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Zhang Z, Kuang D, Xu X, Zhan Z, Ren H, Shi C. Dissemination of IncC plasmids in Salmonella enterica serovar Thompson recovered from seafood and human diarrheic patients in China. Int J Food Microbiol 2024; 417:110708. [PMID: 38653121 DOI: 10.1016/j.ijfoodmicro.2024.110708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024]
Abstract
Salmonella Thompson is a prevalent foodborne pathogen and a major threat to food safety and public health. This study aims to reveal the dissemination mechanism of S. Thompson with co-resistance to ceftriaxone and ciprofloxacin. In this study, 181 S. Thompson isolates were obtained from a retrospective screening on 2118 serotyped Salmonella isolates from foods and patients, which were disseminated in 12 of 16 districts in Shanghai, China. A total of 10 (5.5 %) S. Thompson isolates exhibited resistance to ceftriaxone (MIC ranging from 8 to 32 μg/mL) and ciprofloxacin (MIC ranging from 2 to 8 μg/mL). The AmpC β-lactamase gene blaCMY-2 and plasmid-mediated quinolone resistance (PMQR) genes of qnrS and qepA were identified in the 9 isolates. Conjugation results showed that the co-transfer of blaCMY-2, qnrS, and qepA occurred on the IncC plasmids with sizes of ∼150 (n = 8) or ∼138 (n = 1) kbp. Three typical modules of ISEcp1-blaCMY-2-blc-sugE, IS26-IS15DIV-qnrS-ISKpn19, and ISCR3-qepA-intl1 were identified in an ST3 IncC plasmid pSH11G0791. Phylogenetic analysis indicated that IncC plasmids evolved into Lineages 1, 2, and 3. IncC plasmids from China including pSH11G0791 in this study fell into Lineage 1 with those from the USA, suggesting their close genotype relationship. In conclusion, to our knowledge, it is the first report of the co-existence of blaCMY-2, qnrS, and qepA in IncC plasmids, and the conjugational transfer contributed to their dissemination in S. Thompson. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by IncC plasmids bearing blaCMY-2, qnrS, and qepA.
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Affiliation(s)
- Zengfeng Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dai Kuang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China; National Health Commission (NHC) Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, China
| | - Xuebin Xu
- Laboratory of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200050, China
| | - Zeqiang Zhan
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Ren
- Xianyang Center for Food and Drug Control, Shaanxi, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
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Han Y, Gao YF, Xu HT, Li JP, Li C, Song CL, Lei CW, Chen X, Wang Q, Ma BH, Wang HN. Characterization and risk assessment of novel SXT/R391 integrative and conjugative elements with multidrug resistance in Proteus mirabilis isolated from China, 2018-2020. Microbiol Spectr 2024; 12:e0120923. [PMID: 38197656 PMCID: PMC10871549 DOI: 10.1128/spectrum.01209-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 11/09/2023] [Indexed: 01/11/2024] Open
Abstract
Proteus mirabilis can transfer transposons, insertion sequences, and gene cassettes to the chromosomes of other hosts through SXT/R391 integrative and conjugative elements (ICEs), significantly increasing the possibility of antibiotic resistance gene (ARG) evolution and expanding the risk of ARGs transmission among bacteria. A total of 103 strains of P. mirabilis were isolated from 25 farms in China from 2018 to 2020. The positive detection rate of SXT/R391 ICEs was 25.2% (26/103). All SXT/R391 ICEs positive P. mirabilis exhibited a high level of overall drug resistance. Conjugation experiments showed that all 26 SXT/R391 ICEs could efficiently transfer to Escherichia coli EC600 with a frequency of 2.0 × 10-7 to 6.0 × 10-5. The acquired ARGs, genetic structures, homology relationships, and conservation sequences of 26 (19 different subtypes) SXT/R391 ICEs were investigated by high-throughput sequencing, whole-genome typing, and phylogenetic tree construction. ICEPmiChnHBRJC2 carries erm (42), which have never been found within an SXT/R391 ICE in P. mirabilis, and ICEPmiChnSC1111 carries 19 ARGs, including clinically important cfr, blaCTX-M-65, and aac(6')-Ib-cr, making it the ICE with the most ARGs reported to date. Through genetic stability, growth curve, and competition experiments, it was found that the transconjugant of ICEPmiChnSCNNC12 did not have a significant fitness cost on the recipient bacterium EC600 and may have a higher risk of transmission and dissemination. Although the transconjugant of ICEPmiChnSCSZC20 had a relatively obvious fitness cost on EC600, long-term resistance selection pressure may improve bacterial fitness through compensatory adaptation, providing scientific evidence for risk assessment of horizontal transfer and dissemination of SXT/R391 ICEs in P. mirabilis.IMPORTANCEThe spread of antibiotic resistance genes (ARGs) is a major public health concern. The study investigated the prevalence and genetic diversity of integrative and conjugative elements (ICEs) in Proteus mirabilis, which can transfer ARGs to other hosts. The study found that all of the P. mirabilis strains carrying ICEs exhibited a high level of drug resistance and a higher risk of transmission and dissemination of ARGs. The analysis of novel multidrug-resistant ICEs highlighted the potential for the evolution and spread of novel resistance mechanisms. These findings emphasize the importance of monitoring the spread of ICEs carrying ARGs and the urgent need for effective strategies to combat antibiotic resistance. Understanding the genetic diversity and potential for transmission of ARGs among bacteria is crucial for developing targeted interventions to mitigate the threat of antibiotic resistance.
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Affiliation(s)
- Yun Han
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yu-Feng Gao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - He-ting Xu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jin-Peng Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Cai-Liang Song
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chang-Wei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xuan Chen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qin Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Bo-Heng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hong-Ning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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Ryan MP, Carraro N, Slattery S, Pembroke JT. Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria. Crit Rev Microbiol 2024; 50:105-126. [PMID: 36634159 DOI: 10.1080/1040841x.2022.2161870] [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: 08/20/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.
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Affiliation(s)
- Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon, Limerick, Ireland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Shannon Slattery
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
| | - J Tony Pembroke
- Department of Chemical Sciences, School of Natural Sciences, University of Limerick, Ireland
- Bernal Institute, University of Limerick, Ireland
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Tamayo-Leiva J, Alcorta J, Sepúlveda F, Fuentes-Alburquenque S, Arroyo JI, González-Pastor JE, Díez B. Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton. ISME COMMUNICATIONS 2024; 4:ycae059. [PMID: 38770060 PMCID: PMC11104534 DOI: 10.1093/ismeco/ycae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024]
Abstract
Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.
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Affiliation(s)
- Javier Tamayo-Leiva
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
| | - Jaime Alcorta
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
| | - Felipe Sepúlveda
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
| | - Sebastián Fuentes-Alburquenque
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O’Higgins, Santiago, Chile
- Departamento de Matemáticas y Ciencias de la Ingeniería, Facultad de Ingeniería, Ciencia y Tecnología, Universidad Bernardo O’Higgins, Santiago, Chile
| | - José Ignacio Arroyo
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- The Santa Fe Institute, Santa Fe, NM 87131, United States
- Centro de Modelamiento Matemático, Universidad de Chile, IRL 2807 CNRS Beauchef 851, Santiago, Chile
| | - José Eduardo González-Pastor
- Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA. Carretera de Ajalvir km 4, Torrejón de Ardoz 28850 Madrid, Spain
| | - Beatriz Díez
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
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Zheng Q, Li L, Yin X, Che Y, Zhang T. Is ICE hot? A genomic comparative study reveals integrative and conjugative elements as "hot" vectors for the dissemination of antibiotic resistance genes. mSystems 2023; 8:e0017823. [PMID: 38032189 PMCID: PMC10734551 DOI: 10.1128/msystems.00178-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/14/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Different from other extensively studied mobile genetic elements (MGEs) whose discoveries were initiated decades ago (1950s-1980s), integrative and conjugative elements (ICEs), a diverse array of more recently identified elements that were formally termed in 2002, have aroused increasing concern for their crucial contribution to the dissemination of antibiotic resistance genes (ARGs). However, the comprehensive understanding on ICEs' ARG profile across the bacterial tree of life is still blurred. Through a genomic study by comparison with two key MGEs, we, for the first time, systematically investigated the ARG profile as well as the host range of ICEs and also explored the MGE-specific potential to facilitate ARG propagation across phylogenetic barriers. These findings could serve as a theoretical foundation for risk assessment of ARGs mediated by distinct MGEs and further to optimize therapeutic strategies aimed at restraining antibiotic resistance crises.
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Affiliation(s)
- Qi Zheng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| | - Liguan Li
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| | - You Che
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| | - Tong Zhang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
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van Dijk B, Buffard P, Farr AD, Giersdorf F, Meijer J, Dutilh BE, Rainey PB. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome. ISME COMMUNICATIONS 2023; 3:90. [PMID: 37640834 PMCID: PMC10462680 DOI: 10.1038/s43705-023-00294-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.
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Affiliation(s)
- Bram van Dijk
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
| | - Pauline Buffard
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Andrew D Farr
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Franz Giersdorf
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jeroen Meijer
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL CNRS, Paris, France.
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Fu J, Liu Y, Wang F, Zong G, Wang Z, Zhong C, Cao G. Glabridin inhibited the spread of polymyxin-resistant Enterobacterium carrying ICE MmoMP63. Front Microbiol 2023; 14:1188900. [PMID: 37283918 PMCID: PMC10239875 DOI: 10.3389/fmicb.2023.1188900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction The role of integrative and conjugative elements (ICEs) in antibiotic resistance in Morganella morganii is unknown. This study aimed to determine whether an ICE identified in the M. morganii genome contributed to the polymyxin resistance. Methods Whole-genome sequencing was performed followed by bioinformatics analyses to identify ICEs and antibiotic resistance genes. Conjugation assays were performed to analyze the transferability of a discovered ICE. A drug transporter encoded on the ICE was heterogeneously expressed in Escherichia coli, minimum inhibitory concentrations of antibiotics were determined, and a traditional Chinese medicine library was screened for potential efflux pump inhibitors. Results An antibiotic resistance-conferring ICE, named ICEMmoMP63, was identified. ICEMmoMP63 was verified to be horizontally transferred among Enterobacteriaceae bacteria. G3577_03020 in ICEMmoMP63 was found to mediate multiple antibiotic resistances, especially polymyxin resistance. However, natural compound glabridin was demonstrated to inhibit polymyxin resistance. Discussion Our findings support the need for monitoring dissemination of ICEMmoMP63 in Enterobacteriaceae bacteria. Combined glabridin and polymyxin may have therapeutic potential for treating infections from multi-drug resistant bacteria carrying ICEMmoMP63.
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Affiliation(s)
- Jiafang Fu
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- National Health Commission (NHC) Key Laboratory of Biotechnology Drugs. Shandong Academy of Medical Sciences, Jinan, China
| | - Yayu Liu
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- National Health Commission (NHC) Key Laboratory of Biotechnology Drugs. Shandong Academy of Medical Sciences, Jinan, China
| | | | - Gongli Zong
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- National Health Commission (NHC) Key Laboratory of Biotechnology Drugs. Shandong Academy of Medical Sciences, Jinan, China
| | - Zhen Wang
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Chuanqing Zhong
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China
| | - Guangxiang Cao
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- National Health Commission (NHC) Key Laboratory of Biotechnology Drugs. Shandong Academy of Medical Sciences, Jinan, China
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Han K, Li Y, Zhang Z, Sun L, Wang ET, Li Y. Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids. Microb Genom 2023; 9. [PMID: 37133904 DOI: 10.1099/mgen.0.001004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The successful symbiosis between the partners mainly depends on the nod and nif genes in rhizobia, while the specific symbiosis is mainly determined by the structure of Nod factors and the corresponding secretion systems (type III secretion system; T3SS), etc. These symbiosis genes are usually located on symbiotic plasmids or a chromosomal symbiotic island, both could be transferred interspecies. In our previous studies, Sesbania cannabina-nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of Rhizobium spp., harboured extraordinarily highly conserved symbiosis genes, suggesting that horizontal transfer of symbiosis genes might have happened among them. In order to learn the genomic basis of diversification of rhizobia under the selection of host specificity, we performed this study to compare the complete genome sequences of four Rhizobium strains associated with S. cannabina, YTUBH007, YTUZZ027, YTUHZ044 and YTUHZ045. Their complete genomes were sequenced and assembled at the replicon level. Each strain represents a different species according to the average nucleotide identity (ANI) values calculated using the whole-genome sequences; furthermore, except for YTUBH007, which was classified as Rhizobium binae, the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345-402 kb containing complete nod, nif, fix, T3SS and conjugal transfer genes was detected in each strain. The high ANI and amino acid identity (AAI) values, as well as the close phylogenetic relationships among the entire symbiotic plasmid sequences, indicate that they have the same origin and the entire plasmid has been transferred among different Rhizobium species. These results indicate that S. cannabina stringently selects a certain symbiosis gene background of the rhizobia for nodulation, which might have forced the symbiosis genes to transfer from some introduced rhizobia to the related native or local-condition-adapted bacteria. The existence of almost complete conjugal transfer related elements, but not the gene virD, indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a virD-independent pathway or through another unidentified gene. This study provides insight for the better understanding of high-frequency symbiotic plasmid transfer, host-specific nodulation and the host shift for rhizobia.
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Affiliation(s)
- Kunming Han
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - Zhenpeng Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, PR China
| | - Liqin Sun
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Yan Li
- Yantai Key Laboratory of Characteristic Agricultural Bioresource Conservation & Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, Shandong 264005, PR China
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Lekired A, Cherif-Silini H, Silini A, Ben Yahia H, Ouzari HI. Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments. Genomics 2023; 115:110579. [PMID: 36792019 DOI: 10.1016/j.ygeno.2023.110579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.
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Affiliation(s)
- Abdelmalek Lekired
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hafsa Cherif-Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Allaoua Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Hamza Ben Yahia
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hadda-Imene Ouzari
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia.
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10
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McKeithen-Mead SA, Grossman AD. Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host. PLoS Genet 2023; 19:e1010524. [PMID: 36780569 PMCID: PMC9956884 DOI: 10.1371/journal.pgen.1010524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/24/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are major contributors to genome plasticity in bacteria. ICEs reside integrated in the chromosome of a host bacterium and are passively propagated during chromosome replication and cell division. When activated, ICEs excise from the chromosome and may be transferred through the ICE-encoded conjugation machinery into a recipient cell. Integration into the chromosome of the new host generates a stable transconjugant. Although integration into the chromosome of a new host is critical for the stable acquisition of ICEs, few studies have directly investigated the molecular events that occur in recipient cells during generation of a stable transconjugant. We found that integration of ICEBs1, an ICE of Bacillus subtilis, occurred several generations after initial transfer to a new host. Premature integration in new hosts led to cell death and hence decreased fitness of the ICE and transconjugants. Host lethality due to premature integration was caused by rolling circle replication that initiated in the integrated ICEBs1 and extended into the host chromosome, resulting in catastrophic genome instability. Our results demonstrate that the timing of integration of an ICE is linked to cessation of autonomous replication of the ICE, and that perturbing this linkage leads to a decrease in ICE and host fitness due to a loss of viability of transconjugants. Linking integration to cessation of autonomous replication appears to be a conserved regulatory scheme for mobile genetic elements that both replicate and integrate into the chromosome of their host.
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Affiliation(s)
- Saria A. McKeithen-Mead
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Alan D. Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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11
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Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [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: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
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Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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12
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Zhang F, Ye X, Yin Z, Hu M, Wang B, Liu W, Li B, Ren H, Jin Y, Yue J. Comparative genomics reveals new insights into the evolution of the IncA and IncC family of plasmids. Front Microbiol 2022; 13:1045314. [PMID: 36466664 PMCID: PMC9709138 DOI: 10.3389/fmicb.2022.1045314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/24/2022] [Indexed: 06/13/2024] Open
Abstract
Incompatibility groups IncA and IncC plasmids are of great concern due to their ability to disseminate antibiotic resistance in bacteria via conjugative transfer. A deep understanding of their genomic structures and evolutionary characteristics is of great significance for improving our knowledge about its multidrug-resistance evolution and dissemination. However, current knowledge of their backbone structure, features of core functional modules and the characteristics of variable regions is based on a few plasmids, which highlights the need for a comprehensive systematic study. The present study thoroughly compared and analysed 678 IncA and IncC plasmid genomes. We found that their core functional genes were occasionally deficient and sometimes existed as multiple functional copies/multiple families, which resulted in much diversity. The phylogeny of 13 core functional genes corresponded well to the plasmid subtypes. The conjugative transfer system gained diverse complexity and exhibited many previously unnoticed types with multiple combinations. The insertion of mobile genetic elements (MGEs) in plasmids varied between types and was present in 4 insertion spots in different types of plasmids with certain types of transposons, integrons and insertion sequences. The impact of gene duplication, deletion, the insertion of MGEs, genome rearrangement and recombination resulted in the complex dynamic variable backbone of IncA and IncC plasmids. And IncA and IncC plasmids were more complex than their closest relative SXT/R391 integrative conjugative elements (ICEs), which included nearly all of the diversity of SXT/R391 in key systems. Our work demonstrated a global and systematic view of the IncA and IncC plasmids and provides many new insights into their genome evolution.
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Affiliation(s)
- Fengwei Zhang
- Medical College of Guizhou University, Guiyang, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Xianwei Ye
- Medical College of Guizhou University, Guiyang, China
- Guizhou Provincial People’s Hospital, Guiyang, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, China
| | - Mingda Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Boqian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Wenting Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Beiping Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hongguang Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yuan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Yue
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
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13
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Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria. Mob DNA 2022; 13:19. [PMID: 35962419 PMCID: PMC9373382 DOI: 10.1186/s13100-022-00275-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/22/2022] [Indexed: 11/29/2022] Open
Abstract
Background ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact. Results Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants. Conclusions Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00275-1.
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Mohapatra B, Malhotra H, Phale PS. Life Within a Contaminated Niche: Comparative Genomic Analyses of an Integrative Conjugative Element ICE nahCSV86 and Two Genomic Islands From Pseudomonas bharatica CSV86 T Suggest Probable Role in Colonization and Adaptation. Front Microbiol 2022; 13:928848. [PMID: 35875527 PMCID: PMC9298801 DOI: 10.3389/fmicb.2022.928848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022] Open
Abstract
Comparative genomic and functional analyses revealed the presence of three genomic islands (GIs, >50 Kb size): ICEnahCSV86, Pseudomonas bharatica genomic island-1 (PBGI-1), and PBGI-2 in the preferentially aromatic-degrading soil bacterium, Pseudomonas bharatica CSV86T. Site-specific genomic integration at or near specific transfer RNAs (tRNAs), near-syntenic structural modules, and phylogenetic relatedness indicated their evolutionary lineage to the type-4 secretion system (T4SS) ICEclc family, thus predicting these elements to be integrative conjugative elements (ICEs). These GIs were found to be present as a single copy in the genome and the encoded phenotypic traits were found to be stable, even in the absence of selection pressure. ICEnahCSV86 harbors naphthalene catabolic (nah-sal) cluster, while PBGI-1 harbors Co-Zn-Cd (czc) efflux genes as cargo modules, whereas PBGI-2 was attributed to as a mixed-function element. The ICEnahCSV86 has been reported to be conjugatively transferred (frequency of 7 × 10–8/donor cell) to Stenotrophomonas maltophilia CSV89. Genome-wide comparative analyses of aromatic-degrading bacteria revealed nah-sal clusters from several Pseudomonas spp. as part of probable ICEs, syntenic to conjugatively transferable ICEnahCSV86 of strain CSV86T, suggesting it to be a prototypical element for naphthalene degradation. It was observed that the plasmids harboring nah-sal clusters were phylogenetically incongruent with predicted ICEs, suggesting genetic divergence of naphthalene metabolic clusters in the Pseudomonas population. Gene synteny, divergence estimates, and codon-based Z-test indicated that ICEnahCSV86 is probably derived from PBGI-2, while multiple recombination events masked the ancestral lineage of PBGI-1. Diversifying selection pressure (dN-dS = 2.27–4.31) imposed by aromatics and heavy metals implied the modular exchange-fusion of various cargo clusters through events like recombination, rearrangement, domain reshuffling, and active site optimization, thus allowing the strain to evolve, adapt, and maximize the metabolic efficiency in a contaminated niche. The promoters (Pnah and Psal) of naphthalene cargo modules (nah, sal) on ICEnahCSV86 were proved to be efficient for heterologous protein expression in Escherichia coli. GI-based genomic plasticity expands the metabolic spectrum and versatility of CSV86T, rendering efficient adaptation to the contaminated niche. Such isolate(s) are of utmost importance for their application in bioremediation and are the probable ideal host(s) for metabolic engineering.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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15
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Wang Q, Li T, Zhu C, Huang X, Yang G. Molecular insights for uranium(VI) adsorption at nano-TiO2 surfaces and reduction by alcohols and biomass sugars. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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16
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Liu M, Liu J, Liu G, Wang H, Wang X, Deng Z, He Y, Ou HY. ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. Sci Data 2022; 9:11. [PMID: 35058462 PMCID: PMC8776819 DOI: 10.1038/s41597-021-01112-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Abstract
Bacterial integrative and conjugative elements (ICEs) are highly modular mobile genetic elements critical to the horizontal transfer of antibiotic resistance and virulence factor genes. To better understand and analyze the ongoing increase of ICEs, we developed an Integrative and Conjugative Element Ontology (ICEO) to represent the gene components, functional modules, and other information of experimentally verified ICEs. ICEO is aligned with the upper-level Basic Formal Ontology and reuses existing reliable ontologies. There are 31,081 terms, including 26,814 classes from 14 ontologies and 4128 ICEO-specific classes, representing the information of 271 known experimentally verified ICEs from 235 bacterial strains in ICEO currently and 311 predicted ICEs of 272 completely sequenced Klebsiella pneumoniae strains. Three ICEO use cases were illustrated to investigate complex joins of ICEs and their harboring antibiotic resistance or virulence factor genes by using SPARQL or DL query. ICEO has been approved as an Open Biomedical Ontology library ontology. It may be dedicated to facilitating systematical ICE knowledge representation, integration, and computer-assisted queries.
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Affiliation(s)
- Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jialin Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guitian Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Hui Wang
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xiaoli Wang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yongqun He
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
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17
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Fu X, Lyu L, Wang Y, Zhang Y, Guo X, Chen Q, Liu C. Safety assessment and probiotic characteristics of Enterococcus lactis JDM1. Microb Pathog 2022; 163:105380. [PMID: 34979271 DOI: 10.1016/j.micpath.2021.105380] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVE The aims of this study were to evaluate the safety and probiotic characteristics of the newly isolated Enterococcus lactis strain JDM1. METHODS Safety assessment of E. lactis JDM1 was accomplished by the combination of whole genome sequence information analysis and phenotypic assays, including antimicrobial susceptibility test, haemolysis assay, biogenic amine production assay, cytotoxicity assay. The bacteriostatic experiment and gastrointestinal tolerance experiment were also conducted to evaluate its applicability. RESULTS E. lactis JDM1 possesses good gastrointestinal tolerance and can inhibit the growth of the pathogenic bacteria Clostridioides difficile and Listeria monocytogenes. The chromosome size of JDM1 was 2,570,998 bp with a GC content of 38.46%, which contained a plasmid. One intact prophage, 13 genomic islands and 19 IS elements were predicted in the JDM1 chromosome. Five resistance-related genes and seven virulence-related genes were predicted in the genome. Most resistance genes were conserved, and virulence factors were not related to functional pathogenicity. Antimicrobial susceptibility tests showed that JDM1 was sensitive to tedizolid, ciprofloxacin, levofloxacin, penicillin, ampicillin, vancomycin, linezolid, tetracycline, high-level gentamicin and high-level streptomycin. Genes encoding putative enzymes responsible for adverse metabolites were not found and JDM1 was unable to produce the six main biogenic amines. Cytotoxicity test showed that the JDM1 supernatant had no toxic effect. CONCLUSION E. lactis JDM1 is expected to be developed as a probiotic, and its probiotic properties are worthy of further exploration.
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Affiliation(s)
- Xiaomei Fu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Lyu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Wang
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yan Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qian Chen
- Institute of Intestinal Diseases, Shanghai Tenth People's Hospital Affiliated to Tongji University, Shanghai, 200072, China.
| | - Chang Liu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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18
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Ramsay JP, Bastholm TR, Verdonk CJ, Tambalo DD, Sullivan JT, Harold LK, Panganiban BA, Colombi E, Perry BJ, Jowsey W, Morris C, Hynes MF, Bond CS, Cameron ADS, Yost CK, Ronson CW. An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element. Nucleic Acids Res 2021; 50:975-988. [PMID: 34904658 PMCID: PMC8789080 DOI: 10.1093/nar/gkab1217] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore, QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.
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Affiliation(s)
- Joshua P Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Tahlia R Bastholm
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Callum J Verdonk
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.,Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Dinah D Tambalo
- Biology Department, University of Regina, Regina, SK S4S 0A2, Canada
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Beatrice A Panganiban
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Elena Colombi
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Benjamin J Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - William Jowsey
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Calum Morris
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 4V8, Canada
| | - Charles S Bond
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | | | | | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
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The Facts and Family Secrets of Plasmids That Replicate via the Rolling-Circle Mechanism. Microbiol Mol Biol Rev 2021; 86:e0022220. [PMID: 34878299 DOI: 10.1128/mmbr.00222-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plasmids are self-replicative DNA elements that are transferred between bacteria. Plasmids encode not only antibiotic resistance genes but also adaptive genes that allow their hosts to colonize new niches. Plasmid transfer is achieved by conjugation (or mobilization), phage-mediated transduction, and natural transformation. Thousands of plasmids use the rolling-circle mechanism for their propagation (RCR plasmids). They are ubiquitous, have a high copy number, exhibit a broad host range, and often can be mobilized among bacterial species. Based upon the replicon, RCR plasmids have been grouped into several families, the best known of them being pC194 and pUB110 (Rep_1 family), pMV158 and pE194 (Rep_2 family), and pT181 and pC221 (Rep_trans family). Genetic traits of RCR plasmids are analyzed concerning (i) replication mediated by a DNA-relaxing initiator protein and its interactions with the cognate DNA origin, (ii) lagging-strand origins of replication, (iii) antibiotic resistance genes, (iv) mobilization functions, (v) replication control, performed by proteins and/or antisense RNAs, and (vi) the participating host-encoded functions. The mobilization functions include a relaxase initiator of transfer (Mob), an origin of transfer, and one or two small auxiliary proteins. There is a family of relaxases, the MOBV family represented by plasmid pMV158, which has been revisited and updated. Family secrets, like a putative open reading frame of unknown function, are reported. We conclude that basic research on RCR plasmids is of importance, and our perspectives contemplate the concept of One Earth because we should incorporate bacteria into our daily life by diminishing their virulence and, at the same time, respecting their genetic diversity.
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20
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van Vliet AHM, Charity OJ, Reuter M. A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare? Microb Genom 2021; 7. [PMID: 34766904 PMCID: PMC8743540 DOI: 10.1099/mgen.0.000729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICEs) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanisms such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of the pVir, pTet and PCC42 plasmids and a new 70–129 kb ICE (CampyICE1) in the foodborne bacterial pathogens Campylobacter jejuni and Campylobacter coli. CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli. CampyICE1 is conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5829 (2.3 %) C. jejuni genomes and 92/1347 (6.8 %) C. coli genomes. Similar ICEs were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries three separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer-variant families. A total of 69 spacers and 10 spacer-variant families (63.7 %) were predicted to target Campylobacter plasmids. The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of the pVir, pTet and pCC42 plasmids (188/214 genomes, 87.9 %), suggesting that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter.
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Affiliation(s)
- Arnoud H M van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Oliver J Charity
- Quadram Institute Bioscience, Microbes in the Food Chain programme, Norwich, UK
| | - Mark Reuter
- Quadram Institute Bioscience, Microbes in the Food Chain programme, Norwich, UK
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21
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Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants. THE ISME JOURNAL 2021; 15:2817-2829. [PMID: 33820946 PMCID: PMC8443634 DOI: 10.1038/s41396-021-00969-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 02/01/2023]
Abstract
Antibiotic subsistence in bacteria represents an alternative resistance machinery, while paradoxically, it is also a cure for environmental resistance. Antibiotic-subsisting bacteria can detoxify antibiotic-polluted environments and prevent the development of antibiotic resistance in environments. However, progress toward efficient in situ engineering of antibiotic-subsisting bacteria is hindered by the lack of mechanistic and predictive understanding of the assembly of the functioning microbiome. By top-down manipulation of wastewater microbiomes using sulfadiazine as the single limiting source, we monitored the ecological selection process that forces the wastewater microbiome to perform efficient sulfadiazine subsistence. We found that the community-level assembly selects for the same three families rising to prominence across different initial pools of microbiomes. We further analyzed the assembly patterns using a linear model. Detailed inspections of the sulfonamide metabolic gene clusters in individual genomes of isolates and assembled metagenomes reveal limited transfer potential beyond the boundaries of the Micrococcaceae lineage. Our results open up new possibilities for engineering specialist bacteria for environmental applications.
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22
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Genomic characterization of an extensively drug-resistant chicken-borne Salmonella Indiana isolate carrying an IncHI2-IncHI2A plasmid. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Zhu C, Huang X, Li T, Wang Q, Yang G. Mechanisms for Cr(VI) reduction by alcohols over clay edges: Reactive differences between ethanol and ethanediol, and selective conversions to Cr(IV), Cr(III) and Cr(II) species. J Colloid Interface Sci 2021; 603:37-47. [PMID: 34186408 DOI: 10.1016/j.jcis.2021.06.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
Catalytic reduction by alcohols over clay minerals works efficiently under a wide range of pH and represents an emerging approach to control Cr(VI) contamination. Herein, mechanisms for Cr(VI) adsorption and reduction at clay edges are addressed by dispersion-corrected periodic DFT calculations, considering different active sites, and types (monohydric and polyhydric) and coverage of alcohols. Cr(VI) adsorbs favorably at clay edges, forming direct bonds and strong H-bonds. Mechanisms for Cr(VI) reduction by alcohols are largely determined by π-conjugation development, and efficient conversion conduces to Cr(VI) removal. Cr(II), Cr(III) and Cr(IV) are useful for different purposes, and high selectivity towards these products is realized through rational catalysts design: 1) Cr(IV) dominates at Al3+ site with all ethanol coverage, Al3+ site with high-coverage ethanediol, and Mg2+ site with low-coverage ethanol; 2) Cr(III) dominates at Al3+ and Mg2+ sites with low-coverage ethanediol; 3) Cr(II) dominates at Mg2+ site with high-coverage ethanol or ethanediol. Results agree finely with experimental observations available, and significant new insights have been provided for Cr management and recycling. Detailed electronic structure and vibrational analyses, which can also guide future experimental studies, manifest that Cr(VI) reduction progresses are effectively monitored by ESR and FT-IR techniques.
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Affiliation(s)
- Chang Zhu
- College of Resources and Environments & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, Chongqing 400715, China
| | - Xiaoxiao Huang
- College of Resources and Environments & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, Chongqing 400715, China
| | - Tingting Li
- College of Resources and Environments & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, Chongqing 400715, China
| | - Qian Wang
- College of Resources and Environments & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, Chongqing 400715, China
| | - Gang Yang
- College of Resources and Environments & Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, Southwest University, Chongqing 400715, China.
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24
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Shang D, Zhao H, Xu X, Arunachalam K, Chang J, Bai L, Shi C. Conjugative IncHI2 plasmid harboring novel class 1 integron mediated dissemination of multidrug resistance genes in Salmonella Typhimurium. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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25
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Geng P, Cheng J, Yuan Z, Xiong H, Wang H, Hu X. Horizontal transfer of large plasmid with type IV secretion system and mosquitocidal genomic island with excision and integration capabilities in Lysinibacillus sphaericus. Environ Microbiol 2021; 23:5131-5146. [PMID: 33728723 DOI: 10.1111/1462-2920.15467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/05/2021] [Accepted: 03/14/2021] [Indexed: 01/09/2023]
Abstract
We identified a ~30-kb genomic island (named GI8) carrying the binary toxin gene operon binA/binB on both the chromosome and large pBsph plasmid in the mosquitocidal Lysinibacillus sphaericus C3-41 strain. We found that GI8 is related to the occurrence of binA/binB within L. sphaericus and displays excision and integration capability by recognizing the attB region, which consists of a 2-nt target site (AT) flanked by an 11-nt imperfect inverted repeat. pBsph and two pBsph-like plasmids (p2362 and p1593) were found to carry a type IV secretion system (T4SS) and displayed transmissibility within a narrow host range specific to L. sphaericus. GI8 can be co-transferred with pBsph as a composite element by integration into its attB site, then excised from pBsph and re-integrated into the chromosomal attB site in the new host. The potential hosts of GI8, regardless of whether they are toxic or non-toxic to mosquito larvae, share good collinearity at the chromosomal level. Data indicated that the appearance of the mosquitocidal L. sphaericus lineage was driven by horizontal transfer of the T4SS-type conjugative plasmid and GI8 with excision and specific integration capability.
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Affiliation(s)
- Peiling Geng
- College of Life Science, South-Central University for Nationalities, Wuhan, 430074, China
| | - Jiao Cheng
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhiming Yuan
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hairong Xiong
- College of Life Science, South-Central University for Nationalities, Wuhan, 430074, China
| | - Haiying Wang
- College of Life Science, South-Central University for Nationalities, Wuhan, 430074, China
| | - Xiaomin Hu
- College of Life Science, South-Central University for Nationalities, Wuhan, 430074, China
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26
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Valdelvira R, Bordanaba-Ruiseco L, Martín-Huestamendía C, Ruiz-Masó JA, Del Solar G. Acidic pH Decreases the Endonuclease Activity of Initiator RepB and Increases the Stability of the Covalent RepB-DNA Intermediate while Has Only a Limited Effect on the Replication of Plasmid pMV158 in Lactococcus lactis. Front Mol Biosci 2021; 8:634461. [PMID: 33889596 PMCID: PMC8056398 DOI: 10.3389/fmolb.2021.634461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/27/2021] [Indexed: 11/28/2022] Open
Abstract
Plasmid vectors constitute a valuable tool for homologous and heterologous gene expression, for characterization of promoter and regulatory regions, and for genetic manipulation and labeling of bacteria. During the last years, a series of vectors based on promiscuous replicons of the pMV158 family have been developed for their employment in a variety of Gram-positive bacteria and proved to be useful for all above applications in lactic acid bacteria. A proper use of the plasmid vectors requires detailed knowledge of their main replicative features under the changing growth conditions of the studied bacteria, such as the acidification of the culture medium by lactic acid production. Initiation of pMV158 rolling-circle replication is catalyzed by the plasmid-encoded RepB protein, which performs a sequence-specific cleavage on one of the parental DNA strands and, as demonstrated in this work, establishes a covalent bond with the 5′-P end generated in the DNA. This covalent adduct must last until the leading-strand termination stage, where a new cleavage on the regenerated nick site and a subsequent strand-transfer reaction result in rejoining of the ends of the cleaved parental strand, whereas hydrolysis of the newly-generated adduct would release the protein from a nicked double-stranded DNA plasmid form. We have analyzed here the effect of pH on the different in vitro reactions catalyzed by RepB and on the in vivo replication ability of plasmid pMV158. We show that acidic pH greatly impairs the catalytic activity of the protein and reduces hydrolysis of the covalent RepB-DNA adduct, as expected for the nucleophilic nature of these reactions. Conversely, the ability of pMV158 to replicate in vivo, as monitored by the copy number and segregational stability of the plasmid in Lactococcus lactis, remains almost intact at extracellular pHs ranging from 7.0 to 5.0, and a significant reduction (by ∼50%) in the plasmid copy number per chromosome equivalent is only observed at pH 4.5. Moreover, the RepB to pMV158 molar ratio is increased at pH 4.5, suggesting the existence of compensatory mechanisms that operate in vivo to allow pMV158 replication at pH values that severely disturb the catalytic activity of the initiator protein.
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Affiliation(s)
- Rafael Valdelvira
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Lorena Bordanaba-Ruiseco
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Cristina Martín-Huestamendía
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Angel Ruiz-Masó
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gloria Del Solar
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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27
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Szabó M, Murányi G, Kiss J. IncC helper dependent plasmid-like replication of Salmonella Genomic Island 1. Nucleic Acids Res 2021; 49:832-846. [PMID: 33406256 PMCID: PMC7826253 DOI: 10.1093/nar/gkaa1257] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/24/2020] [Accepted: 12/17/2020] [Indexed: 12/16/2022] Open
Abstract
The Salmonella genomic island 1 (SGI1) and its variants are mobilized by IncA and IncC conjugative plasmids. SGI1-family elements and their helper plasmids are effective transporters of multidrug resistance determinants. SGI1 exploits the transfer apparatus of the helper plasmid and hijacks its activator complex, AcaCD, to trigger the expression of several SGI1 genes. In this way, SGI1 times its excision from the chromosome to the helper entry and expresses mating pore components that enhance SGI1 transfer. The SGI1-encoded T4SS components and the FlhDC-family activator proved to be interchangeable with their IncC-encoded homologs, indicating multiple interactions between SGI1 and its helpers. As a new aspect of this crosstalk, we report here the helper-induced replication of SGI1, which requires both activators, AcaCD and FlhDCSGI1, and significantly increases the stability of SGI1 when coexists with the helper plasmid. We have identified the oriVSGI1 and shown that S004-repA operon encodes for a translationally coupled leader protein and an IncN2/N3-related RepA that are expressed under the control of the AcaCD-responsive promoter PS004. This replicon transiently maintains SGI1 as a 4–8-copy plasmid, not only stabilizing the island but also contributing to the fast displacement of the helper plasmid.
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Affiliation(s)
- Mónika Szabó
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - Gábor Murányi
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - János Kiss
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
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28
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Co-existence of mphA, oqxAB and blaCTX-M-65 on the IncHI2 Plasmid in highly drug-resistant Salmonella enterica serovar Indiana ST17 isolated from retail foods and humans in China. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107269] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania.,The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania.,Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania.,The Research Institute of the University of Bucharest, Bucharest, Romania
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30
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Grüll MP, Mulligan ME, Lang AS. Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents. FEMS Microbiol Lett 2019; 365:5067299. [PMID: 30085064 DOI: 10.1093/femsle/fny192] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/04/2018] [Indexed: 12/18/2022] Open
Abstract
Bacteria are known to release different types of particles that serve various purposes such as the processing of metabolites, communication, and the transfer of genetic material. One of the most interesting aspects of the production of such particles is the biogenesis and trafficking of complex particles that can carry DNA, RNA, proteins or toxins into the surrounding environment to aid in bacterial survival or lead to gene transfer. Two important bacterial extracellular complexes are membrane vesicles and gene transfer agents. In this review, we will discuss the production, contents and functions of these two types of particles as related to their abilities to facilitate horizontal gene transfer.
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Affiliation(s)
| | - M E Mulligan
- Biochemistry, Memorial University of Newfoundland, St John's, NL, Canada
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31
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Li X, Xie Y, Liu M, Tai C, Sun J, Deng Z, Ou HY. oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. Nucleic Acids Res 2019; 46:W229-W234. [PMID: 29733379 PMCID: PMC6030822 DOI: 10.1093/nar/gky352] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
oriTfinder is a web server that facilitates the rapid identification of the origin of transfer site (oriT) of a conjugative plasmid or chromosome-borne integrative and conjugative element. The utilized back-end database oriTDB was built upon more than one thousand known oriT regions of bacterial mobile genetic elements (MGEs) as well as the known MGE-encoding relaxases and type IV coupling proteins (T4CP). With a combination of similarity searches for the oriTDB-archived oriT nucleotide sequences and the co-localization of the flanking relaxase homologous genes, the oriTfinder can predict the oriT region with high accuracy in the DNA sequence of a bacterial plasmid or chromosome in minutes. The server also detects the other transfer-related modules, including the potential relaxase gene, T4CP gene and the type IV secretion system gene cluster, and the putative genes coding for virulence factors and acquired antibiotic resistance determinants. oriTfinder may contribute to meeting the increasing demands of re-annotations for bacterial conjugative, mobilizable or non-transferable elements and aid in the rapid risk accession of disease-relevant trait dissemination in pathogenic bacteria of interest. oriTfinder is freely available to all users without any login requirement at http://bioinfo-mml.sjtu.edu.cn/oriTfinder.
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Affiliation(s)
- Xiaobin Li
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yingzhou Xie
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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32
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
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33
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Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist Updat 2019. [DOI: 10.1016/j.drup.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Kohler V, Keller W, Grohmann E. Regulation of Gram-Positive Conjugation. Front Microbiol 2019; 10:1134. [PMID: 31191478 PMCID: PMC6540685 DOI: 10.3389/fmicb.2019.01134] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/03/2019] [Indexed: 12/20/2022] Open
Abstract
Type IV Secretion Systems (T4SSs) are membrane-spanning multiprotein complexes dedicated to protein secretion or conjugative DNA transport (conjugation systems) in bacteria. The prototype and best-characterized T4SS is that of the Gram-negative soil bacterium Agrobacterium tumefaciens. For Gram-positive bacteria, only conjugative T4SSs have been characterized in some biochemical, structural, and mechanistic details. These conjugation systems are predominantly encoded by self-transmissible plasmids but are also increasingly detected on integrative and conjugative elements (ICEs) and transposons. Here, we report regulatory details of conjugation systems from Enterococcus model plasmids pIP501 and pCF10, Bacillus plasmid pLS1, Clostridium plasmid pCW3, and staphylococcal plasmid pSK41. In addition, regulation of conjugative processes of ICEs (ICEBs1, ICESt1, ICESt3) by master regulators belonging to diverse repressor families will be discussed. A special focus of this review lies on the comparison of regulatory mechanisms executed by proteins belonging to the RRNPP family. These regulators share a common fold and govern several essential bacterial processes, including conjugative transfer.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, BioTechMed Graz, University of Graz, Graz, Austria
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed Graz, University of Graz, Graz, Austria
| | - Elisabeth Grohmann
- Life Sciences and Technology, Beuth University of Applied Sciences Berlin, Berlin, Germany
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35
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Zhu D, Wan J, Yang Z, Xu J, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Chen X, Cheng A. First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China. Front Vet Sci 2019; 6:128. [PMID: 31069241 PMCID: PMC6491836 DOI: 10.3389/fvets.2019.00128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
We report for the first time the occurrence of integrative conjugative elements (ICEs) in Riemerella anatipestifer (R.anatipestifer) isolated from diseased ducks in China. For this purpose, a total of 48 genome sequences were investigated, which comprised 30 publicly available R. anatipestifer genome sequences, and 18 clinical isolates genomes sequences. Two ICEs, named ICERanRCAD0133-1 and ICERanRCAD0179-1 following the classic nomenclature system, were identified in R. anatipestifer through the use of bioinformatics tools. Comparative analysis revealed that three ICEs in Ornithobacterium rhinotracheale showed a high degree of conservation with the core genes of ICERanRCAD0133-1, while 13 ICEs with high similarity to ICERanRCAD0179-1 were found in Bacteroidetes. Based on the definition of ICE family, ICERanRCAD0179-1 was grouped in CTnDOT/ERL family; however, ICERanRCAD0133-1, which had no significant similarity with known ICEs, might be classified into a novel ICE family. The sequences of ICERanRCAD0133-1 and ICERanRCAD0179-1 were 70890 bp and 49166 bp in length, had 33.14 and 50.34% GC content, and contained 77 CDSs and 51 CDSs, respectively. Cargo genes carried by these two ICEs were predicted to encode: R-M systems, IS elements, a putative TonB-dependent receptor, a bacteriocin/lantibiotic efflux ABC transporter, a tetracycline resistance gene and more. In addition, phylogenetic analyses revealed that ICERanRCAD0179-1 and related ICEs were derived from a common ancestor, which may have undergone divergence prior to integartation into the host bacterial chromosome, and that the core genes co-evolved via a related evolutionary process or experienced only a low degree of recombination events during spread from a common CTnDOT/ERL family ancestor. Collectively, this study is the first identification and characterization of ICEs in R. anatipestifer; and provides new insights into the genetic diversity, evolution, adaptation, antimicrobial resistance, and virulence of R. anatipestifer.
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Affiliation(s)
- Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Jianbang Wan
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jinge Xu
- Guizhou Animal Husbandry and Veterinary Research Institute, Guiyang, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Abstract
The study of the genetics of enterococci has focused heavily on mobile genetic elements present in these organisms, the complex regulatory circuits used to control their mobility, and the antibiotic resistance genes they frequently carry. Recently, more focus has been placed on the regulation of genes involved in the virulence of the opportunistic pathogenic species Enterococcus faecalis and Enterococcus faecium. Little information is available concerning fundamental aspects of DNA replication, partition, and division; this article begins with a brief overview of what little is known about these issues, primarily by comparison with better-studied model organisms. A variety of transcriptional and posttranscriptional mechanisms of regulation of gene expression are then discussed, including a section on the genetics and regulation of vancomycin resistance in enterococci. The article then provides extensive coverage of the pheromone-responsive conjugation plasmids, including sections on regulation of the pheromone response, the conjugative apparatus, and replication and stable inheritance. The article then focuses on conjugative transposons, now referred to as integrated, conjugative elements, or ICEs, and concludes with several smaller sections covering emerging areas of interest concerning the enterococcal mobilome, including nonpheromone plasmids of particular interest, toxin-antitoxin systems, pathogenicity islands, bacteriophages, and genome defense.
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Abstract
Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.
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Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
- Corresponding author: E-mail:
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
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Botelho J, Roberts AP, León-Sampedro R, Grosso F, Peixe L. Carbapenemases on the move: it's good to be on ICEs. Mob DNA 2018; 9:37. [PMID: 30574213 PMCID: PMC6299553 DOI: 10.1186/s13100-018-0141-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022] Open
Abstract
Background The evolution and spread of antibiotic resistance is often mediated by mobile genetic elements. Integrative and conjugative elements (ICEs) are the most abundant conjugative elements among prokaryotes. However, the contribution of ICEs to horizontal gene transfer of antibiotic resistance has been largely unexplored. Results Here we report that ICEs belonging to mating-pair formation (MPF) classes G and T are highly prevalent among the opportunistic pathogen Pseudomonas aeruginosa, contributing to the spread of carbapenemase-encoding genes (CEGs). Most CEGs of the MPFG class were encoded within class I integrons, which co-harbour genes conferring resistance to other antibiotics. The majority of the integrons were located within Tn3-like and composite transposons. Conserved attachment site could be predicted for the MPFG class ICEs. MPFT class ICEs carried the CEGs within composite transposons which were not associated with integrons. Conclusions The data presented here provides a global snapshot of the different CEG-harbouring ICEs and sheds light on the underappreciated contribution of these elements to the evolution and dissemination of antibiotic resistance on P. aeruginosa. Electronic supplementary material The online version of this article (10.1186/s13100-018-0141-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- João Botelho
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Adam P Roberts
- 2Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK.,3Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ricardo León-Sampedro
- 4Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Filipa Grosso
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Luísa Peixe
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
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Botelho J, Grosso F, Quinteira S, Brilhante M, Ramos H, Peixe L. Two decades of blaVIM-2-producing Pseudomonas aeruginosa dissemination: an interplay between mobile genetic elements and successful clones. J Antimicrob Chemother 2018; 73:873-882. [DOI: 10.1093/jac/dkx517] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/08/2017] [Indexed: 12/30/2022] Open
Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Sandra Quinteira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto (CIBIO/UP)/InBio Laboratório Associado, Vairão, Portugal
- Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Porto, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra, PRD, Portugal
| | - Michael Brilhante
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Helena Ramos
- Serviço de Microbiologia, Centro Hospitalar do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Wawrzyniak P, Płucienniczak G, Bartosik D. The Different Faces of Rolling-Circle Replication and Its Multifunctional Initiator Proteins. Front Microbiol 2017; 8:2353. [PMID: 29250047 PMCID: PMC5714925 DOI: 10.3389/fmicb.2017.02353] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Horizontal gene transfer (HGT) contributes greatly to the plasticity and evolution of prokaryotic and eukaryotic genomes. The main carriers of foreign DNA in HGT are mobile genetic elements (MGEs) that have extremely diverse genetic structures and properties. Various strategies are used for the maintenance and spread of MGEs, including (i) vegetative replication, (ii) transposition (and other types of recombination), and (iii) conjugal transfer. In many MGEs, all of these processes are dependent on rolling-circle replication (RCR). RCR is one of the most well characterized models of DNA replication. Although many studies have focused on describing its mechanism, the role of replication initiator proteins has only recently been subject to in-depth analysis, which indicates their involvement in multiple biological process associated with RCR. In this review, we present a general overview of RCR and its impact in HGT. We focus on the molecular characteristics of RCR initiator proteins belonging to the HUH and Rep_trans protein families. Despite analogous mechanisms of action these are distinct groups of proteins with different catalytic domain structures. This is the first review describing the multifunctional character of various types of RCR initiator proteins, including the latest discoveries in the field. Recent reports provide evidence that (i) proteins initiating vegetative replication (Rep) or mobilization for conjugal transfer (Mob) may also have integrase (Int) activity, (ii) some Mob proteins are capable of initiating vegetative replication (Rep activity), and (iii) some Rep proteins can act like Mob proteins to mobilize plasmid DNA for conjugal transfer. These findings have significant consequences for our understanding of the role of RCR, not only in DNA metabolism but also in the biology of many MGEs.
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Affiliation(s)
- Paweł Wawrzyniak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland.,Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Grażyna Płucienniczak
- Department of Bioengineering, Institute of Biotechnology and Antibiotics, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems. Genes (Basel) 2017; 8:genes8110337. [PMID: 29165361 PMCID: PMC5704250 DOI: 10.3390/genes8110337] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution.
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42
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Haskett TL, Ramsay JP, Bekuma AA, Sullivan JT, O'Hara GW, Terpolilli JJ. Evolutionary persistence of tripartite integrative and conjugative elements. Plasmid 2017; 92:30-36. [DOI: 10.1016/j.plasmid.2017.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/28/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
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