1
|
Cyriaque V, Ibarra-Chávez R, Kuchina A, Seelig G, Nesme J, Madsen JS. Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation. Nat Commun 2024; 15:5853. [PMID: 38997267 PMCID: PMC11245611 DOI: 10.1038/s41467-024-49793-x] [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: 03/13/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024] Open
Abstract
Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.
Collapse
Affiliation(s)
- Valentine Cyriaque
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, Mons, Belgium.
| | | | - Anna Kuchina
- Institute for Systems Biology, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School for Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | |
Collapse
|
2
|
Lin Z, Zhou Z, Shuai X, Zeng G, Bao R, Chen H. Landscape of plasmids encoding β-lactamases in disinfection residual Enterobacteriaceae from wastewater treatment plants. WATER RESEARCH 2024; 255:121549. [PMID: 38564891 DOI: 10.1016/j.watres.2024.121549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Conventional disinfection processes, such as chlorination and UV radiation, are ineffective in controling antibiotic-resistant bacteria, especially disinfection residual Enterobacteriaceae (DRE) encoding β-lactamases, some of which have been classified as "critical priority pathogens" by the World Health Organization. However, few studies have focused on the transferability, phenotype, and genetic characteristics of DRE-derived plasmids encoding β-lactamases, especially extended-spectrum β-lactamases and carbapenemases. In this study, we isolated 10 typical DRE harboring plasmid-mediated blaNDM, blaCTX-M, or blaTEM in post-disinfection effluent from two wastewater treatment plants (WWTPs), with transfer frequency ranging from 1.69 × 10-6 to 3.02 × 10-5. According to genomic maps of plasmids, all blaNDM and blaTEM were cascaded with IS26, and blaCTX-M was adjacent to ISEcp1 or IS26, indicating the important role of these elements in the movement of β-lactamase-encoding genes. The presence of intact class 1 integrons on pWTPN-01 and pWTPC-03 suggested the ability of these DRE-derived plasmids to integrate other exogenous antibiotic resistance genes (ARGs). The coexistence of antibiotic, disinfectant, and heavy metal resistance genes on the same plasmid (e.g., pWTPT-03) implied the facilitating role of disinfectants and heavy metals in the transmission of DRE-derived ARGs. Notably, two plasmid transconjugants exhibited no discernible competitive fitness cost, suggesting a heightened environmental persistence. Furthermore, enhanced virulence induced by β-lactamase-encoding plasmids in their hosts was confirmed using Galleria mellonella infection models, which might be attributed to plasmid-mediated virulence genes. Overall, this study describes the landscape of β-lactamase-encoding plasmids in DRE, and highlights the urgent need for advanced control of DRE to keep environmental and ecological security.
Collapse
Affiliation(s)
- Zejun Lin
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhenchao Zhou
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinyi Shuai
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Guangshu Zeng
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ruiqi Bao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hong Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou 310058, China; International Cooperation Base of Environmental Pollution and Ecological Health, Science and Technology Agency of Zhejiang, Zhejiang University, China.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Abstract
Biological rapid sand filtration is a commonly employed method for the removal of organic and inorganic impurities in water which relies on the degradative properties of microorganisms for the removal of diverse contaminants, but their bioremediation capabilities vary greatly across waterworks. Bioaugmentation efforts with degradation-proficient bacteria have proven difficult due to the inability of the exogenous microbes to stably colonize the sand filters. Plasmids are extrachromosomal DNA elements that can often transfer between bacteria and facilitate the flow of genetic information across microbiomes, yet their ability to spread within rapid sand filters has remained unknown. Here, we examine the permissiveness of rapid sand filter communities toward four environmentally transmissible plasmids, RP4, RSF1010, pKJK5, and TOL (pWWO), using a dual-fluorescence bioreporter platform combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results reveal that plasmids can transfer at high frequencies and across distantly related taxa from rapid sand filter communities, emphasizing their potential suitability for introducing bioremediation determinants in the microbiomes of underperforming water purification plants.
Collapse
|
5
|
Cyriaque V, Madsen JS, Fievez L, Leroy B, Hansen LH, Bureau F, Sørensen SJ, Wattiez R. Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community. Front Microbiol 2021; 12:655903. [PMID: 34122370 PMCID: PMC8195591 DOI: 10.3389/fmicb.2021.655903] [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] [Received: 01/19/2021] [Accepted: 04/06/2021] [Indexed: 01/01/2023] Open
Abstract
Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a Pseudomonas putida KT2440 plasmid donor and two distinct recipients, Variovorax paradoxus B4 or Delftia acidovorans SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance pbrTRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For V. paradoxus, the pbr operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the pbr operon to D. acidovorans SPH-1 and P. putida KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to D. acidovorans SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-gfp. Conversely, the pbr operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the pbr carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.
Collapse
Affiliation(s)
- Valentine Cyriaque
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium.,Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laurence Fievez
- Cellular and Molecular Immunology Service, GIGA Research, University of Liège (ULG), Liège, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Lars H Hansen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fabrice Bureau
- Cellular and Molecular Immunology Service, GIGA Research, University of Liège (ULG), Liège, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| |
Collapse
|
6
|
Cyriaque V, Géron A, Billon G, Nesme J, Werner J, Gillan DC, Sørensen SJ, Wattiez R. Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. FEMS Microbiol Ecol 2020; 96:5826176. [PMID: 32343356 DOI: 10.1093/femsec/fiaa076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.
Collapse
Affiliation(s)
- Valentine Cyriaque
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Augustin Géron
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium.,Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling,FK9 4LA, UK
| | - Gabriel Billon
- Univ. Lille, CNRS, UMR 8516 - LASIRE - LAboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, F-59000 Lille, France
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, D-18119 Rostock, Germany
| | - David C Gillan
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ruddy Wattiez
- Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium
| |
Collapse
|
7
|
Piotrowska M, Dziewit L, Ostrowski R, Chmielowska C, Popowska M. Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland). Antibiotics (Basel) 2020; 9:antibiotics9090613. [PMID: 32957637 PMCID: PMC7557826 DOI: 10.3390/antibiotics9090613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
Abstract
As small, mobilizable replicons with a broad host range, IncQ plasmids are widely distributed among clinical and environmental bacteria. They carry antibiotic resistance genes, and it has been shown that they confer resistance to β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, sulphonamides, and tetracycline. The previously proposed classification system divides the plasmid group into four subgroups, i.e., IncQ-1, IncQ-2, IncQ-3, and IncQ-4. The last two subgroups have been poorly described so far. The aim of this study was to analyze five newly identified IncQ-3 plasmids isolated from a wastewater treatment plant in Poland and to compare them with all known plasmids belonging to the IncQ-3 subgroup whose sequences were retrieved from the NCBI database. The complete nucleotide sequences of the novel plasmids were annotated and bioinformatic analyses were performed, including identification of core genes and auxiliary genetic load. Furthermore, functional experiments testing plasmid mobility were carried out. Phylogenetic analysis based on three core genes (repA, mobA/repB, and mobC) revealed the presence of three main clusters of IncQ-3 replicons. Apart from having a highly conserved core, the analyzed IncQ-3 plasmids were vectors of antibiotic resistance genes, including (I) the qnrS2 gene that encodes fluoroquinolone resistance and (II) β-lactam, trimethoprim, and aminoglycoside resistance genes within integron cassettes.
Collapse
Affiliation(s)
- Marta Piotrowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Rafał Ostrowski
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Cora Chmielowska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| |
Collapse
|