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Martínez-Renau E, Martín-Platero AM, Bodawatta KH, Martín-Vivaldi M, Martínez-Bueno M, Poulsen M, Soler JJ. Social environment influences microbiota and potentially pathogenic bacterial communities on the skin of developing birds. Anim Microbiome 2024; 6:47. [PMID: 39148142 PMCID: PMC11325624 DOI: 10.1186/s42523-024-00327-2] [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: 08/24/2023] [Accepted: 06/28/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Animal bacterial symbionts are established early in life, either through vertical transmission and/or by horizontal transmission from both the physical and the social environment, such as direct contact with con- or heterospecifics. The social environment particularly can influence the acquisition of both mutualistic and pathogenic bacteria, with consequences for the stability of symbiotic communities. However, segregating the effects of the shared physical environment from those of the social interactions is challenging, limiting our current knowledge on the role of the social environment in structuring bacterial communities in wild animals. Here, we take advantage of the avian brood-parasite system of Eurasian magpies (Pica pica) and great spotted cuckoos (Clamator glandarius) to explore how the interspecific social environment (magpie nestlings developing with or without heterospecifics) affects bacterial communities on uropygial gland skin. RESULTS We demonstrated interspecific differences in bacterial community compositions in members of the two species when growing up in monospecific nests. However, the bacterial community of magpies in heterospecific nests was richer, more diverse, and more similar to their cuckoo nest-mates than when growing up in monospecific nests. These patterns were alike for the subset of microbes that could be considered core, but when looking at the subset of potentially pathogenic bacterial genera, cuckoo presence reduced the relative abundance of potentially pathogenic bacterial genera on magpies. CONCLUSIONS Our findings highlight the role of social interactions in shaping the assembly of the avian skin bacterial communities during the nestling period, as exemplified in a brood parasite-host system.
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Affiliation(s)
- Ester Martínez-Renau
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), 04120, Almería, Spain.
| | - Antonio M Martín-Platero
- Departamento de Microbiología, Universidad de Granada, 18071, Granada, Spain
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain
| | - Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Martín-Vivaldi
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain
- Departamento de Zoología, Universidad de Granada, 18071, Granada, Spain
| | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, 18071, Granada, Spain
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Juan José Soler
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), 04120, Almería, Spain.
- Unidad Asociada (CSIC): Coevolución: Cucos, Hospedadores y Bacterias Simbiontes, Universidad de Granada, 18071, Granada, Spain.
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2
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Leinweber A, Laffont C, Lardi M, Eberl L, Pessi G, Kümmerli R. RNA-Seq reveals that Pseudomonas aeruginosa mounts growth medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia. Commun Biol 2024; 7:995. [PMID: 39143311 PMCID: PMC11324955 DOI: 10.1038/s42003-024-06618-3] [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: 05/05/2023] [Accepted: 07/23/2024] [Indexed: 08/16/2024] Open
Abstract
Most habitats host diverse bacterial communities, offering opportunities for inter-species interactions. While competition might often dominate such interactions, little is known about whether bacteria can sense competitors and mount adequate responses. The competition sensing hypothesis proposes that bacteria can use cues such as nutrient stress and cell damage to prepare for battle. Here, we tested this hypothesis by measuring transcriptome changes in Pseudomonas aeruginosa exposed to the supernatant of its competitor Burkholderia cenocepacia. We found that P. aeruginosa exhibited significant growth-medium-dependent transcriptome changes in response to competition. In an iron-rich medium, P. aeruginosa upregulated genes encoding the type-VI secretion system and the siderophore pyoverdine, whereas genes encoding phenazine toxins and hydrogen cyanide were upregulated under iron-limited conditions. Moreover, general stress response and quorum sensing regulators were upregulated upon supernatant exposure. Altogether, our results reveal nuanced competitive responses of P. aeruginosa when confronted with B. cenocepacia supernatant, integrating both environmental and social cues.
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Affiliation(s)
- Anne Leinweber
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Clémentine Laffont
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
- Department of Quantitative Biomedicine, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
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3
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Talukdar A, Kundu P, Bhattacharjee S, Dey S, Dey A, Biswas JK, Chaudhuri P, Bhattacharya S. Microplastics in mangroves with special reference to Asia: Occurrence, distribution, bioaccumulation and remediation options. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166165. [PMID: 37574065 DOI: 10.1016/j.scitotenv.2023.166165] [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: 05/01/2023] [Revised: 07/15/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
Microplastics (MPs) are a new and lesser-known pollutant that has intrigued the interest of scientists all over the world in recent decades. MP (<5mm in size) can enter marine environments such as mangrove forests in a variety of ways, interfering with the health of the environment and organisms. Mangroves are now getting increasingly exposed to microplastic contamination due to their proximity to human activities and their position as critical transitional zones between land and sea. The present study reviews the status of MPs contamination specifically in mangrove ecosystems situated in Asia. Different sources and characteristics of MPs, subsequent deposition of MPs in mangrove water and sediments, bioaccumulation in different organisms are discussed in this context. MP concentrations in sediments and organisms were higher in mangrove forests exposed to fishing, coastal tourism, urban, and industrial wastewater than in pristine areas. The distribution of MPs varies from organism to organism in mangrove ecosystems, and is significantly influenced by their morphometric characteristics, feeding habits, dwelling environment etc. Mangrove plants can accumulate microplastics in their roots, stem and leaves through absorption, adsorption and entrapment helping in reducing abundance of microplastic in the surrounding environment. Several bacterial and fungal species are reported from these mangrove ecosystems, which are capable of degrading MPs. The bioremediation potential of mangrove plants offers an innovative and sustainable approach to mitigate microplastic pollution. Diverse mechanisms of MP biodegradation by mangrove dwelling organisms are discussed in this context. Biotechnological applications can be utilized to explore the genetic potential of the floral and faunal species found in the Asian mangroves. Detailed studies are required to monitor, control, and evaluate MP pollution in sediments and various organisms in mangrove ecosystems in Asia as well as in other parts of the world.
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Affiliation(s)
| | - Pritha Kundu
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar 803116, India
| | - Shrayan Bhattacharjee
- Ecosystem and Ecology Laboratory, Post-graduate Department of Zoology, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118, India
| | - Satarupa Dey
- Department of Botany, Shyampur Siddheswari Mahavidyalaya, Howrah 711301, West Bengal, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Jayanta Kumar Biswas
- Enviromicrobiology, Ecotoxicology & Ecotechnology Research Laboratory (3E-MicroToxTech Lab), Department of Ecological Studies, and International Centre for Ecological Engineering, University of Kalyani, Nadia, West Bengal 741235, India
| | - Punarbasu Chaudhuri
- Department of Environmental Science, University of Calcutta, Kolkata 700019, West Bengal, India
| | - Sayan Bhattacharya
- School of Ecology and Environment Studies, Nalanda University, Rajgir, Nalanda, Bihar 803116, India.
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4
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Zhang Z, Liu Y, Zhao W, Ji M. Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers. MICROBIOME 2023; 11:228. [PMID: 37848997 PMCID: PMC10583317 DOI: 10.1186/s40168-023-01621-y] [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: 04/06/2023] [Accepted: 07/14/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood. RESULTS Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms. CONCLUSION These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.
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Affiliation(s)
- Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mukan Ji
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
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5
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Fang GY, Mu XJ, Huang BW, Jiang YJ. Monitoring Longitudinal Trends and Assessment of the Health Risk of Shigella flexneri Antimicrobial Resistance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4971-4983. [PMID: 36929874 DOI: 10.1021/acs.est.2c08766] [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: 06/18/2023]
Abstract
Shigella flexneri infection is the main cause of diarrhea in humans worldwide. The emergence of antimicrobial resistance (AMR) of S. flexneri is a growing public health threat worldwide, while large-scale studies monitoring the longitudinal AMR trends of isolates remain scarce. Here, the AMR gene (ARG) profiles of 717 S. flexneri isolates from 1920 to 2020 worldwide were determined. The results showed that the average number of ARGs in isolates has increased significantly, from 19.2 ± 2.4 before 1970 to 29.6 ± 5.3 after 2010. In addition, mobile genetic elements were important contributors to ARGs in S. flexneri isolates. The results of the structural equation model showed that the human development index drove the consumption of antibiotics and indirectly promoted the antibiotic resistance. Finally, a machine learning algorithm was used to predict the antibiotic resistance risk of global terrestrial S. flexneri isolates and successfully map the antibiotic resistance threats in global land habitats with over 80% accuracy. Collectively, this study monitored the longitudinal AMR trends, quantitatively surveilled the health risk of S. flexneri AMR, and provided a theoretical basis for mitigating the threat of antibiotic resistance.
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Affiliation(s)
- Guan-Yu Fang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
- Suzhou Precision Biotech Co., Ltd, Suzhou 215000, P. R. China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
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6
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Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of
Clostridium
in an Artificial Ecosystem for Liquor Production. mSystems 2022; 7:e0029722. [PMID: 35491831 PMCID: PMC9238394 DOI: 10.1128/msystems.00297-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pit mud is a typical artificial ecosystem for Chinese liquor production.
Clostridium
inhabiting pit mud plays essential roles in the flavor formation of strong-flavor baijiu. The relative abundance of
Clostridium
increased with pit mud quality, further influencing the quality of baijiu.
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7
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Werner KA, Schneider D, Poehlein A, Diederich N, Feyen L, Axtmann K, Hübner T, Brüggemann N, Prost K, Daniel R, Grohmann E. Metagenomic Insights Into the Changes of Antibiotic Resistance and Pathogenicity Factor Pools Upon Thermophilic Composting of Human Excreta. Front Microbiol 2022; 13:826071. [PMID: 35432262 PMCID: PMC9009411 DOI: 10.3389/fmicb.2022.826071] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/17/2022] [Indexed: 01/12/2023] Open
Abstract
In times of climate change, practicing a form of sustainable, climate-resilient and productive agriculture is of primordial importance. Compost could be one form of sustainable fertilizer, which is increasing humus, water holding capacity, and nutrient contents of soils. It could thereby strengthen agriculture toward the adverse effects of climate change, especially when additionally combined with biochar. To get access to sufficient amounts of suitable materials for composting, resources, which are currently treated as waste, such as human excreta, could be a promising option. However, the safety of the produced compost regarding human pathogens, pharmaceuticals (like antibiotics) and related resistance genes must be considered. In this context, we have investigated the effect of 140- and 154-days of thermophilic composting on the hygienization of human excreta and saw dust from dry toilets together with straw and green cuttings with and without addition of biochar. Compost samples were taken at the beginning and end of the composting process and metagenomic analysis was conducted to assess the fate of antibiotic resistance genes (ARGs) and pathogenicity factors of the microbial community over composting. Potential ARGs conferring resistance to major classes of antibiotics, such as beta-lactam antibiotics, vancomycin, the MLSB group, aminoglycosides, tetracyclines and quinolones were detected in all samples. However, relative abundance of ARGs decreased from the beginning to the end of composting. This trend was also found for genes encoding type III, type IV, and type VI secretion systems, that are involved in pathogenicity, protein effector transport into eukaryotic cells and horizontal gene transfer between bacteria, respectively. The results suggest that the occurrence of potentially pathogenic microorganisms harboring ARGs declines during thermophilic composting. Nevertheless, ARG levels did not decline below the detection limit of quantitative PCR (qPCR). Thresholds for the usage of compost regarding acceptable resistance gene levels are yet to be evaluated and defined.
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Affiliation(s)
- Katharina A. Werner
- Department of Microbiology, Faculty of Life Sciences and Technology, Berliner Hochschule für Technik, Berlin, Germany
| | - Dominik Schneider
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Nina Diederich
- Department of Microbiology, Faculty of Life Sciences and Technology, Berliner Hochschule für Technik, Berlin, Germany
| | - Lara Feyen
- Department of Microbiology, Faculty of Life Sciences and Technology, Berliner Hochschule für Technik, Berlin, Germany
| | - Katharina Axtmann
- Institute for Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Tobias Hübner
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research GmbH—Umweltforschungszentrum Leipzig (UFZ), Leipzig, Germany
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences—Agrosphere (IBG-3), Forschungszentrum Jülich, Jülich, Germany
| | - Katharina Prost
- Institute of Bio- and Geosciences—Agrosphere (IBG-3), Forschungszentrum Jülich, Jülich, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Elisabeth Grohmann
- Department of Microbiology, Faculty of Life Sciences and Technology, Berliner Hochschule für Technik, Berlin, Germany
- *Correspondence: Elisabeth Grohmann,
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8
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Virieux-Petit M, Hammer-Dedet F, Aujoulat F, Jumas-Bilak E, Romano-Bertrand S. From Copper Tolerance to Resistance in Pseudomonas aeruginosa towards Patho-Adaptation and Hospital Success. Genes (Basel) 2022; 13:genes13020301. [PMID: 35205346 PMCID: PMC8872213 DOI: 10.3390/genes13020301] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
The hospital environment constitutes a reservoir of opportunistic pathogens responsible for healthcare-associated infections (HCAI) such as Pseudomonas aeruginosa (Pa). Pa persistence within technological niches, the increasing emergence of epidemic high-risk clones in HCAI, the epidemiological link between plumbing strains and clinical strains, make it a major nosocomial pathogen. Therefore, understanding the mechanisms of Pa adaptation to hospital water systems would be useful in preventing HCAI. This review deciphers how copper resistance contributes to Pa adaptation and persistence in a hospital environment, especially within copper water systems, and ultimately to its success as a causative agent of HCAI. Numerous factors are involved in copper homeostasis in Pa, among which active efflux conferring copper tolerance, and copper-binding proteins regulating the copper compartmentalization between periplasm and cytoplasm. The functional harmony of copper homeostasis is regulated by several transcriptional regulators. The genomic island GI-7 appeared as especially responsible for the copper resistance in Pa. Mechanisms of copper and antibiotic cross-resistance and co-resistance are also identified, with potential co-regulation processes between them. Finally, copper resistance of Pa confers selective advantages in colonizing and persisting in hospital environments but also appears as an asset at the host/pathogen interface that helps in HCAI occurrence.
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Affiliation(s)
- Maxine Virieux-Petit
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Florence Hammer-Dedet
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Fabien Aujoulat
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
- Hospital Hygiene and Infection Control Team, University Hospital of Montpellier, 34093 Montpellier, France
| | - Sara Romano-Bertrand
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
- Hospital Hygiene and Infection Control Team, University Hospital of Montpellier, 34093 Montpellier, France
- UMR 5151 HSM, Equipe Pathogènes Hydriques Santé et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
- Correspondence: ; Tel.: +33-4-11-75-94-30
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9
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Aeromonas: the multifaceted middleman in the One Health world. Curr Opin Microbiol 2021; 65:24-32. [PMID: 34717260 DOI: 10.1016/j.mib.2021.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023]
Abstract
Aeromonas is at the interface of all the One Health components and represents an amazingly sound test case in the One Health approach, from economic loss in aquaculture tochallenges related to antibiotic-resistant bacteria selected from the environment. In human health, infections following leech therapy is an outstanding example of such One Health challenges. Aeromonads are not only ubiquitous environmental bacteria, able to rapidly colonize and cause opportunistic infections in humans and animals, they are also capable of promoting interactions and gene exchanges between the One Health components. This makes this genus a key amplifier of genetic transfer, especially of antibiotic resistance genes.
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10
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Petitjean M, Juarez P, Meunier A, Daguindau E, Puja H, Bertrand X, Valot B, Hocquet D. The rise and the fall of a Pseudomonas aeruginosa endemic lineage in a hospital. Microb Genom 2021; 7. [PMID: 34473016 PMCID: PMC8715434 DOI: 10.1099/mgen.0.000629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The biological features that allow a pathogen to survive in the hospital environment are mostly unknown. The extinction of bacterial epidemics in hospitals is mostly attributed to changes in medical practice, including infection control, but the role of bacterial adaptation has never been documented. We analysed a collection of Pseudomonas aeruginosa isolates belonging to the Besançon Epidemic Strain (BES), responsible for a 12year nosocomial outbreak, using a genotype-to-phenotype approach. Bayesian analysis estimated the emergence of the clone in the hospital 5 years before its opening, during the creation of its water distribution network made of copper. BES survived better than the reference strains PAO1 and PA14 in a copper solution due to a genomic island containing 13 metal-resistance genes and was specifically able to proliferate in the ubiquitous amoeba Vermamoeba vermiformis. Mutations affecting amino-acid metabolism, antibiotic resistance, lipopolysaccharide biosynthesis, and regulation were enriched during the spread of BES. Seven distinct regulatory mutations attenuated the overexpression of the genes encoding the efflux pump MexAB-OprM over time. The fitness of BES decreased over time in correlation with its genome size. Overall, the resistance to inhibitors and predators presumably aided the proliferation and propagation of BES in the plumbing system of the hospital. The pathogen further spread among patients via multiple routes of contamination. The decreased prevalence of patients infected by BES mirrored the parallel and convergent genomic evolution and reduction that affected bacterial fitness. Along with infection control measures, this may have participated in the extinction of BES in the hospital setting.
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Affiliation(s)
- Marie Petitjean
- Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.,UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Paulo Juarez
- UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Alexandre Meunier
- Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France
| | - Etienne Daguindau
- UMR INSERM 1098, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Hélène Puja
- UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Xavier Bertrand
- Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.,UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Benoit Valot
- UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France.,Bioinformatique et Big Data au Service de la Santé, UFR Science de la Santé, Université de Bourgogne Franche-Comté, 25030 Besançon, France
| | - Didier Hocquet
- Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.,UMR CNRS 6249, Université de Bourgogne Franche-Comté, 25030 Besançon, France.,Bioinformatique et Big Data au Service de la Santé, UFR Science de la Santé, Université de Bourgogne Franche-Comté, 25030 Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Universitaire, 25030 Besançon, France
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11
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Kouvela A, Zaravinos A, Stamatopoulou V. Adaptor Molecules Epitranscriptome Reprograms Bacterial Pathogenicity. Int J Mol Sci 2021; 22:8409. [PMID: 34445114 PMCID: PMC8395126 DOI: 10.3390/ijms22168409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 11/16/2022] Open
Abstract
The strong decoration of tRNAs with post-transcriptional modifications provides an unprecedented adaptability of this class of non-coding RNAs leading to the regulation of bacterial growth and pathogenicity. Accumulating data indicate that tRNA post-transcriptional modifications possess a central role in both the formation of bacterial cell wall and the modulation of transcription and translation fidelity, but also in the expression of virulence factors. Evolutionary conserved modifications in tRNA nucleosides ensure the proper folding and stability redounding to a totally functional molecule. However, environmental factors including stress conditions can cause various alterations in tRNA modifications, disturbing the pathogen homeostasis. Post-transcriptional modifications adjacent to the anticodon stem-loop, for instance, have been tightly linked to bacterial infectivity. Currently, advances in high throughput methodologies have facilitated the identification and functional investigation of such tRNA modifications offering a broader pool of putative alternative molecular targets and therapeutic avenues against bacterial infections. Herein, we focus on tRNA epitranscriptome shaping regarding modifications with a key role in bacterial infectivity including opportunistic pathogens of the human microbiome.
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Affiliation(s)
- Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece;
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
- Cancer Genetics, Genomics and Systems Biology Group, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
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12
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Pseudomonas aeruginosa Consumption of Airway Metabolites Promotes Lung Infection. Pathogens 2021; 10:pathogens10080957. [PMID: 34451421 PMCID: PMC8401524 DOI: 10.3390/pathogens10080957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/03/2022] Open
Abstract
Prevailing dogma indicates that the lung of cystic fibrosis (CF) individuals is infected by multiple pathogens due to the abundant accumulation of mucus, which traps most of inhaled organisms. However, this hypothesis does not explain how specific opportunists, like Pseudomonas aeruginosa, are selected in the CF lung to cause chronic disease. This strongly suggests that other factors than mucus are accrued in the human airway and might predispose to bacterial disease, especially by P. aeruginosa. In this review we discuss the role of macrophage metabolites, like succinate and itaconate, in P. aeruginosa pneumonia. We analyze how dysfunction of the CF transmembrane conductance regulator (CFTR) favors release of these metabolites into the infected airway, and how P. aeruginosa exploits these elements to induce transcriptomic and metabolic changes that increase its capacity to cause intractable disease. We describe the host and pathogen pathways associated with succinate and itaconate catabolism, mechanisms of bacterial adaptation to these determinants, and suggest how both experimental settings and future therapies should consider macrophage metabolites abundance to better study P. aeruginosa pathogenesis.
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13
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Talagrand-Reboul E, Colston SM, Graf J, Lamy B, Jumas-Bilak E. Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas. Genome Biol Evol 2021; 12:535-552. [PMID: 32196086 PMCID: PMC7250499 DOI: 10.1093/gbe/evaa055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Aeromonads are ubiquitous aquatic bacteria that cause opportunistic infections in humans, but their pathogenesis remains poorly understood. A pathogenomic approach was undertaken to provide insights into the emergence and evolution of pathogenic traits in aeromonads. The genomes of 64 Aeromonas strains representative of the whole genus were analyzed to study the distribution, phylogeny, and synteny of the flanking sequences of 13 virulence-associated genes. The reconstructed evolutionary histories varied markedly depending on the gene analyzed and ranged from vertical evolution, which followed the core genome evolution (alt and colAh), to complex evolution, involving gene loss by insertion sequence-driven gene disruption, horizontal gene transfer, and paraphyly with some virulence genes associated with a phylogroup (aer, ser, and type 3 secretion system components) or no phylogroup (type 3 secretion system effectors, Ast, ExoA, and RtxA toxins). The general pathogenomic overview of aeromonads showed great complexity with diverse evolution modes and gene organization and uneven distribution of virulence genes in the genus; the results provided insights into aeromonad pathoadaptation or the ability of members of this group to emerge as pathogens. Finally, these findings suggest that aeromonad virulence-associated genes should be examined at the population level and that studies performed on type or model strains at the species level cannot be generalized to the whole species.
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Affiliation(s)
- Emilie Talagrand-Reboul
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Laboratoire de Bactériologie, Hôpitaux universitaires de Strasbourg, France
| | - Sophie M Colston
- US Naval Research Laboratory, National Academy of Sciences, National Research Council, Washington, District of Columbia
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut
| | - Brigitte Lamy
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Département de Bactériologie, CHU de Nice and Université Côte d'Azur, INSERM, C3M, Nice, France
| | - Estelle Jumas-Bilak
- Équipe Pathogènes Hydriques Santé Environnements, UMR 5569 HSM, University of Montpellier, France.,Département d'Hygiène Hospitalière, CHRU de Montpellier, France
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14
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Menetrey Q, Sorlin P, Jumas-Bilak E, Chiron R, Dupont C, Marchandin H. Achromobacter xylosoxidans and Stenotrophomonas maltophilia: Emerging Pathogens Well-Armed for Life in the Cystic Fibrosis Patients' Lung. Genes (Basel) 2021; 12:610. [PMID: 33919046 PMCID: PMC8142972 DOI: 10.3390/genes12050610] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
In patients with cystic fibrosis (CF), the lung is a remarkable ecological niche in which the microbiome is subjected to important selective pressures. An inexorable colonization by bacteria of both endogenous and environmental origin is observed in most patients, leading to a vicious cycle of infection-inflammation. In this context, long-term colonization together with competitive interactions among bacteria can lead to over-inflammation. While Pseudomonas aeruginosa and Staphylococcus aureus, the two pathogens most frequently identified in CF, have been largely studied for adaptation to the CF lung, in the last few years, there has been a growing interest in emerging pathogens of environmental origin, namely Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The aim of this review is to gather all the current knowledge on the major pathophysiological traits, their supporting mechanisms, regulation and evolutionary modifications involved in colonization, virulence, and competitive interactions with other members of the lung microbiota for these emerging pathogens, with all these mechanisms being major drivers of persistence in the CF lung. Currently available research on A. xylosoxidans complex and S. maltophilia shows that these emerging pathogens share important pathophysiological features with well-known CF pathogens, making them important members of the complex bacterial community living in the CF lung.
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Affiliation(s)
- Quentin Menetrey
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Pauline Sorlin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, 34093 Montpellier, France; (Q.M.); (P.S.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Raphaël Chiron
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Chloé Dupont
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Department d’Hygiène Hospitalière, CHU Montpellier, 34093 Montpellier, France; (E.J.-B.); (C.D.)
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France
- UMR 5151 HydroSciences Montpellier, Equipe Pathogènes Hydriques Santé Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université de Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
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15
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Proteomic profiling of clinical and environmental strains of Pseudomonas aeruginosa. Mol Biol Rep 2021; 48:2325-2333. [PMID: 33728559 DOI: 10.1007/s11033-021-06262-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
Pseudomonas aeruginosa is a ubiquitous bacterium, which is able to change its physiological characteristics in response to different habitats. Environmental strains are presumably less pathogenic than clinical strains and whether or not the clinical strains originate from the environment or through inter-host transmission remains poorly understood. To minimize the risk of infection, a better understanding of proteomic profiling of P. aeruginosa is necessary for elucidating the correlation between environmental and clinical strains. Based on antimicrobial susceptibility and patterns of virulence, we selected 12 clinical and environmental strains: (i) environmental, (ii) multidrug resistant (MDR) clinical and (iii) susceptible clinical strains. Whole-cell protein was extracted from each strain and subjected to two-dimensional differential gel electrophoresis (2-D DIGE) and liquid chromatography tandem mass spectrometry quadrupole time-of-flight (LC-MS QTOF). All 12 strains were clustered into 3 distinct groups based on their variance in protein expression. A total of 526 matched spots were detected and four differentially expressed protein spots (p < 0.05) were identified and all differential spots were downregulated in MDR strain J3. Upregulation of chitin binding and BON domain proteins was present in the environmental and some MDR strains, whereas the clinical strains exhibited distinct proteomic profiles with increased expression of serine protein kinase and arginine/ornithine transport ATP-binding proteins. Significant difference in expression was observed between susceptible clinical and MDR strains, as well as susceptible clinical and environmental strains. Transition from an environmental saprophyte to a clinical strain could alter its physiological characteristics to further increase its adaptation.
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16
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Ouahrani-Bettache S, Jiménez De Bagüés MP, De La Garza J, Freddi L, Bueso JP, Lyonnais S, Al Dahouk S, De Biase D, Köhler S, Occhialini A. Lethality of Brucella microti in a murine model of infection depends on the wbkE gene involved in O-polysaccharide synthesis. Virulence 2020; 10:868-878. [PMID: 31635539 PMCID: PMC6844557 DOI: 10.1080/21505594.2019.1682762] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Brucella microti was isolated a decade ago from wildlife and soil in Europe. Compared to the classical Brucella species, it exhibits atypical virulence properties such as increased growth in human and murine macrophages and lethality in experimentally infected mice. A spontaneous rough (R) mutant strain, derived from the smooth reference strain CCM4915T, showed increased macrophage colonization and was non-lethal in murine infections. Whole-genome sequencing and construction of an isogenic mutant of B. microti and Brucella suis 1330 revealed that the R-phenotype was due to a deletion in a single gene, namely wbkE (BMI_I539), encoding a putative glycosyltransferase involved in lipopolysaccharide (LPS) O-polysaccharide biosynthesis. Complementation of the R-strains with the wbkE gene restored the smooth phenotype and the ability of B. microti to kill infected mice. LPS with an intact O-polysaccharide is therefore essential for lethal B. microti infections in the murine model, demonstrating its importance in pathogenesis.
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Affiliation(s)
| | - María P Jiménez De Bagüés
- Unidad de Tecnología en Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria, Instituto Agroalimentario de Aragón, Universidad de Zaragoza, Zaragoza, Spain
| | | | - Luca Freddi
- IRIM, CNRS, University Montpellier, INSERM, Montpellier, France
| | - Juan P Bueso
- Laboratorio Agroalimentario, Gobierno de Aragón, Zaragoza, Spain
| | | | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Laboratory affiliated to the Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Latina, Italy
| | - Stephan Köhler
- IRIM, CNRS, University Montpellier, INSERM, Montpellier, France
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17
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Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex. Appl Environ Microbiol 2020; 86:AEM.02919-19. [PMID: 32198168 DOI: 10.1128/aem.02919-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/02/2020] [Indexed: 01/17/2023] Open
Abstract
The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic environmental Gram-negative bacilli responsible for a variety of infections in both humans and animals. Beyond its large genetic diversity, its genetic organization in genogroups was recently confirmed through the whole-genome sequencing of human and environmental strains. As they are poorly represented in these analyses, we sequenced the whole genomes of 93 animal strains to determine their genetic background and characteristics. Combining these data with 81 newly sequenced human strains and the genomes available from RefSeq, we performed a genomic analysis that included 375 nonduplicated genomes with various origins (animal, 104; human, 226; environment, 30; unknown, 15). Phylogenetic analysis and clustering based on genome-wide average nucleotide identity confirmed and specified the genetic organization of Smc in at least 20 genogroups. Two new genogroups were identified, and two previously described groups were further divided into two subgroups each. Comparing the strains isolated from different host types and their genogroup affiliation, we observed a clear disequilibrium in certain groups. Surprisingly, some antimicrobial resistance genes, integrons, and/or clusters of attC sites lacking integron-integrase (CALIN) sequences targeting antimicrobial compounds extensively used in animals were mainly identified in animal strains. We also identified genes commonly found in animal strains coding for efflux systems. The result of a large whole-genome analysis performed by us supports the hypothesis of the putative contribution of animals as a reservoir of Stenotrophomonas maltophilia complex strains and/or resistance genes for strains in humans.IMPORTANCE Given its naturally large antimicrobial resistance profile, the Stenotrophomonas maltophilia complex (Smc) is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As it is group of environmental microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The previously reported genomic organization was incomplete, as data from animal strains were underrepresented. We added the missing piece of the puzzle with whole-genome sequencing of 93 strains of animal origin. Beyond describing the phylogenetic organization, we confirmed the genetic diversity of the Smc, which could not be estimated through routine phenotype- or matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF)-based laboratory tests. Animals strains seem to play a key role in the diversity of Smc and could act as a reservoir for mobile resistance genes. Some genogroups seem to be associated with particular hosts; the genetic support of this association and the role of the determinants/corresponding genes need to be explored.
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18
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Thöming JG, Tomasch J, Preusse M, Koska M, Grahl N, Pohl S, Willger SD, Kaever V, Müsken M, Häussler S. Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. NPJ Biofilms Microbiomes 2020; 6:2. [PMID: 31934344 PMCID: PMC6954232 DOI: 10.1038/s41522-019-0113-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/16/2019] [Indexed: 01/28/2023] Open
Abstract
Studying parallel evolution of similar traits in independent within-species lineages provides an opportunity to address evolutionary predictability of molecular changes underlying adaptation. In this study, we monitored biofilm forming capabilities, motility, and virulence phenotypes of a plethora of phylogenetically diverse clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. We also recorded biofilm-specific and planktonic transcriptional responses. We found that P. aeruginosa isolates could be stratified based on the production of distinct organismal traits. Three major biofilm phenotypes, which shared motility and virulence phenotypes, were produced repeatedly in several isolates, indicating that the phenotypes evolved via parallel or convergent evolution. Of note, while we found a restricted general response to the biofilm environment, the individual groups of biofilm phenotypes reproduced biofilm transcriptional profiles that included the expression of well-known biofilm features, such as surface adhesive structures and extracellular matrix components. Our results provide insights into distinct ways to make a biofilm and indicate that genetic adaptations can modulate multiple pathways for biofilm development that are followed by several independent clinical isolates. Uncovering core regulatory pathways that drive biofilm-associated growth and tolerance towards environmental stressors promises to give clues to host and environmental interactions and could provide useful targets for new clinical interventions.
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Affiliation(s)
- Janne G. Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michal Koska
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Nora Grahl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sarah Pohl
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sven D. Willger
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Mathias Müsken
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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19
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Sentausa E, Basso P, Berry A, Adrait A, Bellement G, Couté Y, Lory S, Elsen S, Attrée I. Insertion sequences drive the emergence of a highly adapted human pathogen. Microb Genom 2019; 6. [PMID: 30946644 PMCID: PMC7643977 DOI: 10.1099/mgen.0.000265] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas aeruginosa is a highly adaptive opportunistic pathogen that can have serious health consequences in patients with lung disorders. Taxonomic outliers of P. aeruginosa of environmental origin have recently emerged as infectious for humans. Here, we present the first genome-wide analysis of an isolate that caused fatal haemorrhagic pneumonia. In two clones, CLJ1 and CLJ3, sequentially recovered from a patient with chronic pulmonary disease, insertion of a mobile genetic element into the P. aeruginosa chromosome affected major virulence-associated phenotypes and led to increased resistance to the antibiotics used to combat the infection. Comparative genome, proteome and transcriptome analyses revealed that this ISL3-family insertion sequence disrupted the genes for flagellar components, type IV pili, O-specific antigens, translesion polymerase and enzymes producing hydrogen cyanide. Seven-fold more insertions were detected in the later isolate, CLJ3, than in CLJ1, some of which modified strain susceptibility to antibiotics by disrupting the genes for the outer-membrane porin OprD and the regulator of β-lactamase expression AmpD. In the Galleria mellonella larvae model, the two strains displayed different levels of virulence, with CLJ1 being highly pathogenic. This study revealed insertion sequences to be major players in enhancing the pathogenic potential of a P. aeruginosa taxonomic outlier by modulating both its virulence and its resistance to antimicrobials, and explains how this bacterium adapts from the environment to a human host.
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Affiliation(s)
- Erwin Sentausa
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Present address: Evotec ID (Lyon) SAS, Marcy l'Étoile, France
| | - Pauline Basso
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Present address: Department of Microbiology and Immunology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Alice Berry
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
| | - Annie Adrait
- Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Gwendoline Bellement
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France.,Present address: Biozentrum, University of Basel, Basel, Switzerland
| | - Yohann Couté
- Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Stephen Lory
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
| | - Ina Attrée
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
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20
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Hui N, Grönroos M, Roslund MI, Parajuli A, Vari HK, Soininen L, Laitinen OH, Sinkkonen A. Diverse Environmental Microbiota as a Tool to Augment Biodiversity in Urban Landscaping Materials. Front Microbiol 2019; 10:536. [PMID: 30967847 PMCID: PMC6438878 DOI: 10.3389/fmicb.2019.00536] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/01/2019] [Indexed: 01/16/2023] Open
Abstract
Human activities typically lead to simplified urban diversity, which in turn reduces microbial exposure and increases the risk to urban dwellers from non-communicable diseases. To overcome this, we developed a microbial inoculant from forest and agricultural materials that resembles microbiota in organic soils. Three different sand materials (sieved, safety, and sandbox) commonly used in playgrounds and other public spaces were enriched with 5% of the inoculant. Skin microbiota on fingers (identified from bacterial 16S rDNA determined using Illumina MiSeq sequencing) was compared after touching non-enriched and microbial inoculant-enriched sands. Exposure to the non-enriched materials changed the skin bacterial community composition in distinct ways. When the inoculant was added to the materials, the overall shift in community composition was larger and the differences between different sand materials almost disappeared. Inoculant-enriched sand materials increased bacterial diversity and richness but did not affect evenness at the OTU level on skin. The Firmicutes/Bacteroidetes ratio was higher after touching inoculant-enriched compared to non-enriched sand materials. The relative abundance of opportunistic pathogens on skin was 40–50% before touching sand materials, but dropped to 14 and 4% after touching standard and inoculant-enriched sand materials, respectively. When individual genera were analyzed, Pseudomonas sp. and Sphingomonas sp. were more abundant after touching standard, non-enriched sand materials, while only the relative abundance of Chryseobacterium sp. increased after touching the inoculant-enriched materials. As Chryseobacterium is harmless for healthy persons, and as standard landscaping materials and normal skin contain genera that include severe pathogens, the inoculant-enriched materials can be considered safe. Microbial inoculants could be specifically created to increase the proportion of non-pathogenic bacterial taxa and minimize the transfer of pathogenic taxa. We recommend further study into the usability of inoculant-enriched materials and their effects on the bacterial community composition of human skin and on the immune response.
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Affiliation(s)
- Nan Hui
- Nature-Based Solutions Research Group, Ecology and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Mira Grönroos
- Nature-Based Solutions Research Group, Ecology and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Marja I Roslund
- Nature-Based Solutions Research Group, Ecology and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Anirudra Parajuli
- Nature-Based Solutions Research Group, Ecology and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Heli K Vari
- Nature-Based Solutions Research Group, Ecology and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Laura Soininen
- Nature-Based Solutions Research Group, Ecology and Environment Research Programme, University of Helsinki, Lahti, Finland
| | - Olli H Laitinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Aki Sinkkonen
- Nature-Based Solutions Research Group, Ecology and Environment Research Programme, University of Helsinki, Lahti, Finland
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21
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Genome-Guided Characterization of Ochrobactrum sp. POC9 Enhancing Sewage Sludge Utilization-Biotechnological Potential and Biosafety Considerations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15071501. [PMID: 30013002 PMCID: PMC6069005 DOI: 10.3390/ijerph15071501] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/07/2018] [Accepted: 07/12/2018] [Indexed: 11/17/2022]
Abstract
Sewage sludge is an abundant source of microorganisms that are metabolically active against numerous contaminants, and thus possibly useful in environmental biotechnologies. However, amongst the sewage sludge isolates, pathogenic bacteria can potentially be found, and such isolates should therefore be carefully tested before their application. A novel bacterial strain, Ochrobactrum sp. POC9, was isolated from a sewage sludge sample collected from a wastewater treatment plant. The strain exhibited lipolytic, proteolytic, cellulolytic, and amylolytic activities, which supports its application in biodegradation of complex organic compounds. We demonstrated that bioaugmentation with this strain substantially improved the overall biogas production and methane content during anaerobic digestion of sewage sludge. The POC9 genome content analysis provided a deeper insight into the biotechnological potential of this bacterium and revealed that it is a metalotolerant and a biofilm-producing strain capable of utilizing various toxic compounds. The strain is resistant to rifampicin, chloramphenicol and β-lactams. The corresponding antibiotic resistance genes (including blaOCH and cmlA/floR) were identified in the POC9 genome. Nevertheless, as only few genes in the POC9 genome might be linked to pathogenicity, and none of those genes is a critical virulence factor found in severe pathogens, the strain appears safe for application in environmental biotechnologies.
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Jayol A, Corlouer C, Haenni M, Darty M, Maillard K, Desroches M, Lamy B, Jumas-Bilak E, Madec JY, Decousser JW. Are animals a source of Stenotrophomonas maltophilia in human infections? Contributions of a nationwide molecular study. Eur J Clin Microbiol Infect Dis 2018; 37:1039-1045. [PMID: 29488120 DOI: 10.1007/s10096-018-3203-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/26/2018] [Indexed: 01/25/2023]
Abstract
Stenotrophomonas maltophilia (Sm) is an archetypal environmental opportunistic bacterium responsible for health care-associated infections. The role of animals in human Sm infections is unknown. This study aims to reveal the genetic and phylogenetic relationships between pathogenic strains of Sm, both animal and human, and identify a putative role for animals as a reservoir in human infection. We phenotypically and genotypically characterized 61 Sm strains responsible for animal infections (mainly respiratory tract infections in horses) from a French nationwide veterinary laboratory network. We tested antimicrobial susceptibility and performed MLST and genogrouping using the concatenation of the seven housekeeping genes from the original MLST scheme. Excluding the eight untypeable strains owing to the lack of gene amplification, only 10 out of the 53 strains yielded a known ST (ST5, ST39, ST162, ST8, ST27, ST126, ST131). The genogroup distribution highlighted not only genogroups (genogroups 5 and 9) comprised exclusively of animal strains but also genogroups shared by human and animal strains. Interestingly, these shared genogroups were primarily groups 2 and 6, which have previously been identified as the two most frequent genogroups among human-pathogenic Sm strains, especially among respiratory pathogens. The antimicrobial susceptibility testing underlined the presence of acquired resistance: 18.8 and 7.5% of the tested isolates were resistant to the sulfonamide-trimethoprim combination and ciprofloxacin, respectively. Animal strains of Sm shared phylogenetic traits with some of the most successful human strains. The exact relationships between the human and animal strains, and the genetic support of these common traits, need to be determined.
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Affiliation(s)
- Aurélie Jayol
- Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, 94000, Créteil, France
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- INSERM European Unit (LEA-IAME Paris, France), University of Fribourg, Fribourg, Switzerland
| | - Camille Corlouer
- Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, 94000, Créteil, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES, Lyon, France
| | - Mélanie Darty
- Next Generation Sequencing Platform, University Hospital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
| | | | - Marine Desroches
- Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, 94000, Créteil, France
| | - Brigitte Lamy
- Department of Bacteriology, Archet 2 Hospital, Nice Academic Hospital, Nice, France
- INSERM U1065, C3M, Team 6, Nice, France
| | - Estelle Jumas-Bilak
- Infection Control Department, Montpellier University Hospital, Montpellier, France
- UMR5569 HydroSciences Montpellier, Equipe «Pathogènes Hydriques Santé Environnements», Faculté de Pharmacie, 15 Avenue Charles Flahault BP 14491 34093 Montpellier UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES, Lyon, France
| | - Jean-Winoc Decousser
- Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, University Hospital Henri Mondor, 94000, Créteil, France.
- EA 7380 Dynamyc Université Paris-Est Créteil (UPEC), Ecole nationale vétérinaire d'Alfort (EnvA), Faculté de Médecine de Créteil, 8 rue du Général Sarrail, 94010, Créteil, France.
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Taylor-Mulneix DL, Hamidou Soumana I, Linz B, Harvill ET. Evolution of Bordetellae from Environmental Microbes to Human Respiratory Pathogens: Amoebae as a Missing Link. Front Cell Infect Microbiol 2017; 7:510. [PMID: 29322035 PMCID: PMC5732149 DOI: 10.3389/fcimb.2017.00510] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/27/2017] [Indexed: 12/16/2022] Open
Abstract
The genus Bordetella comprises several bacterial species that colonize the respiratory tract of mammals. It includes B. pertussis, a human-restricted pathogen that is the causative agent of Whooping Cough. In contrast, the closely related species B. bronchiseptica colonizes a broad range of animals as well as immunocompromised humans. Recent metagenomic studies have identified known and novel bordetellae isolated from different environmental sources, providing a new perspective on their natural history. Using phylogenetic analysis, we have shown that human and animal pathogenic bordetellae have most likely evolved from ancestors that originated from soil and water. Our recent study found that B. bronchiseptica can evade amoebic predation and utilize Dictyostelium discoideum as an expansion and transmission vector, which suggests that the evolutionary pressure to evade the amoebic predator enabled the rise of bordetellae as respiratory pathogens. Interactions with amoeba may represent the starting point for bacterial adaptation to eukaryotic cells. However, as bacteria evolve and adapt to a novel host, they can become specialized and restricted to a specific host. B. pertussis is known to colonize and cause infection only in humans, and this specialization to a closed human-to-human lifecycle has involved genome reduction and the loss of ability to utilize amoeba as an environmental reservoir. The discoveries from studying the interaction of Bordetella species with amoeba will elicit a better understanding of the evolutionary history of these and other important human pathogens.
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Affiliation(s)
- Dawn L Taylor-Mulneix
- Department of Infectious Diseases, Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Illiassou Hamidou Soumana
- Department of Infectious Diseases, Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Bodo Linz
- Department of Infectious Diseases, Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Eric T Harvill
- Department of Infectious Diseases, Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Retief L, Bennett NC, Jarvis JUM, Bastos ADS. Subterranean Mammals: Reservoirs of Infection or Overlooked Sentinels of Anthropogenic Environmental Soiling? ECOHEALTH 2017; 14:662-674. [PMID: 29094221 DOI: 10.1007/s10393-017-1281-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 07/16/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
Global reports of emergent pathogens in humans have intensified efforts to identify wildlife reservoirs. Subterranean mammals, such as bathyergid mole rats, are largely overlooked, despite their high-level exposure to soil-dwelling microbes. Initial assessment of bathyergid reservoir potential was determined using a broad-range 16S rRNA PCR approach, which revealed an 83% PCR-positivity for the 234 bathyergid lung samples evaluated. The presence of the Bacillus cereus complex, a ubiquitous bacterial assemblage, containing pathogenic and zoonotic species, was confirmed through nucleotide sequencing, prior to group- and species-specific PCR sequencing. The latter allowed for enhanced placement and prevalence estimations of Bacillus in four bathyergid species sampled across a range of transformed landscapes in the Western Cape Province, South Africa. Two novel Bacillus strains (1 and 2) identified on the basis of the concatenated 16S rRNA-groEL-yeaC data set (2066 nucleotides in length), clustered with B. mycoides (ATCC 6462) and B. weihenstephanensis (WSBC 10204), within a well-supported monophyletic lineage. The levels of co-infection, evaluated with a groEL strain-specific assay, developed specifically for this purpose, were high (71%). The overall Bacillus presence of 17.95% (ranging from 0% for Georychus capensis to 45.35% for Bathyergus suillus) differed significantly between host species (χ2 = 69.643; df = 3; P < 0.05), being significantly higher in bathyergids sampled near an urban informal settlement (χ2 = 70.245; df = 3; P < 0.05). The results highlight the sentinel potential of soil-dwelling mammals for monitoring anthropogenically introduced, opportunistic pathogens and the threats they pose to vulnerable communities, particularly in the developing world.
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Affiliation(s)
- Liezl Retief
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Private Bag 20, Hatfield, 0028, South Africa
| | - Nigel C Bennett
- South African Research Chair of Mammal Behavioural Ecology and Physiology, Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Hatfield, 0028, South Africa
| | - Jennifer U M Jarvis
- Department of Zoology, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Armanda D S Bastos
- Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Private Bag 20, Hatfield, 0028, South Africa.
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25
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Auta HS, Emenike CU, Fauziah SH. Screening of Bacillus strains isolated from mangrove ecosystems in Peninsular Malaysia for microplastic degradation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1552-1559. [PMID: 28964604 DOI: 10.1016/j.envpol.2017.09.043] [Citation(s) in RCA: 234] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 09/13/2017] [Accepted: 09/13/2017] [Indexed: 05/06/2023]
Abstract
The continuous accumulation of microplastics in the environment poses ecological threats and has been an increasing problem worldwide. In this study, eight bacterial strains were isolated from mangrove sediment in Peninsular Malaysia to mitigate the environmental impact of microplastics and develop a clean-up option. The bacterial isolates were screened for their potential to degrade UV-treated microplastics from polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), and polystyrene (PS). Only two isolates, namely, Bacillus cereus and Bacillus gottheilii, grew on a synthetic medium containing different microplastic polymers as the sole carbon source. A shake flask experiment was carried out to further evaluate the biodegradability potential of the isolates. Degradation was monitored by recording the weight loss of microplastics and the growth pattern of the isolates in the mineral medium. The biodegradation extent was validated by assessment of the morphological and structural changes through scanning electron microscopy and Fourier transform infrared spectroscopy analyses. The calculated weight loss percentages of the microplastic particles by B. cereus after 40 days were 1.6%, 6.6%, and 7.4% for PE, PET, and PS, respectively. B. gottheilii recorded weight loss percentages of 6.2%, 3.0%, 3.6%, and 5.8% for PE, PET, PP, and PS, respectively. The designated isolates degraded the microplastic material and exhibited potential for remediation of microplastic-contaminated environment. Biodegradation tests must be conducted to characterize the varied responses of microbes toward pollutants, such as microplastics. Hence, a novel approach for biodegradation of microplastics must be developed to help mitigate the environmental impact of plastics and microplastic polymers.
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Affiliation(s)
- H S Auta
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; Department of Microbiology, Federal University of Technology, Minna, Nigeria.
| | - C U Emenike
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; Centre for Research in Waste Management, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
| | - S H Fauziah
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia; Centre for Research in Waste Management, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
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26
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Abdouchakour F, Aujoulat F, Licznar-Fajardo P, Marchandin H, Toubiana M, Parer S, Lotthé A, Jumas-Bilak E. Intraclonal variations of resistance and phenotype in Pseudomonas aeruginosa epidemic high-risk clone ST308: A key to success within a hospital? Int J Med Microbiol 2017; 308:279-289. [PMID: 29276044 DOI: 10.1016/j.ijmm.2017.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/28/2017] [Accepted: 11/19/2017] [Indexed: 10/18/2022] Open
Abstract
Most multidrug-resistant (MDR) and extensively drug-resistant (XDR) P. aeruginosa strains belonged to epidemic high-risk (EHR) clones that succeeded worldwide in the context of hospital outbreaks. In order to study the intraclonal diversity in EHR P. aeruginosa, we selected clinical and environmental strains of the EHR clone ST308 that caused outbreak clusters over five years in a hospital and then persisted in the hospital environment during four additional years, causing sporadic infections. Unexpectedly, resistance phenotype was very diverse within the population, independently of the origin (environmental or human) and the period of isolation (during or after outbreaks). Most MDR/XDR strains belonged to clusters in pulsed-field gel electrophoresis (PFGE) while singleton strains instead displayed susceptible or moderately resistant phenotypes. High diversity was observed for motility and biofilm formation without correlation with the origin and the period. Resistance to biocides was not linked to epidemic success or to environmental persistence. Finally, the EHR clone ST308 did not display common adaptive traits, nor traits related to an origin or a period of isolation in the hospital. The major character of this EHR clone ST308 is its intraclonal diversity that probably warrants its adaptation and persistence in hospital whatever the conditions and therefore its epidemic behaviour. This diversity could result from adaptive radiation with the evolution of multiple lineages that fill available niches within a complex ecosystem such as a hospital.
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Affiliation(s)
- F Abdouchakour
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - F Aujoulat
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - P Licznar-Fajardo
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Département d'Hygiène Hospitalière, CHRU Montpellier, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34090 Montpellier, France
| | - H Marchandin
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Department of Microbiology, Nîmes University Hospital, Place du Professeur Robert Debré, 30029 Nîmes, France
| | - M Toubiana
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France
| | - S Parer
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Département d'Hygiène Hospitalière, CHRU Montpellier, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34090 Montpellier, France
| | - A Lotthé
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Département d'Hygiène Hospitalière, CHRU Montpellier, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34090 Montpellier, France
| | - E Jumas-Bilak
- Université de Montpellier, UMR 5569 HydroSciences, équipe Pathogènes Hydriques Santé Environnements, 15, Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 5, France; Département d'Hygiène Hospitalière, CHRU Montpellier, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34090 Montpellier, France.
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27
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Freddi L, Damiano MA, Chaloin L, Pennacchietti E, Al Dahouk S, Köhler S, De Biase D, Occhialini A. The Glutaminase-Dependent System Confers Extreme Acid Resistance to New Species and Atypical Strains of Brucella. Front Microbiol 2017; 8:2236. [PMID: 29187839 PMCID: PMC5695133 DOI: 10.3389/fmicb.2017.02236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/31/2017] [Indexed: 11/28/2022] Open
Abstract
Neutralophilic bacteria have developed specific mechanisms to cope with the acid stress encountered in environments such as soil, fermented foods, and host compartments. In Escherichia coli, the glutamate decarboxylase (Gad)-dependent system is extremely efficient: it requires the concerted action of glutamate decarboxylase (GadA/GadB) and of the glutamate (Glu)/γ-aminobutyrate antiporter, GadC. Notably, this system is operative also in new strains/species of Brucella, among which Brucella microti, but not in the “classical” species, with the exception of marine mammals strains. Recently, the glutaminase-dependent system (named AR2_Q), relying on the deamination of glutamine (Gln) into Glu and on GadC activity, was described in E. coli. In Brucella genomes, a putative glutaminase (glsA)-coding gene is located downstream of the gadBC genes. We found that in B. microti these genes are expressed as a polycistronic transcript. Moreover, using a panel of Brucella genus-representative strains, we show that the AR2_Q system protects from extreme acid stress (pH ≤2.5), in the sole presence of Gln, only the Brucella species/strains predicted to have functional glsA and gadC. Indeed, mutagenesis approaches confirmed the involvement of glsA and gadC of B. microti in AR2_Q and that the acid-sensitive phenotype of B. abortus can be ascribed to a Ser248Leu substitution in GlsA, leading to loss of glutaminase activity. Furthermore, we found that the gene BMI_II339, of unknown function and downstream of the gadBC–glsA operon, positively affects Gad- and GlsA-dependent AR. Thus, we identified novel determinants that allow newly discovered and marine mammals Brucella strains to be better adapted to face hostile acidic environments. As for significance, this work may contribute to the understanding of the host preferences of Brucella species and opens the way to alternative diagnostic targets in epidemiological surveillance of brucellosis.
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Affiliation(s)
- Luca Freddi
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Maria A Damiano
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Laurent Chaloin
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Eugenia Pennacchietti
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Laboratory Affiliated to the Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Latina, Italy
| | | | - Stephan Köhler
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Laboratory Affiliated to the Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Latina, Italy
| | - Alessandra Occhialini
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
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Bragonzi A, Paroni M, Pirone L, Coladarci I, Ascenzioni F, Bevivino A. Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice. Int J Mol Sci 2017; 18:ijms18112417. [PMID: 29135920 PMCID: PMC5713385 DOI: 10.3390/ijms18112417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 01/17/2023] Open
Abstract
Burkholderia cenocepacia is an important opportunistic pathogen in cystic fibrosis (CF) patients, and has also been isolated from natural environments. In previous work, we explored the virulence and pathogenic potential of environmental B. cenocepacia strains and demonstrated that they do not differ from clinical strains in some pathogenic traits. Here, we investigated the ability of the environmental B. cenocepacia Mex1 strain, isolated from the maize rhizosphere, to persist and increase its virulence after serial passages in a mouse model of chronic infection. B. cenocepacia Mex1 strain, belonging to the recA lineage IIIA, was embedded in agar beads and challenged into the lung of C57Bl/6 mice. The mice were sacrificed after 28 days from infection and their lungs were tested for bacterial loads. Agar beads containing the pool of B. cenocepacia colonies from the four sequential passages were used to infect the mice. The environmental B. cenocepacia strain showed a low incidence of chronic infection after the first passage; after the second, third and fourth passages in mice, its ability to establish chronic infection increased significantly and progressively up to 100%. Colonial morphology analysis and genetic profiling of the Mex1-derived clones recovered after the fourth passage from infected mice revealed that they were indistinguishable from the challenged strain both at phenotypic and genetic level. By testing the virulence of single clones in the Galleria mellonella infection model, we found that two Mex1-derived clones significantly increased their pathogenicity compared to the parental Mex1 strain and behaved similarly to the clinical and epidemic B. cenocepacia LMG16656T. Our findings suggest that serial passages of the environmental B. cenocepacia Mex1 strain in mice resulted in an increased ability to determine chronic lung infection and the appearance of clonal variants with increased virulence in non-vertebrate hosts.
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Affiliation(s)
- Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Moira Paroni
- Infections and Cystic Fibrosis Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
- Department of Biosciences, University of Milan, 20133 Milan, Italy.
| | - Luisa Pirone
- Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy.
| | - Ivan Coladarci
- Biology and Biotechnology Department "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Fiorentina Ascenzioni
- Biology and Biotechnology Department "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Annamaria Bevivino
- Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy.
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Patel S, Mathivanan N, Goyal A. Bacterial adhesins, the pathogenic weapons to trick host defense arsenal. Biomed Pharmacother 2017; 93:763-771. [DOI: 10.1016/j.biopha.2017.06.102] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/23/2017] [Accepted: 06/29/2017] [Indexed: 12/18/2022] Open
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30
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Chaix G, Roger F, Berthe T, Lamy B, Jumas-Bilak E, Lafite R, Forget-Leray J, Petit F. Distinct Aeromonas Populations in Water Column and Associated with Copepods from Estuarine Environment (Seine, France). Front Microbiol 2017; 8:1259. [PMID: 28744262 PMCID: PMC5504101 DOI: 10.3389/fmicb.2017.01259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 06/23/2017] [Indexed: 11/13/2022] Open
Abstract
Aeromonas spp. are ubiquitous bacteria primarily recovered from aquatic ecosystems. They are found in fresh water as well as estuarine and marine waters, and in association with numerous autochthonous aquatic organisms in these environments. However, aeromonads are also etiologic agents of fish diseases and are now recognized as emerging pathogens in humans. The estuary is therefore a key environment, harboring autochthonous aeromonads, and aeromonads originating from humans and animals, mainly released by treated WWTP effluent or watershed run-off via tributaries. The present study compares the abundance and the diversity of Aeromonas populations. Over 2 years of monitoring (eight campaigns from February 2013 to November 2015), the occurrence of Aeromonas was investigated within the water column (water and fluid mud) and in association with copepods. Moreover, the diversity of Aeromonas populations was ascertained by analyzing gyrB and radA sequences, and the antibiotic-resistance phenotypes were determined using the disk diffusion method. This study shows, for the first time, the presence of Aeromonas spp. in water (1.1 × 102 to 1.2 ± 0.3 × 103 CFU.100 mL-1), fluid mud (2.6 ± 2.6 × 102 to 9.8 ± 0.9 × 103 CFU.g-1) and in association with living copepods (1.9 ± 0.7 × 102 to >1.1 × 104 CFU.g-1) in the Seine estuary. Moreover, the diversity study, conducted on 36 strains isolated from the water column and 47 strains isolated from copepods, indicates distinct populations within these two compartments. Strains distributed in five clusters corresponding to A. bestiarum (n = 6; 5.45%), A. encheleia (n = 1; 0.91%), A. media (n = 22; 20.0%), A. rivipollensis (n = 34; 30.91%) and A. salmonicida (n = 47; 42.73%). A. salmonicida is the most abundant species associated with Eurytemora affinis (n = 35; 74.47%). In contrast, A. salmonicida accounts for only 30.56% (n = 11) of isolates in the water column. This study shows the coexistence of distinct populations of Aeromonas in the oligohaline area of an anthropized estuary. Moreover, A. media, a putative human pathogen, present in the water column and abundant in the WWTP samples, was not detected in association with living copepods.
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Affiliation(s)
- Gautier Chaix
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie UniversitéRouen, France
| | - Frédéric Roger
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie UniversitéRouen, France
| | - Thierry Berthe
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie UniversitéRouen, France
| | - Brigitte Lamy
- CNRS 5569 HSM, Équipe Pathogènes Hydriques Santé Environnements, Université de MontpellierMontpellier, France.,Laboratoire de Bactériologie, CHU de NiceNice, France
| | - Estelle Jumas-Bilak
- CNRS 5569 HSM, Équipe Pathogènes Hydriques Santé Environnements, Université de MontpellierMontpellier, France.,Département d'Hygiène Hospitalière, CHRU de MontpellierMontpellier, France
| | - Robert Lafite
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie UniversitéRouen, France
| | | | - Fabienne Petit
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie UniversitéRouen, France.,UPMC, CNRS, EPHE, UMR 7619 METIS, Sorbonne UniversitésParis, France
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Przybyłek M, Bakar M, Mendrycka M, Kosikowska U, Malm A, Worzakowska M, Szymborski T, Kędra-Królik K. Rubber elastomeric nanocomposites with antimicrobial properties. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 76:269-277. [PMID: 28482527 DOI: 10.1016/j.msec.2017.03.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/27/2016] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
Abstract
In this paper we show an elastomeric nanocomposite that exhibits antibacterial and antifungal activity. It comprises a rubber blend matrix and a nanofiller, which is a modified bentonite clay (Nanobent® ZR2). We have developed innovative technology for the nanofiller incorporation into the rubber matrix. This new approach was successfully implemented in pilot production at the Polish chemical manufacturer Spoiwo (Spoldzielnia Pracy Chemiczno-Wytworczej 'Spoiwo', Radom, Poland). Here we reveal that addition of the functionalised bentonite affects the mechanical and thermal behaviour of elastomers. For example, by adding 1-3% of bentonite nanoparticles we strongly enhanced elongation and tensile stress at break, whereas stiffness remained unchanged. We observed improvement of the thermal properties of the nanocomposites yielded and extension of the temperature usage range (from -29 to 311°C). As a proof of concept we present the antimicrobial effect of elastomeric nanocomposites verified on a wide range of both pathogenic and opportunistic reference bacteria strains, as well as reference strains of yeasts. The proposed method of hydrophilic nanofiller introduction into the rubber elastomer is economically viable and enables fabrication of elastomeric elements with high added value. Their significant antibacterial and antifungal activity makes them desirable in medicine, biomedical engineering, and the food industry.
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Affiliation(s)
- Małgorzata Przybyłek
- Faculty of Material Science, Technology and Design, Kazimierz Pulaski University of Technology and Humanities, Chrobrego Str. 27, 26-600 Radom, Poland.
| | - Mohamed Bakar
- Faculty of Material Science, Technology and Design, Kazimierz Pulaski University of Technology and Humanities, Chrobrego Str. 27, 26-600 Radom, Poland
| | - Mariola Mendrycka
- Faculty of Health Sciences and Physical Culture, Kazimierz Pulaski University of Technology and Humanities, Chrobrego Str. 27, 26-600 Radom, Poland
| | - Urszula Kosikowska
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, W. Chodzki Str. 1, 20-093 Lublin, Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, W. Chodzki Str. 1, 20-093 Lublin, Poland
| | - Marta Worzakowska
- Department of Polymer Chemistry, Faculty of Chemistry, Maria Curie-Sklodowska University, M. Curie-Sklodowska Sq. 5, 20-031 Lublin, Poland
| | - Tomasz Szymborski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Karolina Kędra-Królik
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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Patel S. Letter to the editor on ‘The necessity of overhaul in perception of microbiological culture methods’. Microb Pathog 2017; 102:A1-A2. [DOI: 10.1016/j.micpath.2016.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 12/01/2022]
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Wong YC, Abd El Ghany M, Naeem R, Lee KW, Tan YC, Pain A, Nathan S. Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS. Front Microbiol 2016; 7:1288. [PMID: 27597847 PMCID: PMC4993015 DOI: 10.3389/fmicb.2016.01288] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/04/2016] [Indexed: 12/13/2022] Open
Abstract
Burkholderia cenocepacia infection often leads to fatal cepacia syndrome in cystic fibrosis patients. However, antibiotic therapy rarely results in complete eradication of the pathogen due to its intrinsic resistance to many clinically available antibiotics. Recent attention has turned to the identification of essential genes as the proteins encoded by these genes may serve as potential targets for development of novel antimicrobials. In this study, we utilized TraDIS (Transposon Directed Insertion-site Sequencing) as a genome-wide screening tool to facilitate the identification of B. cenocepacia genes essential for its growth and viability. A transposon mutant pool consisting of approximately 500,000 mutants was successfully constructed, with more than 400,000 unique transposon insertion sites identified by computational analysis of TraDIS datasets. The saturated library allowed for the identification of 383 genes that were predicted to be essential in B. cenocepacia. We extended the application of TraDIS to identify conditionally essential genes required for in vitro growth and revealed an additional repertoire of 439 genes to be crucial for B. cenocepacia growth under nutrient-depleted conditions. The library of B. cenocepacia mutants can subsequently be subjected to various biologically related conditions to facilitate the discovery of genes involved in niche adaptation as well as pathogenicity and virulence.
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Affiliation(s)
- Yee-Chin Wong
- Faculty of Science and Technology, School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia Bangi, Malaysia
| | - Moataz Abd El Ghany
- Chemical and Life Sciences and Engineering Division, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia; The Westmead Institute for Medical Research and The Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, SydneyNSW, Australia
| | - Raeece Naeem
- Chemical and Life Sciences and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | | | | | - Arnab Pain
- Chemical and Life Sciences and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Sheila Nathan
- Faculty of Science and Technology, School of Biosciences and Biotechnology, Universiti Kebangsaan Malaysia Bangi, Malaysia
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Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland. Genome Res 2016; 26:1101-9. [PMID: 27432456 PMCID: PMC4971767 DOI: 10.1101/gr.205245.116] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 06/13/2016] [Indexed: 01/16/2023]
Abstract
Serratia marcescens, a member of the Enterobacteriaceae family, is a Gram-negative bacterium responsible for a wide range of nosocomial infections. The emergence of multidrug-resistant strains is an increasing danger to public health. To design effective means to control the dissemination of S. marcescens, an in-depth analysis of the population structure and variation is required. Utilizing whole-genome sequencing, we characterized the population structure and variation, as well as the antimicrobial resistance determinants, of a systematic collection of antimicrobial-resistant S. marcescens associated with bloodstream infections in hospitals across the United Kingdom and Ireland between 2001 and 2011. Our results show that S. marcescens is a diverse species with a high level of genomic variation. However, the collection was largely composed of a limited number of clones that emerged from this diverse background within the past few decades. We identified potential recent transmissions of these clones, within and between hospitals, and showed that they have acquired antimicrobial resistance determinants for different beta-lactams, ciprofloxacin, and tetracyclines on multiple occasions. The expansion of these multidrug-resistant clones suggests that the treatment of S. marcescens infections will become increasingly difficult in the future.
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Syal K, Maiti K, Naresh K, Avaji PG, Chatterji D, Jayaraman N. Synthetic arabinomannan glycolipids impede mycobacterial growth, sliding motility and biofilm structure. Glycoconj J 2016; 33:763-77. [DOI: 10.1007/s10719-016-9670-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/17/2016] [Accepted: 04/26/2016] [Indexed: 11/24/2022]
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Hocquet D, Petitjean M, Rohmer L, Valot B, Kulasekara HD, Bedel E, Bertrand X, Plésiat P, Köhler T, Pantel A, Jacobs MA, Hoffman LR, Miller SI. Pyomelanin-producing Pseudomonas aeruginosa selected during chronic infections have a large chromosomal deletion which confers resistance to pyocins. Environ Microbiol 2016; 18:3482-3493. [PMID: 27119970 DOI: 10.1111/1462-2920.13336] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 12/31/2022]
Abstract
When bacterial lineages make the transition from free-living to permanent association with hosts, they can undergo massive gene losses, for which the selective forces within host tissues are unknown. We identified here melanogenic clinical isolates of Pseudomonas aeruginosa with large chromosomal deletions (66 to 270 kbp) and characterized them to investigate how they were selected. When compared with their wild-type parents, melanogenic mutants (i) exhibited a lower fitness in growth conditions found in human tissues, such as hyperosmolarity and presence of aminoglycoside antibiotics, (ii) narrowed their metabolic spectrum with a growth disadvantage with particular carbon sources, including aromatic amino acids and acyclic terpenes, suggesting a reduction of metabolic flexibility. Despite an impaired fitness in rich media, melanogenic mutants can inhibit their wild-type parents and compete with them in coculture. Surprisingly, melanogenic mutants became highly resistant to two intraspecific toxins, the S-pyocins AP41 and S1. Our results suggest that pyocins produced within a population of infecting P. aeruginosa may have selected for bacterial mutants that underwent massive gene losses and that were adapted to the life in diverse bacterial communities in the human host. Intraspecific interactions may therefore be an important factor driving the continuing evolution of pathogens during host infections.
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Affiliation(s)
- Didier Hocquet
- UMR CNRS 6249, Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France. .,Service d' Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.
| | - Marie Petitjean
- UMR CNRS 6249, Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France.,Service d' Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Laurence Rohmer
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Benoît Valot
- UMR CNRS 6249, Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France
| | | | - Elodie Bedel
- UMR CNRS 6249, Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France.,Service d' Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Xavier Bertrand
- UMR CNRS 6249, Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France.,Service d' Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Patrick Plésiat
- Service de Bactériologie, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Thilo Köhler
- Département de Génétique et de Microbiologie, Centre Médical Universitaire, Genève, Suisse
| | - Alix Pantel
- Service de Microbiologie, Centre Hospitalier Régional Universitaire, Nîmes, France.,UMR INSERM U1047, Université de Montpellier, Nîmes, France
| | - Michael A Jacobs
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Samuel I Miller
- Department of Microbiology, University of Washington, Seattle, WA, USA
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Lund-Palau H, Turnbull AR, Bush A, Bardin E, Cameron L, Soren O, Wierre-Gore N, Alton EWFW, Bundy JG, Connett G, Faust SN, Filloux A, Freemont P, Jones A, Khoo V, Morales S, Murphy R, Pabary R, Simbo A, Schelenz S, Takats Z, Webb J, Williams HD, Davies JC. Pseudomonas aeruginosa infection in cystic fibrosis: pathophysiological mechanisms and therapeutic approaches. Expert Rev Respir Med 2016; 10:685-97. [PMID: 27175979 DOI: 10.1080/17476348.2016.1177460] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pseudomonas aeruginosa is a remarkably versatile environmental bacterium with an extraordinary capacity to infect the cystic fibrosis (CF) lung. Infection with P. aeruginosa occurs early, and although eradication can be achieved following early detection, chronic infection occurs in over 60% of adults with CF. Chronic infection is associated with accelerated disease progression and increased mortality. Extensive research has revealed complex mechanisms by which P. aeruginosa adapts to and persists within the CF airway. Yet knowledge gaps remain, and prevention and treatment strategies are limited by the lack of sensitive detection methods and by a narrow armoury of antibiotics. Further developments in this field are urgently needed in order to improve morbidity and mortality in people with CF. Here, we summarize current knowledge of pathophysiological mechanisms underlying P. aeruginosa infection in CF. Established treatments are discussed, and an overview is offered of novel detection methods and therapeutic strategies in development.
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Affiliation(s)
- Helena Lund-Palau
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Andrew R Turnbull
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK.,b Department of Respiratory Paediatrics , Royal Brompton and Harefield NHS Foundation Trust , London , UK
| | - Andrew Bush
- b Department of Respiratory Paediatrics , Royal Brompton and Harefield NHS Foundation Trust , London , UK.,c National Heart and Lung Institute, Imperial College , London , UK
| | - Emmanuelle Bardin
- d Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College , London , UK
| | - Loren Cameron
- e Department of Medicine , Imperial College , London , UK
| | - Odel Soren
- f Biological Sciences, Institute for Life Sciences , University of Southampton , Southampton , UK
| | | | - Eric W F W Alton
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Jacob G Bundy
- c National Heart and Lung Institute, Imperial College , London , UK
| | - Gary Connett
- g NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust , University of Southampton , Southampton , UK
| | - Saul N Faust
- g NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust , University of Southampton , Southampton , UK
| | - Alain Filloux
- h Department of Life Sciences , Imperial College , London , UK
| | - Paul Freemont
- e Department of Medicine , Imperial College , London , UK
| | - Andy Jones
- i Department of Respiratory Medicine , Royal Brompton Hospital , London , UK
| | - Valerie Khoo
- c National Heart and Lung Institute, Imperial College , London , UK
| | | | - Ronan Murphy
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Rishi Pabary
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Ameze Simbo
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK
| | - Silke Schelenz
- k Department of Microbiology , Royal Brompton Hospital , London UK
| | - Zoltan Takats
- d Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine , Imperial College , London , UK
| | - Jeremy Webb
- k Department of Microbiology , Royal Brompton Hospital , London UK
| | - Huw D Williams
- g NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust , University of Southampton , Southampton , UK
| | - Jane C Davies
- a Department of Gene Therapy, National Heart and Lung Institute , Imperial College , London , UK.,b Department of Respiratory Paediatrics , Royal Brompton and Harefield NHS Foundation Trust , London , UK
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Guilbaud C, Morris CE, Barakat M, Ortet P, Berge O. Isolation and identification of Pseudomonas syringae facilitated by a PCR targeting the whole P. syringae group. FEMS Microbiol Ecol 2015; 92:fiv146. [PMID: 26610434 DOI: 10.1093/femsec/fiv146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2015] [Indexed: 11/13/2022] Open
Abstract
We present a reliable PCR-based method to avoid the biases related to identification based on the conventional phenotypes currently used in the identification of Pseudomonas syringae sensu lato, a ubiquitous environmental bacterium including plant pathogens. We identified a DNA target suitable for this purpose by applying a comparative genomic pipeline to Pseudomonas genomes. We designed primers and developed PCR conditions that led to a clean and strong PCR product from 97% of the 185 strains of P. syringae strains tested and gave a clear negative result for the 31 non-P. syringae strains tested. The sensitivity of standard PCR was determined with pure strains to be 10(6) bacteria mL(-1) or 0.4 ng of DNA μL(-1). Sensitivity could be improved with the touchdown method. The new PCR-assisted isolation of P. syringae was efficient when deployed on an environmental sample of river water as compared to the isolation based on phenotypes. This innovation eliminates the need for extensive expertise in isolating P. syringae colonies, was simpler, faster and very reliable. It will facilitate discovery of more diversity of P. syringae and research on emergence, dispersion and evolution to understand the varied functions of this environmental bacterium.
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Affiliation(s)
| | - Cindy E Morris
- INRA, UR0407 Pathologie Végétale, F-84143 Montfavet cedex, France
| | - Mohamed Barakat
- CEA, IBEB, Lab Ecol Microb Rhizosphere and Environ Extrem, Saint-Paul-lez-Durance, F-13108, France CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Philippe Ortet
- CEA, IBEB, Lab Ecol Microb Rhizosphere and Environ Extrem, Saint-Paul-lez-Durance, F-13108, France CNRS, UMR 7265 Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Odile Berge
- INRA, UR0407 Pathologie Végétale, F-84143 Montfavet cedex, France
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Synthetic glycolipids and (p)ppGpp analogs: development of inhibitors for mycobacterial growth, biofilm and stringent response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 842:309-27. [PMID: 25408352 DOI: 10.1007/978-3-319-11280-0_20] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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41
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Dupont C, Michon AL, Jumas-Bilak E, Nørskov-Lauritsen N, Chiron R, Marchandin H. Intrapatient diversity of Achromobacter spp. involved in chronic colonization of Cystic Fibrosis airways. INFECTION GENETICS AND EVOLUTION 2015; 32:214-23. [PMID: 25791931 DOI: 10.1016/j.meegid.2015.03.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/27/2015] [Accepted: 03/09/2015] [Indexed: 11/28/2022]
Abstract
Achromobacter spp. are increasingly identified in Cystic Fibrosis (CF) patients and their ability to persistently colonize the CF respiratory tract (CFRT) suggests that Achromobacter species possess adaptive characteristics. We studied genome dynamics in 118 isolates recovered from 13 patients with Achromobacter chronic colonization (5-26 isolates per patient recovered over 13-61 months). Isolates were identified to species level by nrdA gene sequencing, subjected to Pulsed-Field Gel Electrophoresis (PFGE) and multiplex rep-PCR (MR-PCR), and rrs intragenomic diversity was studied by PCR-Temporal Temperature Gel Electrophoresis (TTGE). Intrapatient diversity was assessed: (i) from dynamics of XbaI and/or SpeI-based pulsotypes, (ii) from comparison of MR-PCR profiles, and (iii) by longitudinal analysis of rrs intragenomic diversity. Patients were chronically colonized by Achromobacter xylosoxidans (n=10), Achromobacter dolens (n=1) or Achromobacter insuavis (n=2). All strains displayed genomic diversification over time but A. insuavis showed higher pulsotype diversity compared to other species. Intragenomic rrs heterogeneity was found in strains from 6 of 13 patients and may be persistently observed. Achromobacter genome evolution observed during chronic colonization of the CFRT warrants further investigation of the adaptation features of the different species, as well as of the selective forces driving this adaptation in the CFRT.
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Affiliation(s)
- Chloé Dupont
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Anne-Laure Michon
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Estelle Jumas-Bilak
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Saint-Eloi, Laboratoire d'Hygiène hospitalière, 80 avenue Augustin Fliche, 34295 Montpellier Cedex 5, France
| | - Niels Nørskov-Lauritsen
- Department of Clinical Microbiology, Aarhus University Hospital, Skejby, 8200 Aarhus, Denmark
| | - Raphaël Chiron
- Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Centre de Ressources et de Compétences de la Mucoviscidose, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - Hélène Marchandin
- Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France; Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France.
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Niches, population structure and genome reduction in Ochrobactrum intermedium: clues to technology-driven emergence of pathogens. PLoS One 2014; 9:e83376. [PMID: 24465379 PMCID: PMC3894950 DOI: 10.1371/journal.pone.0083376] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 11/01/2013] [Indexed: 12/21/2022] Open
Abstract
Ochrobactrum intermedium is considered as an emerging human environmental opportunistic pathogen with mild virulence. The distribution of isolates and sequences described in literature and databases showed frequent association with human beings and polluted environments. As population structures are related to bacterial lifestyles, we investigated by multi-locus approach the genetic structure of a population of 65 isolates representative of the known natural distribution of O. intermedium. The population was further surveyed for genome dynamics using pulsed-field gel electrophoresis and genomics. The population displayed a clonal epidemic structure with events of recombination that occurred mainly in clonal complexes. Concerning biogeography, clones were shared by human and environments and were both cosmopolitan and local. The main cosmopolitan clone was genetically and genomically stable, and grouped isolates that all harbored an atypical insertion in the rrs. Ubiquitism and stability of this major clone suggested a clonal succes in a particular niche. Events of genomic reduction were detected in the population and the deleted genomic content was described for one isolate. O. intermedium displayed allopatric characters associated to a tendancy of genome reduction suggesting a specialization process. Considering its relatedness with Brucella, this specialization might be a commitment toward pathogenic life-style that could be driven by technological selective pressure related medical and industrial technologies.
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Martino ME, Fasolato L, Montemurro F, Novelli E, Cardazzo B. Aeromonasspp.: ubiquitous or specialized bugs? Environ Microbiol 2013; 16:1005-18. [DOI: 10.1111/1462-2920.12215] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Maria Elena Martino
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
| | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
| | - Filomena Montemurro
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
| | - Enrico Novelli
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science; University of Padova; Legnaro 35020 Italy
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Roger F, Lamy B, Jumas-Bilak E, Kodjo A, Marchandin H. Ribosomal multi-operon diversity: an original perspective on the genus Aeromonas. PLoS One 2012; 7:e46268. [PMID: 23032081 PMCID: PMC3459834 DOI: 10.1371/journal.pone.0046268] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/28/2012] [Indexed: 12/31/2022] Open
Abstract
16S rRNA gene (rrs) is considered of low taxonomic interest in the genus Aeromonas. Here, 195 Aeromonas strains belonging to populations structured by multilocus phylogeny were studied using an original approach that considered Ribosomal Multi-Operon Diversity. This approach associated pulsed-field gel electrophoresis (PFGE) to assess rrn operon number and distribution across the chromosome and PCR-temporal temperature gel electrophoresis (TTGE) to assess rrs V3 region heterogeneity. Aeromonads harbored 8 to 11 rrn operons, 10 operons being observed in more than 92% of the strains. Intraspecific variability was low or nul except for A. salmonicida and A. aquariorum suggesting that large chromosomic rearrangements might occur in these two species while being extremely rarely encountered in the evolution of other taxa. rrn operon number at 8 as well as PFGE patterns were shown valuable for taxonomic purpose allowing resolution of species complexes. PCR-TTGE revealed a high rate of strains (41.5%) displaying intragenomic rrs heterogeneity. Strains isolated from human samples more frequently displayed intragenomic heterogeneity than strains recovered from non-human and environmental specimens. Intraspecific variability ranged from 0 to 76.5% of the strains. The observation of species-specific TTGE bands, the recovery of identical V3 regions in different species and the variability of intragenomic heterogeneity (1-13 divergent nucleotides) supported the occurrence of mutations and horizontal transfer in aeromonad rrs evolution. Altogether, the presence of a high number of rrn operon, the high proportion of strains harboring divergent rrs V3 region and the previously demonstrated high level of genetic diversity argued in favor of highly adaptative capabilities of aeromonads. Outstanding features observed for A. caviae supported the ongoing process of adaptation to a specialized niche represented by the gut, previously hypothesized. 16S rRNA gene is an informative marker in the genus Aeromonas for both evolutionary and polyphasic taxonomic studies provided that multi-operon fingerprinting approaches are used.
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Affiliation(s)
- Frédéric Roger
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
| | - Brigitte Lamy
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
- Groupe d’Etude Français des Aeromonas (GFA), Lyon, France
| | - Estelle Jumas-Bilak
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire d’Hygiène hospitalière, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
| | - Angeli Kodjo
- Groupe d’Etude Français des Aeromonas (GFA), Lyon, France
- CNRS UMR 5557 Ecologie microbienne, VetAgro Sup Campus vétérinaire de Lyon, Université Claude Bernard Lyon 1, Marcy-l’Étoile, France
| | | | - Hélène Marchandin
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
- * E-mail:
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