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Li F, Deng J, Zhang Z, Wang C, Mao Y. FabV, the Unique Enoyl-Acyl Carrier Protein Reductase in Xanthomonas arboricola pv. juglandis Associated with Walnut Bacterial Blight, Is Essential for the Growth and Confers Triclosan Resistance to the Strain. PHYTOPATHOLOGY 2024; 114:780-791. [PMID: 37913555 DOI: 10.1094/phyto-08-23-0272-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: 11/03/2023]
Abstract
Walnut bacterial blight caused by Xanthomonas arboricola pv. juglandis (Xaj) is one of the most prevalent diseases of walnut (Juglans spp.), causing significant reductions in nut yield and important losses in economy. Enoyl-acyl carrier protein (ACP) reductase (ENR) is one of the key enzymes involved in the biosynthesis of bacterial fatty acids. In this study, we identified a single ENR-encoding gene, RS10040, in the genome of the XajDW3F3 strain. Sequence alignment analysis suggested RS10040 as a candidate fabV gene in Xaj. Expression of XajfabV restored the growth of the Escherichia coli fabI temperature-sensitive mutant under a nonpermissive growth condition. In vitro assays demonstrated that XajFabV catalyzed enoyl-ACPs of various chain lengths to acyl-ACPs, demonstrating its role in de novo fatty acid biosynthesis. Furthermore, we confirmed that XajfabV is an essential gene for growth, as no XajfabV deletion mutant could be obtained, although XajfabV in the chromosome could be deleted after compensating with a functional ENR-encoding gene via an exogenous plasmid. The fabV replacement mutants showed similar growth characteristic and fatty acid compositions. Our data further identified that fabV conferred Xaj with tolerance to various environmental stresses. Although XajFabV conferred Xaj with triclosan resistance, the resistance of Xaj was weaker than that found for Pseudomonas aeruginosa. Moreover, triclosan exhibited a control effect against infection of the ΔfabV/EcfabI to its host walnut. This study revealed the function of XajFabV and laid a theoretical foundation for the fatty acid synthesis mechanism of Xaj.
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Affiliation(s)
- Feng Li
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Jiangli Deng
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Zhilin Zhang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Cheng Wang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Yahui Mao
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
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Huang G, Khan R, Zheng Y, Lee PC, Li Q, Khan I. Exploring the role of gut microbiota in advancing personalized medicine. Front Microbiol 2023; 14:1274925. [PMID: 38098666 PMCID: PMC10720646 DOI: 10.3389/fmicb.2023.1274925] [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: 08/09/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023] Open
Abstract
Ongoing extensive research in the field of gut microbiota (GM) has highlighted the crucial role of gut-dwelling microbes in human health. These microbes possess 100 times more genes than the human genome and offer significant biochemical advantages to the host in nutrient and drug absorption, metabolism, and excretion. It is increasingly clear that GM modulates the efficacy and toxicity of drugs, especially those taken orally. In addition, intra-individual variability of GM has been shown to contribute to drug response biases for certain therapeutics. For instance, the efficacy of cyclophosphamide depends on the presence of Enterococcus hirae and Barnesiella intestinihominis in the host intestine. Conversely, the presence of inappropriate or unwanted gut bacteria can inactivate a drug. For example, dehydroxylase of Enterococcus faecalis and Eggerthella lenta A2 can metabolize L-dopa before it converts into the active form (dopamine) and crosses the blood-brain barrier to treat Parkinson's disease patients. Moreover, GM is emerging as a new player in personalized medicine, and various methods are being developed to treat diseases by remodeling patients' GM composition, such as prebiotic and probiotic interventions, microbiota transplants, and the introduction of synthetic GM. This review aims to highlight how the host's GM can improve drug efficacy and discuss how an unwanted bug can cause the inactivation of medicine.
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Affiliation(s)
- Gouxin Huang
- Clinical Research Center, Shantou Central Hospital, Shantou, China
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Yilin Zheng
- Clinical Research Center, Shantou Central Hospital, Shantou, China
| | - Ping-Chin Lee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Qingnan Li
- Clinical Research Center, Shantou Central Hospital, Shantou, China
- Department of Pharmacy, Shantou Central Hospital, Shantou, China
| | - Imran Khan
- Department of Biotechnology, Faculty of Chemical and Life Sciences, Abdul Wali Khan University Mardan, Mardan, Pakistan
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Li S, Wang S, Pan C, Luo Y, Liang S, Long S, Yang X, Wang B. Differences in Physiological Performance and Gut Microbiota between Deep-Sea and Coastal Aquaculture of Thachinotus Ovatus: A Metagenomic Approach. Animals (Basel) 2023; 13:3365. [PMID: 37958120 PMCID: PMC10648977 DOI: 10.3390/ani13213365] [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: 09/01/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Aquaculture has become the fastest growing sector in global agriculture. The environmental degradation, diseases, and high density of mariculture has made for an inevitable shift in mariculture production from coastal to deep-sea areas. The influence that traditional coastal and emerging deep-sea farming environments exert on aquatic growth, immunity and gut microbial flora is unclear. To address this question, we compared the growth performance, physiological indicators and intestinal microbiological differences of deep-sea and coastal aquaculture in the Guangxi Beibu Gulf of China. The results showed that the growth performance and the complement of C3 and C4 (C3, C4), superoxide dismutase (SOD), and lysozyme (LYS), these physiological and biochemical indicators in the liver, kidney, and muscle of Trachinotus ovatus (T. ovatus), showed significant differences under different rearing conditions. Metagenome sequencing analysis showed Ascomycota, Pseudomonadota, and Bacillota were the three dominant phyla, accounting for 52.98/53.32 (coastal/deep sea), 24.30/22.13, and 10.39/11.82%, respectively. Aligned against the CARD database, a total of 23/2 (coastal/deep-sea) antibiotic resistance genes were screened and grouped into 4/2 genotypes. It indicated that compared with deep-sea fish, higher biological oxygen levels (3.10 times), inorganic nitrogen (110.00 times) and labile phosphate levels (29.00 times) in coastal waters might contributed to the existence of eutrophication with antibiotic resistance. The results of the study can provide complementary data on the study of the difference between deep-sea farming and traditional coastal farming, serving as a reference to future in-depth work on the transformation of fisheries development and scientific standardization of deep-sea farming.
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Affiliation(s)
- Shuangfei Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.L.); (S.W.); (C.P.); (Y.L.); (S.L.); (S.L.)
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Shilin Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.L.); (S.W.); (C.P.); (Y.L.); (S.L.); (S.L.)
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Cong Pan
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.L.); (S.W.); (C.P.); (Y.L.); (S.L.); (S.L.)
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Yanqing Luo
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.L.); (S.W.); (C.P.); (Y.L.); (S.L.); (S.L.)
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Shitong Liang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.L.); (S.W.); (C.P.); (Y.L.); (S.L.); (S.L.)
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Siru Long
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.L.); (S.W.); (C.P.); (Y.L.); (S.L.); (S.L.)
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Xuewei Yang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.L.); (S.W.); (C.P.); (Y.L.); (S.L.); (S.L.)
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Boyu Wang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (S.L.); (S.W.); (C.P.); (Y.L.); (S.L.); (S.L.)
- Shenzhen Key Laboratory of Marine Biological Resources and Ecology Environment, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China
- Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
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Sun C, Zhang T, Zhou Y, Liu ZF, Zhang Y, Bian Y, Feng XS. Triclosan and related compounds in the environment: Recent updates on sources, fates, distribution, analytical extraction, analysis, and removal techniques. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 870:161885. [PMID: 36731573 DOI: 10.1016/j.scitotenv.2023.161885] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Triclosan (TCS) has been widely used in daily life because of its broad-spectrum antibacterial activities. The residue of TCS and related compounds in the environment is one of the critical environmental safety problems, and the pandemic of COVID-19 aggravates the accumulation of TCS and related compounds in the environment. Therefore, detecting TCS and related compound residues in the environment is of great significance to human health and environmental safety. The distribution of TCS and related compounds are slightly different worldwide, and the removal methods also have advantages and disadvantages. This paper summarized the research progress on the source, distribution, degradation, analytical extraction, detection, and removal techniques of TCS and related compounds in different environmental samples. The commonly used analytical extraction methods for TCS and related compounds include solid-phase extraction, liquid-liquid extraction, solid-phase microextraction, liquid-phase microextraction, and so on. The determination methods include liquid chromatography coupled with different detectors, gas chromatography and related methods, sensors, electrochemical method, capillary electrophoresis. The removal techniques in various environmental samples mainly include biodegradation, advanced oxidation, and adsorption methods. Besides, both the pros and cons of different techniques have been compared and summarized, and the development and prospect of each technique have been given.
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Affiliation(s)
- Chen Sun
- School of Pharmacy, China Medical University, Shenyang 110122, China; Department of Pharmaceutics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Ting Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yu Zhou
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhi-Fei Liu
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Yuan Zhang
- School of Pharmacy, China Medical University, Shenyang 110122, China.
| | - Yu Bian
- School of Pharmacy, China Medical University, Shenyang 110122, China.
| | - Xue-Song Feng
- School of Pharmacy, China Medical University, Shenyang 110122, China.
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Khan R, Shah MD, Shah L, Lee PC, Khan I. Bacterial polysaccharides-A big source for prebiotics and therapeutics. Front Nutr 2022; 9:1031935. [PMID: 36407542 PMCID: PMC9671505 DOI: 10.3389/fnut.2022.1031935] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/11/2022] [Indexed: 07/29/2023] Open
Abstract
Bacterial polysaccharides are unique due to their higher purity, hydrophilic nature, and a finer three-dimensional fibrous structure. Primarily, these polymers provide protection, support, and energy to the microorganism, however, more recently several auxiliary properties of these biopolymers have been unmasked. Microbial polysaccharides have shown therapeutic abilities against various illnesses, augmented the healing abilities of the herbal and Western medicines, improved overall health of the host, and have exerted positive impact on the growth of gut dwelling beneficial bacteria. Specifically, the review is discussing the mechanism through which bacterial polysaccharides exert anti-inflammatory, antioxidant, anti-cancer, and anti-microbial properties. In addition, they are holding promising application in the 3D printing. The review is also discussing a perspective about the metagenome-based screening of polysaccharides, their integration with other cutting-edge tools, and synthetic microbiome base intervention of polysaccharides as a strategy for prebiotic intervention. This review has collected interesting information about the bacterial polysaccharides from Google Scholar, PubMed, Scopus, and Web of Science databases. Up to our knowledge, this is the first of its kind review article that is summarizing therapeutic, prebiotics, and commercial application of bacterial polysaccharides.
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Affiliation(s)
- Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Muhammad Dawood Shah
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Luqman Shah
- Department of Biochemistry, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Ping-Chin Lee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Imran Khan
- Department of Biotechnology, Faculty of Chemical and Life Sciences, Abdul Wali Khan University Mardan, Mardan, Pakistan
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Hopf FSM, Roth CD, de Souza EV, Galina L, Czeczot AM, Machado P, Basso LA, Bizarro CV. Bacterial Enoyl-Reductases: The Ever-Growing List of Fabs, Their Mechanisms and Inhibition. Front Microbiol 2022; 13:891610. [PMID: 35814645 PMCID: PMC9260719 DOI: 10.3389/fmicb.2022.891610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Enoyl-ACP reductases (ENRs) are enzymes that catalyze the last step of the elongation cycle during fatty acid synthesis. In recent years, new bacterial ENR types were discovered, some of them with structures and mechanisms that differ from the canonical bacterial FabI enzymes. Here, we briefly review the diversity of structural and catalytic properties of the canonical FabI and the new FabK, FabV, FabL, and novel ENRs identified in a soil metagenome study. We also highlight recent efforts to use the newly discovered Fabs as targets for drug development and consider the complex evolutionary history of this diverse set of bacterial ENRs.
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Affiliation(s)
- Fernanda S. M. Hopf
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Candida D. Roth
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Eduardo V. de Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiza Galina
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexia M. Czeczot
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pablo Machado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz A. Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristiano V. Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Cristiano V. Bizarro,
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Khan R, Yee AL, Gilbert JA, Haider A, Jamal SB, Muhammad F. Triclosan-containing sutures: safety and resistance issues need to be addressed prior to generalized use. APPLIED NANOSCIENCE 2021. [DOI: 10.1007/s13204-021-01979-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Li XH, Huang YY, Lu LM, Zhao LJ, Luo XK, Li RJ, Dai YY, Qin C, Huang YQ, Chen H. Early genetic diagnosis of clarithromycin resistance in Helicobacter pylori. World J Gastroenterol 2021; 27:3595-3608. [PMID: 34239272 PMCID: PMC8240046 DOI: 10.3748/wjg.v27.i24.3595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/13/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The drug resistance rate of clinical Helicobacter pylori (H. pylori) isolates has increased. However, the mechanism of drug resistance remains unclear. In this study, drug-resistant H. pylori strains were isolated from different areas and different populations of Chinese for genomic analysis.
AIM To investigate drug-resistant genes in H. pylori and find the genes for the early diagnosis of clarithromycin resistance.
METHODS Three drug-resistant H. pylori strains were isolated from patients with gastritis in Bama County, China. Minimal inhibitory concentrations of clarithromycin, metronidazole, and levofloxacin were determined and complete genome sequencing was performed with annotation. Hp1181 and hp1184 genes were found in these strains and then detected by reverse transcription polymerase chain reaction. The relationships between hp1181 or hp1184 and clarithromycin resistance were ascertained with gene mutant and drug-resistant strains. The homology of the strains with hp26695 was assessed through complete genome detection and identification. Differences in genome sequences, gene quantity, and gene characteristics were detected amongst the three strains. Prediction and analysis of the function of drug-resistant genes indicated that the RNA expression of hp1181 and hp1184 increased in the three strains, which was the same in the artificially induced clarithromycin-resistant bacteria. After gene knockout, the drug sensitivity of the strains was assessed.
RESULTS The strains showing a high degree of homology with hp26695, hp1181, and hp1184 genes were found in these strains; the expression of the genes hp1184 and hp1181 was associated with clarithromycin resistance.
CONCLUSION Hp1181 and hp1184 mutations may be the earliest and most persistent response to clarithromycin resistance, and they may be the potential target genes for the diagnosis, prevention, and treatment of clarithromycin resistance.
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Affiliation(s)
- Xiao-Hua Li
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yong-Yi Huang
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Lin-Ming Lu
- Department of Pathology, Wannan Medical College, Wuhu 241002, Anhui Province, China
| | - Li-Juan Zhao
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Xian-Ke Luo
- Department of Gastroenterology, National Hospital of Guangxi Zhuang Autonomous Region, Nanning Guangxi Zhuang Autonomous Region, 530001, China
| | - Ru-Jia Li
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yuan-Yuan Dai
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Chun Qin
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yan-Qiang Huang
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Hao Chen
- Department of Pathology, Wannan Medical College, Wuhu 241002, Anhui Province, China
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Leyn SA, Zlamal JE, Kurnasov OV, Li X, Elane M, Myjak L, Godzik M, de Crecy A, Garcia-Alcalde F, Ebeling M, Osterman AL. Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance. Microb Genom 2021; 7. [PMID: 33945454 PMCID: PMC8209735 DOI: 10.1099/mgen.0.000553] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the dynamics and mechanisms of acquired drug resistance across major classes of antibiotics and bacterial pathogens is of critical importance for the optimization of current anti-infective therapies and the development of novel ones. To systematically address this challenge, we developed a workflow combining experimental evolution in a morbidostat continuous culturing device with deep genomic sequencing of population samples collected in time series. This approach was applied to the experimental evolution of six populations of Escherichia coli BW25113 towards acquiring resistance to triclosan (TCS), an antibacterial agent in various consumer products. This study revealed the rapid emergence and expansion (up to 100% in each culture within 4 days) of missense mutations in the fabI gene, encoding enoyl-acyl carrier protein reductase, the known TCS molecular target. A follow-up analysis of isolated clones showed that distinct amino acid substitutions increased the drug IC90 in a 3-16-fold range, reflecting their proximity to the TCS-binding site. In contrast to other antibiotics, efflux-upregulating mutations occurred only rarely and with low abundance. Mutations in several other genes were detected at an earlier stage of evolution. Most notably, three distinct amino acid substitutions were mapped in the C-terminal periplasmic domain of CadC protein, an acid stress-responsive transcriptional regulator. While these mutations do not confer robust TCS resistance, they appear to play a certain, yet unknown, role in adaptation to relatively low drug pressure. Overall, the observed evolutionary trajectories suggest that the FabI enzyme is the sole target of TCS (at least up to the ~50 µm level), and amino acid substitutions in the TCS-binding site represent the main mechanism of robust TCS resistance in E. coli. This model study illustrates the potential utility of the established morbidostat-based approach for uncovering resistance mechanisms and target identification for novel drug candidates with yet unknown mechanisms of action.
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Affiliation(s)
- Semen A Leyn
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jaime E Zlamal
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Oleg V Kurnasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Xiaoqing Li
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Marinela Elane
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lourdes Myjak
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Mikolaj Godzik
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Fernando Garcia-Alcalde
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology, Roche Innovation Center, Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center, Basel, Switzerland
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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10
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McFarland AG, Bertucci HK, Littman E, Shen J, Huttenhower C, Hartmann EM. Triclosan Tolerance Is Driven by a Conserved Mechanism in Diverse Pseudomonas Species. Appl Environ Microbiol 2021; 87:e02924-20. [PMID: 33483311 PMCID: PMC8091609 DOI: 10.1128/aem.02924-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/20/2021] [Indexed: 02/04/2023] Open
Abstract
Perturbation of natural microbial communities by antimicrobials, such as triclosan, can result in selection for antibiotic tolerance, which is of particular concern when pathogens are present. Members of the genus Pseudomonas are found in many natural microbial communities and frequently demonstrate increased abundance following triclosan exposure. The pathogen and well-studied model organism Pseudomonas aeruginosa exhibits high triclosan tolerance; however, it is unknown if all Pseudomonas species share this trait or if there are susceptible strains. We characterized the triclosan tolerance phenotypes of diverse Pseudomonas isolates obtained from triclosan-exposed built environments and identified both tolerant and sensitive strains. High tolerance is associated with carriage of the enoyl-acyl carrier reductase (ENR) isozyme gene fabV, compared to the lesser protective effects of efflux or presence of ENRs. Given its unique importance, we examined fabV distribution throughout Pseudomonas species using large-scale phylogenomic analyses. We find fabV presence or absence is largely invariant at the species level but demonstrates multiple gain and loss events in its evolutionary history. We further provide evidence of its presence on mobile genetic elements. Our results demonstrate the surprising variability in triclosan tolerance in Pseudomonas and confirm fabV to be a useful indicator for high triclosan tolerance in Pseudomonas These findings provide a framework for better monitoring of Pseudomonas in triclosan-exposed environments and interpreting effects on species and gene composition.IMPORTANCE Closely related species are typically assumed to demonstrate similar phenotypes driven by underlying conserved genotypes. When monitoring for the effect of antimicrobials on the types of species that may be selected for, this assumption may prove to be incorrect, and identification of additional genetic markers may be necessary. We isolated several phylogenetically diverse members of Pseudomonas from indoor environments and tested their phenotypic tolerance toward the commonly used antimicrobial triclosan. Although Pseudomonas isolates are broadly regarded to be highly triclosan tolerant, we demonstrate the presence of both triclosan-tolerant and -susceptible strains, separated by a difference in tolerance of nearly 3 orders of magnitude. Bioinformatic and experimental investigation demonstrated that the presence of the gene fabV was associated with high tolerance. We demonstrate that fabV is not evenly distributed in all Pseudomonas species and that its presence could be a useful predictor of high triclosan tolerance suitable for antimicrobial monitoring efforts involving triclosan.
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Affiliation(s)
- Alexander G McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Hanna K Bertucci
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Erica Littman
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
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11
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Blaustein RA, Michelitsch LM, Glawe AJ, Lee H, Huttelmaier S, Hellgeth N, Ben Maamar S, Hartmann EM. Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota. MICROBIOME 2021; 9:32. [PMID: 33517907 PMCID: PMC7849112 DOI: 10.1186/s40168-020-00983-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/16/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. RESULTS Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features. CONCLUSIONS Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.
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Affiliation(s)
- Ryan A. Blaustein
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | | | - Adam J. Glawe
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Hansung Lee
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Stefanie Huttelmaier
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Nancy Hellgeth
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL USA
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12
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Demissie R, Kabre P, Fung LWM. Nonactive-Site Mutations in S. aureus FabI That Induce Triclosan Resistance. ACS OMEGA 2020; 5:23175-23183. [PMID: 32954168 PMCID: PMC7495757 DOI: 10.1021/acsomega.0c02942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
The wide use of the antimicrobial agent/biocide, triclosan, promotes triclosan-resistant bacterial strains, including Staphylococcus aureus, as well as leads to accumulation in the aquatic and terrestrial environments. Knowledge of the molecular actions of triclosan on S. aureus is needed to understand the consequence of triclosan resistance and environmental accumulation of triclosan on S. aureus resistant strains, as well as to develop biphenyl ether analogs as antibiotic candidates. Triclosan inhibits an essential enzyme in the fatty acid biosynthetic pathway, the reduced nicotinamide adenine dinucleotide (NADH)/reduced nicotinamide adenine dinucleotide phosphate (NADPH)-dependent enoyl-acyl carrier protein (enoyl-ACP) reductase, or FabI. In this study, we used error-prone polymerase chain reaction (epPCR) to generate mutations in the S. aureus FabI enzyme. Instead of using an elaborate FabI enzyme activity assay that involves ACP-linked substrates to determine whether triclosan inhibits the enzyme activities of individual FabI mutants, we used an efficient and economical assay that we developed, based on thermal shift principles, to screen for triclosan binding to FabI mutants in cells. We identified four active-site mutations. More interestingly, we also identified nine triclosan-resistant mutations distant from the active site (G113V, Y123H, S166N, N220I, G227C, A230T, V241I, F252I, and H253P) but located in disparate positions in the monomer-monomer and dimer-dimer interface regions in S. aureus FabI. We suggest that these sites may serve as potential allosteric sites for designing potential therapeutic inhibitors that offer advantages in selectivity since allosteric sites are less evolutionarily conserved.
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Affiliation(s)
- Robel Demissie
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | | | - Leslie W.-M. Fung
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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13
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Mahalak KK, Firrman J, Lee JJ, Bittinger K, Nuñez A, Mattei LM, Zhang H, Fett B, Bobokalonov J, Arango-Argoty G, Zhang L, Zhang G, Liu LS. Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro. PLoS One 2020; 15:e0234046. [PMID: 32585680 PMCID: PMC7316517 DOI: 10.1371/journal.pone.0234046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/17/2020] [Indexed: 12/17/2022] Open
Abstract
The recent ban of the antimicrobial compound triclosan from use in consumer soaps followed research that showcased the risk it poses to the environment and to human health. Triclosan has been found in human plasma, urine and milk, demonstrating that it is present in human tissues. Previous work has also demonstrated that consumption of triclosan disrupts the gut microbial community of mice and zebrafish. Due to the widespread use of triclosan and ubiquity in the environment, it is imperative to understand the impact this chemical has on the human body and its symbiotic resident microbes. To that end, this study is the first to explore how triclosan impacts the human gut microbial community in vitro both during and after treatment. Through our in vitro system simulating three regions of the human gut; the ascending colon, transverse colon, and descending colon regions, we found that treatment with triclosan significantly impacted the community structure in terms of reduced population, diversity, and metabolite production, most notably in the ascending colon region. Given a 2 week recovery period, most of the population levels, community structure, and diversity levels were recovered for all colon regions. Our results demonstrate that the human gut microbial community diversity and population size is significantly impacted by triclosan at a high dose in vitro, and that the community is recoverable within this system.
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Affiliation(s)
- Karley K. Mahalak
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Jenni Firrman
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Alberto Nuñez
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Bryton Fett
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jamshed Bobokalonov
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Gustavo Arango-Argoty
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, United States of America
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Lin Shu Liu
- United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
- * E-mail:
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14
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Kim SH, Khan R, Choi K, Lee SW, Rhee S. A triclosan-resistance protein from the soil metagenome is a novel enoyl-acyl carrier protein reductase: Structure-guided functional analysis. FEBS J 2020; 287:4710-4728. [PMID: 32112503 DOI: 10.1111/febs.15267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/05/2020] [Accepted: 02/27/2020] [Indexed: 11/28/2022]
Abstract
The synthetic biocide triclosan targets enoyl-acyl carrier protein reductase(s) (ENR) in bacterial type II fatty acid biosynthesis. Screening and sequence analyses of the triclosan resistome from the soil metagenome identified a variety of triclosan-resistance ENRs. Interestingly, the mode of triclosan resistance by one hypothetical protein was elusive, mainly due to a lack of sequence similarity with other proteins that mediate triclosan resistance. Here, we carried out a structure-based function prediction of the hypothetical protein, herein referred to as FabMG, and in vivo and in vitro functional analyses. The crystal structure of FabMG showed limited structural homology with FabG and FabI, which are also involved in type II fatty acid synthesis. In vivo complementation and in vitro activity assays indicated that FabMG is functionally a FabI-type ENR that employs NADH as a coenzyme. Variations in the sequence and structure of FabMG are likely responsible for inefficient binding of triclosan, resulting in triclosan resistance. These data unravel a previously uncharacterized FabMG, which is prevalent in various microbes in triclosan-contaminated environments and provide mechanistic insight into triclosan resistance.
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Affiliation(s)
- Sang-Hoon Kim
- Department of Agricultural Biotechnology, Seoul National University, Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan, Korea.,Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan, Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan, Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Korea
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15
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Zadeh Hosseingholi E, Zarrini G, Pashazadeh M, Gheibi Hayat SM, Molavi G. In Silico Identification of Probable Drug and Vaccine Candidates Against Antibiotic-Resistant Acinetobacter baumannii. Microb Drug Resist 2019; 26:456-467. [PMID: 31742478 DOI: 10.1089/mdr.2019.0236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acinetobacter baumannii is known as a Gram-negative bacterium that has become one of the most important health problems due to antibiotic resistance. Today, numerous efforts are being made to find new antibiotics against this nosocomial pathogen. As an alternative solution, finding bacterial target(s), necessary for survival and spread of most resistant strains, can be a benefit exploited in drug and vaccine design. In this study, a list of extensive drug-resistant and carbapenem-resistant (multidrug resistant) A. bumannii strains with complete sequencing of genome were prepared and common hypothetical proteins (HPs) composed of more than 200 amino acids were selected. Then, a number of bioinformatics tools were combined for functional assignments of HPs using their sequence. Overall, among 18 in silico investigated proteins, the results showed that 7 proteins implicated in transcriptional regulation, pilus assembly, protein catabolism, fatty acid biosynthesis, adhesion, urea catalysis, and hydrolysis of phosphate monoesters have theoretical potential of involvement in successful survival and pathogenesis of A. baumannii. In addition, immunological analyses with prediction softwares indicated 4 HPs to be probable vaccine candidates. The outcome of this work will be helpful to find novel vaccine design candidates and therapeutic targets for A. baumannii through experimental investigations.
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Affiliation(s)
| | - Gholamreza Zarrini
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Marayam Pashazadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Seyed Mohammad Gheibi Hayat
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Science, Yazd, Iran
| | - Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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16
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Weitekamp CA, Phelps D, Swank A, McCord J, Sobus JR, Catron T, Keely S, Brinkman N, Zurlinden T, Wheaton E, Strynar M, McQueen C, Wood CE, Tal T. Triclosan-Selected Host-Associated Microbiota Perform Xenobiotic Biotransformations in Larval Zebrafish. Toxicol Sci 2019; 172:109-122. [PMID: 31504981 PMCID: PMC10461336 DOI: 10.1093/toxsci/kfz166] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/17/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Microbiota regulate important physiologic processes during early host development. They also biotransform xenobiotics and serve as key intermediaries for chemical exposure. Antimicrobial agents in the environment may disrupt these complex interactions and alter key metabolic functions provided by host-associated microbiota. To examine the role of microbiota in xenobiotic metabolism, we exposed zebrafish larvae to the antimicrobial agent triclosan. Conventionally colonized (CC), microbe-free axenic (AX), or axenic colonized on day 1 (AC1) zebrafish were exposed to 0.16-0.30 µM triclosan or vehicle on days 1, 6, 7, 8, and 9 days post fertilization (dpf). After 6 and 10 dpf, host-associated microbial community structure and putative function were assessed by 16S rRNA gene sequencing. At 10 dpf, triclosan exposure selected for bacterial taxa, including Rheinheimera. Triclosan-selected microbes were predicted to be enriched in pathways related to mechanisms of antibiotic resistance, sulfonation, oxidative stress, and drug metabolism. Furthermore, at 10 dpf, colonized zebrafish contained 2.5-3 times more triclosan relative to AX larvae. Nontargeted chemical analysis revealed that, relative to AX larvae, both cohorts of colonized larvae showed elevations in 23 chemical features, including parent triclosan and putative triclosan sulfate. Taken together, these data suggest that triclosan exposure selects for microbes that harbor the capacity to biotransform triclosan into chemical metabolites with unknown toxicity profiles. More broadly, these data support the concept that microbiota modify the toxicokinetics of xenobiotic exposure.
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Affiliation(s)
- Chelsea A. Weitekamp
- Oak Ridge Institute for Science and Education/U.S. EPA/ORD/NHEERL/ISTD, Research Triangle Park, North Carolina, 27711
| | - Drake Phelps
- Oak Ridge Institute for Science and Education/U.S. EPA/ORD/NHEERL/ISTD, Research Triangle Park, North Carolina, 27711
| | - Adam Swank
- U.S. EPA/ORD/NHEERL/RCU, Research Triangle Park, North Carolina, 27711
| | - James McCord
- Oak Ridge Institute for Science and Education/U.S. EPA/ORD/NHEERL/ISTD, Research Triangle Park, North Carolina, 27711
| | - Jon R. Sobus
- U.S. EPA/ORD/NERL/EMMD, Research Triangle Park, North Carolina, 27711
| | - Tara Catron
- Oak Ridge Institute for Science and Education/U.S. EPA/ORD/NHEERL/ISTD, Research Triangle Park, North Carolina, 27711
| | - Scott Keely
- U.S. EPA/ORD/NERL/SED, Cincinnati, Ohio, 45220
| | | | - Todd Zurlinden
- U.S. EPA/ORD/NCCT, Research Triangle Park, North Carolina, 27711
| | | | - Mark Strynar
- U.S. EPA/ORD/NERL/EMMD, Research Triangle Park, North Carolina, 27711
| | - Charlene McQueen
- University of Arizona, Department of Pharmacology and Toxicology, Tucson, Arizona, 85721
| | - Charles E. Wood
- University of Arizona, Department of Pharmacology and Toxicology, Tucson, Arizona, 85721
| | - Tamara Tal
- U.S. EPA/ORD/NHEERL/ISTD, Research Triangle Park, North Carolina, 27711
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17
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Biochemical and Structural Insights Concerning Triclosan Resistance in a Novel YX 7K Type Enoyl-Acyl Carrier Protein Reductase from Soil Metagenome. Sci Rep 2019; 9:15401. [PMID: 31659200 PMCID: PMC6817880 DOI: 10.1038/s41598-019-51895-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/08/2019] [Indexed: 11/08/2022] Open
Abstract
Enoyl-acyl carrier protein reductase (ENR) catalyzes the last reduction step in the bacterial type II fatty acid biosynthesis cycle. ENRs include FabI, FabL, FabL2, FabK, and FabV. Previously, we reported a unique triclosan (TCL) resistant ENR homolog that was predominant in obligate intracellular pathogenic bacteria and Apicomplexa. Herein, we report the biochemical and structural basis of TCL resistance in this novel ENR. The purified protein revealed NADH-dependent ENR activity and shared similarity to prototypic FabI. Thus, this metagenome-derived ENR was designated FabI2. Unlike other prototypic bacterial ENRs with the YX6K type catalytic domain, FabI2 possessed a unique YX7K type catalytic domain. Computational modeling followed by site-directed mutagenesis revealed that mild resistance (20 µg/ml of minimum inhibitory concentration) of FabI2 to TCL was confined to the relatively less bulky side chain of A128. Substitution of A128 in FabI2 with bulky valine (V128) elevated TCL resistance. Phylogenetic analysis further suggested that the novel FabI2 and prototypical FabI evolved from a common short-chain dehydrogenase reductase family. To our best knowledge, FabI2 is the only known ENR shared by intracellular pathogenic prokaryotes, intracellular pathogenic lower eukaryotes, and a few higher eukaryotes. This suggests that the ENRs of prokaryotes and eukaryotes diverged from a common ancestral ENR of FabI2.
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18
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Cabral L, Noronha MF, de Sousa STP, Lacerda-Júnior GV, Richter L, Fostier AH, Andreote FD, Hess M, Oliveira VMD. The metagenomic landscape of xenobiotics biodegradation in mangrove sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 179:232-240. [PMID: 31051396 DOI: 10.1016/j.ecoenv.2019.04.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/08/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Metagenomics is a powerful approach to study microorganisms present in any given environment and their potential to maintain and improve ecosystem health without the need of cultivating these microorganisms in the laboratory. In this study, we combined a cultivation-independent metagenomics approach with functional assays to identify the detoxification potential of microbial genes evaluating their potential to contribute to xenobiotics resistance in oil-impacted mangrove sediments. A metagenomic fosmid library containing 12,960 clones from highly contaminated mangrove sediment was used in this study. For assessment of metal resistance, clones were grown in culture medium with increasing concentrations of mercury. The analyses metagenomic library sequences revealed the presence of genes related to heavy metals and antibiotics resistance in the oil-impacted mangrove microbiome. The taxonomic profiling of these sequences suggests that at the genus level, Geobacter was the most abundant genus in our dataset. A functional screening assessment of the metagenomic library successfully detected 24 potential heavy metal tolerant clones, six of which were capable of growing with increased concentrations of mercury. The genetic characterization of selected clones allowed the detection of genes related to detoxification processes, such as chromate transport protein ChrA, haloacid dehalogenase-like hydrolase, lipopolysaccharide transport system, and 3-oxoacyl-[acyl-carrier-protein] reductase. Clones were capable of growing in medium containing increased concentrations of metals and antibiotics, but none manifested strong mercury removal from culture medium characteristic of mercuric reductase activity. These results suggest that resistance to xenobiotic stress varies greatly and that additional studies to elucidate the potential of metal biotransformation need to be carried out with the goal of improving bioremediation application.
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Affiliation(s)
- Lucélia Cabral
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB)- University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Melline Fontes Noronha
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB)- University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Sanderson Tarciso Pereira de Sousa
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB)- University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gileno Vieira Lacerda-Júnior
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Institute of Biology (IB)- University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Larissa Richter
- Institute of Chemistry - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Anne Hélène Fostier
- Institute of Chemistry - University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, ''Luiz de Queiroz'' College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Matthias Hess
- University of California, Davis, Department of Animal Science, Davis, CA, USA
| | - Valéria Maia de Oliveira
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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19
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Functional screening for triclosan resistance in a wastewater metagenome and isolates of Escherichia coli and Enterococcus spp. from a large Canadian healthcare region. PLoS One 2019; 14:e0211144. [PMID: 30677104 PMCID: PMC6345445 DOI: 10.1371/journal.pone.0211144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/07/2019] [Indexed: 01/31/2023] Open
Abstract
The biocide triclosan is in many consumer products and is a frequent contaminant of wastewater (WW) such that there is concern that triclosan promotes resistance to important antibiotics. This study identified functional mechanisms of triclosan resistance (TCSR) in WW metagenomes, and assessed the frequency of TCSR in WW-derived and clinical isolates of Escherichia coli and Enterococcus spp. Metagenomic DNA extracted from WW was used to profile the microbiome and construct large-insert cosmid libraries, which were screened for TCSR. Resistant cosmids were sequenced and the TCSR determinant identified by transposon mutagenesis. Wastewater Enterococcus spp. (N = 94) and E. coli (N = 99) and clinical Enterococcus spp. (N = 146) and vancomycin-resistant E. faecium (VRE; N = 149) were collected and tested for resistance to triclosan and a comprehensive drug panel. Functional metagenomic screening revealed diverse FabV homologs as major WW TCSR determinants. Resistant clones harboured sequences likely originating from Aeromonas spp., a common WW microbe. The triclosan MIC90s for E. coli, E. faecalis, and E. faecium isolates were 0.125, 32, and 32 mg/L, respectively. For E. coli, there was no correlation between the triclosan MIC and any drug tested. Negative correlations were detected between the triclosan MIC and levofloxacin resistance for E. faecalis, and between triclosan and vancomycin, teicoplanin, and ampicillin resistance for E. faecium. Thus, FabV homologs were the major contributor to the WW triclosan resistome and high-level TCSR was not observed in WW or clinical isolates. Elevated triclosan MICs were not positively correlated with antimicrobial resistance to any drug tested.
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20
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Phandanouvong-Lozano V, Sun W, Sanders JM, Hay AG. Biochar does not attenuate triclosan's impact on soil bacterial communities. CHEMOSPHERE 2018; 213:215-225. [PMID: 30223126 DOI: 10.1016/j.chemosphere.2018.08.132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/24/2018] [Accepted: 08/26/2018] [Indexed: 06/08/2023]
Abstract
Triclosan, a broad-spectrum antimicrobial, has been widely used in pharmaceutical and personal care products. It undergoes limited degradation during wastewater treatment and is present in biosolids, most of which are land applied in the United States. This study assessed the impact of triclosan (0-100 mg kg-1) with and without biochar on soil bacterial communities. Very little 14C-triclosan was mineralized to 14CO2 (<7%) over the course of the study (42 days). While biochar (1%) significantly lowered mineralization of triclosan, analysis of 16S rRNA gene sequences revealed that biochar impacted very few OTUs and did not alter the overall structure of the community. Triclosan, on the other hand, significantly affected bacterial diversity and community structure (alpha diversity, ANOVA, p < 0.001; beta diversity, AMOVA, p < 0.01). Dirichlet multinomial mixtures (DMM) modeling and complete linkage clustering (CLC) revealed a dose-dependent impact of triclosan. Non-Parametric Metastats (NPM) analysis showed that 150 of 734 OTUs from seven main phyla were significantly impacted by triclosan (adjusted p < 0.05). Genera harboring opportunistic pathogens such as Flavobacterium were enriched in the presence of triclosan, as was Stenotrophomonas. The latter has previously been implicated in triclosan degradation via stable isotope probing. Surprisingly, Sphingomonads, which include well-characterized triclosan degraders were negatively impacted by even low doses of triclosan. Analyses of published genomes showed that triclosan resistance determinants were rare in Sphingomonads which may explain why they were negatively impacted by triclosan in our soil.
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Affiliation(s)
| | - Wen Sun
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Jennie M Sanders
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Anthony G Hay
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.
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21
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Fujimoto M, Carey DE, McNamara PJ. Metagenomics reveal triclosan-induced changes in the antibiotic resistome of anaerobic digesters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 241:1182-1190. [PMID: 30029328 DOI: 10.1016/j.envpol.2018.06.048] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/15/2018] [Accepted: 06/16/2018] [Indexed: 06/08/2023]
Abstract
Triclosan (TCS) is a broad-spectrum antimicrobial used in a variety of consumer products. While it was recently banned from hand soaps in the US, it is still a key ingredient in a top-selling toothpaste. TCS is a hydrophobic micropollutant that is recalcitrant under anaerobic digestion thereby resulting in high TCS concentrations in biosolids. The objective of this study was to determine the impact of TCS on the antibiotic resistome and potential cross-protection in lab-scale anaerobic digesters using shotgun metagenomics. It was hypothesized that metagenomics would reveal selection for antibiotic resistance genes (ARGs) not previously found in pure culture studies or mixed-culture studies using targeted qPCR. In this study, four different levels of TCS were continuously fed to triplicate lab-scale anaerobic digesters to assess the effect of TCS levels on the antibiotic resistance gene profiles (resistome). Blasting metagenomic reads against antibiotic/metal resistance gene database (BacMet) revealed that ARG diversity and abundance changed along the TCS concentration gradient. While loss of bacterial diversity and digester function were observed in the digester treated with the highest TCS concentration, FabV, which is a known TCS resistance gene, increased in this extremely high TCS environment. The abundance of several other known ARG or metal resistance genes (MRGs), including corA and arsB, also increased as the concentrations of TCS increased. Analysis of other functional genes using SEED database revealed the increase of potentially key genes for resistance including different types of transporters and transposons. These results indicate that antimicrobials can alter the abundance of multiple resistance genes in anaerobic digesters even when function (i.e. methane production) is maintained. This study also suggests that enriched ARGs could be released into environments with biosolids land application.
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Affiliation(s)
- Masanori Fujimoto
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA; Soil and Water Sciences Department, University of Florida, Gainesville, FL, USA
| | - Daniel E Carey
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA; Brown & Caldwell, Charlotte, NC, USA
| | - Patrick J McNamara
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, WI, USA.
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22
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Biochemical and Structural Basis of Triclosan Resistance in a Novel Enoyl-Acyl Carrier Protein Reductase. Antimicrob Agents Chemother 2018; 62:AAC.00648-18. [PMID: 29891603 DOI: 10.1128/aac.00648-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Enoyl-acyl carrier protein reductases (ENR), such as FabI, FabL, FabK, and FabV, catalyze the last reduction step in bacterial type II fatty acid biosynthesis. Previously, we reported metagenome-derived ENR homologs resistant to triclosan (TCL) and highly similar to 7-α hydroxysteroid dehydrogenase (7-AHSDH). These homologs are commonly found in Epsilonproteobacteria, a class that contains several human-pathogenic bacteria, including the genera Helicobacter and Campylobacter Here we report the biochemical and predicted structural basis of TCL resistance in a novel 7-AHSDH-like ENR. The purified protein exhibited NADPH-dependent ENR activity but no 7-AHSDH activity, despite its high homology with 7-AHSDH (69% to 96%). Because this ENR was similar to FabL (41%), we propose that this metagenome-derived ENR be referred to as FabL2. Homology modeling, molecular docking, and molecular dynamic simulation analyses revealed the presence of an extrapolated six-amino-acid loop specific to FabL2 ENR, which prevented the entry of TCL into the active site of FabL2 and was likely responsible for TCL resistance. Elimination of this extrapolated loop via site-directed mutagenesis resulted in the complete loss of TCL resistance but not enzyme activity. Phylogenetic analysis suggested that FabL, FabL2, and 7-AHSDH diverged from a common short-chain dehydrogenase reductase family. This study is the first to report the role of the extrapolated loop of FabL2-type ENRs in conferring TCL resistance. Thus, the FabL2 ENR represents a new drug target specific for pathogenic Epsilonproteobacteria.
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23
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Ribado JV, Ley C, Haggerty TD, Tkachenko E, Bhatt AS, Parsonnet J. Household triclosan and triclocarban effects on the infant and maternal microbiome. EMBO Mol Med 2018; 9:1732-1741. [PMID: 29030459 PMCID: PMC5709730 DOI: 10.15252/emmm.201707882] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In 2016, the US Food and Drug Administration banned the use of specific microbicides in some household and personal wash products due to concerns that these chemicals might induce antibiotic resistance or disrupt human microbial communities. Triclosan and triclocarban (referred to as TCs) are the most common antimicrobials in household and personal care products, but the extent to which TC exposure perturbs microbial communities in humans, particularly during infant development, was unknown. We conducted a randomized intervention of TC‐containing household and personal care products during the first year following birth to characterize whether TC exposure from wash products perturbs microbial communities in mothers and their infants. Longitudinal survey of the gut microbiota using 16S ribosomal RNA amplicon sequencing showed that TC exposure from wash products did not induce global reconstruction or loss of microbial diversity of either infant or maternal gut microbiotas. Broadly antibiotic‐resistant species from the phylum Proteobacteria, however, were enriched in stool samples from mothers in TC households after the introduction of triclosan‐containing toothpaste. When compared by urinary triclosan level, agnostic to treatment arm, infants with higher triclosan levels also showed an enrichment of Proteobacteria species. Despite the minimal effects of TC exposure from wash products on the gut microbial community of infants and adults, detected taxonomic differences highlight the need for consumer safety testing of antimicrobial self‐care products on the human microbiome and on antibiotic resistance.
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Affiliation(s)
| | - Catherine Ley
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas D Haggerty
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ekaterina Tkachenko
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA .,Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Julie Parsonnet
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA .,Division of Epidemiology, Department of Health Research and Policy, Stanford University, Stanford, CA, USA
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24
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Khan R, Roy N, Choi K, Lee SW. Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis. PLoS One 2018; 13:e0192277. [PMID: 29420585 PMCID: PMC5805296 DOI: 10.1371/journal.pone.0192277] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022] Open
Abstract
The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed. Further, the excessive use of this biocide in natural environments may selectively enrich for not only TCS-resistant bacterial pathogens, but possibly for additional resistance to multiple antibiotics.
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Affiliation(s)
- Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Nazish Roy
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
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25
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Lee MH, Khan R, Tao W, Choi K, Lee SY, Lee JW, Hwang EC, Lee SW. Soil metagenome-derived 3-hydroxypalmitic acid methyl ester hydrolases suppress extracellular polysaccharide production in Ralstonia solanacearum. J Biotechnol 2018; 270:30-38. [PMID: 29407418 DOI: 10.1016/j.jbiotec.2018.01.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
Abstract
Autoinducers are indispensable for bacterial cell-cell communication. However, due to the reliance on culture-based techniques, few autoinducer-hydrolyzing enzymes are known. In this study, we characterized soil metagenome-derived unique enzymes capable of hydrolyzing 3-hydroxypalmitic acid methyl ester (3-OH PAME), an autoinducer of the plant pathogenic bacterium Ralstonia solanacearum. Among 146 candidate lipolytic clones from a soil metagenome library, 4 unique enzymes capable of hydrolyzing the autoinducer 3-OH PAME, termed ELP86, ELP96, ELP104, and EstDL33, were selected and characterized. Phylogenetic analysis revealed that metagenomic enzymes were novel esterase/lipase candidates as they clustered as novel subfamilies of family I, V, X, and family XI. The purified enzymes displayed various levels of hydrolytic activities towards 3-OH PAME with optimum activity at 40-50 °C and pH 7-10. Interestingly, ELP104 also displayed N-(3-oxohexanoyl)-L-homoserine lactone hydrolysis activity. Heterologous expression of the gene encoding 3-OH PAME hydrolase in R. solanacearum significantly decreased exopolysaccharide production without affecting bacterial growth. mRNA transcription analysis revealed that genes regulated by quorum-sensing, such as phcA and xpsR, were significantly down-regulated in the stationary growth phase of R. solanacearum. Therefore, metagenomic enzymes are capable of quorum-quenching by hydrolyzing the autoinducer 3-OH PAME, which could be used as a biocontrol strategy against bacterial wilt.
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Affiliation(s)
- Myung Hwan Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Weixin Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Wuhan University, Wuhan, 430072, China
| | - Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Jae Wook Lee
- Department of Chemistry, Dong-A University, Busan 49315, Republic of Korea
| | - Eul Chul Hwang
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea.
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