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Sengupta P, Muthamilselvi Sivabalan SK, Singh NK, Raman K, Venkateswaran K. Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station. MICROBIOME 2024; 12:62. [PMID: 38521963 PMCID: PMC10960378 DOI: 10.1186/s40168-024-01777-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/08/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO2 levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board. One microorganism of particular interest in our study is Enterobacter bugandensis, primarily found in clinical specimens including the human gastrointestinal tract, and also reported to possess pathogenic traits, leading to a plethora of infections. RESULTS Distinct from their Earth counterparts, ISS E. bugandensis strains have exhibited resistance mechanisms that categorise them within the ESKAPE pathogen group, a collection of pathogens recognised for their formidable resistance to antimicrobial treatments. During the 2-year Microbial Tracking 1 mission, 13 strains of multidrug-resistant E. bugandensis were isolated from various locations within the ISS. We have carried out a comprehensive study to understand the genomic intricacies of ISS-derived E. bugandensis in comparison to terrestrial strains, with a keen focus on those associated with clinical infections. We unravel the evolutionary trajectories of pivotal genes, especially those contributing to functional adaptations and potential antimicrobial resistance. A hypothesis central to our study was that the singular nature of the stresses of the space environment, distinct from any on Earth, could be driving these genomic adaptations. Extending our investigation, we meticulously mapped the prevalence and distribution of E. bugandensis across the ISS over time. This temporal analysis provided insights into the persistence, succession, and potential patterns of colonisation of E. bugandensis in space. Furthermore, by leveraging advanced analytical techniques, including metabolic modelling, we delved into the coexisting microbial communities alongside E. bugandensis in the ISS across multiple missions and spatial locations. This exploration revealed intricate microbial interactions, offering a window into the microbial ecosystem dynamics within the ISS. CONCLUSIONS Our comprehensive analysis illuminated not only the ways these interactions sculpt microbial diversity but also the factors that might contribute to the potential dominance and succession of E. bugandensis within the ISS environment. The implications of these findings are twofold. Firstly, they shed light on microbial behaviour, adaptation, and evolution in extreme, isolated environments. Secondly, they underscore the need for robust preventive measures, ensuring the health and safety of astronauts by mitigating risks associated with potential pathogenic threats. Video Abstract.
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Affiliation(s)
- Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India
| | | | - Nitin Kumar Singh
- NASA Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr, Pasadena, 91109, CA, USA
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India.
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India.
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, 600036, Tamil Nadu, India.
- Wadhwani School of Data Science and AI, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India.
| | - Kasthuri Venkateswaran
- NASA Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr, Pasadena, 91109, CA, USA.
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Han M, Zarkani AA, Duan Y, Grimm M, Trotereau J, Virlogeux-Payant I, Schikora A. Bidirectional Comparisons Revealed Functional Patterns in Interaction between Salmonella enterica and Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:414. [PMID: 38337947 PMCID: PMC10857149 DOI: 10.3390/plants13030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Plants may harbor the human pathogen Salmonella enterica. Interactions between S. enterica and different plant species have been studied in individual reports. However, disparities arising from the distinct experimental conditions may render a meaningful comparison very difficult. This study explored interaction patterns between different S. enterica strains including serovars Typhimurium 14028s and LT2 and serovar Senftenberg, and different plants (Arabidopsis, lettuce, and tomato) in one approach. Better persistence of S. enterica serovar Typhimurium strains was observed in all tested plants, whereas the resulting symptoms varied depending on plant species. Genes encoding pathogenesis-related proteins were upregulated in plants inoculated with Salmonella. Furthermore, transcriptome of tomato indicated dynamic responses to Salmonella, with strong and specific responses already 24 h after inoculation. By comparing with publicly accessible Arabidopsis and lettuce transcriptome results generated in a similar manner, constants and variables were displayed. Plants responded to Salmonella with metabolic and physiological adjustments, albeit with variability in reprogrammed orthologues. At the same time, Salmonella adapted to plant leaf-mimicking media with changes in biosynthesis of cellular components and adjusted metabolism. This study provides insights into the Salmonella-plant interaction, allowing for a direct comparison of responses and adaptations in both organisms.
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Affiliation(s)
- Min Han
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany; (M.H.)
- INRAE Val de Loire, Université de Tours, L’Unité Mixte de Recherche Infectiologie et Santé Publique (UMR ISP), 37380 Nouzilly, France
| | - Azhar A. Zarkani
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany; (M.H.)
| | - Yongming Duan
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany; (M.H.)
| | - Maja Grimm
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany; (M.H.)
| | - Jérôme Trotereau
- INRAE Val de Loire, Université de Tours, L’Unité Mixte de Recherche Infectiologie et Santé Publique (UMR ISP), 37380 Nouzilly, France
| | - Isabelle Virlogeux-Payant
- INRAE Val de Loire, Université de Tours, L’Unité Mixte de Recherche Infectiologie et Santé Publique (UMR ISP), 37380 Nouzilly, France
| | - Adam Schikora
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany; (M.H.)
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Deblais L, Ranjit S, Vrisman C, Antony L, Scaria J, Miller SA, Rajashekara G. Role of Stress-Induced Proteins RpoS and YicC in the Persistence of Salmonella enterica subsp. enterica Serotype Typhimurium in Tomato Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:109-118. [PMID: 36394339 DOI: 10.1094/mpmi-07-22-0152-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Understanding the functional role of bacterial genes in the persistence of Salmonella in plant organs can facilitate the development of agricultural practices to mitigate food safety risks associated with the consumption of fresh produce contaminated with Salmonella spp. Our study showed that Salmonella enterica subsp. enterica serotype Typhimurium (strain MDD14) persisted less in inoculated tomato plants than other Salmonella Typhimurium strains tested (JSG210, JSG626, JSG634, JSG637, JSG3444, and EV030415; P < 0.01). In-vitro assays performed in limited-nutrient conditions (growth rate, biofilm production, and motility) were inconclusive in explaining the in-planta phenotype observed with MDD14. Whole-genome sequencing combined with non-synonymous single nucleotide variations analysis was performed to identify genomic differences between MDD14 and the other Salmonella Typhimurium strains. The genome of MDD14 contained a truncated version (123 bp N-terminal) of yicC and a mutated version of rpoS (two non-synonymous substitutions, i.e., G66E and R82C), which are two stress-induced proteins involved in iron acquisition, environmental sensing, and cell envelope integrity. The rpoS and yicC genes were deleted in Salmonella Typhimurium JSG210 with the Lambda Red recombining system. Both mutants had limited persistence in tomato plant organs, similar to that of MDD14. In conclusion, we demonstrated that YicC and RpoS are involved in the persistence of Salmonella in tomato plants in greenhouse conditions and, thus, could represent potential targets to mitigate persistence of Salmonella spp. in planta. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Loïc Deblais
- Department of Animal Sciences, The Ohio State University, Wooster, OH, U.S.A
| | - Sochina Ranjit
- Department of Animal Sciences, The Ohio State University, Wooster, OH, U.S.A
| | - Claudio Vrisman
- Department of Plant Pathology, The Ohio State University, Wooster, OH, U.S.A
| | - Linto Antony
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, U.S.A
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, U.S.A
| | - Sally A Miller
- Department of Plant Pathology, The Ohio State University, Wooster, OH, U.S.A
| | - Gireesh Rajashekara
- Department of Animal Sciences, The Ohio State University, Wooster, OH, U.S.A
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Liu X, Li Y, Micallef SA. Developmentally related and drought-induced shifts in the kale metabolome limited Salmonella enterica association, providing novel insights to enhance food safety. Food Microbiol 2022; 108:104113. [DOI: 10.1016/j.fm.2022.104113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/22/2022] [Accepted: 08/07/2022] [Indexed: 11/27/2022]
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Micallef SA, Han S, Martinez L. Tomato Cultivar Nyagous Fruit Surface Metabolite Changes during Ripening Affect Salmonella Newport. J Food Prot 2022; 85:1604-1613. [PMID: 36048925 DOI: 10.4315/jfp-22-160] [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: 05/25/2022] [Accepted: 08/30/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Tomatoes are a valuable crop consumed year-round. Ripe fruit is picked for local sale, whereas tomatoes intended for transit may be harvested at late mature green or breaker stages when fruit firmness preserves quality. In this study, we evaluated Solanum lycopersicum cv. BHN602 association with three Salmonella serotypes and S. lycopersicum cv. Nyagous with Salmonella Newport using fruit at two ripeness stages. Counts of Salmonella Javiana and Typhimurium were higher from red ripe fruit surfaces of BHN602, and counts of Salmonella Newport were higher from ripe Nyagous fruit than from mature green fruit (P < 0.05). Aqueous fruit washes containing fruit surface compounds collected from ripe Nyagous fruit supported more Salmonella Newport growth than green fruit washes (P < 0.05). Growth curve analysis showed that between 2 and 6 h, Salmonella Newport grew at a rate of 0.25 log CFU/h in red fruit wash compared with 0.17 log CFU/h in green fruit wash (P < 0.05). The parallel trend in Salmonella interaction between fruit and wash suggested that surface metabolite differences between unripe and ripe fruit affect Salmonella dynamics. Untargeted phytochemical profiling of tomato fruit surface washes with gas chromatography time-of-flight mass spectrometry showed that ripe fruit had threefold-lower amino acid and fourfold-higher sugar (fructose, glucose, and xylose) levels than green fruit. Green fruit had higher levels of lauric, palmitic, margaric, and arachidic acids, whereas red fruit had more capric acid. The phenolics ferulic, chlorogenic, and vanillic acid, as well as tyrosol, also decreased with ripening. Although limitations of this study preclude conclusions on how specific compounds affect Salmonella, our study highlights the complexity of the plant niche for foodborne pathogens and the importance of understanding the metabolite landscape Salmonella encounters on fresh produce. Fruit surface phytochemical profiling generated testable hypotheses for future studies exploring the differential Salmonella interactions with tomato varieties and fruit at various ripeness stages. HIGHLIGHTS
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Affiliation(s)
- Shirley A Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA.,Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland 20742, USA
| | - Sanghyun Han
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA
| | - Louisa Martinez
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA
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George AS, Brandl MT. Plant Bioactive Compounds as an Intrinsic and Sustainable Tool to Enhance the Microbial Safety of Crops. Microorganisms 2021; 9:2485. [PMID: 34946087 PMCID: PMC8704493 DOI: 10.3390/microorganisms9122485] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 12/25/2022] Open
Abstract
Outbreaks of produce-associated foodborne illness continue to pose a threat to human health worldwide. New approaches are necessary to improve produce safety. Plant innate immunity has potential as a host-based strategy for the deactivation of enteric pathogens. In response to various biotic and abiotic threats, plants mount defense responses that are governed by signaling pathways. Once activated, these result in the release of reactive oxygen and nitrogen species in addition to secondary metabolites that aim at tempering microbial infection and pest attack. These phytochemicals have been investigated as alternatives to chemical sanitization, as many are effective antimicrobial compounds in vitro. Their antagonistic activity toward enteric pathogens may also provide an intrinsic hurdle to their viability and multiplication in planta. Plants can detect and mount basal defenses against enteric pathogens. Evidence supports the role of plant bioactive compounds in the physiology of Salmonella enterica, Escherichia coli, and Listeria monocytogenes as well as their fitness on plants. Here, we review the current state of knowledge of the effect of phytochemicals on enteric pathogens and their colonization of plants. Further understanding of the interplay between foodborne pathogens and the chemical environment on/in host plants may have lasting impacts on crop management for enhanced microbial safety through translational applications in plant breeding, editing technologies, and defense priming.
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Affiliation(s)
| | - Maria T. Brandl
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA 94710, USA;
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Zarkani AA, Schikora A. Mechanisms adopted by Salmonella to colonize plant hosts. Food Microbiol 2021; 99:103833. [PMID: 34119117 DOI: 10.1016/j.fm.2021.103833] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022]
Abstract
Fruits and vegetables consumed fresh or as minimally-processed produce, have multiple benefits for our diet. Unfortunately, they bring a risk of food-borne diseases, for example salmonellosis. Interactions between Salmonella and crop plants are indeed a raising concern for the global health. Salmonella uses multiple strategies to manipulate the host defense system, including plant's defense responses. The main focus of this review are strategies used by this bacterium during the interaction with crop plants. Emphasis was put on how Salmonella avoids the plant defense responses and successfully colonizes plants. In addition, several factors were reviewed assessing their impact on Salmonella persistence and physiological adaptation to plants and plant-related environment. The understanding of those mechanisms, their regulation and use by the pathogen, while in contact with plants, has significant implication on the growth, harvest and processing steps in plant production system. Consequently, it requires both the authorities and science to advance and definite methods aiming at prevention of crop plants contamination. Thus, minimizing and/or eliminating the potential of human diseases.
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Affiliation(s)
- Azhar A Zarkani
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany; University of Baghdad, Department of Biotechnology, 10071, Baghdad, Iraq.
| | - Adam Schikora
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany.
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He Y, Chen R, Qi Y, Salazar JK, Zhang S, Tortorello ML, Deng X, Zhang W. Survival and transcriptomic response of Salmonella enterica on fresh-cut fruits. Int J Food Microbiol 2021; 348:109201. [PMID: 33930836 DOI: 10.1016/j.ijfoodmicro.2021.109201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 01/21/2023]
Abstract
Salmonella enterica is frequently implicated in foodborne disease outbreaks associated with fresh-cut fruits. In the U.S., more than one third of fruit-related outbreaks have been linked to two S. enterica serotypes Newport and Typhimurium. Approximately 80% of fruit-related human salmonellosis cases were associated with tomatoes, cantaloupes and cucumbers. In this study, we investigated the population dynamics of S. Newport and S. Typhimurium on fresh-cut tomato, cantaloupe, cucumber and apple under short-term storage conditions. We further compared the transcriptomic profiles of a S. Newport strain on fresh-cut tomato and cantaloupe using high-throughput RNA-seq. We demonstrated that both S. enterica Newport and Typhimurium survived well on various fresh-cut fruit items under refrigeration storage conditions, independent of inoculation levels. However, S. enterica displayed variable survival behaviors on different types of fruits. For example, at 7 d storage, the population of S. enterica reduced less than 0.2 log (p > 0.05) on fresh-cut tomato and cantaloupe, in contrast to ~0.5 log (p < 0.05) on cucumber and apple. RNA-seq analysis suggested that S. enterica mediates its survival on fresh-cut fruits through differentially regulating genes involved in specific carbon utilization and metabolic pathways. Several known bacterial virulence factors (e.g., pag gene) were found to be differentially regulated on fresh-cut tomato and cantaloupe, suggesting a link between the events of food contamination and subsequent human infection. Findings from this study contribute to a better understanding of S. enterica survival mechanisms on fresh-cut produce.
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Affiliation(s)
- Yingshu He
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA; Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA.
| | - Ruixi Chen
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Yan Qi
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA
| | - Joelle K Salazar
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Shimei Zhang
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Mary Lou Tortorello
- Division of Food Processing Science and Technology, U. S. Food and Drug Administration, Bedford Park, IL, USA
| | - Xiangyu Deng
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, USA
| | - Wei Zhang
- Department of Food Science and Nutrition & Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
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