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Allegrini M, Iocoli GA, Zabaloy MC. Combined use of digestate and inorganic fertilizer alleviates the burden of class 1 integrons in perennial ryegrass rhizosphere without compromising aerial biomass production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34279-6. [PMID: 38985425 DOI: 10.1007/s11356-024-34279-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
Antimicrobial resistance (AMR) is one of the main global health challenges. Anaerobic digestion (AD) can significantly reduce the burden of antibiotic resistance genes (ARGs) in animal manures. However, the reduction is often incomplete. The agronomic use of digestates requires assessments of their effects on soil ARGs. The objective of this study was to assess the effect of digestate on the abundance of ARGs and mobile genetic elements (MGEs) in the rhizosphere of ryegrass (Lolium perenne L.) and to determine whether half-dose replacement of digestate with urea (combined fertilizer) can be implemented as a safer approach while maintaining a similar biomass production. A greenhouse assay was conducted during 190 days under a completely randomized design with two experimental factors: fertilizer type (unfertilized control and fertilized treatments with equal N dose: digestate, urea and combined fertilizer) and sampling date (16 and 148 days after the last application). The results indicated that the digestate significantly increased the abundance of clinical class 1 integrons (intI1 gene) relative to the unfertilized control at both sampling dates (P < 0.05), while the combined fertilizer only increased them at the first sampling. Sixteen days after completing the fertilization scheme only the combined fertilizer and urea significantly increased the biomass production relative to the control (P < 0.05). Additionally, by the end of the assay, the combined fertilizer showed significantly lower levels of the macrolide-resistance gene ermB than digestate and a cumulative biomass similar to urea or digestate. Overall, the combined fertilizer can alleviate the burden of integrons and ermB while simultaneously improving biomass production.
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Affiliation(s)
- Marco Allegrini
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), Universidad Nacional de Rosario (UNR)-CONICET, Zavalla, Argentina
| | - Gastón Alejandro Iocoli
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - María Celina Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina.
- Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina.
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2
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Yang QE, Ma X, Zeng L, Wang Q, Li M, Teng L, He M, Liu C, Zhao M, Wang M, Hui D, Madsen JS, Liao H, Walsh TR, Zhou S. Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study. THE LANCET. MICROBE 2024; 5:e13-e23. [PMID: 38006896 DOI: 10.1016/s2666-5247(23)00227-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-β-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context. METHODS For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli. FINDINGS We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids. INTERPRETATION Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors. FUNDING The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.
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Affiliation(s)
- Qiu E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodan Ma
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingshuang Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinqin Wang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Minchun Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Teng
- Department of Veterinary Medicine, College of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Mingzhen He
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengshi Zhao
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengzhu Wang
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deng Hui
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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3
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Castañeda-Barba S, Top EM, Stalder T. Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era. Nat Rev Microbiol 2024; 22:18-32. [PMID: 37430173 DOI: 10.1038/s41579-023-00926-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/12/2023]
Abstract
Antimicrobial resistance (AMR) poses a substantial threat to human health. The widespread prevalence of AMR is, in part, due to the horizontal transfer of antibiotic resistance genes (ARGs), typically mediated by plasmids. Many of the plasmid-mediated resistance genes in pathogens originate from environmental, animal or human habitats. Despite evidence that plasmids mobilize ARGs between these habitats, we have a limited understanding of the ecological and evolutionary trajectories that facilitate the emergence of multidrug resistance (MDR) plasmids in clinical pathogens. One Health, a holistic framework, enables exploration of these knowledge gaps. In this Review, we provide an overview of how plasmids drive local and global AMR spread and link different habitats. We explore some of the emerging studies integrating an eco-evolutionary perspective, opening up a discussion about the factors that affect the ecology and evolution of plasmids in complex microbial communities. Specifically, we discuss how the emergence and persistence of MDR plasmids can be affected by varying selective conditions, spatial structure, environmental heterogeneity, temporal variation and coexistence with other members of the microbiome. These factors, along with others yet to be investigated, collectively determine the emergence and transfer of plasmid-mediated AMR within and between habitats at the local and global scale.
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Affiliation(s)
- Salvador Castañeda-Barba
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA.
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Sheng H, Wu S, Xue Y, Zhao W, Caplan AB, Hovde CJ, Minnich SA. Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance. PLoS One 2023; 18:e0291520. [PMID: 37699034 PMCID: PMC10497133 DOI: 10.1371/journal.pone.0291520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Pathogenic Escherichia coli and Salmonella enterica pose serious public health threats due to their ability to cause severe gastroenteritis and life-threatening sequela, particularly in young children. Moreover, the emergence and dissemination of antibiotic resistance in these bacteria have complicated control of infections. Alternative strategies that effectively target these enteric pathogens and negate or reduce the need of antibiotics are urgently needed. Such an alternative is the CRISPR-Cas9 system because it can generate sequence-specific lethal double stranded DNA breaks. In this study, two self-transmissible broad host range conjugative plasmids, pRK24 and pBP136, were engineered to deliver multiplexed CRSIPR-Cas9 systems that specifically target Enterohemorrhagic and Enteropathogenic strains of E. coli (EHEC and EPEC), S. enterica, and blaCMY-2 antibiotic resistance plasmids. Using in vitro mating assays, we show that the conjugative delivery of pRK24-CRISPR-Cas9 carrying guide RNAs to the EPEC/EHEC eae (intimin) gene can selectively kill enterohemorrhagic E. coli O157 eae+ cells (3 log kill at 6 h) but does not kill the isogenic Δeae mutant (P<0.001). Similar results were also obtained with a pBP136 derivative, pTF16, carrying multiplexed guide RNAs targeting E. coli eae and the S. enterica ssaN gene coding for the type III secretion ATPase. Another pBP136 derivative, TF18, carries guide RNAs targeting S. enterica ssaN and the antibiotic resistance gene, blaCMY-2, carried on the multi-drug resistant pAR06302. Introduction of pTF18 into bacteria harboring pAR06302 showed plasmids were cured at an efficiency of 53% (P<0.05). Using a murine neonate EPEC infection model, pTF16 was delivered by a murine derived E. coli strain to EPEC infected mice and showed significant reductions of intestinal EPEC (P<0.05). These results suggest that establishing conjugative CRISPR-Cas9 antimicrobials in the intestinal microbiome may provide protection from enteric pathogens and reduce antibiotic resistance without disrupting the normal microbiota.
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Affiliation(s)
- Haiqing Sheng
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah Wu
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Yansong Xue
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Wei Zhao
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Allan B. Caplan
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Carolyn J. Hovde
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Scott A. Minnich
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
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5
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Li L, Liu Y, Xiao Q, Xiao Z, Meng D, Yang Z, Deng W, Yin H, Liu Z. Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota. Front Microbiol 2023; 14:1173748. [PMID: 37485539 PMCID: PMC10361621 DOI: 10.3389/fmicb.2023.1173748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/22/2023] [Indexed: 07/25/2023] Open
Abstract
The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Qinzhi Xiao
- Yongzhou Tobacco Company of Hunan Province, Yongzhou, China
| | - Zhipeng Xiao
- Hengyang Tobacco Company of Hunan Province, Hengyang, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhaoyue Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Wenqiao Deng
- Changsha Institute of Agricultural Science, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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6
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Sánchez-Salazar AM, Taparia T, Olesen AK, Acuña JJ, Sørensen SJ, Jorquera MA. An overview of plasmid transfer in the plant microbiome. Plasmid 2023; 127:102695. [PMID: 37295540 DOI: 10.1016/j.plasmid.2023.102695] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Plant microbiomes are pivotal for healthy plant physiological development. Microbes live in complex co-association with plant hosts, and interactions within these microbial communities vary with plant genotype, plant compartment, phenological stage, and soil properties, among others. Plant microbiomes also harbor a substantial and diverse pool of mobile genes encoded on plasmids. Several plasmid functions attributed to plant-associated bacteria are relatively poorly understood. Additionally, the role of plasmids in disseminating genetic traits within plant compartments is not well known. Here, we present the current knowledge on the occurrence, diversity, function, and transfer of plasmids in plant microbiomes, emphasizing the factors that could modulate gene transfer in-planta. We also describe the role of the plant microbiome as a plasmid reservoir and the dissemination of its genetic material. We include a brief discussion on the current methodological limitations in studying plasmid transfer within plant microbiomes. This information could be useful to elucidate the dynamics of the bacterial gene pools, the adaptations different organisms have made, and variations in bacterial populations that might have never been described before, particularly in complex microbial communities associated with plants in natural and anthropogenic impacted environments.
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Affiliation(s)
- Angela M Sánchez-Salazar
- Programa de Doctorado en Ciencias de Recursos Naturales, Facultad de Ingeniería y Ciencia, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile
| | - Tanvi Taparia
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark
| | - Asmus K Olesen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; The Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile
| | - Søren J Sørensen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; The Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile.
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Moradigaravand D, Li L, Dechesne A, Nesme J, de la Cruz R, Ahmad H, Banzhaf M, Sørensen SJ, Smets BF, Kreft JU. Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning. Bioinformatics 2023; 39:btad400. [PMID: 37348862 PMCID: PMC10318386 DOI: 10.1093/bioinformatics/btad400] [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: 07/09/2022] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 06/24/2023] Open
Abstract
MOTIVATION Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped. RESULTS In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems. AVAILABILITY AND IMPLEMENTATION The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.
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Affiliation(s)
- Danesh Moradigaravand
- Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Liguan Li
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
- Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Joseph Nesme
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Roberto de la Cruz
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Huda Ahmad
- Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jan-Ulrich Kreft
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
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8
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Zheng F, Zhou GW, Zhu D, Neilson R, Zhu YG, Chen B, Yang XR. Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14904-14912. [PMID: 35917301 DOI: 10.1021/acs.est.1c08733] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.
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Affiliation(s)
- Fei Zheng
- School of Life Sciences, Hebei University, Baoding 071002, China
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guo-Wei Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, United Kingdom
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Bing Chen
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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9
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Macedo G, Olesen AK, Maccario L, Hernandez Leal L, v. d. Maas P, Heederik D, Mevius D, Sørensen SJ, Schmitt H. Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11398-11408. [PMID: 35896060 PMCID: PMC9387108 DOI: 10.1021/acs.est.2c02686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The quantification and identification of new plasmid-acquiring bacteria in representative mating conditions is critical to characterize the risk of horizontal gene transfer in the environment. This study aimed to quantify conjugation events resulting from manure application to soils and identify the transconjugants resulting from these events. Conjugation was quantified at multiple time points by plating and flow cytometry, and the transconjugants were recovered by fluorescence-activated cell sorting and identified by 16S rRNA sequencing. Overall, transconjugants were only observed within the first 4 days after manure application and at values close to the detection limits of this experimental system (1.00-2.49 log CFU/g of manured soil, ranging between 10-5 and 10-4 transconjugants-to-donor ratios). In the pool of recovered transconjugants, we found amplicon sequence variants (ASVs) of genera whose origin was traced to soils (Bacillus and Nocardioides) and manure (Comamonas and Rahnella). This work showed that gene transfer from fecal to soil bacteria occurred despite the less-than-optimal conditions faced by manure bacteria when transferred to soils, but these events were rare, mainly happened shortly after manure application, and the plasmid did not colonize the soil community. This study provides important information to determine the risks of AMR spread via manure application.
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Affiliation(s)
- Gonçalo Macedo
- Department
of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
- Wetsus,
European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Asmus K. Olesen
- Department
of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Lorrie Maccario
- Department
of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Lucia Hernandez Leal
- Wetsus,
European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Peter v. d. Maas
- Van
Hall Larenstein, University of Applied Sciences, Agora 1, 8901 BV Leeuwarden, The Netherlands
| | - Dick Heederik
- Institute
for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Dik Mevius
- Department
of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
- Department
of Bacteriology and Epidemiology, Wageningen
Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Søren J. Sørensen
- Department
of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Heike Schmitt
- Wetsus,
European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
- Institute
for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
- Centre
for Infectious Disease Control, National
Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
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10
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Zhou GW, Zheng F, Fan XT, Li MJ, Sun QY, Zhu YG, Yang XR. Host age increased conjugal plasmid transfer in gut microbiota of the soil invertebrate Caenorhabditis elegans. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127525. [PMID: 34879519 DOI: 10.1016/j.jhazmat.2021.127525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/03/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Plasmid conjugation contributes greatly to the spread of antibiotic resistance genes (ARGs) in soils. However, the spread potential in the gut of soil fauna remains poorly studied, and little was known about the impact of host age on ARGs dissemination in the gut microbiota of soil animals. Here, the typical nematode-Caenorhabditis elegans was employed as the model soil animal, aiming to investigate transfer of broad-host-range IncP-1ɛ from Escherichia coli MG1655 to gut microbiota within 6 days under varied temperature gradients (15, 20 and 25 °C) using qPCR combined with plate screening. Results showed that conjugation rates increased with incubation time and rising temperature in the gut of C. elegans, sharing a similar trend with abundances of plasmid conjugation relevant genes such as trbBp (mating pair formation) and trfAp (plasmid replication). Incubation time and temperature significantly shaped the gut microbial community of C. elegans. Core microbiota in the gut of C. elegans, including Enterobacteriaceae, Lactobacillaceae and Leuconostocaceae, constituted a large part of transconjugal pool for plasmid IncP-1ɛ. Our results highlight an important sink of gut microbiota for ARGs dissemination and upregulation of ARGs transfer in the gut microbiota with host age, further potentially stimulating evolution of ARGs in terrestrial environments.
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Affiliation(s)
- Guo-Wei Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Fei Zheng
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; School of Life Sciences, Hebei University, Baoding 071002, China
| | - Xiao-Ting Fan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming-Jun Li
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Qing-Ye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol 2022; 7:34-47. [PMID: 34873292 PMCID: PMC9261505 DOI: 10.1038/s41564-021-01014-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022]
Abstract
Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.
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Affiliation(s)
- Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Spencer Diamond
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Yue Clare Lou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Christine He
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Michael Xu
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zeyi Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sara J Smith
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Kimberly Tang
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Trenton K Owens
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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12
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Pallares-Vega R, Macedo G, Brouwer MSM, Hernandez Leal L, van der Maas P, van Loosdrecht MCM, Weissbrodt DG, Heederik D, Mevius D, Schmitt H. Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains. Front Microbiol 2021; 12:656250. [PMID: 34349732 PMCID: PMC8326584 DOI: 10.3389/fmicb.2021.656250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmid-mediated dissemination of antibiotic resistance among fecal Enterobacteriaceae in natural ecosystems may contribute to the persistence of antibiotic resistance genes in anthropogenically impacted environments. Plasmid transfer frequencies measured under laboratory conditions might lead to overestimation of plasmid transfer potential in natural ecosystems. This study assessed differences in the conjugative transfer of an IncP-1 (pKJK5) plasmid to three natural Escherichia coli strains carrying extended-spectrum beta-lactamases, by filter mating. Matings were performed under optimal laboratory conditions (rich LB medium and 37°C) and environmentally relevant temperatures (25, 15 and 9°C) or nutrient regimes mimicking environmental conditions and limitations (synthetic wastewater and soil extract). Under optimal nutrient conditions and temperature, two recipients yielded high transfer frequencies (5 × 10-1) while the conjugation frequency of the third strain was 1000-fold lower. Decreasing mating temperatures to psychrophilic ranges led to lower transfer frequencies, albeit all three strains conjugated under all the tested temperatures. Low nutritive media caused significant decreases in transconjugants (-3 logs for synthetic wastewater; -6 logs for soil extract), where only one of the strains was able to produce detectable transconjugants. Collectively, this study highlights that despite less-than-optimal conditions, fecal organisms may transfer plasmids in the environment, but the transfer of pKJK5 between microorganisms is limited mainly by low nutrient conditions.
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Affiliation(s)
- Rebeca Pallares-Vega
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gonçalo Macedo
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Michael S. M. Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Lucia Hernandez Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
| | - Peter van der Maas
- Van Hall Larenstein, University of Applied Sciences, Leeuwarden, Netherlands
| | | | - David G. Weissbrodt
- Department Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
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13
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D'Aeth JC, van der Linden MPG, McGee L, de Lencastre H, Turner P, Song JH, Lo SW, Gladstone RA, Sá-Leão R, Ko KS, Hanage WP, Breiman RF, Beall B, Bentley SD, Croucher NJ. The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci. eLife 2021; 10:e67113. [PMID: 34259624 PMCID: PMC8321556 DOI: 10.7554/elife.67113] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
Multidrug-resistant Streptococcus pneumoniae emerge through the modification of core genome loci by interspecies homologous recombinations, and acquisition of gene cassettes. Both occurred in the otherwise contrasting histories of the antibiotic-resistant S. pneumoniae lineages PMEN3 and PMEN9. A single PMEN3 clade spread globally, evading vaccine-induced immunity through frequent serotype switching, whereas locally circulating PMEN9 clades independently gained resistance. Both lineages repeatedly integrated Tn916-type and Tn1207.1-type elements, conferring tetracycline and macrolide resistance, respectively, through homologous recombination importing sequences originating in other species. A species-wide dataset found over 100 instances of such interspecific acquisitions of resistance cassettes and flanking homologous arms. Phylodynamic analysis of the most commonly sampled Tn1207.1-type insertion in PMEN9, originating from a commensal and disrupting a competence gene, suggested its expansion across Germany was driven by a high ratio of macrolide-to-β-lactam consumption. Hence, selection from antibiotic consumption was sufficient for these atypically large recombinations to overcome species boundaries across the pneumococcal chromosome.
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Affiliation(s)
- Joshua C D'Aeth
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Mark PG van der Linden
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital RWTH AachenAachenGermany
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller UniversityNew YorkUnited States
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for ChildrenSiem ReapCambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Jae-Hoon Song
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - Stephanie W Lo
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Rebecca A Gladstone
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de LisboaOeirasPortugal
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of MedicineSuwonRepublic of Korea
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory UniversityAtlantaUnited States
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and PreventionAtlantaUnited States
| | - Stephen D Bentley
- Parasites & Microbes, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
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14
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Contagious Antibiotic Resistance: Plasmid Transfer among Bacterial Residents of the Zebrafish Gut. Appl Environ Microbiol 2021; 87:AEM.02735-20. [PMID: 33637574 DOI: 10.1128/aem.02735-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/20/2021] [Indexed: 01/12/2023] Open
Abstract
By characterizing the trajectories of antibiotic resistance gene transfer in bacterial communities such as the gut microbiome, we will better understand the factors that influence this spread of resistance. Our aim was to investigate the host network of a multidrug resistance broad-host-range plasmid in the culturable gut microbiome of zebrafish. This was done through in vitro and in vivo conjugation experiments with Escherichia coli as the donor of the plasmid pB10::gfp When this donor was mixed with the extracted gut microbiome, only transconjugants of Aeromonas veronii were detected. In separate matings between the same donor and four prominent isolates from the gut microbiome, the plasmid transferred to two of these four isolates, A. veronii and Plesiomonas shigelloides, but not to Shewanella putrefaciens and Vibrio mimicus When these A. veronii and P. shigelloides transconjugants were the donors in matings with the same four isolates, the plasmid now also transferred from A. veronii to S. putrefaciens P. shigelloides was unable to donate the plasmid, and V. mimicus was unable to acquire it. Finally, when the E. coli donor was added in vivo to zebrafish through their food, plasmid transfer was observed in the gut, but only to Achromobacter, a rare member of the gut microbiome. This work shows that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome depends on the donor-recipient species combinations and therefore their spatial arrangement. It also suggests that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.IMPORTANCE To understand how antibiotic resistance plasmids end up in human pathogens, it is crucial to learn how, where, and when they are transferred and maintained in members of bacterial communities such as the gut microbiome. To gain insight into the network of plasmid-mediated antibiotic resistance sharing in the gut microbiome, we investigated the transferability and maintenance of a multidrug resistance plasmid among the culturable bacteria of the zebrafish gut. We show that the success of plasmid-mediated antibiotic resistance spread in a gut microbiome can depend on which species are involved, as some are important nodes in the plasmid-host network and others are dead ends. Our findings also suggest that rare gut microbiome members should not be ignored as potential reservoirs of multidrug resistance plasmids from food.
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15
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Bravo G, Vega-Celedón P, Gentina JC, Seeger M. Bioremediation by Cupriavidus metallidurans Strain MSR33 of Mercury-Polluted Agricultural Soil in a Rotary Drum Bioreactor and Its Effects on Nitrogen Cycle Microorganisms. Microorganisms 2020; 8:E1952. [PMID: 33316980 PMCID: PMC7763483 DOI: 10.3390/microorganisms8121952] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022] Open
Abstract
Nitrogen cycle microorganisms are essential in agricultural soils and may be affected by mercury pollution. The aims of this study are to evaluate the bioremediation of mercury-polluted agricultural soil using Cupriavidus metallidurans MSR33 in a rotary drum bioreactor (RDB) and to characterize the effects of mercury pollution and bioremediation on nitrogen cycle microorganisms. An agricultural soil was contaminated with mercury (II) (20-30 ppm) and subjected to bioremediation using strain MSR33 in a custom-made RDB. The effects of mercury and bioremediation on nitrogen cycle microorganisms were studied by qPCR. Bioremediation in the RDB removed 82% mercury. MSR33 cell concentrations, thioglycolate, and mercury concentrations influence mercury removal. Mercury pollution strongly decreased nitrogen-fixing and nitrifying bacterial communities in agricultural soils. Notably, after soil bioremediation process nitrogen-fixing and nitrifying bacteria significantly increased. Diverse mercury-tolerant strains were isolated from the bioremediated soil. The isolates Glutamicibacter sp. SB1a, Brevundimonas sp. SB3b, and Ochrobactrum sp. SB4b possessed the merG gene associated with the plasmid pTP6, suggesting the horizontal transfer of this plasmid to native gram-positive and gram-negative bacteria. Bioremediation by strain MSR33 in an RDB is an attractive and innovative technology for the clean-up of mercury-polluted agricultural soils and the recovery of nitrogen cycle microbial communities.
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Affiliation(s)
- Guillermo Bravo
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile;
| | - Paulina Vega-Celedón
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile;
| | - Juan Carlos Gentina
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso 2362803, Chile;
| | - Michael Seeger
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso 2390123, Chile;
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16
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Song J, Klümper U, Riber L, Dechesne A, Smets BF, Sørensen SJ, Brandt KK. A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination. FEMS Microbiol Ecol 2020; 96:5917080. [PMID: 33002118 DOI: 10.1093/femsec/fiaa200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 09/28/2020] [Indexed: 12/29/2022] Open
Abstract
Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg-1) soil compared to corresponding communities extracted from moderately (458 mg kg-1) Cu contaminated soil and a low Cu reference soil (15 mg kg-1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.
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Affiliation(s)
- Jianxiao Song
- School of Ecology and Environment, Northwestern Polytechnical University, 1 Dongxiang Road, Chang'an District, Xi'an Shaanxi,710129, P.R. China.,Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.,Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, Dresden 01217, Germany.,Environment and Sustainability Institute, Medical School, University of Exeter, Penryn Campus, Cornwall, TR10 9FE, UK
| | - Leise Riber
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.,Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej Building 115, 2800 Kgs. Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej Building 115, 2800 Kgs. Lyngby, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Kristian K Brandt
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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17
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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18
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Buckner MMC, Ciusa ML, Meek RW, Moorey AR, McCallum GE, Prentice EL, Reid JP, Alderwick LJ, Di Maio A, Piddock LJV. HIV Drugs Inhibit Transfer of Plasmids Carrying Extended-Spectrum β-Lactamase and Carbapenemase Genes. mBio 2020; 11:e03355-19. [PMID: 32098822 PMCID: PMC7042701 DOI: 10.1128/mbio.03355-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial-resistant (AMR) infections pose a serious risk to human and animal health. A major factor contributing to this global crisis is the sharing of resistance genes between different bacteria via plasmids. The WHO lists Enterobacteriaceae, such as Escherichia coli and Klebsiella pneumoniae, producing extended-spectrum β-lactamases (ESBL) and carbapenemases as "critical" priorities for new drug development. These resistance genes are most often shared via plasmid transfer. However, finding methods to prevent resistance gene sharing has been hampered by the lack of screening systems for medium-/high-throughput approaches. Here, we have used an ESBL-producing plasmid, pCT, and a carbapenemase-producing plasmid, pKpQIL, in two different Gram-negative bacteria, E. coli and K. pneumoniae Using these critical resistance-pathogen combinations, we developed an assay using fluorescent proteins, flow cytometry, and confocal microscopy to assess plasmid transmission inhibition within bacterial populations in a medium-throughput manner. Three compounds with some reports of antiplasmid properties were tested; chlorpromazine reduced transmission of both plasmids and linoleic acid reduced transmission of pCT. We screened the Prestwick library of over 1,200 FDA-approved drugs/compounds. From this, we found two nucleoside analogue drugs used to treat HIV, abacavir and azidothymidine (AZT), which reduced plasmid transmission (AZT, e.g., at 0.25 μg/ml reduced pCT transmission in E. coli by 83.3% and pKpQIL transmission in K. pneumoniae by 80.8% compared to untreated controls). Plasmid transmission was reduced by concentrations of the drugs which are below peak serum concentrations and are achievable in the gastrointestinal tract. These drugs could be used to decolonize humans, animals, or the environment from AMR plasmids.IMPORTANCE More and more bacterial infections are becoming resistant to antibiotics. This has made treatment of many infections very difficult. One of the reasons this is such a large problem is that bacteria are able to share their genetic material with other bacteria, and these shared genes often include resistance to a variety of antibiotics, including some of our drugs of last resort. We are addressing this problem by using a fluorescence-based system to search for drugs that will stop bacteria from sharing resistance genes. We uncovered a new role for two drugs used to treat HIV and show that they are able to prevent the sharing of two different types of resistance genes in two unique bacterial strains. This work lays the foundation for future work to reduce the prevalence of resistant infections.
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Affiliation(s)
- Michelle M C Buckner
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - M Laura Ciusa
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Richard W Meek
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Alice R Moorey
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Gregory E McCallum
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Emma L Prentice
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Jeremy P Reid
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Luke J Alderwick
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Alessandro Di Maio
- Birmingham Advanced Light Microscopy, School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Laura J V Piddock
- Institute of Microbiology & Infection, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
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19
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Blau K, Jechalke S, Smalla K. Detection, Isolation, and Characterization of Plasmids in the Environment. Methods Mol Biol 2020; 2075:39-60. [PMID: 31584153 DOI: 10.1007/978-1-4939-9877-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Plasmids play a major role in the bacterial adaptation to changing and stressful environmental conditions caused by antibiotics, heavy metals, and disinfectants. However, the investigation of the ecology and diversity of environmental plasmids is challenging due to their typically low abundance in soil bacterial communities and the low cultivability of their hosts. Here we discuss the potentials and limitations of cultivation-dependent and cultivation-independent approaches for detecting and quantifying plasmids in total community DNA from environmental samples. Protocols for PCR-based detection of plasmid-specific sequences in total community DNA are presented. Furthermore, protocols to obtain and characterize plasmids either from isolates (endogenous plasmid isolation) or by capturing into a recipient strain by biparental and triparental mating will be provided.
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Affiliation(s)
- Khald Blau
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Sven Jechalke
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany.
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20
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Yang Y, Ashworth AJ, Willett C, Cook K, Upadhyay A, Owens PR, Ricke SC, DeBruyn JM, Moore PA. Review of Antibiotic Resistance, Ecology, Dissemination, and Mitigation in U.S. Broiler Poultry Systems. Front Microbiol 2019; 10:2639. [PMID: 31803164 PMCID: PMC6872647 DOI: 10.3389/fmicb.2019.02639] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 10/30/2019] [Indexed: 12/24/2022] Open
Abstract
Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.
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Affiliation(s)
- Yichao Yang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Amanda J Ashworth
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Fayetteville, AR, United States
| | - Cammy Willett
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Kimberly Cook
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Abhinav Upadhyay
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Phillip R Owens
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Dale Bumpers Small Farms Research Center, Booneville, AR, United States
| | - Steven C Ricke
- Department of Food Science and Center for Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Philip A Moore
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Fayetteville, AR, United States
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21
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Measuring Plasmid Conjugation Using Fluorescent Reporters. Methods Mol Biol 2019. [PMID: 31584157 DOI: 10.1007/978-1-4939-9877-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorescence-based methods are increasingly popular because they (1) offer a faster alternative to labor-intensive traditional methods, (2) enable the development of automated high-throughput screening procedures, and (3) allow direct visualization of biological processes. Here we describe three fluorescence-based methods applicable for the detection and quantitation of plasmid conjugation. The first method uses flow cytometry as a fast and reliable alternative to traditional plating methods. A second one employs fluorescence expression for high-throughput analysis of plasmid conjugation. Finally we review a third method that enables direct visualization of plasmid transfer under the microscope.
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22
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González-Plaza JJ, Blau K, Milaković M, Jurina T, Smalla K, Udiković-Kolić N. Antibiotic-manufacturing sites are hot-spots for the release and spread of antibiotic resistance genes and mobile genetic elements in receiving aquatic environments. ENVIRONMENT INTERNATIONAL 2019; 130:104735. [PMID: 31260930 DOI: 10.1016/j.envint.2019.04.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 05/24/2023]
Abstract
High antibiotic releases from manufacturing facilities have been identified as a risk factor for antibiotic resistance development in bacterial pathogens. However, the role of antibiotic pollution in selection and transferability of antibiotic resistance genes (ARGs) is still limited. In this study, we analyzed effluents from azithromycin-synthesis and veterinary-drug formulation facilities as well as sediments from receiving river and creek taken at the effluent discharge sites, upstream and downstream of discharge. Culturing showed that the effluent discharge significantly increased the proportion of antibiotic resistant bacteria in exposed sediments compared to the upstream ones. Quantitative real-time PCR revealed that effluents from both industries contained high and similar relative abundances of resistance genes [sul1, sul2, qacE/qacEΔ1, tet(A)], class 1 integrons (intI1) and IncP-1 plasmids (korB). Consequently, these genes significantly increased in relative abundances in receiving sediments, with more pronounced effects being observed for river than for creek sediments due to lower background levels of the investigated genes in the river. In addition, effluent discharge considerably increased transfer frequencies of captured ARGs from exposed sediments into Escherichia coli CV601 recipient as shown by biparental mating experiments. Most plasmids exogenously captured from effluent and polluted sediments belonged to the broad host range IncP-1ε plasmid group, conferred multiple antibiotic resistance and harbored class 1 integrons. Discharge of pharmaceutical waste from antibiotic manufacturing sites thus poses a risk for development and dissemination of multi-resistant bacteria, including pathogens.
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Affiliation(s)
| | - Khald Blau
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tamara Jurina
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
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23
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Bañuelos-Vazquez LA, Torres Tejerizo G, Cervantes-De La Luz L, Girard L, Romero D, Brom S. Conjugative transfer between Rhizobium etli endosymbionts inside the root nodule. Environ Microbiol 2019; 21:3430-3441. [PMID: 31037804 DOI: 10.1111/1462-2920.14645] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/05/2019] [Accepted: 04/26/2019] [Indexed: 11/30/2022]
Abstract
Since the discovery that biological nitrogen fixation ensues in nodules resulting from the interaction of rhizobia with legumes, nodules were thought to be exclusive for hosting nitrogen-fixing and plant growth promoting bacteria. In this work, we uncover a novel function of nodules, as a niche permissive to acquisition of plasmids via conjugative transfer. We used Rhizobium etli CFN42, which nodulates Phaseolus vulgaris. The genome of R. etli CFN42 contains a chromosome and six plasmids. pRet42a is a conjugative plasmid regulated by Quorum-Sensing (QS), and pRet42d is the symbiotic plasmid. Here, using confocal microscopy and flow cytometry, we show that pRet42a transfers on the root's surface, and unexpectedly, inside the nodules. Conjugation still took place inside nodules, even when it was restricted on the plant surface by placing the QS traI regulator under the promoter of the nitrogenase gene, which is only expressed inside the nodules, or by inhibiting the QS transcriptional induction of transfer genes with a traM antiactivator on an unstable vector maintained on the plant surface and lost inside the nodules. These results conclusively confirm the occurrence of conjugation in these structures, defining them as a protected environment for bacterial diversification.
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Affiliation(s)
- Luis Alfredo Bañuelos-Vazquez
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Gonzalo Torres Tejerizo
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Laura Cervantes-De La Luz
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lourdes Girard
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - David Romero
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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24
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Fleitas Martínez O, Cardoso MH, Ribeiro SM, Franco OL. Recent Advances in Anti-virulence Therapeutic Strategies With a Focus on Dismantling Bacterial Membrane Microdomains, Toxin Neutralization, Quorum-Sensing Interference and Biofilm Inhibition. Front Cell Infect Microbiol 2019; 9:74. [PMID: 31001485 PMCID: PMC6454102 DOI: 10.3389/fcimb.2019.00074] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance constitutes one of the major challenges facing humanity in the Twenty-First century. The spread of resistant pathogens has been such that the possibility of returning to a pre-antibiotic era is real. In this scenario, innovative therapeutic strategies must be employed to restrict resistance. Among the innovative proposed strategies, anti-virulence therapy has been envisioned as a promising alternative for effective control of the emergence and spread of resistant pathogens. This review presents some of the anti-virulence strategies that are currently being developed, it will cover strategies focused on quench pathogen quorum sensing (QS) systems, disassemble of bacterial functional membrane microdomains (FMMs), disruption of biofilm formation and bacterial toxin neutralization.
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Affiliation(s)
- Osmel Fleitas Martínez
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Marlon Henrique Cardoso
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Suzana Meira Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Octavio Luiz Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
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25
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Fan XT, Li H, Chen QL, Zhang YS, Ye J, Zhu YG, Su JQ. Fate of Antibiotic Resistant Pseudomonas putida and Broad Host Range Plasmid in Natural Soil Microcosms. Front Microbiol 2019; 10:194. [PMID: 30881351 PMCID: PMC6407330 DOI: 10.3389/fmicb.2019.00194] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/23/2019] [Indexed: 12/03/2022] Open
Abstract
Plasmid conjugation is one of the dominant mechanisms of horizontal gene transfer, playing a noticeable role in the rapid spread of antibiotic resistance genes (ARGs). Broad host range plasmids are known to transfer to diverse bacteria in extracted soil bacterial communities when evaluated by filter mating incubation. However, the persistence and dissemination of broad range plasmid in natural soil has not been well studied. In this study, Pseudomonas putida with a conjugative antibiotic resistance plasmid RP4 was inoculated into a soil microcosm, the fate and persistence of P. putida and RP4 were monitored by quantitative PCR. The concentrations of P. putida and RP4 both rapidly decreased within 15-day incubation. P. putida then decayed at a significantly lower rate during subsequent incubation, however, no further decay of RP4 was observed, resulting in an elevated RP4/P. putida ratio (up to 10) after 75-day incubation, which implied potential transfer of RP4 to soil microbiota. We further sorted RP4 recipient bacteria from the soil microcosms by fluorescence-activated cell sorting. Spread of RP4 increased during 75-day microcosm operation and was estimated at around 10-4 transconjugants per recipient at the end of incubation. Analysis of 16S rRNA gene sequences of transconjugants showed that host bacteria of RP4 were affiliated to more than 15 phyla, with increased diversity and shift in the composition of host bacteria. Proteobacteria was the most dominant phylum in the transconjugant pools. Transient transfer of RP4 to some host bacteria was observed. These results emphasize the prolonged persistence of P. putida and RP4 in natural soil microcosms, and highlight the potential risks of increased spread potential of plasmid and broader range of host bacteria in disseminating ARGs in soil.
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Affiliation(s)
- Xiao-Ting Fan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yu-Sen Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Ye
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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26
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Ravasi D, König R, Principi P, Perale G, Demarta A. Effect of Powdered Activated Carbon as Advanced Step in Wastewater Treatments on Antibiotic Resistant Microorganisms. Curr Pharm Biotechnol 2019; 20:63-75. [PMID: 30727884 PMCID: PMC6637097 DOI: 10.2174/1389201020666190207095556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/16/2018] [Accepted: 01/19/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Conventional wastewater treatment plants discharge significant amounts of antibiotic resistant bacteria and antibiotic resistance genes into natural water bodies contributing to the spread of antibiotic resistance. Some advanced wastewater treatment technologies have been shown to effectively decrease the number of bacteria. Nevertheless, there is still a lack of knowledge about the effectiveness of these treatments on antibiotic resistant bacteria and antibiotic resistant genes. To the best of our knowledge, no specific studies have considered how powdered activated carbon (PAC) treatments can act on antibiotic resistant bacteria, although it is essential to assess the impact of this wastewater treatment on the spread of antibiotic resistant bacteria. METHODS To address this gap, we evaluated the fate and the distribution of fluorescent-tagged antibiotic/ antimycotic resistant microorganisms in a laboratory-scale model simulating a process configuration involving powdered activated carbon as advanced wastewater treatment. Furthermore, we studied the possible increase of naturally existing antibiotic resistant bacteria during the treatment implementing PAC recycling. RESULTS The analysis of fluorescent-tagged microorganisms demonstrated the efficacy of the PAC adsorption treatment in reducing the load of both susceptible and resistant fluorescent microorganisms in the treated water, reaching a removal efficiency of 99.70%. Moreover, PAC recycling did not increase the resistance characteristics of cultivable bacteria neither in the sludge nor in the treated effluent. CONCLUSION Results suggest that wastewater PAC treatment is a promising technology not only for the removal of micropollutants but also for its effect in decreasing antibiotic resistant bacteria release.
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Affiliation(s)
- Damiana Ravasi
- Laboratory of Applied Microbiology, Department of Environment, Construction and Design, University of Applied Sciences and Arts of Southern Switzerland, Via Mirasole 22a, 6501 Bellinzona, Switzerland
| | - Roger König
- Department of Innovative Technologies, Bio-Environmental Technologies Laboratory, Mechanical Engineering and Materials Technology Institute, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, 6928 Manno, Switzerland
| | - Pamela Principi
- Department of Innovative Technologies, Bio-Environmental Technologies Laboratory, Mechanical Engineering and Materials Technology Institute, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, 6928 Manno, Switzerland
| | - Giuseppe Perale
- Department of Innovative Technologies, Bio-Environmental Technologies Laboratory, Mechanical Engineering and Materials Technology Institute, University of Applied Sciences and Arts of Southern Switzerland, Galleria 2, Via Cantonale 2c, 6928 Manno, Switzerland
| | - Antonella Demarta
- Laboratory of Applied Microbiology, Department of Environment, Construction and Design, University of Applied Sciences and Arts of Southern Switzerland, Via Mirasole 22a, 6501 Bellinzona, Switzerland
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27
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Qiu Y, Zhang J, Li B, Wen X, Liang P, Huang X. A novel microfluidic system enables visualization and analysis of antibiotic resistance gene transfer to activated sludge bacteria in biofilm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:582-590. [PMID: 29909325 DOI: 10.1016/j.scitotenv.2018.06.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 05/25/2023]
Abstract
Antibiotic resistance genes (ARGs) in environment have become a growing public concern, due to their potential to be obtained by pathogens and their duplication along cell division. Horizontal gene transfer (HGT) was reported to be responsible for ARGs dissemination in microbes, but the HGT feature in environmental biofilm was still unclear due to insufficient assay tools. To address this challenge, we applied a novel microfluidic system to cultivate thin biofilm by continuous supply of nutrients and close contact between cells. Resembling the living state of biofilm in open environment, this chip visualized the transfer of ARG-encoded plasmids RP4 and pKJK5 to the receptors, e.g., activated sludge bacteria. The average plasmid transfer frequency per receptor (T/R) from RP4-hosted Pseudomonas putida KT2440 to activated sludge bacteria was quantified to be 2.5 × 10-3 via flow cytometry, and T/R for pKJK5-hosted Escherichia coli MG1655 was 8.9 × 10-3, while the corresponding average frequencies per donor (T/D) were diverse for the two host strains as 4.3 × 10-3 and 1.4 × 10-1 respectively. The difference between T/R and T/D was explained by the plasmid transfer kinetics, implying specific purposes of the two calculations. Finally, we collected the transconjugants by fluorescent activated cell sorting and further sequenced their 16S rDNA. Bacteria from phyla Proteobacteria and Firmicutes were found more susceptible to be transconjugants than those from Bacteroidetes. Our work demonstrated that microfluidic system was advantageous in biofilm HGT study, which can provide more insights into environmental ARG control.
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Affiliation(s)
- Yong Qiu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jing Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Xianghua Wen
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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28
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Begum J, Mir NA, Dev K, Khan IA. Dynamics of antibiotic resistance with special reference to Shiga toxin-producing Escherichia coli infections. J Appl Microbiol 2018; 125:1228-1237. [PMID: 29957827 DOI: 10.1111/jam.14034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/21/2018] [Accepted: 06/26/2018] [Indexed: 11/26/2022]
Abstract
The discovery of antibiotics was paralleled by the evolution of antibiotic resistance which is probably the best example of contemporary evolution in action. The selection pressure, imposed by indiscriminate use of antibiotics, has changed the scale, mode and tempo of antibiotic resistance evolution. The presence of multidrug resistance, wide range of adaptability features and the infectivity make antibiotic resistance of Shiga toxin-producing Escherichia coli (STEC) more dangerous. The characterization, prevalence and the virulence factors of STEC have been profusely reported, whereas, the antibiotic resistance has been largely ignored because the antibiotic use in STEC infections is controversial. Thus, the current review has focussed on the source, evolution, persistence, mechanism, dissemination and control of antibiotic resistance viz-a-viz the STEC infections. The resistance development occurs by the inactivation of antibiotics, regulating the membrane permeability, modification of natural antibiotic targets or the use of efflux pumps against antibiotics. And, the dissemination of resistance genes occurs vertically by DNA replication and horizontally by conjugation, transduction and transformation. The prevention of development and dissemination of antibiotic resistance needs international public health bodies to rationalize the antibiotic use, prevent the flux of antibiotics into the environment, develop the rapid diagnostics tests, undertake proper surveillance of antibiotic resistance, promote the research on antibiotic resistance prevention, promote the research and development of novel alternative antibiotics, and encourage the widespread social awareness campaigns against the inappropriate antibiotic usage.
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Affiliation(s)
- J Begum
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, GBPUAT, Panthnagar, Udham Singh Nagar, Uttarakhand, India
| | - N A Mir
- ICAR- Central Avian Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - K Dev
- ICAR- Central Avian Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - I A Khan
- ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
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Pinilla-Redondo R, Cyriaque V, Jacquiod S, Sørensen SJ, Riber L. Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives. Plasmid 2018; 99:56-67. [PMID: 30086339 DOI: 10.1016/j.plasmid.2018.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 10/28/2022]
Abstract
The emergence of antimicrobial resistant bacteria constitutes an increasing global health concern. Although it is well recognized that the cornerstone underlying this phenomenon is the dissemination of antimicrobial resistance via plasmids and other mobile genetic elements, the antimicrobial resistance transfer routes remain largely uncharted. In this review, we describe different methods for assessing the transfer frequency and host ranges of plasmids within complex microbiomes. The discussion is centered around the critical evaluation of recent advances for monitoring the fate of fluorescently tagged plasmids in bacterial communities through the coupling of fluorescence activated cell sorting and next generation sequencing techniques. We argue that this approach constitutes an exceptional tool for obtaining quantitative data regarding the extent of plasmid transfer, key disseminating taxa, and possible propagation routes. The integration of this information will provide valuable insights on how to develop alternative avenues for fighting the rise of antimicrobial resistant pathogens, as well as the means for constructing more comprehensive risk assessment models.
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Affiliation(s)
| | - Valentine Cyriaque
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, Mons, Belgium
| | | | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Leise Riber
- Section for Functional Genomics, University of Copenhagen, Copenhagen, Denmark.
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30
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Manirajan BA, Maisinger C, Ratering S, Rusch V, Schwiertz A, Cardinale M, Schnell S. Diversity, specificity, co-occurrence and hub taxa of the bacterial–fungal pollen microbiome. FEMS Microbiol Ecol 2018; 94:5033679. [DOI: 10.1093/femsec/fiy112] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/31/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Binoy Ambika Manirajan
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Corinna Maisinger
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Volker Rusch
- Institut für Integrative Biologie, Stiftung Old Herborn University, Herborn, Germany
| | - Andreas Schwiertz
- MVZ Institut für Mikroökologie GmbH, D-35745 Herborn, Auf den Lüppen 8, Germany,
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
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31
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Arias-Andres M, Klümper U, Rojas-Jimenez K, Grossart HP. Microplastic pollution increases gene exchange in aquatic ecosystems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 237:253-261. [PMID: 29494919 DOI: 10.1016/j.envpol.2018.02.058] [Citation(s) in RCA: 282] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/26/2018] [Accepted: 02/19/2018] [Indexed: 05/20/2023]
Abstract
Pollution by microplastics in aquatic ecosystems is accumulating at an unprecedented scale, emerging as a new surface for biofilm formation and gene exchange. In this study, we determined the permissiveness of aquatic bacteria towards a model antibiotic resistance plasmid, comparing communities that form biofilms on microplastics vs. those that are free-living. We used an exogenous and red-fluorescent E. coli donor strain to introduce the green-fluorescent broad-host-range plasmid pKJK5 which encodes for trimethoprim resistance. We demonstrate an increased frequency of plasmid transfer in bacteria associated with microplastics compared to bacteria that are free-living or in natural aggregates. Moreover, comparison of communities grown on polycarbonate filters showed that increased gene exchange occurs in a broad range of phylogenetically-diverse bacteria. Our results indicate horizontal gene transfer in this habitat could distinctly affect the ecology of aquatic microbial communities on a global scale. The spread of antibiotic resistance through microplastics could also have profound consequences for the evolution of aquatic bacteria and poses a neglected hazard for human health.
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Affiliation(s)
- Maria Arias-Andres
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, 16775 Stechlin, Germany; Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, D-14469 Potsdam, Germany; Central American Institute for Studies on Toxic Substances, Universidad Nacional, Campus Omar Dengo, P.O. Box 86-3000, Heredia, Costa Rica
| | - Uli Klümper
- European Centre for Environment and Human Health, University of Exeter, Medical School, Royal Cornwall Hospital, Truro, United Kingdom; ESI & CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall, United Kingdom
| | - Keilor Rojas-Jimenez
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, 16775 Stechlin, Germany; Universidad Latina de Costa Rica, Campus San Pedro, Apdo. 10138-1000, San José, Costa Rica
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, 16775 Stechlin, Germany; Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, D-14469 Potsdam, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research - BBIB, Freie Universität Berlin, Altensteinstr. 34, 14195 Berlin, Germany.
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32
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Wolters B, Jacquiod S, Sørensen SJ, Widyasari-Mehta A, Bech TB, Kreuzig R, Smalla K. Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization. FEMS Microbiol Ecol 2018; 94:4867966. [DOI: 10.1093/femsec/fiy027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/15/2018] [Indexed: 12/30/2022] Open
Affiliation(s)
- Birgit Wolters
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11–12, 38104 Braunschweig, Germany
- Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry, Hagenring 30, 38106 Braunschweig, Germany
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Arum Widyasari-Mehta
- Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry, Hagenring 30, 38106 Braunschweig, Germany
| | - Tina B Bech
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Øster Voldgade 10, 1350 Copenhagen K, Denmark
| | - Robert Kreuzig
- Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry, Hagenring 30, 38106 Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11–12, 38104 Braunschweig, Germany
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33
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Leite DCA, Salles JF, Calderon EN, van Elsas JD, Peixoto RS. Specific plasmid patterns and high rates of bacterial co-occurrence within the coral holobiont. Ecol Evol 2018; 8:1818-1832. [PMID: 29435256 PMCID: PMC5792611 DOI: 10.1002/ece3.3717] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 12/24/2022] Open
Abstract
Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co-occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples collected from Mussismilia hispida colonies on two reefs located in Bahia, Brazil, to disentangle their associated bacterial communities, intertaxa correlations, and plasmid patterns. Proxies for two broad-host-range (BHR) plasmid groups, IncP-1β and PromA, were screened. Both groups were significantly (up to 252 and 100%, respectively) more abundant in coral mucus than in seawater. Notably, the PromA plasmid group was detected only in coral mucus samples. The core bacteriome of M. hispida mucus was composed primarily of members of the Proteobacteria, followed by those of Firmicutes. Significant host specificity and co-occurrences among different groups of the dominant phyla (e.g., Bacillaceae and Pseudoalteromonadaceae and the genera Pseudomonas, Bacillus, and Vibrio) were detected. These relationships were observed for both the most abundant phyla and the bacteriome core, in which most of the operational taxonomic units showed intertaxa correlations. The observed evidence of host-specific bacteriome and co-occurrence (and potential symbioses or niche space co-dominance) among the most dominant members indicates a taxonomic selection of members of the stable bacterial community. In parallel, host-specific plasmid patterns could also be, independently, related to the assembly of members of the coral microbiome.
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Affiliation(s)
- Deborah C. A. Leite
- Institute of MicrobiologyFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Joana F. Salles
- Genomics Research in Ecology and Evolution in Nature ‐ Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Emiliano N. Calderon
- NUPEM/MacaéFederal University of Rio de JaneiroRio de JaneiroBrazil
- Instituto Coral VivoSanta Cruz CabráliaBrazil
| | - Jan D. van Elsas
- Genomics Research in Ecology and Evolution in Nature ‐ Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Raquel S. Peixoto
- Institute of MicrobiologyFederal University of Rio de JaneiroRio de JaneiroBrazil
- IMAM‐AquaRio – Rio Marine Aquarium Research CenterRio de JaneiroBrazil
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34
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Jacquiod S, Brejnrod A, Morberg SM, Abu Al-Soud W, Sørensen SJ, Riber L. Deciphering conjugative plasmid permissiveness in wastewater microbiomes. Mol Ecol 2017; 26:3556-3571. [DOI: 10.1111/mec.14138] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/30/2017] [Accepted: 03/30/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Samuel Jacquiod
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Asker Brejnrod
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Stefan M. Morberg
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Waleed Abu Al-Soud
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Søren J. Sørensen
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Leise Riber
- Section of Microbiology; Department of Biology; University of Copenhagen; Copenhagen Denmark
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35
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Ambika Manirajan B, Ratering S, Rusch V, Schwiertz A, Geissler-Plaum R, Cardinale M, Schnell S. Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity. Environ Microbiol 2016; 18:5161-5174. [DOI: 10.1111/1462-2920.13524] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/04/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Binoy Ambika Manirajan
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Volker Rusch
- Institut für Integrative Biologie, Stiftung Old Herborn University; Herborn Germany
| | | | - Rita Geissler-Plaum
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig-University; Giessen Germany
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36
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Wolters B, Widyasari-Mehta A, Kreuzig R, Smalla K. Contaminations of organic fertilizers with antibiotic residues, resistance genes, and mobile genetic elements mirroring antibiotic use in livestock? Appl Microbiol Biotechnol 2016; 100:9343-9353. [DOI: 10.1007/s00253-016-7742-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/10/2016] [Accepted: 07/12/2016] [Indexed: 11/29/2022]
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Abstract
Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.
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38
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von Wintersdorff CJH, Penders J, van Niekerk JM, Mills ND, Majumder S, van Alphen LB, Savelkoul PHM, Wolffs PFG. Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Front Microbiol 2016; 7:173. [PMID: 26925045 PMCID: PMC4759269 DOI: 10.3389/fmicb.2016.00173] [Citation(s) in RCA: 721] [Impact Index Per Article: 90.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antibiotic resistance among pathogenic bacteria has been a rising problem for public health in recent decades. It is becoming increasingly recognized that not only antibiotic resistance genes (ARGs) encountered in clinical pathogens are of relevance, but rather, all pathogenic, commensal as well as environmental bacteria—and also mobile genetic elements and bacteriophages—form a reservoir of ARGs (the resistome) from which pathogenic bacteria can acquire resistance via horizontal gene transfer (HGT). HGT has caused antibiotic resistance to spread from commensal and environmental species to pathogenic ones, as has been shown for some clinically important ARGs. Of the three canonical mechanisms of HGT, conjugation is thought to have the greatest influence on the dissemination of ARGs. While transformation and transduction are deemed less important, recent discoveries suggest their role may be larger than previously thought. Understanding the extent of the resistome and how its mobilization to pathogenic bacteria takes place is essential for efforts to control the dissemination of these genes. Here, we will discuss the concept of the resistome, provide examples of HGT of clinically relevant ARGs and present an overview of the current knowledge of the contributions the various HGT mechanisms make to the spread of antibiotic resistance.
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Affiliation(s)
- Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+ Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands
| | - Julius M van Niekerk
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Nathan D Mills
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Snehali Majumder
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Lieke B van Alphen
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology and Infection Control, VU University Medical CenterAmsterdam, Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands
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39
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Dealtry S, Nour EH, Holmsgaard PN, Ding GC, Weichelt V, Dunon V, Heuer H, Hansen LH, Sørensen SJ, Springael D, Smalla K. Exploring the complex response to linuron of bacterial communities from biopurification systems by means of cultivation-independent methods. FEMS Microbiol Ecol 2015; 92:fiv157. [DOI: 10.1093/femsec/fiv157] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 02/03/2023] Open
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40
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Ulrich A, Becker R, Ulrich K, Ewald D. Conjugative transfer of a derivative of the IncP-1α plasmid RP4 and establishment of transconjugants in the indigenous bacterial community of poplar plants. FEMS Microbiol Lett 2015; 362:fnv201. [PMID: 26490946 PMCID: PMC4643746 DOI: 10.1093/femsle/fnv201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/09/2015] [Accepted: 10/16/2015] [Indexed: 12/14/2022] Open
Abstract
The persistence of traits introduced into the indigenous bacterial community of poplar plants was investigated using bioluminescence mediated by the luc gene. Three endophytic bacterial strains provided with the IncP-1α plasmid RP4-Tn-luc were used to inoculate poplar cuttings at different phenological stages. Screening of isolates by bioluminescence and real-time PCR detection of the luc gene revealed stable persistence for at least 10 weeks. Although the inoculated strains became established with a high population density after inoculation at leaf development (April) and senescence (October), the strains were suppressed by the indigenous bacteria at stem elongation (June). Transconjugants could be detected only at this phenological stage. Indigenous bacteria harbouring RP4-Tn-luc became established with densities ranging from 2 × 10(5) to 9 × 10(6) CFU g(-1) fresh weight 3 and 10 weeks after inoculation. The increased colonization of the cuttings by indigenous bacteria at stem elongation seemed to strongly compete with the introduced strains. Otherwise, the phenological stage of the plants as well as the density of the indigenous recipients could serve as the driver for a more frequent conjugative plasmid transfer. A phylogenetic assignment of transconjugants indicated the transfer of RP4-Tn-luc into six genera of Proteobacteria, mainly Sphingomonas, Stenotrophomonas and Xanthomonas.
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Affiliation(s)
- Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, D-15374 Müncheberg, Germany
| | - Regina Becker
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, D-15374 Müncheberg, Germany
| | - Kristina Ulrich
- Johann Heinrich von Thünen-Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Forest Genetics, Waldsieversdorf D-15377, Germany
| | - Dietrich Ewald
- Johann Heinrich von Thünen-Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Forest Genetics, Waldsieversdorf D-15377, Germany
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41
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Tejerizo GT, Bañuelos LA, Cervantes L, Gaytán P, Pistorio M, Romero D, Brom S. Development of molecular tools to monitor conjugative transfer in rhizobia. J Microbiol Methods 2015; 117:155-63. [PMID: 26272377 DOI: 10.1016/j.mimet.2015.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/26/2023]
Abstract
Evolution of bacterial populations has been extensively driven by horizontal transfer events. Conjugative plasmid transfer is considered the principal contributor to gene exchange among bacteria. Several conjugative and mobilizable plasmids have been identified in rhizobia, and two major molecular mechanisms that regulate their transfer have been described, under laboratory conditions. The knowledge of rhizobial plasmid transfer regulation in natural environments is very poor. In this work we developed molecular tools to easily monitor the conjugative plasmid transfer in rhizobia by flow cytometry (FC) or microscopy. 24 cassettes were constructed by combining a variety of promotors, fluorescent proteins and antibiotic resistance genes, and used to tag plasmids and chromosome of donor strains. We were able to detect plasmid transfer after conversion of non-fluorescent recipients into fluorescent transconjugants. Flow cytometry (FC) was optimized to count donor, recipient and transconjugant strains to determine conjugative transfer frequencies. Results were similar, when determined either by FC or by viable counts. Our constructions also allowed the visualization of transconjugants in crosses performed on bean roots. The tools presented here may also be used for other purposes, such as analysis of transcriptional fusions or single-cell tagging. Application of the system will allow the survey of how different environmental conditions or other regulators modulate plasmid transfer in rhizobia.
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Affiliation(s)
- Gonzalo Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata-CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.
| | - Luis Alfredo Bañuelos
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Laura Cervantes
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Paul Gaytán
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata-CONICET, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - David Romero
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca, Morelos, Mexico
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42
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Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community. ISME JOURNAL 2015; 9:934-45. [PMID: 25333461 DOI: 10.1038/ismej.2014.191] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 08/17/2014] [Accepted: 08/21/2014] [Indexed: 11/08/2022]
Abstract
Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.
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Wolters B, Kyselková M, Krögerrecklenfort E, Kreuzig R, Smalla K. Transferable antibiotic resistance plasmids from biogas plant digestates often belong to the IncP-1ε subgroup. Front Microbiol 2015; 5:765. [PMID: 25653641 PMCID: PMC4301011 DOI: 10.3389/fmicb.2014.00765] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/16/2014] [Indexed: 12/30/2022] Open
Abstract
Manure is known to contain residues of antibiotics administered to farm animals as well as bacteria carrying antibiotic resistance genes (ARGs). These genes are often located on mobile genetic elements. In biogas plants (BGPs), organic substrates such as manure and plant material are mixed and fermented in order to provide energy, and resulting digestates are used for soil fertilization. The fate of plasmid carrying bacteria from manure during the fermentation process is unknown. The present study focused on transferable antibiotic resistance plasmids from digestates of seven BGPs, using manure as a co-substrate, and their phenotypic and genotypic characterization. Plasmids conferring resistance to either tetracycline or sulfadiazine were captured by means of exogenous plasmid isolation from digestates into Pseudomonas putida KT2442 and Escherichia coli CV601 recipients, at transfer frequencies ranging from 10(-5) to 10(-7). Transconjugants (n = 101) were screened by PCR-Southern blot hybridization and real-time PCR for the presence of IncP-1, IncP-1ε, IncW, IncN, IncP-7, IncP-9, LowGC, and IncQ plasmids. While 61 plasmids remained unassigned, 40 plasmids belonged to the IncP-1ε subgroup. All these IncP-1ε plasmids were shown to harbor the genes tet(A), sul1, qacEΔ1, intI1, and integron gene cassette amplicons of different size. Further analysis of 16 representative IncP-1ε plasmids showed that they conferred six different multiple antibiotic resistance patterns and their diversity seemed to be driven by the gene cassette arrays. IncP-1ε plasmids displaying similar restriction and antibiotic resistance patterns were captured from different BGPs, suggesting that they may be typical of this environment. Our study showed that BGP digestates are a potential source of transferable antibiotic resistance plasmids, and in particular the broad host range IncP-1ε plasmids might contribute to the spread of ARGs when digestates are used as fertilizer.
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Affiliation(s)
- Birgit Wolters
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics Braunschweig, Germany ; Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry Braunschweig, Germany
| | - Martina Kyselková
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Soil Biology České Budějovice, Czech Republic
| | - Ellen Krögerrecklenfort
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics Braunschweig, Germany
| | - Robert Kreuzig
- Technische Universität Braunschweig, Institute of Environmental and Sustainable Chemistry Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics Braunschweig, Germany
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Protocol for Evaluating the Permissiveness of Bacterial Communities Toward Conjugal Plasmids by Quantification and Isolation of Transconjugants. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/8623_2014_36] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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Załuga J, Stragier P, Baeyen S, Haegeman A, Van Vaerenbergh J, Maes M, De Vos P. Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle. BMC Genomics 2014; 15:392. [PMID: 24885539 PMCID: PMC4059874 DOI: 10.1186/1471-2164-15-392] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/09/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The genus Clavibacter harbors economically important plant pathogens infecting agricultural crops such as potato and tomato. Although the vast majority of Clavibacter strains are pathogenic, there is an increasing number of non-pathogenic isolates reported. Non-pathogenic Clavibacter strains isolated from tomato seeds are particularly problematic because they affect the current detection and identification tests for Clavibacter michiganensis subsp. michiganensis (Cmm), which is regulated with a zero tolerance in tomato seed. Their misidentification as pathogenic Cmm hampers a clear judgment on the seed quality and health. RESULTS To get more insight in the genetic features linked to the lifestyle of these bacteria, a whole-genome sequence of the tomato seed-borne non-pathogenic Clavibacter LMG 26808 was determined. To gain a better understanding of the molecular determinants of pathogenicity, the genome sequence of LMG 26808 was compared with that of the pathogenic Cmm strain (NCPPB 382). The comparative analysis revealed that LMG 26808 does not contain plasmids pCM1 and pCM2 and also lacks the majority of important virulence factors described so far for pathogenic Cmm. This explains its apparent non-pathogenic nature in tomato plants. Moreover, the genome analysis of LMG 26808 detected sequences from a plasmid originating from a member of Enterobacteriaceae/Klebsiella relative. Genes received that way and coding for antibiotic resistance may provide a competitive advantage for survival of LMG 26808 in its ecological niche. Genetically, LMG 26808 was the most similar to the pathogenic Cmm NCPPB 382 but contained more mobile genetic elements. The genome of this non-pathogenic Clavibacter strain contained also a high number of transporters and regulatory genes. CONCLUSIONS The genome sequence of the non-pathogenic Clavibacter strain LMG 26808 and the comparative analyses with other pathogenic Clavibacter strains provided a better understanding of the genetic bases of virulence and adaptation mechanisms present in the genus Clavibacter.
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Affiliation(s)
- Joanna Załuga
- />Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent, B-9000 Belgium
| | - Pieter Stragier
- />Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent, B-9000 Belgium
| | - Steve Baeyen
- />Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research - ILVO, Burg. Van Gansberghelaan 96, Merelbeke, B-9820 Belgium
| | - Annelies Haegeman
- />Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research - ILVO, Burg. Van Gansberghelaan 96, Merelbeke, B-9820 Belgium
| | - Johan Van Vaerenbergh
- />Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research - ILVO, Burg. Van Gansberghelaan 96, Merelbeke, B-9820 Belgium
| | - Martine Maes
- />Plant Sciences Unit - Crop Protection, Institute for Agricultural and Fisheries Research - ILVO, Burg. Van Gansberghelaan 96, Merelbeke, B-9820 Belgium
| | - Paul De Vos
- />Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent, B-9000 Belgium
- />BCCM/LMG Bacteria collection - Laboratory of Microbiology Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, Gent, B-9000 Belgium
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Single-cell analyses revealed transfer ranges of IncP-1, IncP-7, and IncP-9 plasmids in a soil bacterial community. Appl Environ Microbiol 2013; 80:138-45. [PMID: 24141122 DOI: 10.1128/aem.02571-13] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conjugative transfer ranges of three different plasmids of the incompatibility groups IncP-1 (pBP136), IncP-7 (pCAR1), and IncP-9 (NAH7) were investigated in soil bacterial communities by culture-dependent and culture-independent methods. Pseudomonas putida, a donor of each plasmid, was mated with soil bacteria, and green fluorescent protein (GFP), encoded on the plasmid, was used as a reporter protein for successful transfer. GFP-expressing transconjugants were detected and separated at the single-cell level by flow cytometry. Each cell was then analyzed by PCR and sequencing of its 16S rRNA gene following either whole-genome amplification or cultivation. A large number of bacteria within the phylum Proteobacteria was identified as transconjugants for pBP136 by both culture-dependent and culture-independent methods. Transconjugants belonging to the phyla Actinobacteria, Bacteroidetes, and Firmicutes were detected only by the culture-independent method. Members of the genus Pseudomonas (class Gammaproteobacteria) were identified as major transconjugants of pCAR1 and NAH7 by both methods, whereas Delftia species (class Betaproteobacteria) were detected only by the culture-independent method. The transconjugants represented a minority of the soil bacteria. Although pCAR1-containing Delftia strains could not be cultivated after a one-to-one filter mating assay between the donor and cultivable Delftia strains as recipients, fluorescence in situ hybridization detected pCAR1-containing Delftia cells, suggesting that Delftia was a "transient" host of pCAR1.
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Møller AK, Barkay T, Hansen MA, Norman A, Hansen LH, Sørensen SJ, Boyd ES, Kroer N. Mercuric reductase genes (merA) and mercury resistance plasmids in High Arctic snow, freshwater and sea-ice brine. FEMS Microbiol Ecol 2013; 87:52-63. [DOI: 10.1111/1574-6941.12189] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/18/2013] [Accepted: 07/29/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Annette K. Møller
- Department of Environmental Science; Aarhus University; Roskilde Denmark
| | - Tamar Barkay
- Department of Environmental Science; Aarhus University; Roskilde Denmark
- Department of Biochemistry and Microbiology; Rutgers; The State University of New Jersey; New Brunswick NJ USA
| | - Martin A. Hansen
- Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Anders Norman
- Department of Biology; University of Copenhagen; Copenhagen Denmark
| | - Lars H. Hansen
- Department of Biology; University of Copenhagen; Copenhagen Denmark
| | | | - Eric S. Boyd
- Department of Chemistry and Biochemistry; Montana State University; Bozeman MT USA
| | - Niels Kroer
- Department of Environmental Science; Aarhus University; Roskilde Denmark
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Dunon V, Sniegowski K, Bers K, Lavigne R, Smalla K, Springael D. High prevalence of IncP-1 plasmids and IS1071 insertion sequences in on-farm biopurification systems and other pesticide-polluted environments. FEMS Microbiol Ecol 2013; 86:415-31. [PMID: 23802695 DOI: 10.1111/1574-6941.12173] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 04/22/2013] [Accepted: 06/18/2013] [Indexed: 11/26/2022] Open
Abstract
Mobile genetic elements (MGEs) are considered as key players in the adaptation of bacteria to degrade organic xenobiotic recalcitrant compounds such as pesticides. We examined the prevalence and abundance of IncP-1 plasmids and IS1071, two MGEs that are frequently linked with organic xenobiotic degradation, in laboratory and field ecosystems with and without pesticide pollution history. The ecosystems included on-farm biopurification systems (BPS) processing pesticide-contaminated wastewater and soil. Comparison of IncP-1/IS1071 prevalence between pesticide-treated and nontreated soil and BPS microcosms suggested that both IncP-1 and IS1071 proliferated as a response to pesticide treatment. The increased prevalence of IncP-1 plasmids and IS1071-specific sequences in treated systems was accompanied by an increase in the capacity to mineralize the applied pesticides. Both elements were also encountered in high abundance in field BPS ecosystems that were in operation at farmyards and that showed the capacity to degrade/mineralize a wide range of chlorinated aromatics and pesticides. In contrast, IS1071 and especially IncP-1, MGE were less abundant in field ecosystems without pesticide history although some of them still showed a high IS1071 abundance. Our data suggest that MGE-containing organisms were enriched in pesticide-contaminated environments like BPS where they might contribute to spreading of catabolic genes and to pathway assembly.
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Affiliation(s)
- Vincent Dunon
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
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Quantification of IncP-1 plasmid prevalence in environmental samples. Appl Environ Microbiol 2012; 79:1410-3. [PMID: 23241977 DOI: 10.1128/aem.03728-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To study the role of broad-host-range IncP-1 plasmids in bacterial adaptability to irregular environmental challenges, a quantitative real-time PCR assay was developed that specifically detects the korB gene, which is conserved in all IncP-1 plasmids, in environmental samples. IncP-1 plasmid dynamics in a biopurification system for pesticide wastes were analyzed.
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de la Cruz-Perera CI, Ren D, Blanchet M, Dendooven L, Marsch R, Sørensen SJ, Burmølle M. The ability of soil bacteria to receive the conjugative IncP1 plasmid, pKJK10, is different in a mixed community compared to single strains. FEMS Microbiol Lett 2012; 338:95-100. [PMID: 23106414 DOI: 10.1111/1574-6968.12036] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 10/25/2012] [Indexed: 11/30/2022] Open
Abstract
Horizontal gene transfer by conjugation is common among bacterial populations in soil. It is well known that the host range of plasmids depends on several factors, including the identity of the plasmid host cell. In the present study, however, we demonstrate that the composition of the recipient community is also determining for the dissemination of a conjugative plasmid. We isolated 15 different bacterial strains from soil and assessed the conjugation frequencies of the IncP1 plasmid, pKJK10, by flow cytometry, from two different donors, Escherichia coli and Pseudomonas putida, to either 15 different bacterial strains or to the mixed community composed of all the 15 strains. We detected transfer of pKJK10 from P. putida to Stenotrophomonas rhizophila in a diparental mating, but no transfer was observed to the mixed community. In contrast, for E. coli, transfer was observed only to the mixed community, where Ochrobactrum rhizosphaerae was identified as the dominating plasmid recipient. Our results indicate that the presence of a bacterial community impacts the plasmid permissiveness by affecting the ability of strains to receive the conjugative plasmid.
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