiotic therapy failure is often caused by the presence of persister cells, which are metabolically-dormant bacteria capable of surviving exposure to antimicrobials. Under favorable conditions, persisters can resume growth leading to recurrent infections. Moreover, several studies have indicated that persisters may promote the evolution of antimicrobial resistance and facilitate the selection of specific resistant mutants; therefore, in light of the increasing numbers of multidrug-resistant infections worldwide, developing efficient strategies against dormant cells is of paramount importance. In this review, we present and discuss the efficacy of various agents whose antimicrobial activity is independent of the metabolic status of the bacteria as they target cell envelope structures. Since the biofilm-environment is favorable for the formation of dormant subpopulations, anti-persister strategies should also include agents that destroy the biofilm matrix or inhibit biofilm development. This article reviews examples of selected cell wall hydrolases, polysaccharide depolymerases and antimicrobial peptides. Their combination with standard antibiotics seems to be the most promising approach in combating persistent infections.
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Affiliation(s)
- Karolina Stojowska-Swędrzyńska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dorota Kuczyńska-Wiśnik
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Ewa Laskowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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