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Yao S, Yu J, Zhang T, Xie J, Yan C, Ni X, Guo B, Cui C. Comprehensive analysis of distribution characteristics and horizontal gene transfer elements of bla NDM-1-carrying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:173907. [PMID: 38906294 DOI: 10.1016/j.scitotenv.2024.173907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/08/2024] [Accepted: 06/08/2024] [Indexed: 06/23/2024]
Abstract
The worldwide dissemination of New Delhi metallo-β-lactamase-1 (NDM-1), which mediates resistance to almost all clinical β-lactam antibiotics, is a major public health problem. The global distribution, species, sources, and potential transfer risk of blaNDM-1-carrying bacteria are unclear. Results of a comprehensive analysis of literature in 2010-2022 showed that a total of 6002 blaNDM-1 carrying bacteria were widely distributed around 62 countries with a high trend in the coastal areas. Opportunistic pathogens or pathogens like Klebsiella sp., Escherichia sp., Acinetobacter sp. and Pseudomonas sp. were the four main species indicating the potential microbial risk. Source analysis showed that 86.45 % of target bacteria were isolated from the source of hospital (e.g., Hospital patients and wastewater) and little from surface water (5.07 %) and farms (3.98 %). A plasmid-encoded blaNDM-1Acinetobacter sp. with the resistance mechanisms of antibiotic efflux pump, antibiotic target change and antibiotic degradation was isolated from the wastewater of a typical tertiary hospital. Insertion sequences (IS3 and IS30) located in the adjacent 5 kbp of blaNDM-1-bleMBL gene cluster indicating the transposon-mediated horizontal gene transfer risk. These results showed that the worldwide spread of blaNDM-1-carrying bacteria and its potential horizontal gene transfer risk deserve good control.
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Affiliation(s)
- Shijie Yao
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaqin Yu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Tianyang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jianhao Xie
- Children's Hospital of Fudan University, Shanghai 200233, China
| | - Chicheng Yan
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xuan Ni
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bingbing Guo
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Changzheng Cui
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China; Shanghai environmental protection key laboratory on environmental standard and risk management of chemical pollutants, East China University of Science & Technology, Shanghai 200237, China.
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2
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Selinidis MA, Corliss AC, Chappell J, Silberg JJ. Ribozyme-Mediated Gene-Fragment Complementation for Nondestructive Reporting of DNA Transfer within Soil. ACS Synth Biol 2024. [PMID: 39145471 DOI: 10.1021/acssynbio.4c00264] [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: 08/16/2024]
Abstract
Enzymes that produce volatile metabolites can be coded into genetic circuits to report nondisruptively on microbial behaviors in hard-to-image soils. However, these enzyme reporters remain challenging to apply in gene transfer studies due to leaky off states that can lead to false positives. To overcome this problem, we designed a reporter that uses ribozyme-mediated gene-fragment complementation of a methyl halide transferase (MHT) to regulate the synthesis of methyl halide gases. We split the mht gene into two nonfunctional fragments and attached these to a pair of splicing ribozyme fragments. While the individual mht-ribozyme fragments did not produce methyl halides when transcribed alone in Escherichia coli, coexpression resulted in a spliced transcript that translated the MHT reporter. When cells containing one mht-ribozyme fragment transcribed from a mobile plasmid were mixed with cells that transcribed the second mht-ribozyme fragment, methyl halides were only detected following rare conjugation events. When conjugation was performed in soil, it led to a 16-fold increase in methyl halides in the soil headspace. These findings show how ribozyme-mediated gene-fragment complementation can achieve tight control of protein reporter production, a level of control that will be critical for monitoring the effects of soil conditions on gene transfer and the fidelity of biocontainment measures developed for environmental applications.
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Affiliation(s)
- Malyn A Selinidis
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
| | - Andrew C Corliss
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
| | - James Chappell
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of BioSciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, MS-362, 6100 Main Street, Houston, Texas 77005, United States
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3
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Li HZ, Li WJ, Wang ZJ, Chen QL, Staal Jensen MK, Qiao M, Cui L. Integrating Multiple Bacterial Phenotypes and Bayesian Network for Analyzing Health Risks of Pathogens in Plastisphere. Anal Chem 2024; 96:11374-11382. [PMID: 38949233 DOI: 10.1021/acs.analchem.4c01433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Plastic pollution represents a critical threat to soil ecosystems and even humans, as plastics can serve as a habitat for breeding and refuging pathogenic microorganisms against stresses. However, evaluating the health risk of plastispheres is difficult due to the lack of risk factors and quantification model. Here, DNA sequencing, single-cell Raman-D2O labeling, and transformation assay were used to quantify key risk factors of plastisphere, including pathogen abundance, phenotypic resistance to various stresses (antibiotic and pesticide), and ability to acquire antibiotic resistance genes. A Bayesian network model was newly introduced to integrate these three factors and infer their causal relationships. Using this model, the risk of pathogen in the plastisphere is found to be nearly 3 magnitudes higher than that in free-living state. Furthermore, this model exhibits robustness for risk prediction, even in the absence of one factor. Our framework offers a novel and practical approach to assessing the health risk of plastispheres, contributing to the management of plastic-related threats to human health.
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Affiliation(s)
- Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Wen-Jing Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Jian Wang
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Qing-Lin Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Mia Kristine Staal Jensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Min Qiao
- Research Center for Eco-Environmental Sciences Chinese Academy of Sciences, Beijing 100085, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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Shi J, Sun C, An T, Jiang C, Mei S, Lv B. Unraveling the effect of micro/nanoplastics on the occurrence and horizontal transfer of environmental antibiotic resistance genes: Advances, mechanisms and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174466. [PMID: 38964386 DOI: 10.1016/j.scitotenv.2024.174466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Microplastics can not only serve as vectors of antibiotic resistance genes (ARGs), but also they and even nanoplastics potentially affect the occurrence of ARGs in indigenous environmental microorganisms, which have aroused great concern for the development of antibiotic resistance. This article specifically reviews the effects of micro/nanoplastics (concentration, size, exposure time, chemical additives) and their interactions with other pollutants on environmental ARGs dissemination. The changes of horizontal genes transfer (HGT, i.e., conjugation, transformation and transduction) of ARGs caused by micro/nanoplastics were also summarized. Further, this review systematically sums up the mechanisms of micro/nanoplastics regulating HGT process of ARGs, including reactive oxygen species production, cell membrane permeability, transfer-related genes expression, extracellular polymeric substances production, and ARG donor-recipient adsorption/contaminants adsorption/biofilm formation. The underlying mechanisms in changes of bacterial communities induced by micro/nanoplastics were also discussed as it was an important factor for structuring the profile of ARGs in the actual environment, including causing environmental stress, providing carbon sources, forming biofilms, affecting pollutants distribution and environmental factors. This review contributes to a systematical understanding of the potential risks of antibiotic resistance dissemination caused by micro/nanoplastics and provokes thinking about perspectives for future research and the management of micro/nanoplastics and plastics.
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Affiliation(s)
- Jianhong Shi
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Chaoli Sun
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Tingxuan An
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Changhai Jiang
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Shenglong Mei
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), Shanghai Maritime University, Shanghai 201306, China.
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Muñoz-Gutiérrez I, Cantu L, Shanahan J, Girguis M, de la Cruz M, Mota-Bravo L. Cryptic environmental conjugative plasmid recruits a novel hybrid transposon resulting in a new plasmid with higher dispersion potential. mSphere 2024; 9:e0025224. [PMID: 38771049 PMCID: PMC11332342 DOI: 10.1128/msphere.00252-24] [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: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 05/22/2024] Open
Abstract
Cryptic conjugative plasmids lack antibiotic-resistance genes (ARGs). These plasmids can capture ARGs from the vast pool of the environmental metagenome, but the mechanism to recruit ARGs remains to be elucidated. To investigate the recruitment of ARGs by a cryptic plasmid, we sequenced and conducted mating experiments with Escherichia coli SW4848 (collected from a lake) that has a cryptic IncX (IncX4) plasmid and an IncF (IncFII/IncFIIB) plasmid with five genes that confer resistance to aminoglycosides (strA and strB), sulfonamides (sul2), tetracycline [tet(A)], and trimethoprim (dfrA5). In a conjugation experiment, a novel hybrid Tn21/Tn1721 transposon of 22,570 bp (designated Tn7714) carrying the five ARG mobilized spontaneously from the IncF plasmid to the cryptic IncX plasmid. The IncF plasmid was found to be conjugative when it was electroporated into E. coli DH10B (without the IncX plasmid). Two parallel conjugations with the IncF and the new IncX (carrying the novel Tn7714 transposon) plasmids in two separate E. coli DH10B as donors and E. coli J53 as the recipient revealed that the conjugation rate of the new IncX plasmid (with the novel Tn7714 transposon and five ARGs) is more than two orders of magnitude larger than the IncF plasmid. For the first time, this study shows experimental evidence that cryptic environmental plasmids can capture and transfer transposons with ARGs to other bacteria, creating novel multidrug-resistant conjugative plasmids with higher dispersion potential. IMPORTANCE Cryptic conjugative plasmids are extrachromosomal DNA molecules without antibiotic-resistance genes (ARGs). Environmental bacteria carrying cryptic plasmids with a high conjugation rate threaten public health because they can capture clinically relevant ARGs and rapidly spread them to pathogenic bacteria. However, the mechanism to recruit ARG by cryptic conjugative plasmids in environmental bacteria has not been observed experimentally. Here, we document the first translocation of a transposon with multiple clinically relevant ARGs to a cryptic environmental conjugative plasmid. The new multidrug-resistant conjugative plasmid has a conjugation rate that is two orders of magnitude higher than the original plasmid that carries the ARG (i.e., the new plasmid from the environment can spread ARG more than two orders of magnitude faster). Our work illustrates the importance of studying the mobilization of ARGs in environmental bacteria. It sheds light on how cryptic conjugative plasmids recruit ARGs, a phenomenon at the root of the antibiotic crisis.
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Affiliation(s)
- Iván Muñoz-Gutiérrez
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Luis Cantu
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Jack Shanahan
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Miray Girguis
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Marlene de la Cruz
- School of Biological Sciences, University of California, Irvine, California, USA
| | - Luis Mota-Bravo
- School of Biological Sciences, University of California, Irvine, California, USA
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Moussa J, Gargallo-Viola D, Thomsen LE. A novel high-throughput screening method for identifying compounds that inhibit plasmid conjugation. MethodsX 2024; 12:102740. [PMID: 38737486 PMCID: PMC11087957 DOI: 10.1016/j.mex.2024.102740] [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: 02/21/2024] [Accepted: 05/01/2024] [Indexed: 05/14/2024] Open
Abstract
Plasmid conjugation is an important contributing factor to the spread of antibiotic resistance among bacteria, posing a significant global health threat. Our method introduces an innovative high-throughput screening approach to identify compounds that inhibit or reduce conjugation, addressing the need for new strategies against the spread of antimicrobial resistance. Using Escherichia coli strains as donor and recipient, we screened 3500 compounds from a library provided by ABAC Therapeutics. Each 96 -well plate was loaded with 88 different compounds and bacterial cultures. Every plate also included negative and positive controls of conjugation. After an hour, cultures from wells were spotted on agar plates and assessed visually. Compounds that showed a visible effect on conjugation were retested. Six compounds targeting conjugation were found, showing promise for further analysis.
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Affiliation(s)
- Jennifer Moussa
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | | | - Line Elnif Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
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7
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Ghaly TM, Gillings MR, Rajabal V, Paulsen IT, Tetu SG. Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange. Front Microbiol 2024; 15:1338026. [PMID: 38741746 PMCID: PMC11089894 DOI: 10.3389/fmicb.2024.1338026] [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: 11/14/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence plant health outcomes, driving the spread of both plant growth-promoting and phytopathogenic traits. However, community dynamics, including the range of genetic elements and bacteria involved in this process are still poorly understood. Integrons are genetic elements recently shown to be abundant in plant microbiomes, and are associated with HGT across broad phylogenetic boundaries. They facilitate the spread of gene cassettes, small mobile elements that collectively confer a diverse suite of adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes to investigate the prevalence and functional diversity of integrons in this niche. We found that integrons are particularly abundant in the genomes of Pseudomonadales, Burkholderiales, and Xanthomonadales. In total, we detected nearly 9,000 gene cassettes, and found that many could be involved in plant growth promotion or phytopathogenicity, suggesting that integrons might play a role in bacterial mutualistic or pathogenic lifestyles. The rhizosphere was enriched in cassettes involved in the transport and metabolism of diverse substrates, suggesting that they may aid in adaptation to this environment, which is rich in root exudates. We also found that integrons facilitate cross-species HGT, which is particularly enhanced in the phyllosphere. This finding may provide an ideal opportunity to promote plant growth by fostering the spread of genes cassettes relevant to leaf health. Together, our findings suggest that integrons are important elements in plant microbiomes that drive HGT, and have the potential to facilitate plant host adaptation.
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Affiliation(s)
- Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
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8
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Zorea A, Pellow D, Levin L, Pilosof S, Friedman J, Shamir R, Mizrahi I. Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. Nat Commun 2024; 15:3147. [PMID: 38605009 PMCID: PMC11009399 DOI: 10.1038/s41467-024-47272-x] [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: 08/17/2023] [Accepted: 03/25/2024] [Indexed: 04/13/2024] Open
Abstract
Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid dispersal is predominantly stochastic, indicating neutral processes as the primary driver of their wide distribution. We find that only 20-25% of plasmid DNA is being selected in various disease states, constraining its distribution across hosts. Selective pressures shape specific plasmid segments with distinct ecological functions, influenced by plasmid mobilization lifestyle, antibiotic usage, and inflammatory gut diseases. Notably, these elements are more commonly shared within groups of individuals with similar health conditions, such as Inflammatory Bowel Disease (IBD), regardless of geographic location across continents. These segments contain essential genes such as iron transport mechanisms- a distinctive gut signature of IBD that impacts the severity of inflammation. Our findings shed light on mechanisms driving plasmid dispersal and selection in the human gut, highlighting their role as carriers of vital gene pools impacting bacterial hosts and ecosystem dynamics.
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Affiliation(s)
- Alvah Zorea
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - David Pellow
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - Shai Pilosof
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel
| | - Jonathan Friedman
- Institute of Environmental Sciences, Hebrew University, Rehovot, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Itzhak Mizrahi
- National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
- The Goldman Sonnenfeldt School of Sustainability and Climate Change, Ben-Gurion University of the Negev, 8410501, Be'er Sheva, Israel.
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9
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Liu F, Luo Y, Xu T, Lin H, Qiu Y, Li B. Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment. Front Microbiol 2024; 15:1371388. [PMID: 38638913 PMCID: PMC11025395 DOI: 10.3389/fmicb.2024.1371388] [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: 01/16/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024] Open
Abstract
The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.
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Affiliation(s)
- Fan Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
| | - Yuqiu Luo
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
| | - Tiansi Xu
- School of Environment, Tsinghua University, Beijing, China
| | - Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
| | - Yong Qiu
- School of Environment, Tsinghua University, Beijing, China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China
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10
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Ormsby MJ, Woodford L, Quilliam RS. Can plastic pollution drive the emergence and dissemination of novel zoonotic diseases? ENVIRONMENTAL RESEARCH 2024; 246:118172. [PMID: 38220083 DOI: 10.1016/j.envres.2024.118172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
As the volume of plastic in the environment increases, so too does human interactions with plastic pollution. Similarly, domestic, feral, and wild animals are increasingly interacting with plastic pollution, highlighting the potential for contamination of plastic wastes with animal faeces, urine, saliva, and blood. Substantial evidence indicates that once in the environment, plastics rapidly become colonised by microbial biofilm (the so-called 'plastisphere), which often includes potentially harmful microbial pathogens (including pathogens that are zoonotic in nature). Climate change, increased urbanisation, and the intensification of agriculture, mean that the three-way interactions between humans, animals, and plastic pollution are becoming more frequent, which is significant as almost 60% of emerging human infectious diseases during the last century have been zoonotic. Here, we critically review the potential for contaminated environmental plastics to facilitate the evolution of novel pathogenic strains of microorganisms, and the subsequent role of plastic pollution in the cyclical dissemination of zoonotic pathogens. As the interactions between humans, animals, and plastic pollution continues to grow, and the volume of plastics entering the environment increases, there is clearly an urgent need to better understand the role of plastic waste in facilitating zoonotic pathogen evolution and dissemination, and the effect this can have on environmental and human health.
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Affiliation(s)
- Michael J Ormsby
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - Luke Woodford
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Richard S Quilliam
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
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11
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Zhang L, Yan C, Wen C. Vertical distribution characteristics and transport paths of antibiotic resistance genes in constructed wetland system. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133555. [PMID: 38262322 DOI: 10.1016/j.jhazmat.2024.133555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Although the migration and diffusion of antibiotic resistance genes (ARGs) in soil-plant systems have attracted much attention, the migration and diffusion characteristics between constructed wetlands and soil-plant systems differ greatly. Therefore, it is necessary to conduct research on vertical transmission and diffusion of ARGs in constructed wetlands. The vertical distribution and transmission of ARGs in constructed wetlands were explored via metagenomic analysis. The results showed that the proportion of multidrug ARGs was the largest, ranging from 24.2% to 47.5%. The shared characteristics of ARGs were similar to those of bacteria, and there were fewer unique ARGs and microbial species in mesophyll tissue. Sourcetracker analysis revealed that ARGs transfer between plants and atmosphere was bidirectional, but the diffusion of ARGs to atmosphere through plants was relatively weak. ARGs were mainly transmitted to atmosphere/surrounding environment through substrate and influent, and the contributions of substrate to ARGs in atmosphere/surrounding environment were 59.2% and 78.6%, respectively. ARGs involved in foliar attachment mainly originated from peripheral inputs. ARGs showed nonspecific selection for the host at phylum, class and order levels. These findings suggest that more attention should be given to the potential risks of ARGs in constructed wetlands, to formulate effective control and management strategies.
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Affiliation(s)
- Ling Zhang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Materials Sciences and Engineering, Xinxiang Engineering Research Center for Wastewater Treatment Energy Saving and Emission Reduction, Henan Institute of Technology, Xinxiang 453003, China
| | - Changzhou Yan
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Ce Wen
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Surekha S, Lamiyan AK, Gupta V. Antibiotic Resistant Biofilms and the Quest for Novel Therapeutic Strategies. Indian J Microbiol 2024; 64:20-35. [PMID: 38468748 PMCID: PMC10924852 DOI: 10.1007/s12088-023-01138-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/03/2023] [Indexed: 03/13/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the major leading causes of death around the globe. Present treatment pipelines are insufficient to overcome the critical situation. Prominent biofilm forming human pathogens which can thrive in infection sites using adaptive features results in biofilm persistence. Considering the present scenario, prudential investigations into the mechanisms of resistance target them to improve antibiotic efficacy is required. Regarding this, developing newer and effective treatment options using edge cutting technologies in medical research is the need of time. The reasons underlying the adaptive features in biofilm persistence have been centred on different metabolic and physiological aspects. The high tolerance levels against antibiotics direct researchers to search for novel bioactive molecules that can help combat the problem. In view of this, the present review outlines the focuses on an opportunity of different strategies which are in testing pipeline can thus be developed into products ready to use.
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Affiliation(s)
- Saumya Surekha
- Department of Biochemistry, Panjab University, Chandigarh, India
| | | | - Varsha Gupta
- GMCH: Government Medical College and Hospital, Chandigarh, India
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13
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Røder HL, Christidi E, Amador CI, Music S, Olesen AK, Svensson B, Madsen JS, Herschend J, Kreft JU, Burmølle M. Flagellar interference with plasmid uptake in biofilms: a joint experimental and modeling study. Appl Environ Microbiol 2024; 90:e0151023. [PMID: 38095456 PMCID: PMC10807428 DOI: 10.1128/aem.01510-23] [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: 09/04/2023] [Accepted: 10/30/2023] [Indexed: 01/25/2024] Open
Abstract
Plasmid conjugation is a key facilitator of horizontal gene transfer (HGT), and plasmids encoding antibiotic resistance drive the increasing prevalence of antibiotic resistance. In natural, engineered, and clinical environments, bacteria often grow in protective biofilms. Therefore, a better understanding of plasmid transfer in biofilms is needed. Our aim was to investigate plasmid transfer in a biofilm-adapted wrinkly colony mutant of Xanthomonas retroflexus (XRw) with enhanced matrix production and reduced motility. We found that XRw biofilms had an increased uptake of the broad host-range IncP-1ϵ plasmid pKJK5 compared to the wild type (WT). Proteomics revealed fewer flagellar-associated proteins in XRw, suggesting that flagella were responsible for reducing plasmid uptake. This was confirmed by the higher plasmid uptake of non-flagellated fliM mutants of the X. retroflexus wrinkly mutant as well as the wild type. Moreover, testing several flagellar mutants of Pseudomonas putida suggested that the flagellar effect was more general. We identified seven mechanisms with the potential to explain the flagellar effect and simulated them in an individual-based model. Two mechanisms could thus be eliminated (increased distances between cells and increased lag times due to flagella). Another mechanism identified as viable in the modeling was eliminated by further experiments. The possibility of steric hindrance of pilus movement and binding by flagella, reducing the frequency of contact and thus plasmid uptake, proved viable, and the three other viable mechanisms had a reduced probability of plasmid transfer in common. Our findings highlight the important yet complex effects of flagella during bacterial conjugation in biofilms.IMPORTANCEBiofilms are the dominant form of microbial life and bacteria living in biofilms are markedly different from their planktonic counterparts, yet the impact of the biofilm lifestyle on horizontal gene transfer (HGT) is still poorly understood. Horizontal gene transfer by conjugative plasmids is a major driver in bacterial evolution and adaptation, as exemplified by the troubling spread of antibiotic resistance. To either limit or promote plasmid prevalence and dissemination, we need a better understanding of plasmid transfer between bacterial cells, especially in biofilms. Here, we identified a new factor impacting the transfer of plasmids, flagella, which are required for many types of bacterial motility. We show that their absence or altered activity can lead to enhanced plasmid uptake in two bacterial species, Xanthomonas retroflexus and Pseudomonas putida. Moreover, we demonstrate the utility of mathematical modeling to eliminate hypothetical mechanisms.
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Affiliation(s)
- Henriette Lyng Røder
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eleni Christidi
- School of Biosciences & Institute of Microbiology and Infection & Centre for Computational Biology, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | - Samra Music
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Jakob Herschend
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan-Ulrich Kreft
- School of Biosciences & Institute of Microbiology and Infection & Centre for Computational Biology, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Mette Burmølle
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Libante V, Dechêne-Tempier M, Leblond-Bourget N, Payot S. Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes. Methods Mol Biol 2024; 2815:79-91. [PMID: 38884912 DOI: 10.1007/978-1-0716-3898-9_7] [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] [Indexed: 06/18/2024]
Abstract
Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.
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Affiliation(s)
| | - Manon Dechêne-Tempier
- Université de Lorraine, INRAE, DynAMic, Nancy, France
- Anses, Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, Ploufragan, France
| | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, Nancy, France.
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Yang QE, Ma X, Zeng L, Wang Q, Li M, Teng L, He M, Liu C, Zhao M, Wang M, Hui D, Madsen JS, Liao H, Walsh TR, Zhou S. Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study. THE LANCET. MICROBE 2024; 5:e13-e23. [PMID: 38006896 DOI: 10.1016/s2666-5247(23)00227-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-β-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context. METHODS For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli. FINDINGS We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids. INTERPRETATION Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors. FUNDING The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.
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Affiliation(s)
- Qiu E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodan Ma
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingshuang Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinqin Wang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Minchun Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Teng
- Department of Veterinary Medicine, College of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Mingzhen He
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengshi Zhao
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengzhu Wang
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deng Hui
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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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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17
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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18
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Kraychete GB, Bonelli RR, Picão RC. Green light for improving our understanding of AMR spread. THE LANCET. MICROBE 2024; 5:e2-e3. [PMID: 38006897 DOI: 10.1016/s2666-5247(23)00331-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/27/2023]
Affiliation(s)
- Gabriela B Kraychete
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Raquel R Bonelli
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Renata C Picão
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
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Chen X, Wang X, Huang Y, Zhu Z, Li T, Cai Z, Li M, Gong H, Yan M. Combined effects of microplastics and antibiotic-resistant bacteria on Daphnia magna growth and expression of functional genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166880. [PMID: 37709097 DOI: 10.1016/j.scitotenv.2023.166880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023]
Abstract
Microplastics could act as vectors for the transport of harmful bacteria, such as pathogens and antibiotic resistance bacteria (ARB), but their combined effects have not been reported yet. Here, ARB Shigella flexneri with sulfonamides resistance and micro-polystyrene (micro-PS) were used to investigate their possible combined effects on the growth and expression of functional genes in Daphnia magna. Results showed that micro-PS colonized with S. flexneri were ingested by D. magna and blocked in their intestine after 24 h exposure. Changes were observed in the life history and morphology of D. magna, as well as the expression of functional genes in all treatments, but with no difference in the survival rate. We also determined the expression of six functional genes involved in energy and metabolism (arginine kinase, AK) and oxidative stress response (thioredoxin reductase, TRxR, catalase, CAT, and glutathione S-transferases, GSTs), as well as in growth, development and reproduction (vitellogenin, Vtg1 and ecdysone receptor, EcR). AK and Vtg1 did not show significant differences, however, EcR was down-regulated and the other three genes (TRxR, CAT, GSTs) were up-regulated in the combined-treated group. Antibiotic resistance gene (ARGs) sul1 was detected when exposed to micro-PS colonized with S. flexneri., suggesting that D. magna could acquire resistance genes through microplastic biofilms. These results indicated that MPs could act as a carrier of ARB to transfer ARGs into D. magna, and affect the life history, morphology, and the expression of related functional genes of D. magna, to adapt to the stress caused by MPs and ARB.
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Affiliation(s)
- Xiaofeng Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Xiaocui Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Yuanyin Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Ziying Zhu
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Tianmu Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Zeming Cai
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Minqian Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China
| | - Han Gong
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China.
| | - Muting Yan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510641, China.
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20
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Li XY, Wu WF, Wu CY, Hu Y, Xiang Q, Li G, Lin XY, Zhu YG. Seeds Act as Vectors for Antibiotic Resistance Gene Dissemination in a Soil-Plant Continuum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21358-21369. [PMID: 38078407 DOI: 10.1021/acs.est.3c05678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Though the evidence for antibiotic resistance spread via plant microbiome is mounting, studies regarding antibiotic resistome in the plant seed, a reproductive organ and important food resource, are still in their infancy. This study investigated the effects of long-term organic fertilization on seed bacterial endophytes, resistome, and their intergenerational transfer in the microcosm. A total of 99 antibiotic resistance genes (ARGs) and 26 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR. The amount of organic fertilizer applied was positively correlated to the number and relative abundance of seed-associated ARGs and MGEs. Moreover, the transmission of ARGs from the rhizosphere to the seed was mainly mediated by the shared bacteria and MGEs. Notably, the rhizosphere of progeny seedlings derived from seeds harboring abundant ARGs was found to have a higher relative abundance of ARGs. Using structural equation models, we further revealed that seed resistome and MGEs were key factors affecting the ARGs in the progeny rhizosphere, implying the seed was a potential resistome reservoir for rhizosphere soil. This study highlights the overlooked role of seed endophytes in the dissemination of resistome in the soil-plant continuum, and more attention should be paid to plant seeds as vectors of ARGs within the "One-Health" framework.
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Affiliation(s)
- Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Yan Hu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Guo Y, Wu C, Wang Z, Shi Y, Sun J. Co-occurrence of toxic metals, bacterial communities and metal resistance genes in coastal sediments from Bohai bay. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122666. [PMID: 37788796 DOI: 10.1016/j.envpol.2023.122666] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
Sediment heavy metal contamination poses substantial risks to microbial community composition and functional gene distribution. Bohai Bay (BHB), the second-largest bay in the Bohai Sea, is subject to severe anthropogenic pollution. However, to date, there have been no studies conducted to evaluate the distribution of metal resistance genes (MRGs) and bacterial communities in the coastal sediments of BHB. In this study, we employed high-throughput sequencing based on 16S rRNA genes and real-time quantitative PCR (qPCR) to provide a comprehensive view of toxic metals, MRGs, and bacterial communities in BHB's coastal sediment samples across two seasons. We detected high levels of Cd in the summer samples and As in the autumn samples. The metal content in most autumn samples and all summer samples, based on ecological indices, indicated low ecological risk. Proteobacteria dominated all samples, followed by Desulfobacterota, Bacteroidota and Campilobacterota. Bacterial community variability was higher between autumn sampling sites but more stable in summer. We detected 9 MRG subtypes in all samples, with abundances ranging from 4.58 × 10-1 to 2.25 copies/16S rRNA copies. arsB exhibited the highest relative abundance, followed by acr3, czcA and arrA. The efflux mechanism is a common mechanism for sediment resistance to metal stress in Bohai Bay. Procrustes analysis indicated that bacterial community composition may be a determinant of MRGs composition in BHB sediments. Network analysis suggested that eight classes could be potential hosts for six MRGs. However, this type of correlation requires further validation. To summarize, our study offers preliminary insights into bacterial community and MRG distribution patterns in heavy metal-exposed sediments, laying the groundwork for understanding microbial community adaptations in multi-metal polluted environments and supporting ecological restoration efforts.
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Affiliation(s)
- Yiyan Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China
| | - Chao Wu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Zhi Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China
| | - Yifeng Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China
| | - Jun Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China.
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Skoog EJ, Fournier GP, Bosak T. Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia. Genes (Basel) 2023; 14:2168. [PMID: 38136990 PMCID: PMC10742547 DOI: 10.3390/genes14122168] [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: 10/20/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.
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Affiliation(s)
- Emilie J. Skoog
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Gregory P. Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (G.P.F.); (T.B.)
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23
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Jing K, Li Y, Yao C, Jiang C, Li J. Towards the fate of antibiotics and the development of related resistance genes in stream biofilms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165554. [PMID: 37454845 DOI: 10.1016/j.scitotenv.2023.165554] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/01/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Antibiotics are ubiquitously found in natural surface waters and cause great harm to aquatic organisms. Stream biofilm is a complex and active community composed of algae, bacteria, fungi and other microorganisms, which mainly adheres to solid substances such as rocks and sediments. The durability and diverse structural and metabolic characteristics of biofilms make them a representative of microbial life in aquatic micrecosystems and can reflect major ecosystem processes. Microorganisms and extracellular polymeric substances in biofilms can adsorb and actively accumulate antibiotics. Therefore, biofilms are excellent biological indicators for detecting antibiotic in polluted aquatic environments, but the biotransformation potential of stream biofilms for antibiotics has not been fully explored in the aquatic environment. The characteristics of stream biofilm, such as high abundance and activity of bacterial community, wide contact area with pollutants, etc., which increases the opportunity of biotransformation of antibiotics in biofilm and contribute to bioremediation to improve ecosystem health. Recent studies have demonstrated that both exposure to high and sub-minimum inhibitory concentrations of antibiotics may drive the development of antibiotic resistance genes (ARGs) in natural stream biofilms, which are susceptible to the effects of antibiotic residues, microbial communities and mobile genetic elements, etc. On the basis of peer-reviewed papers, this review explores the distribution behavior of antibiotics in stream biofilms and the contribution of biofilms to the acquisition and spread of antibiotic resistance. Considering that antibiotics and ARGs alter the structure and ecological functions of natural microbial communities and pose a threat to river organisms and human health, our research findings provide comprehensive insights into the migration, transformation, and bioavailability of antibiotics in biofilms.
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Affiliation(s)
- Ke Jing
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, HoHai University, Nanjing 210098, China
| | - Ying Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, HoHai University, Nanjing 210098, China.
| | - Chi Yao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, HoHai University, Nanjing 210098, China
| | - Chenxue Jiang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, HoHai University, Nanjing 210098, China
| | - Jing Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, HoHai University, Nanjing 210098, China
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24
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Sun H, Li H, Zhang X, Liu Y, Chen H, Zheng L, Zhai Y, Zheng H. The honeybee gut resistome and its role in antibiotic resistance dissemination. Integr Zool 2023; 18:1014-1026. [PMID: 36892101 DOI: 10.1111/1749-4877.12714] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.
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Affiliation(s)
- Huihui Sun
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Hu Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yan Liu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Hao Chen
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Li Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Hao Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
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25
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Liu L, Zhang QH, Li RT. In Situ and Individual-Based Analysis of the Influence of Polystyrene Microplastics on Escherichia coli Conjugative Gene Transfer at the Single-Cell Level. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15936-15944. [PMID: 37801563 DOI: 10.1021/acs.est.3c05476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
The impact of microplastic particles of micro- and nanometer sizes on microbial horizontal gene transfer (HGT) remains a controversial topic. Existing studies rely on traditional approaches, which analyze population behavior, leading to conflicting conclusions and a limited understanding. The present study addressed these limitations by employing a novel microfluidic chamber system for in situ visualization and precise quantification of the effects of different concentrations of polystyrene (PS) microbeads on microbial HGT at the single-cell level. The statistical analysis indicated no significant difference in the division times of both the donor and recipient bacteria across different PS microbead concentrations. However, as the concentration of PS microbeads increased from 0 to 2000 mg L-1, the average conjugation frequency of Escherichia coli decreased from 0.028 ± 0.015 to 0.004 ± 0.003. Our observations from the microfluidic experiments revealed that 500 nm PS microbeads created a barrier effect on bacterial conjugative transfer. The presence of microbeads resulted in reduced contact and interaction between the donor and recipient strains, thereby causing a decrease in the conjugation transfer frequency. These findings were validated by an individual-based modeling framework parameterized by the data from the individual-level microfluidic experiments. Overall, this study offers a fresh perspective and strategy for investigating the risks associated with the dissemination of antibiotic resistance genes related to microplastics.
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Affiliation(s)
- Li Liu
- School of Chemistry, Beihang University, Beijing 100191, P. R. China
| | - Qiang-Hong Zhang
- School of Chemistry, Beihang University, Beijing 100191, P. R. China
| | - Rui-Tong Li
- School of Chemistry, Beihang University, Beijing 100191, P. R. China
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26
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Shi J, Lv B, Wang B, Xie B. Insight into the responses of antibiotic resistance genes in microplastic biofilms to zinc oxide nanoparticles and zinc ions pressures in landfill leachate. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132096. [PMID: 37480611 DOI: 10.1016/j.jhazmat.2023.132096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Microplastic (MP) biofilms are hotspots of antibiotic resistance genes (ARGs) in landfill environment. MP biofilms in landfill leachate coexist with heavy metals and metallic nanoparticles (NPs) that considered to be the selective agents of ARGs. However, the effects of these selective pressures on ARGs in MP biofilms and their differences in MP-surrounding leachate have not been well understood. Herein, the changes of ARG abundances in MP biofilms and corresponding leachate under zinc oxide (ZnO) NPs and zinc ion (Zn2+) pressures were comparatively analyzed. The presence of ZnO NPs and Zn2+ promoted the enrichment of ARGs in MP biofilms, and the enrichment was more pronounced in ZnO NPs groups. ZnO NPs and especially Zn2+ mainly decreased the abundances of ARGs in leachate. The increase of integron abundances and reactive oxygen species production in MP biofilms implied the enhanced potential for horizontal transfer of ARGs under ZnO NPs and Zn2+ pressures. Meanwhile, the co-occurrence pattern between ARGs and bacterial genera in MP biofilms with more diverse potential ARG hosts was more complex than in leachate, and the enrichment of ARG-hosting bacteria in MP biofilms under ZnO NPs and Zn2+ pressures supported the enrichment of ARGs.
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Affiliation(s)
- Jianhong Shi
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Binghan Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China.
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27
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Kuznetsova MV, Pospelova JS, Maslennikova IL, Starčič Erjavec M. Dual-Species Biofilms: Biomass, Viable Cell Ratio/Cross-Species Interactions, Conjugative Transfer. Int J Mol Sci 2023; 24:14497. [PMID: 37833945 PMCID: PMC10572544 DOI: 10.3390/ijms241914497] [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: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
Biofilms as a form of adaptation are beneficial for bacterial survival and may be hot spots for horizontal gene transfer, including conjugation. The aim of this research was to characterize the biofilm biomass, viable cell ratios and conjugative transfer of the pOX38 plasmid, an F-plasmid derivative, from the Escherichia coli N4i pOX38 strain (donor) into a uropathogenic E. coli DL82 strain (recipient) within dual-species biofilms with one of the following opportunistic pathogenic bacteria: Klebsiella pneumoniae, Enterococcus faecalis or Pseudomonas aeruginosa. Dual-species biofilms of E. coli with K. pneumoniae or P. aeruginosa but not E. faecalis were more massive and possessed more exopolysaccharide matrix compared to single-species biofilms of donor and recipient cells. Correlation between biofilm biomass and exopolysaccharide matrix was rs = 0.888 in dual-species biofilms. In dual-species biofilm with E. faecalis the proportion of E. coli was the highest, while in the biofilm with P. aeruginosa and K. pneumoniae, the E. coli was less abundant. The conjugative frequencies of plasmid transfer in dual-species biofilms of E. coli with E. faecalis and P. aeruginosa were reduced. A decrease in conjugative frequency was also observed when cell-free supernatants (CFSs) of E. faecalis and P. aeruginosa were added to the E. coli conjugation mixture. Further, the activity of the autoinducer AI-2 in the CFSs of the E. coli conjugation mixture was reduced when bacteria or CFSs of E. faecalis and P. aeruginosa were added to the E. coli conjugation mixture. Hence, the intercellular and interspecies interactions in dual-species biofilms depend on the partners involved.
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Affiliation(s)
- Marina V Kuznetsova
- Institute of Ecology and Genetics of Microorganisms Ural Branch Russian Academy of Sciences, 614081 Perm, Russia
| | | | - Irina L Maslennikova
- Institute of Ecology and Genetics of Microorganisms Ural Branch Russian Academy of Sciences, 614081 Perm, Russia
| | - Marjanca Starčič Erjavec
- Department of Microbiology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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28
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Loret S, Habib B, Romain P, Roba A, Reboul A. Prevention of horizontal transfer of laboratory plasmids to environmental bacteria: comparison of the effectiveness of a few disinfection approaches to degrade DNA. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:89369-89380. [PMID: 37450185 DOI: 10.1007/s11356-023-28733-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The routine work of any molecular biology laboratory includes the daily use of microorganisms, including strains of E. coli, transformed with a variety of plasmids expressing at least one antibiotic resistance gene (ARG). Therefore, to avoid the accidental release of ARGs into environmental water, methods for disinfection of liquid laboratory waste must be effective in destroying nucleic acids. In support of this recommendation, the origin of replication of Enterobacteriaceae plasmids has been detected in strains of non-Enterobacteriaceae bacteria isolated from wastewater from laboratories and research institutes, suggesting that interspecific transfer of laboratory plasmids had occurred. Using quantitative polymerase chain reaction, we determined the decimal reduction value (D value, expressed as concentration of disinfectant or length of physical treatment) of several decontamination methods for their DNA degradation effect on cultures of E. coli Top10 transformed with a kanamycin resistant plasmid (pET28A + or pEGFP-C2). The estimated D values were 0.7 M for sulfuric acid, 6.3% for a commercial P3 disinfectant, 25 min for steam sterilization at 121 °C, and 49 min for disinfection by UVC. A 20-min treatment of bacteria cultures with a final concentration of 1-10% sodium hypochlorite was found to be ineffective in completely destroying a bacteria plasmid gene marker (coding for the pBR322 origin of replication). Residual DNA from NaClO-treated cells was 60%, while it decreased under 10% using the commercial disinfectant P3 diluted at 5%. As the degradation was incomplete in both cases, we recommend avoiding discharge of disinfected liquid waste to wastewater (even after chemical neutralization) without additional plasmid destruction treatment, to prevent horizontal transfer of laboratory ARGs to environmental bacteria.
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Affiliation(s)
- Suzanne Loret
- Health and Safety Department, Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Biosafety Office, Rue de Bruxelles 61, B 5000, Namur, Belgium.
| | - Boutaina Habib
- Science Faculty, University Mohammed V, Avenue Ibn Batouta, BP 1014, Rabat, Morocco
| | - Pierre Romain
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Rue de Bruxelles 61, B 5000 , Namur, Belgium
| | - Agnès Roba
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Rue de Bruxelles 61, B 5000 , Namur, Belgium
| | - Angéline Reboul
- Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur (UNamur), Rue de Bruxelles 61, B 5000 , Namur, Belgium
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29
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Tran NN, Morrisette T, Jorgensen SCJ, Orench-Benvenutti JM, Kebriaei R. Current therapies and challenges for the treatment of Staphylococcus aureus biofilm-related infections. Pharmacotherapy 2023; 43:816-832. [PMID: 37133439 DOI: 10.1002/phar.2806] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 05/04/2023]
Abstract
Staphylococcus aureus is a major cause of nosocomial and community-acquired infections and contributes to significant increase in morbidity and mortality especially when associated with medical devices and in biofilm form. Biofilm structure provides a pathway for the enrichment of resistant and persistent phenotypes of S. aureus leading to relapse and recurrence of infection. Minimal diffusion of antibiotics inside biofilm structure leads to heterogeneity and distinct physiological activity. Additionally, horizontal gene transfer between cells in proximity adds to the challenges associated with eradication of biofilms. This narrative review focuses on biofilm-associated infections caused by S. aureus, the impact of environmental conditions on biofilm formation, interactions inside biofilm communities, and the clinical challenges that they present. Conclusively, potential solutions, novel treatment strategies, combination therapies, and reported alternatives are discussed.
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Affiliation(s)
- Nikki N Tran
- Department of Pharmacy, The Ohio State University Wexner Medical Center - The James Cancer Hospital and Solove Research Institute, Columbus, Ohio, USA
| | - Taylor Morrisette
- Department of Clinical Pharmacy and Outcomes Sciences, Medical University of South Carolina College of Pharmacy, Charleston, South Carolina, USA
- Department of Pharmacy Services, Medical University of South Carolina Shawn Jenkins Children's Hospital, Charleston, South Carolina, USA
| | - Sarah C J Jorgensen
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - José M Orench-Benvenutti
- P3 Research Laboratory, Division of Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Razieh Kebriaei
- P3 Research Laboratory, Division of Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
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30
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Alav I, Buckner MMC. Non-antibiotic compounds associated with humans and the environment can promote horizontal transfer of antimicrobial resistance genes. Crit Rev Microbiol 2023:1-18. [PMID: 37462915 DOI: 10.1080/1040841x.2023.2233603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/23/2023] [Accepted: 06/30/2023] [Indexed: 02/15/2024]
Abstract
Horizontal gene transfer plays a key role in the global dissemination of antimicrobial resistance (AMR). AMR genes are often carried on self-transmissible plasmids, which are shared amongst bacteria primarily by conjugation. Antibiotic use has been a well-established driver of the emergence and spread of AMR. However, the impact of commonly used non-antibiotic compounds and environmental pollutants on AMR spread has been largely overlooked. Recent studies found common prescription and over-the-counter drugs, artificial sweeteners, food preservatives, and environmental pollutants, can increase the conjugative transfer of AMR plasmids. The potential mechanisms by which these compounds promote plasmid transmission include increased membrane permeability, upregulation of plasmid transfer genes, formation of reactive oxygen species, and SOS response gene induction. Many questions remain around the impact of most non-antibiotic compounds on AMR plasmid conjugation in clinical isolates and the long-term impact on AMR dissemination. By elucidating the role of routinely used pharmaceuticals, food additives, and pollutants in the dissemination of AMR, action can be taken to mitigate their impact by closely monitoring use and disposal. This review will discuss recent progress on understanding the influence of non-antibiotic compounds on plasmid transmission, the mechanisms by which they promote transfer, and the level of risk they pose.
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Affiliation(s)
- Ilyas Alav
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Michelle M C Buckner
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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31
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Heo S, Oh SE, Lee G, Lee J, Ha NC, Jeon CO, Jeong K, Lee JH, Jeong DW. Staphylococcus equorum plasmid pKS1030-3 encodes auxiliary biofilm formation and trans-acting gene mobilization systems. Sci Rep 2023; 13:11108. [PMID: 37429971 DOI: 10.1038/s41598-023-38274-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
The foodborne bacterium Staphylococcus equorum strain KS1030 harbours plasmid pSELNU1, which encodes a lincomycin resistance gene. pSELNU1 undergoes horizontal transfer between bacterial strains, thus spreading antibiotic resistance. However, the genes required for horizontal plasmid transfer are not encoded in pSELNU1. Interestingly, a relaxase gene, a type of gene related to horizontal plasmid transfer, is encoded in another plasmid of S. equorum KS1030, pKS1030-3. The complete genome of pKS1030-3 is 13,583 bp long and encodes genes for plasmid replication, biofilm formation (the ica operon), and horizontal gene transfer. The replication system of pKS1030-3 possesses the replication protein-encoding gene repB, a double-stranded origin of replication, and two single-stranded origins of replication. The ica operon, relaxase gene, and a mobilization protein-encoding gene were detected in pKS1030-3 strain-specifically. When expressed in S. aureus RN4220, the ica operon and relaxase operon of pKS1030-3 conferred biofilm formation ability and horizontal gene transfer ability, respectively. The results of our analyses show that the horizontal transfer of pSELNU1 of S. equorum strain KS1030 depends on the relaxase encoded by pKS1030-3, which is therefore trans-acting. Genes encoded in pKS1030-3 contribute to important strain-specific properties of S. equorum KS1030. These results could contribute to preventing the horizontal transfer of antibiotic resistance genes in food.
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Affiliation(s)
- Sojeong Heo
- Department of Food and Nutrition, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Seung-Eun Oh
- Department of Food and Nutrition, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Gawon Lee
- Department of Food and Nutrition, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Jinwook Lee
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nam-Chul Ha
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Keuncheol Jeong
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, 16227, Republic of Korea
| | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, 16227, Republic of Korea
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women's University, Seoul, 02748, Republic of Korea.
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32
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Sánchez-Salazar AM, Taparia T, Olesen AK, Acuña JJ, Sørensen SJ, Jorquera MA. An overview of plasmid transfer in the plant microbiome. Plasmid 2023; 127:102695. [PMID: 37295540 DOI: 10.1016/j.plasmid.2023.102695] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Plant microbiomes are pivotal for healthy plant physiological development. Microbes live in complex co-association with plant hosts, and interactions within these microbial communities vary with plant genotype, plant compartment, phenological stage, and soil properties, among others. Plant microbiomes also harbor a substantial and diverse pool of mobile genes encoded on plasmids. Several plasmid functions attributed to plant-associated bacteria are relatively poorly understood. Additionally, the role of plasmids in disseminating genetic traits within plant compartments is not well known. Here, we present the current knowledge on the occurrence, diversity, function, and transfer of plasmids in plant microbiomes, emphasizing the factors that could modulate gene transfer in-planta. We also describe the role of the plant microbiome as a plasmid reservoir and the dissemination of its genetic material. We include a brief discussion on the current methodological limitations in studying plasmid transfer within plant microbiomes. This information could be useful to elucidate the dynamics of the bacterial gene pools, the adaptations different organisms have made, and variations in bacterial populations that might have never been described before, particularly in complex microbial communities associated with plants in natural and anthropogenic impacted environments.
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Affiliation(s)
- Angela M Sánchez-Salazar
- Programa de Doctorado en Ciencias de Recursos Naturales, Facultad de Ingeniería y Ciencia, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile
| | - Tanvi Taparia
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark
| | - Asmus K Olesen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; The Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile
| | - Søren J Sørensen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; The Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile.
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Tripathi A, Kumar D, Chavda P, Rathore DS, Pandit R, Blake D, Tomley F, Joshi M, Joshi CG, Dubey SK. Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121517. [PMID: 36990341 DOI: 10.1016/j.envpol.2023.121517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/26/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.
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Affiliation(s)
- Animesh Tripathi
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Priyank Chavda
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Dalip Singh Rathore
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Damer Blake
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, UK
| | - Fiona Tomley
- Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire, UK
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology; (DST), Government of Gujarat, Gandhinagar, Gujarat, 382011, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Sun J, Yuan Y, Cai L, Zeng M, Li X, Yao F, Chen W, Huang Y, Shafiq M, Xie Q, Zhang Q, Wong N, Wang Z, Jiao X. Metagenomic evidence for antibiotics-driven co-evolution of microbial community, resistome and mobilome in hospital sewage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121539. [PMID: 37019259 DOI: 10.1016/j.envpol.2023.121539] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/11/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Overconsumption of antibiotics is an immediate cause for the emergence of antimicrobial resistance (AMR) and antibiotic resistant bacteria (ARB), though its environmental impact remains inadequately clarified. There is an urgent need to dissect the complex links underpinning the dynamic co-evolution of ARB and their resistome and mobilome in hospital sewage. Metagenomic and bioinformatic methods were employed to analyze the microbial community, resistome and mobilome in hospital sewage, in relation to data on clinical antibiotic use collected from a tertiary-care hospital. In this study, resistome (1,568 antibiotic resistance genes, ARGs, corresponding to 29 antibiotic types/subtypes) and mobilome (247 types of mobile genetic elements, MGEs) were identified. Networks connecting co-occurring ARGs with MGEs encompass 176 nodes and 578 edges, in which over 19 types of ARGs had significant correlations with MGEs. Prescribed dosage and time-dependent antibiotic consumption were associated with the abundance and distributions of ARGs, and conjugative transfer of ARGs via MGEs. Variation partitioning analyses show that effects of conjugative transfer were most likely the main contributors to transient propagation and persistence of AMR. We have presented the first evidence supporting idea that use of clinical antibiotics is a potent driving force for the development of co-evolving resistome and mobilome, which in turn supports the growth and evolution of ARB in hospital sewage. The use of clinical antibiotics calls for greater attention in antibiotic stewardship and management.
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Affiliation(s)
- Jiayu Sun
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China; Guangdong Province Center for Disease Control and Prevention, Guangzhou, 511400, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Leshan Cai
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China; Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, 515041, China
| | - Mi Zeng
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Xin Li
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Fen Yao
- Department of Pharmacology, Shantou University Medical College, Shantou, 515041, China
| | - Weidong Chen
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Yuanchun Huang
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Muhammad Shafiq
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Qingdong Xie
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China
| | - Qiaoxin Zhang
- The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, China
| | - Naikei Wong
- Department of Pharmacology, Shantou University Medical College, Shantou, 515041, China
| | - Zhen Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515041, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, China; Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, 515041, China.
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Pandya A, Shah Y, Kothari N, Postwala H, Shah A, Parekh P, Chorawala MR. The future of cancer immunotherapy: DNA vaccines leading the way. Med Oncol 2023; 40:200. [PMID: 37294501 DOI: 10.1007/s12032-023-02060-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023]
Abstract
Immuno-oncology has revolutionized cancer treatment and has opened up new opportunities for developing vaccination methods. DNA-based cancer vaccines have emerged as a promising approach to activating the bodily immune system against cancer. Plasmid DNA immunizations have shown a favorable safety profile and there occurs induction of generalized as well as tailored immune responses in preclinical and early-phase clinical experiments. However, these vaccines have notable limitations in immunogenicity and heterogeneity and these require refinements. DNA vaccine technology has been focusing on improving vaccine efficacy and delivery, with parallel developments in nanoparticle-based delivery systems and gene-editing technologies such as CRISPR/Cas9. This approach has showcased great promise in enhancing and tailoring the immune response to vaccination. Strategies to enhance the efficacy of DNA vaccines include the selection of appropriate antigens, optimizing insertion in a plasmid, and studying combinations of vaccines with conventional strategies and targeted therapies. Combination therapies have attenuated immunosuppressive activities in the tumor microenvironment and enhanced the capability of immune cells. This review provides an overview of the current framework of DNA vaccines in oncology and focuses on novel strategies, including established combination therapies and those still under development.The challenges that oncologists, scientists, and researchers need to overcome to establish DNA vaccines as an avant-garde approach to defeating cancer, are also emphasized. The clinical implications of the immunotherapeutic approaches and the need for predictive biomarkers have also been reviewed upon. We have also tried to extend the role of Neutrophil extracellular traps (NETs) to the DNA vaccines. The clinical implications of the immunotherapeutic approaches have also been reviewed upon. Ultimately, refining and optimizing DNA vaccines will enable harnessing the immune system's natural ability to recognize and eliminate cancer cells, leading the world towards a revolution in cancer cure.
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Affiliation(s)
- Aanshi Pandya
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Yesha Shah
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Nirjari Kothari
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Humzah Postwala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Aayushi Shah
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Priyajeet Parekh
- AV Pharma LLC, 1545 University Blvd N Ste A, Jacksonville, FL, 32211, USA
| | - Mehul R Chorawala
- Department of Pharmacology and Pharmacy Practice, L. M. College of Pharmacy, Opp. Gujarat University, Ahmedabad, Gujarat, 380009, India.
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Román-Écija M, Navas-Cortés JA, Velasco-Amo MP, Arias-Giraldo LF, Gómez LM, Fuente LDL, Landa BB. Two Xylella fastidiosa subsp. multiplex Strains Isolated from Almond in Spain Differ in Plasmid Content and Virulence Traits. PHYTOPATHOLOGY 2023; 113:960-974. [PMID: 36576402 DOI: 10.1094/phyto-06-22-0234-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The plant-pathogenic bacterium Xylella fastidiosa is a major threat to agriculture and the environment worldwide. Recent devastating outbreaks in Europe highlight the potential of this pathogen to cause emergent diseases. X. fastidiosa subsp. multiplex ESVL and IVIA5901 strains that belong to sequence type 6 were isolated from almond orchards within the outbreak area in Alicante province (Spain). Both strains share more than 99% of the chromosomal sequences (average nucleotide identity), but the ESVL strain harbors two plasmids (pXF64-Hb_ESVL and pUCLA-ESVL). Here, virulence phenotypes and genome content were compared between both strains, using three strains from the United States as a reference for the phenotypic analyses. Experiments in microfluidic chambers, used as a simulation of xylem vessels, showed that twitching motility was absent in the IVIA5901 strain, whereas the ESVL strain had reduced twitching motility. In general, both Spanish strains had less biofilm formation, less cell aggregation, and lower virulence in tobacco compared with U.S. reference strains. Genome analysis of the two plasmids from ESVL revealed 51 unique coding sequences that were absent in the chromosome of IVIA5901. Comparison of the chromosomes of both strains showed some unique coding sequences and single-nucleotide polymorphisms in each strain, with potential deleterious mutations. Genomic differences found in genes previously associated with adhesion and motility might explain the differences in the phenotypic traits studied. Although additional studies are necessary to infer the potential role of X. fastidiosa plasmids, our results indicate that the presence of plasmids should be considered in the study of the mechanisms of pathogenicity and adaptation in X. fastidiosa to new environments. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- M Román-Écija
- Department of Crop Protection, Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - J A Navas-Cortés
- Department of Crop Protection, Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - M P Velasco-Amo
- Department of Crop Protection, Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - L F Arias-Giraldo
- Department of Crop Protection, Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - L M Gómez
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
| | - L De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, U.S.A
| | - B B Landa
- Department of Crop Protection, Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
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Zhou Q, Zhang J, Fang Q, Zhang M, Wang X, Zhang D, Pan X. Microplastic biodegradability dependent responses of plastisphere antibiotic resistance to simulated freshwater-seawater shift in onshore marine aquaculture zones. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 331:121828. [PMID: 37187278 DOI: 10.1016/j.envpol.2023.121828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/09/2023] [Accepted: 05/13/2023] [Indexed: 05/17/2023]
Abstract
MPs carrying ARGs can travel between freshwater and seawater due to intensive land-sea interaction in onshore marine aquaculture zones (OMAZ). However, the response of ARGs in plastisphere with different biodegradability to freshwater-seawater shift is still unknown. In this study, ARG dynamics and associated microbiota on biodegradable poly (butyleneadipate-co-terephthalate) (PBAT) and non-biodegradable polyethylene terephthalate (PET) MPs were investigated through a simulated freshwater-seawater shift. The results exhibited that freshwater-seawater shift significantly influenced ARG abundance in plastisphere. The relative abundance of most studied ARGs decreased rapidly in plastisphere after they entered seawater from freshwater but increased on PBAT after MPs entered freshwater from seawater. Besides, the high relative abundance of multi-drug resistance (MDR) genes occurred in plastisphere, and the co-change between most ARGs and mobile genetic elements indicated the role of horizontal gene transfer on ARG regulation. Proteobacteria was dominant phylum in plastisphere and the dominant genera, such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Afipia, Gemmobacter and Enhydrobacter, were significantly associated with qnrS, tet and MDR genes in plastisphere. Moreover, after MPs entered new water environment, the ARGs and microbiota genera in plastisphere changed significantly and tended to converge with those in receiving water. These results indicated that MP biodegradability and freshwater-seawater interaction influenced potential hosts and distributions of ARGs, of which biodegradable PBAT posed a high risk in ARG dissemination. This study would be helpful for understanding the impact of biodegradable MP pollution on spread of antibiotic resistance in OMAZ.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jun Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qunkai Fang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ming Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaonan Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
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Kosterlitz O, Huisman JS. Guidelines for the estimation and reporting of plasmid conjugation rates. Plasmid 2023; 126:102685. [PMID: 37121291 DOI: 10.1016/j.plasmid.2023.102685] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/15/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
Conjugation is a central characteristic of plasmid biology and an important mechanism of horizontal gene transfer in bacteria. However, there is little consensus on how to accurately estimate and report plasmid conjugation rates, in part due to the wide range of available methods. Given the similarity between approaches, we propose general reporting guidelines for plasmid conjugation experiments. These constitute best practices based on recent literature about plasmid conjugation and methods to measure conjugation rates. In addition to the general guidelines, we discuss common theoretical assumptions underlying existing methods to estimate conjugation rates and provide recommendations on how to avoid violating these assumptions. We hope this will aid the implementation and evaluation of conjugation rate measurements, and initiate a broader discussion regarding the practice of quantifying plasmid conjugation rates.
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Affiliation(s)
- Olivia Kosterlitz
- Department of Biology, University of Washington, 3747 W Stevens Way NE, Life Sciences Bldg, Seattle, Washington, United States of America.
| | - Jana S Huisman
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Universitätsstrasse 16, 8092 Zürich, Switzerland.
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Oliver C, Céspedes C, Santibañez N, Ruiz P, Romero A. Subinhibitory concentrations of florfenicol increase the biofilm formation of Piscirickettsia salmonis. JOURNAL OF FISH DISEASES 2023; 46:591-596. [PMID: 36639965 DOI: 10.1111/jfd.13757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Public health is facing a new challenge due to the increased bacterial resistance to most of the conventional antibacterial agents. Inadequate use of antibiotics in the Chilean aquaculture industry leads to the generation of multidrug resistance bacteria. Many fish pathogenic bacteria produce biofilm upon various sources of stress such as antibiotics, which provides several survival advantages for the bacterial life in community and can constitute a reservoir of pathogens in the marine environment. Being florfenicol a broad-spectrum antibiotic commonly used to treat infections in aquaculture, the aim of this study was to assess whether this antibiotic modulates in vitro the biofilm formation in several isolates of Piscirickettsia salmonis. Standard antibiotic-micro broth 96-flat well plates were used to determinate the minimal inhibitory concentration of florfenicol in eight different P. salmonis isolates. In vitro findings, with P. salmonis growing in the presence and absence of the antibiotic, exhibited a statistically significantly increase (p < .05) in biofilm formation in all the bacterial isolates cultivated with sub-MIC (defined as the half of the minimal inhibitory concentration in the presence of antibiotic) of florfenicol compared with controls (antibiotic-free broth). In conclusion, sub-MIC of florfenicol induced an increased biofilm formation in all P. salmonis isolates tested.
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Affiliation(s)
- Cristian Oliver
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Facultad de Ciencias Veterinarias, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - Constanza Céspedes
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Facultad de Ciencias Veterinarias, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - Natacha Santibañez
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Facultad de Ciencias Veterinarias, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
| | - Pamela Ruiz
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Talcahuano, Chile
| | - Alex Romero
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Facultad de Ciencias Veterinarias, Instituto de Patología Animal, Universidad Austral de Chile, Valdivia, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
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Wedel E, Bernabe-Balas C, Ares-Arroyo M, Montero N, Santos-Lopez A, Mazel D, Gonzalez-Zorn B. Insertion Sequences Determine Plasmid Adaptation to New Bacterial Hosts. mBio 2023:e0315822. [PMID: 37097157 DOI: 10.1128/mbio.03158-22] [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: 04/26/2023] Open
Abstract
Plasmids facilitate the vertical and horizontal spread of antimicrobial resistance genes between bacteria. The host range and adaptation of plasmids to new hosts determine their impact on the spread of resistance. In this work, we explore the mechanisms driving plasmid adaptation to novel hosts in experimental evolution. Using the small multicopy plasmid pB1000, usually found in Pasteurellaceae, we studied its adaptation to a host from a different bacterial family, Escherichia coli. We observed two different mechanisms of adaptation. One mechanism is single nucleotide polymorphisms (SNPs) in the origin of replication (oriV) of the plasmid, which increase the copy number in E. coli cells, elevating the stability, and resistance profile. The second mechanism consists of two insertion sequences (ISs), IS1 and IS10, which decrease the fitness cost of the plasmid by disrupting an uncharacterized gene on pB1000 that is harmful to E. coli. Both mechanisms increase the stability of pB1000 independently, but only their combination allows long-term maintenance. Crucially, we show that the mechanisms have a different impact on the host range of the plasmid. SNPs in oriV prevent the replication in the original host, resulting in a shift of the host range. In contrast, the introduction of ISs either shifts or expands the host range, depending on the IS. While IS1 leads to expansion, IS10 cannot be reintroduced into the original host. This study gives new insights into the relevance of ISs in plasmid-host adaptation to understand the success in spreading resistance. IMPORTANCE ColE1-like plasmids are small, mobilizable plasmids that can be found across at least four orders of Gammaproteobacteria and are strongly associated with antimicrobial resistance genes. Plasmid pB1000 carries the gene blaROB-1, conferring high-level resistance to penicillins and cefaclor. pB1000 has been described in various species of the family Pasteurellaceae, for example, in Haemophilus influenzae, which can cause diseases such as otitis media, meningitis, and pneumonia. To understand the resistance spread through horizontal transfer, it is essential to study the mechanisms of plasmid adaptation to novel hosts. In this work we identify that a gene from pB1000, which encodes a peptide that is toxic for E. coli, and the low plasmid copy number (PCN) of pB1000 in E. coli cells are essential targets in the described plasmid-host adaptation and therefore limit the spread of pB1000-encoded blaROB-1. Furthermore, we show how the interplay of two adaptation mechanisms leads to successful plasmid maintenance in a different bacterial family.
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Affiliation(s)
- Emilia Wedel
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bernabe-Balas
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Natalia Montero
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Alfonso Santos-Lopez
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Didier Mazel
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit (ARU), Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
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Feng L, Aryal N, Li Y, Horn SJ, Ward AJ. Developing a biogas centralised circular bioeconomy using agricultural residues - Challenges and opportunities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161656. [PMID: 36669668 DOI: 10.1016/j.scitotenv.2023.161656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Anaerobic digestion (AD) can be used as a stand-alone process or integrated as part of a larger biorefining process to produce biofuels, biochemicals and fertiliser, and has the potential to play a central role in the emerging circular bioeconomy (CBE). Agricultural residues, such as animal slurry, straw, and grass silage, represent an important resource and have a huge potential to boost biogas and methane yields. Under the CBE concept, there is a need to assess the long-term impact and investigate the potential accumulation of specific unwanted substances. Thus, a comprehensive literature review to summarise the benefits and environmental impacts of using agricultural residues for AD is needed. This review analyses the benefits and potential adverse effects related to developing biogas-centred CBE. The identified potential risks/challenges for developing biogas CBE include GHG emission, nutrient management, pollutants, etc. In general, the environmental risks are highly dependent on the input feedstocks and resulting digestate. Integrated treatment processes should be developed as these could both minimise risks and improve the economic perspective.
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Affiliation(s)
- Lu Feng
- NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway.
| | - Nabin Aryal
- Department of Microsystems, University of South-Eastern Norway, Borre, Norway
| | - Yeqing Li
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Biogas Upgrading Utilization, College of New Energy and Materials, China University of Petroleum Beijing (CUPB), Beijing 102249, PR China
| | - Svein Jarle Horn
- NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1431 Ås, Norway; Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
| | - Alastair James Ward
- Department of Biological and Chemical Engineering, Aarhus University, Denmark
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Qi Q, Ghaly TM, Penesyan A, Rajabal V, Stacey JA, Tetu SG, Gillings MR. Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4870-4879. [PMID: 36912846 DOI: 10.1021/acs.est.2c09739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeremy Ac Stacey
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
| | - Sasha G Tetu
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Michael R Gillings
- School of Natural Sciences, Macquarie University, 14 Eastern Road, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
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43
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Weng Y, Hu P, Hu L. Baicalein Inhibits Plasmid-Mediated Horizontal Transmission of the blaKPC Multidrug Resistance Gene from Klebsiella pneumoniae to Escherichia coli. Biol Pharm Bull 2023; 46:394-398. [PMID: 36543225 DOI: 10.1248/bpb.b22-00500] [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: 12/24/2022]
Abstract
Carbapenem-resistant bacterial infections pose an urgent threat to public health worldwide. Horizontal transmission of the β-lacatamase Klebsiella pneumoniae carbapenemase (blaKPC) multidrug resistance gene is a major mechanism for global dissemination of carbapenem resistance. Here, we investigated the effects of baicalein, an active ingredient of a Chinese herbal medicine, on plasmid-mediated horizontal transmission of blaKPC from a meropenem-resistant K. pneumoniae strain (JZ2157) to a meropenem-sensitive Escherichia coli strain (E600). Baicalein showed no direct effects on the growth of JZ2157 or E600. Co-cultivation of JZ2157 and E600 caused the spread of meropenem resistance from JZ2157 to E600. Baicalein at 40 and 400 µg/mL significantly inhibited the spread of meropenem resistance. Co-cultivation also resulted in plasmid-mediated transmission of blaKPC from JZ2157 to E600, which was inhibited by baicalein. Therefore, baicalein may be used in clinical practice to prevent or contain outbreaks of carbapenem-resistant infections by inhibiting the horizontal transfer of resistance genes across bacteria species.
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Affiliation(s)
- Yuesong Weng
- Department of Laboratory Medicine, Ningbo First Hospital
| | - Pingyi Hu
- Department of Laboratory Medicine, Ningbo First Hospital.,School of Laboratory Medicine and Life Science, Wenzhou Medical University
| | - Liqing Hu
- Department of Laboratory Medicine, Ningbo First Hospital
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44
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Verweij W, Griswold CK. Spatial structure and benefits to hosts allow plasmids with and without post-segregational killing systems to coexist. Biol Lett 2023; 19:20220376. [PMID: 36855853 PMCID: PMC9975649 DOI: 10.1098/rsbl.2022.0376] [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: 08/17/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
To persist, a plasmid relies on being passed on to a daughter cell, but this does not always occur. Plasmids with post-segregational killing (PSK) systems kill a daughter cell if the plasmid has not been passed on. By killing the host, it also kills competing plasmids in the same host, something competing plasmids without a similar system cannot do. Accordingly, plasmids with PSK systems can displace other plasmids. In nature, plasmids with and without PSK systems coexist and prior theory has suggested this is expected to be very rare or unstable, such that one or the other type of plasmid eventually takes over. Here, we show that if there is spatial structure and plasmids confer benefits to hosts, coexistence of plasmids occurs broadly. Often plasmids confer benefits (even ones with a PSK system) and bacteria are often spatially structured. So, our results may be generally applicable.
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Affiliation(s)
- Wilco Verweij
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Cortland K. Griswold
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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45
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Ban O, Bang WY, Jeon HJ, Jung YH, Yang J, Kim DH. Potential of
Bifidobacterium lactis
IDCC 4301 isolated from breast milk‐fed infant feces as a probiotic and functional ingredient. Food Sci Nutr 2023; 11:1952-1964. [PMID: 37051343 PMCID: PMC10084967 DOI: 10.1002/fsn3.3230] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/07/2022] [Accepted: 01/07/2023] [Indexed: 02/10/2023] Open
Abstract
Probiotics provide important health benefits to the host by improving intestinal microbial balance and have been widely consumed as dietary supplements. In this study, we investigated whether Bifidobacterium lactis IDCC 4301 (BL), isolated from feces of breast milk-fed infants, is safe to consume. Based on the guidelines established by the European Food Safety Authority (EFSA), safety tests such as antibiotic susceptibility, hemolysis, toxic compound formation (i.e., biogenic amine and d-lactate), single-dose acute oral toxicity, and extracellular enzymatic activities were performed. In addition, toxigenic genes, antibiotic resistance genes, and mobile genetic elements were investigated by analyzing the genome sequence of BL. BL was susceptible to eight antibiotics except for vancomycin and the absence of transferable resistance in the genome of this strain implied that vancomycin resistance is likely to be intrinsic. With regard to phenotypic characteristics, there was no concern of toxicity of this strain. Furthermore, BL utilized various carbohydrates and their conjugates through the activity of various endogenous carbohydrate-utilizing enzymes. Interestingly, the supernatant of the BL showed strong antipathogenic activity against various infectious pathogens. Therefore, we suggest that BL should be a safe probiotic and can be used as a functional ingredient in the food, cosmetic, and pharmaceutical industries.
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Affiliation(s)
- O‐Hyun Ban
- Ildong Bioscience Gyeonggi‐do South Korea
- School of Food Science and Biotechnology Kyungpook National University Daegu South Korea
| | | | - Hyeon Ji Jeon
- School of Food Science and Biotechnology Kyungpook National University Daegu South Korea
| | - Young Hoon Jung
- School of Food Science and Biotechnology Kyungpook National University Daegu South Korea
| | | | - Dong Hyun Kim
- School of Food Science and Biotechnology Kyungpook National University Daegu South Korea
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46
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Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel) 2023; 12:antibiotics12020328. [PMID: 36830238 PMCID: PMC9952180 DOI: 10.3390/antibiotics12020328] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.
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47
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Flemming HC, van Hullebusch ED, Neu TR, Nielsen PH, Seviour T, Stoodley P, Wingender J, Wuertz S. The biofilm matrix: multitasking in a shared space. Nat Rev Microbiol 2023; 21:70-86. [PMID: 36127518 DOI: 10.1038/s41579-022-00791-0] [Citation(s) in RCA: 161] [Impact Index Per Article: 161.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 01/20/2023]
Abstract
The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates - in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.
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Affiliation(s)
- Hans-Curt Flemming
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | | | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Thomas Seviour
- Aarhus University Centre for Water Technology, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.,Department of Orthopaedics, The Ohio State University, Columbus, OH, USA
| | - Jost Wingender
- University of Duisburg-Essen, Biofilm Centre, Department of Aquatic Microbiology, Essen, Germany
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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48
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Tian S, Sun X, Xiao H, Zhou Y, Huang X, An XL, Liu C, Su JQ. Evaluation of rice straw and its transformation products on norfloxacin degradation and antibiotic resistome attenuation during soil incorporation. CHEMOSPHERE 2023; 313:137451. [PMID: 36464023 DOI: 10.1016/j.chemosphere.2022.137451] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Straw incorporation into reclaimed soils has been demonstrated to increase soil nutrients and has the potential to efficiently increase crop production. However, which incorporation mode is more helpful in the control of antibiotic resistance genes (ARGs) remains unknown. In this study, we systematically compared the occurrence of antibiotic resistome in norfloxacin contaminated soils amended with rice straw (RS) and the transformation products, biochar (RSB) and ash (RSA). RS significantly promoted the degradation of norfloxacin (0.0648 d-1, 3 times faster than control), whereas RSB had little effect and RSA hindered the degradation. Based on metagenomic analysis, RS and RSB significantly reduced the ARGs relative abundance (0.1421 and 0.1991 compared to 0.2540 in control) at the end of soil incubation. Adonis test indicated that all of amendment treatments significantly affect the microbial communities in soils, whereas only RS and RSB significantly affect the variation of antibiotic resistome. Procrustes analysis confirmed the association of microbial communities and ARGs. Network analysis further revealed that the reduction in Actinobacteria was the main reason for the general decrease of ARGs relative abundance during soil incorporation, whereas Proteobacteria and Bacteroidetes were responsible for temporary promotion of ARGs in RS and RSB at the early stage. Finally, scientifically setting up the usage of rice straw and optimizing the preparation process of biochar are suggested for the synchronous control of the risk of antibiotics and ARGs during soil incorporation.
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Affiliation(s)
- Shaohua Tian
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Xuecong Sun
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Hai Xiao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Yanyan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Xu Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China.
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
| | - Chaoxiang Liu
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, 350108, PR China.
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, PR China
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49
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Antimicrobial Resistance and Recent Alternatives to Antibiotics for the Control of Bacterial Pathogens with an Emphasis on Foodborne Pathogens. Antibiotics (Basel) 2023; 12:antibiotics12020274. [PMID: 36830185 PMCID: PMC9952301 DOI: 10.3390/antibiotics12020274] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the most important global public health problems. The imprudent use of antibiotics in humans and animals has resulted in the emergence of antibiotic-resistant bacteria. The dissemination of these strains and their resistant determinants could endanger antibiotic efficacy. Therefore, there is an urgent need to identify and develop novel strategies to combat antibiotic resistance. This review provides insights into the evolution and the mechanisms of AMR. Additionally, it discusses alternative approaches that might be used to control AMR, including probiotics, prebiotics, antimicrobial peptides, small molecules, organic acids, essential oils, bacteriophage, fecal transplants, and nanoparticles.
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50
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Hu X, Zhang Y, Chen Z, Gao Y, Teppen B, Boyd SA, Zhang W, Tiedje JM, Li H. Tetracycline accumulation in biofilms enhances the selection pressure on Escherichia coli for expression of antibiotic resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159441. [PMID: 36252660 DOI: 10.1016/j.scitotenv.2022.159441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Microorganisms are present as either biofilm or planktonic species in natural and engineered environments. Little is known about the selection pressure emanating from exposure to sub-minimal inhibitory concentration of antibiotics on planktonic vs. biofilm bacteria. In this study, an E. coli bioreporter was used to develop biofilms on glass and high-density polyethylene (HDPE) surfaces, and compared with the corresponding planktonic bacteria in antibiotic resistance expression when exposed to a range of μg/L levels of tetracycline. The antibiotic resistance-associated fluorescence emissions from biofilm E. coli reached up to 1.6 times more than those from planktonic bacteria. The intensively developed biofilms on glass surfaces caused the embedded bacteria to experience higher selection pressure and express more antibiotic resistance than those on HDPE surfaces. The temporal pattern of fluorescence emissions from biofilm E. coli was consistent with the biofilm-developing processes during the experimental period. The increased expression of antibiotic resistance from biofilm bacteria could be attributed to the high affinity of tetracycline with extracellular polymeric substances (EPS). The enhanced accumulation of tetracycline in biofilms could exert higher selection pressure on the embedded bacteria. These results suggest that in many natural and engineered systems the higher antibiotic resistance in biofilm bacteria could be attributed partially to the retention antibiotics by the EPS in biofilms.
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Affiliation(s)
- Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Yingjie Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Zeyou Chen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Brian Teppen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Stephen A Boyd
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Wei Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States.
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