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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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García Vázquez A, Mitarai N, Jauffred L. Genetic mixing and demixing on expanding spherical frontiers. ISME COMMUNICATIONS 2024; 4:ycae009. [PMID: 38524760 PMCID: PMC10958774 DOI: 10.1093/ismeco/ycae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 03/26/2024]
Abstract
Genetic fluctuation during range expansion is a key process driving evolution. When a bacterial population is expanding on a 2D surface, random fluctuations in the growth of the pioneers at the front line cause a strong demixing of genotypes. Even when there is no selective advantage, sectors of low genetic diversity are formed. Experimental studies of range expansions in surface-attached colonies of fluorescently labelled micro-organisms have contributed significantly to our understanding of fundamental evolutionary dynamics. However, experimental studies on genetic fluctuations in 3D range expansions have been sparse, despite their importance for tumour or biofilm development. We encapsulated populations of two fluorescent Escherichia coli strains in inoculation droplets (volumes [Formula: see text] nl). The confined ensemble of cells grew when embedded in a hydrogel-with nutrients-and developed 3D colonies with well-defined, sector-like regions. Using confocal laser scanning microscopy, we imaged the development of 3D colonies and the emergence of sectors. We characterized how cell concentration in the inoculation droplet controls sectors, growth rate, and the transition from branched colonies to quasi-spherical colonies. We further analysed how sectors on the surface change over time. We complement these experimental results with a modified 3D Eden growth model. The model in 3D spherical growth predicts a phase, where sectors are merging, followed by a steady increase (constant rate), and the experimentally analysed sectors were consistent with this prediction. Therefore, our results demonstrate qualitative differences between radial (2D) and spherical (3D) range expansions and their importance in gene fixation processes.
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Affiliation(s)
- Alba García Vázquez
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark
| | - Namiko Mitarai
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark
| | - Liselotte Jauffred
- The Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark
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A double layer agar plate method results in an improvement for enumerating Vibrio vulnificus and Vibrio parahaemolyticus exposed to nutrient deficiency and refrigeration temperature. Food Microbiol 2022; 107:104085. [DOI: 10.1016/j.fm.2022.104085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 11/22/2022]
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Fan J, Jia Y, Xu D, Ye Z, Zhou J, Huang J, Fu Y, Shen C. Anaerobic condition induces a viable but nonculturable state of the PCB-degrading Bacteria Rhodococcus biphenylivorans TG9. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142849. [PMID: 33757234 DOI: 10.1016/j.scitotenv.2020.142849] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 06/12/2023]
Abstract
Significant microbial removal of highly chlorinated polychlorinated biphenyls (PCBs) requires the cooperation of anaerobic and aerobic bacteria. During the sequencing process of anaerobic dechlorination and aerobic degradation of PCBs, aerobic degrading bacteria have to undergo anaerobic stress. However, the survival strategy of aerobic degrading bacteria under anaerobic condition is not well-understood. In this study, the culturable cells of Rhodococcus biphenylivorans TG9 decreased from 108 CFU/mL to values below the detection limit after 60 days of anaerobic stress while the viable cells remained 105-106 cells/mL, indicating that anaerobic condition induced TG9 entering into the viable but nonculturable (VBNC) state. Cell resuscitation was observed when oxygen was supplied further confirming the VBNC state of TG9. The results of single-cell Raman spectroscopy combined with heavy water indicated the significant decrease of metabolic activity after TG9 entering into the VBNC state. Additionally, the degradation ability of TG9 in the VBNC state was also significantly reduced, while it recovered after resuscitation. Our research proved that entering into the VBNC state is a survival strategy of TG9 under anaerobic conditions, and the limited culturability and degrading capacity could be overcome by resuscitation. The present study provides new insights for improving the remediation efficiency of PCBs contamination.
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Affiliation(s)
- Jiahui Fan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Yangyang Jia
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Dongdong Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Zhe Ye
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Jiahang Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Jionghao Huang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Yulong Fu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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Song K, Shim J, Jung JY, Lee C, Nam Y. Endowing antifouling properties on metal substrata by creating an artificial barrier layer based on scalable metal oxide nanostructures. BIOFOULING 2020; 36:766-782. [PMID: 32842788 DOI: 10.1080/08927014.2020.1811238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Here, by creating different types of artificial barrier layer against bacterial attachment, anti-biofouling properties were endowed on three metallic surfaces - aluminum, stainless steel and titanium. To each metallic surface, a tailored chemical oxidation process was applied to grow scalable oxide structures with an additional appropriate coating, resulting in three different types of anti-biofouling barrier, a thin water film, an air layer and an oil layer. Fluorescence images of the attached bacteria showed that the water layer improved the anti-biofouling performance up to 8-12 h and the air layer up to 12-24 h, comparable with the lifetime of the air layer. In comparison, the oil layer exhibited the best anti-biofouling performance by suppressing the fouled area by < 10% up to 72 h regardless of the substratum type. The present work provides simple, low-cost, scalable strategies to enhance the anti-biofouling performance of industrially important metallic surfaces. [Formula: see text].
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Affiliation(s)
- Kyounghwan Song
- Department of Mechanical Engineering, Kyung Hee University, Yongin, Republic of Korea
| | - Jaehwan Shim
- Department of Mechanical Engineering, Kyung Hee University, Yongin, Republic of Korea
| | - Jung-Yeul Jung
- Maritime Safety and Environmental Research Division, Korea Research Institute of Ships & Ocean Engineering, Daejeon, Republic of Korea
| | - Choongyeop Lee
- Department of Mechanical Engineering, Kyung Hee University, Yongin, Republic of Korea
| | - Youngsuk Nam
- Department of Mechanical Engineering, Kyung Hee University, Yongin, Republic of Korea
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M Jayakumar J, Balasubramanian D, Reddi G, Almagro-Moreno S. Synergistic role of abiotic factors driving viable but non-culturable Vibrio cholerae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:454-465. [PMID: 32542975 DOI: 10.1111/1758-2229.12861] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/06/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
Vibrio cholerae O1, a natural inhabitant of estuarine environments, is found in a dormant, viable but non-culturable (VBNC) state during interepidemic periods. Although the individual roles of abiotic factors affecting VBNC formation have been extensively studied, their interplay in driving this phenomenon remains largely unaddressed. Here, we identified that major abiotic factors synergize with low nutrient conditions governing entry of cells into the VBNC state. Specifically, V. cholerae cells exposed to a combination of alkaline pH and high salinity under aeration at low temperatures (VBNC-inducing conditions) synergize to facilitate rapid entry into VBNC, whereas the opposite conditions prevented entry into the state. The major virulence regulator ToxR, and the stringent response protein RelA played opposing roles, repressing and facilitating VBNC entry respectively. Further, VBNC-inducing conditions negated the effects of ToxR and RelA, facilitating rapid formation of VBNC cells. In summary, this study highlights the synergy between critical abiotic factors and identified ToxR and RelA as two associated regulators, allowing for the persistence of V. cholerae in aquatic environments. Insights obtained in this study will help better understand environmental survival non-sporulating bacteria and transmission of facultative bacterial pathogens.
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Affiliation(s)
- Jane M Jayakumar
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, 32816
| | - Deepak Balasubramanian
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, 32816
| | - Geethika Reddi
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, 32816
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, 32816
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, FL, 32816
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Kirketerp-Møller K, Stewart PS, Bjarnsholt T. The zone model: A conceptual model for understanding the microenvironment of chronic wound infection. Wound Repair Regen 2020; 28:593-599. [PMID: 32529778 PMCID: PMC7540265 DOI: 10.1111/wrr.12841] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 11/26/2022]
Abstract
In 2008, two articles in Wound Repair and Regeneration changed the clinical perspective on chronic wounds. They stated that chronic wounds that do not heal contain bacterial biofilms and that these biofilms may be one of the reasons for the nonhealing properties of the wounds. However, we still do not understand the exact role biofilms play in the halted healing process, and we are not able to successfully treat them. The reason for this could be that in vivo biofilms differ substantially from in vitro biofilms, and that most of the knowledge about biofilms originates from in vitro research. In this article, we introduce the zone model as a concept for understanding bacterial behavior and the impact of the microenvironment on both the host and the bacteria. Until now, identification of bacteria, gene expression, and postscript regulation have been looking at a bulk of bacteria and averaging the behavior of all the bacteria. As the zone model dictates that every single bacterium reacts to its own microenvironment, the model may facilitate the planning of future research with improved clinical relevance. The zone model integrates physiology and biology from single cells, microbial aggregates, local host response, surrounding tissue, and the systemic context of the whole host. Understanding the mechanisms behind the actions and reactions by a single bacterium when interacting with other neighboring bacteria cells, other microorganisms, and the host will help us overcome the detrimental effects of bacteria in chronic wounds. Furthermore, we propose use of the terminology "bacterial phenotype" when describing the actions and reactions of bacteria, and the term "biofilms" to describe the morphology of the bacterial community.
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Affiliation(s)
| | - Philip S Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, University of Copenhagen and Department of Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
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