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Dong Q, Sun B, Liu Y, Huang X. Sewerage surveillance tracking characteristics of human antibiotic resistance genes in sewer system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175850. [PMID: 39209175 DOI: 10.1016/j.scitotenv.2024.175850] [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: 05/12/2024] [Revised: 07/30/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Sewage surveillance is widely applied to track valid human excretion information and identify public health conditions during corona virus disease 2019 (COVID-19) pandemic. This approach can be applied to monitor the antibiotic resistance level in sewers and to assess the risk of spreading antibiotic resistance in municipal wastewater systems. However, there is still little information about human antibiotic resistance occurrence characteristics in sewer system. This study conducted a field trial for whole year to advance understanding on spatial and temporal occurrence of antibiotic resistance genes (ARGs) in gravity sewerage. The spatial distribution of ARGs along the drainage pipe line (from human settlements to wastewater treatement pant (WWTP)) was insignificant, which may be affected by irregular human emission alongside the pipeline. The correlation between ARGs and antibiotics in sewage was insignificant. The temporal distribution showed that the effect of temperature on ARGs abundance was evident, the ARGs abundance in sewage was generally higher during the cold season. Metagenomic analysis revealed that the detected ARGs were mainly distributed in Proteobacteria (47.51 %) and Antinobacteria (20.11 %). Potential hosts of ARGs in sewage were mainly identified as human gut microorganisms, including human pathogenic bacteria, such as Prevotella, Kocuria, and Propionibacterium, etc. This study provides a new insight into the sewerage surveillance tracking characteristics of human ARGs in sewer system, and suggesting that the sewage-carried ARGs surveillance is a promising method for assessment and management of antibiotic resistance level on population size.
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Affiliation(s)
- Qian Dong
- School of Environment, State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China; Institute of Water Environment Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Bo Sun
- School of Environment, State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Yanchen Liu
- School of Environment, State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China.
| | - Xia Huang
- School of Environment, State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
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2
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Wu J, Hu Y, Perlin MH, Danko D, Lu J, Oliveira M, Werner J, Zambrano MM, Sierra MA, Osuolale OO, Łabaj P, Rascovan N, Hazrin-Chong NH, Jang S, Suzuki H, Nieto-Caballero M, Prithiviraj B, Lee PKH, Chmielarczyk A, Różańska A, Zhao Y, Wang L, Mason CE, Shi T. Landscape of global urban environmental resistome and its association with local socioeconomic and medical status. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1292-1301. [PMID: 38489008 DOI: 10.1007/s11427-023-2504-1] [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: 10/10/2023] [Accepted: 12/06/2023] [Indexed: 03/17/2024]
Abstract
Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.
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Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yige Hu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, 40292, USA
| | - David Danko
- Weill Cornell Medicine, New York, 10065, USA
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA
| | - Jun Lu
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, 4050-290, Portugal
- Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, 4200-465, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4050-290, Portugal
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Maria A Sierra
- Weill Cornell Medicine, New York, 10065, USA
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, 340271, Nigeria
| | - Paweł Łabaj
- Maopolska Centre of Biotechnology, Jagiellonian University, Kraków, 30-005, Poland
| | - Nicolás Rascovan
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, 83041, France
| | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia UKM, 43600, Bangi, Selangor, Malaysia
| | - Soojin Jang
- Institut Pasteur Korea, Seoul, 13488, Republic of Korea
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
| | - Marina Nieto-Caballero
- Civil, Environmental and Architectural Department, University of Colorado at Boulder, Boulder, 80303, USA
| | | | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, 999077, China
| | - Agnieszka Chmielarczyk
- Department of Microbiology, Faculty of Medicine, Jagiellonian University, Krakow, 30-005, Poland
| | - Anna Różańska
- Department of Microbiology, Faculty of Medicine, Jagiellonian University, Krakow, 30-005, Poland
| | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China.
| | - Lan Wang
- College of Architecture and Urban Planning, Tongji University, Shanghai, 200092, China.
| | - Christopher E Mason
- Weill Cornell Medicine, New York, 10065, USA.
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, 10065, USA.
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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3
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Lee K, Raguideau S, Sirén K, Asnicar F, Cumbo F, Hildebrand F, Segata N, Cha CJ, Quince C. Population-level impacts of antibiotic usage on the human gut microbiome. Nat Commun 2023; 14:1191. [PMID: 36864029 PMCID: PMC9981903 DOI: 10.1038/s41467-023-36633-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.
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Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
- CJ Bioscience, Seoul, 04527, Republic of Korea
| | | | - Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Falk Hildebrand
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK.
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4
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Yuan M, Huang Z, Malakar PK, Pan Y, Zhao Y, Zhang Z. Antimicrobial resistomes in food chain microbiomes. Crit Rev Food Sci Nutr 2023; 64:6953-6974. [PMID: 36785889 DOI: 10.1080/10408398.2023.2177607] [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: 02/15/2023]
Abstract
The safety and integrity of the global food system is in a constant state of flux with persistent chemical and microbial risks. While chemical risks are being managed systematically, microbial risks pose extra challenges. Antimicrobial resistant microorganism and persistence of related antibiotic resistance genes (ARGs) in the food chain adds an extra dimension to the management of microbial risks. Because the food chain microbiome is a key interface in the global health system, these microbes can affect health in many ways. In this review, we systematically summarize the distribution of ARGs in foods, describe the potential transmission pathway and transfer mechanism of ARGs from farm to fork, and discuss potential food safety problems and challenges. Modulating antimicrobial resistomes in the food chain facilitates a sustainable global food production system.
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Affiliation(s)
- Mengqi Yuan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zhenhua Huang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pradeep K Malakar
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai Ocean University, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai Ocean University, Shanghai, China
| | - Zhaohuan Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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5
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Pan X, Zhou Z, Liu B, Wu Z. A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases. Front Microbiol 2022; 13:1037389. [DOI: 10.3389/fmicb.2022.1037389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a “reservoir” of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.
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6
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Cho Y, Kim J, Pai H, Rho M. Deciphering Resistome in Patients With Chronic Obstructive Pulmonary Diseases and Clostridioides difficile Infections. Front Microbiol 2022; 13:919907. [PMID: 35983323 PMCID: PMC9378971 DOI: 10.3389/fmicb.2022.919907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/20/2022] [Indexed: 12/03/2022] Open
Abstract
Antibiotics alter the gut microbiome and cause dysbiosis leading to antibiotic-resistant organisms. Different patterns of antibiotic administration cause a difference in bacterial composition and resistome in the human gut. We comprehensively investigated the association between the distribution of antibiotic resistance genes (ARGs), bacterial composition, and antibiotic treatments in patients with chronic obstructive pulmonary diseases (COPD) and Clostridioides difficile infections (CDI) who had chronic or acute intermittent use of antibiotics and compared them with healthy individuals. We analyzed the gut microbiomes of 61 healthy individuals, 16 patients with COPD, and 26 patients with CDI. The COPD patients were antibiotic-free before stool collection for a median of 40 days (Q1: 9.5; Q3: 60 days), while the CDI patients were antibiotic-free for 0 days (Q1: 0; Q3: 0.3). The intra-group beta diversity measured by the median Bray-Curtis index was the lowest for the healthy individuals (0.55), followed by the COPD (0.69) and CDI groups (0.72). The inter-group beta diversity was the highest among the healthy and CDI groups (median index = 0.89). The abundance of ARGs measured by the number of reads per kilobase per million reads (RPKM) was 684.2; 1,215.2; and 2,025.1 for the healthy, COPD, and CDI groups. It was negatively correlated with the alpha diversity of bacterial composition. For the prevalent ARG classes, healthy individuals had the lowest diversity and abundance of aminoglycoside, β-lactam, and macrolide-lincosamide-streptogramin (MLS) resistance genes, followed by the COPD and CDI groups. The abundances of Enterococcus and Escherichia species were positively correlated with ARG abundance and the days of antibiotic treatment, while Bifidobacterium and Ruminococcus showed negative correlations for the same. In addition, we analyzed the mobilome patterns of aminoglycoside and β-lactam resistance gene carriers using metagenomic sequencing data. In conclusion, the ARGs were significantly enhanced in the CDI and COPD groups than in healthy individuals. In particular, aminoglycoside and β-lactam resistance genes were more abundant in the CDI and COPD groups, but the dominant mobile genetic elements that enable the transfer of such genes showed similar prevalence patterns among the groups.
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Affiliation(s)
- Youna Cho
- Department of Computer Science, Hanyang University, Seoul, South Korea
| | - Jieun Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
- Hyunjoo Pai,
| | - Mina Rho
- Department of Computer Science, Hanyang University, Seoul, South Korea
- Department of Biomedical Informatics, Hanyang University, Seoul, South Korea
- *Correspondence: Mina Rho,
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7
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Lawther K, Santos FG, Oyama LB, Rubino F, Morrison S, Creevey CJ, McGrath JW, Huws SA. Resistome Analysis of Global Livestock and Soil Microbiomes. Front Microbiol 2022; 13:897905. [PMID: 35875563 PMCID: PMC9300982 DOI: 10.3389/fmicb.2022.897905] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to public health globally; it is estimated that AMR bacteria caused 1.27 million deaths in 2019, and this is set to rise to 10 million deaths annually. Agricultural and soil environments act as antimicrobial resistance gene (ARG) reservoirs, operating as a link between different ecosystems and enabling the mixing and dissemination of resistance genes. Due to the close interactions between humans and agricultural environments, these AMR gene reservoirs are a major risk to both human and animal health. In this study, we aimed to identify the resistance gene reservoirs present in four microbiomes: poultry, ruminant, swine gastrointestinal (GI) tracts coupled with those from soil. This large study brings together every poultry, swine, ruminant, and soil shotgun metagenomic sequence available on the NCBI sequence read archive for the first time. We use the ResFinder database to identify acquired antimicrobial resistance genes in over 5,800 metagenomes. ARGs were diverse and widespread within the metagenomes, with 235, 101, 167, and 182 different resistance genes identified in the poultry, ruminant, swine, and soil microbiomes, respectively. The tetracycline resistance genes were the most widespread in the livestock GI microbiomes, including tet(W)_1, tet(Q)_1, tet(O)_1, and tet(44)_1. The tet(W)_1 resistance gene was found in 99% of livestock GI tract microbiomes, while tet(Q)_1 was identified in 93%, tet(O)_1 in 82%, and finally tet(44)_1 in 69%. Metatranscriptomic analysis confirmed these genes were "real" and expressed in one or more of the livestock GI tract microbiomes, with tet(40)_1 and tet(O)_1 expressed in all three livestock microbiomes. In soil, the most abundant ARG was the oleandomycin resistance gene, ole(B)_1. A total of 55 resistance genes were shared by the four microbiomes, with 11 ARGs actively expressed in two or more microbiomes. By using all available metagenomes we were able to mine a large number of samples and describe resistomes in 37 countries. This study provides a global insight into the diverse and abundant antimicrobial resistance gene reservoirs present in both livestock and soil microbiomes.
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Affiliation(s)
- Katie Lawther
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Fernanda Godoy Santos
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Linda Boniface Oyama
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Francesco Rubino
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Steven Morrison
- Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Chris J. Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - John W. McGrath
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Sharon Ann Huws
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
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8
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Shuai M, Zhang G, Zeng F, Fu Y, Liang X, Yuan L, Xu F, Gou W, Miao Z, Jiang Z, Wang J, Zhuo L, Chen Y, Ju F, Zheng J. Human Gut Antibiotic Resistome and Progression of Diabetes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104965. [PMID: 35142450 PMCID: PMC9008416 DOI: 10.1002/advs.202104965] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/13/2022] [Indexed: 05/02/2023]
Abstract
The antibiotic resistance crisis underlies globally increasing failures in treating deadly bacterial infections, largely due to the selection of antibiotic resistance genes (ARG) collection, known as the resistome, in human gut microbiota. So far, little is known about the relationship between gut antibiotic resistome and host metabolic disorders such as type 2 diabetes (T2D). Here, metagenomic landscape of gut antibiotic resistome is profiled in a large multiomics human cohort (n = 1210). There is a significant overall shift in gut antibiotic resistome structure among healthy, prediabetes, and T2D groups. It is found that larger ARG diversity is associated with a higher risk of T2D. The novel diabetes ARG score is positively associated with glycemic traits. Longitudinal validation analysis confirms that the ARG score is associated with T2D progression, characterized by the change of insulin resistance. Collectively, the data describe the profiles of gut antibiotic resistome and support its close relationship with T2D progression.
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Affiliation(s)
- Menglei Shuai
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Guoqing Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhou310030China
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhou310024China
| | - Fang‐fang Zeng
- Guangdong Provincial Key Laboratory of FoodNutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat‐sen UniversityGuangzhou510275China
- Department of EpidemiologySchool of MedicineJinan UniversityGuangzhou510632China
| | - Yuanqing Fu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhou310024China
| | - Xinxiu Liang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Ling Yuan
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhou310030China
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhou310024China
| | - Fengzhe Xu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Wanglong Gou
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Zelei Miao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
| | - Zengliang Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhou310024China
| | - Jia‐ting Wang
- Guangdong Provincial Key Laboratory of FoodNutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat‐sen UniversityGuangzhou510275China
| | - Lai‐bao Zhuo
- Guangdong Provincial Key Laboratory of FoodNutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat‐sen UniversityGuangzhou510275China
| | - Yu‐ming Chen
- Guangdong Provincial Key Laboratory of FoodNutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat‐sen UniversityGuangzhou510275China
| | - Feng Ju
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
- Key Laboratory of Coastal Environment and Resources of Zhejiang ProvinceSchool of EngineeringWestlake UniversityHangzhou310030China
- Institute of Advanced TechnologyWestlake Institute for Advanced StudyHangzhou310024China
| | - Ju‐Sheng Zheng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou310030China
- Westlake Intelligent Biomarker Discovery LabWestlake Laboratory of Life Sciences and BiomedicineHangzhou310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhou310024China
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9
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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10
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Ghosh A, Firdous S, Saha S. Bioinformatics for Human Microbiome. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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11
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Ho J, Yeoh YK, Barua N, Chen Z, Lui G, Wong SH, Yang X, Chan MCW, Chan PKS, Hawkey PM, Ip M. Systematic review of human gut resistome studies revealed variable definitions and approaches. Gut Microbes 2020; 12:1700755. [PMID: 31942825 PMCID: PMC7524153 DOI: 10.1080/19490976.2019.1700755] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.
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Affiliation(s)
- Jeffery Ho
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nilakshi Barua
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Grace Lui
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,Department of Medicine & Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,Department of Medicine & Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Martin CW Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul KS Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter M Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,CONTACT Margaret Ip Department of Microbiology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
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12
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Meng X, Zhang G, Cao H, Yu D, Fang X, de Vos WM, Wu H. Gut dysbacteriosis and intestinal disease: mechanism and treatment. J Appl Microbiol 2020; 129:787-805. [PMID: 32277534 PMCID: PMC11027427 DOI: 10.1111/jam.14661] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/14/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022]
Abstract
The gut microbiome functions like an endocrine organ, generating bioactive metabolites, enzymes or small molecules that can impact host physiology. Gut dysbacteriosis is associated with many intestinal diseases including (but not limited to) inflammatory bowel disease, primary sclerosing cholangitis-IBD, irritable bowel syndrome, chronic constipation, osmotic diarrhoea and colorectal cancer. The potential pathogenic mechanism of gut dysbacteriosis associated with intestinal diseases includes the alteration of composition of gut microbiota as well as the gut microbiota-derived signalling molecules. The many correlations between the latter and the susceptibility for intestinal diseases has placed a spotlight on the gut microbiome as a potential novel target for therapeutics. Currently, faecal microbial transplantation, dietary interventions, use of probiotics, prebiotics and drugs are the major therapeutic tools utilized to impact dysbacteriosis and associated intestinal diseases. In this review, we systematically summarized the role of intestinal microbiome in the occurrence and development of intestinal diseases. The potential mechanism of the complex interplay between gut dysbacteriosis and intestinal diseases, and the treatment methods are also highlighted.
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Affiliation(s)
- X Meng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, Changchun, PR China
| | - G Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, Changchun, PR China
| | - H Cao
- InnovHope Inc, Framingham, MA, USA
| | - D Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, Changchun, PR China
| | - X Fang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, Changchun, PR China
| | - W M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - H Wu
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
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13
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Watkins RR, Bonomo RA. Overview: The Ongoing Threat of Antimicrobial Resistance. Infect Dis Clin North Am 2020; 34:649-658. [PMID: 33011053 DOI: 10.1016/j.idc.2020.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effectiveness of antibiotics continues to erode because of the relentless spread of antimicrobial resistance (AMR). Public and private foundations, professional organizations, and international health agencies recognize the threat posed by AMR and have issued calls for action. One of the main drivers of AMR is overprescription of antibiotics, both in human and in veterinary medicine. The One Health concept is a response from a broad group of stakeholders to counter the global health threat posed by AMR. In this article, we discuss current trends in AMR and suggest strategies to mitigate its ongoing dissemination.
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Affiliation(s)
- Richard R Watkins
- Division of Infectious Diseases, Cleveland Clinic Akron General, Akron, OH, USA; Department of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA.
| | - Robert A Bonomo
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Case VA Center for Antimicrobial Resistance and Epidemiology (Case VA-CARES), Case Western Reserve University, Cleveland, OH, USA
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14
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Liu H, Wang HH. Impact of Microbiota Transplant on Resistome of Gut Microbiota in Gnotobiotic Piglets and Human Subjects. Front Microbiol 2020; 11:932. [PMID: 32508773 PMCID: PMC7248251 DOI: 10.3389/fmicb.2020.00932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
Microbiota transplant is becoming a popular process to restore or initiate “healthy” gut microbiota and immunity. But, the potential risks of the related practices need to be carefully evaluated. This study retrospectively examined the resistomes of donated fecal microbiota for treating intestinal disorders, vaginal microbiota of pregnant women, and infant fecal microbiota from rural and urban communities, as well as the impact of transplants on the fecal resistome of human and animal recipients. Antibiotic resistance (AR) genes were found to be abundant in all donor microbiota. An overall surge of resistomes with higher prevalence and abundance of AR genes was observed in the feces of all transplanted gnotobiotic pigs as well as in the feces of infant subjects, compared to those in donor fecal and maternal vaginal microbiota. Surprisingly, transplants using rural Amish microbiota led to more instead of less AR genes in the fecal microbiota of gnotobiotic pigs than did transplants using urban microbiota. New AR gene subtypes undetected originally also appeared in gnotobiotic pigs, in Crohn’s Disease (CD) patients after transplant, and in feces of infant subjects. The data illustrated the key role of the host gastrointestinal tract system in amplifying the ever-increasing AR gene pool, even without antibiotic exposure. The data further suggest that the current approaches of microbiota transplant can introduce significant health risk factor(s) to the recipients, and newborn human and animal hosts with naïve gut microbiota were especially susceptible. Given the illustrated public health risks of microbiota transplant, minimizing massive and unnecessary damages to gut microbiota by oral antibiotics and other gut impacting drugs becomes important. Since eliminating risk factors including AR bacteria and opportunistic pathogens directly from donor microbiota is still difficult to achieve, developing microbial cocktails with defined organisms and functions has further become an urgent need, should microbiota transplantation become necessary.
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Affiliation(s)
- Hu Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Hua H Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
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15
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Ramsheh MY, Haldar K, Bafadhel M, George L, Free RC, John C, Reeve NF, Ziegler-Heitbrock L, Gut I, Singh D, Mistry V, Tobin MD, Oggioni MR, Brightling C, Barer MR. Resistome analyses of sputum from COPD and healthy subjects reveals bacterial load-related prevalence of target genes. Thorax 2019; 75:8-16. [PMID: 31699806 DOI: 10.1136/thoraxjnl-2019-213485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND Antibiotic resistance is a major global threat. We hypothesised that the chronic obstructive pulmonary disease (COPD) airway is a reservoir of antimicrobial resistance genes (ARGs) that associate with microbiome-specific COPD subgroups. OBJECTIVE To determine the resistance gene profiles in respiratory samples from COPD patients and healthy volunteers. METHODS Quantitative PCR targeting 279 specific ARGs was used to profile the resistomes in sputum from subjects with COPD at stable, exacerbation and recovery visits (n=55; COPD-BEAT study), healthy controls with (n=7) or without (n=22) exposure to antibiotics in the preceding 12 months (EXCEED study) and in bronchial brush samples from COPD (n=8) and healthy controls (n=7) (EvA study). RESULTS ARG mean (SEM) prevalence was greater in stable COPD samples (35.2 (1.6)) than in healthy controls (27.6 (1.7); p=0.004) and correlated with total bacterial abundance (r2=0.23; p<0.001). Prevalence of ARG positive signals in individuals was not related to COPD symptoms, lung function or their changes at exacerbation. In the COPD subgroups designated High γProteobacteria and High Firmicutes, ARG prevalence was not different at stable state but significantly declined from stable through exacerbation to recovery in the former (p=0.011) without changes in total bacterial abundance. The ARG patterns were similar in COPD versus health, COPD microbiome-subgroups and between sputum and bronchoscopic samples independent of antibiotic exposure in the last 12 months. CONCLUSIONS ARGs are highly prevalent in sputum, broadly in proportion to bacterial abundance in both healthy and COPD subjects. Thus, COPD appears to be an ARG reservoir due to high levels of bacterial colonisation.
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Affiliation(s)
| | - Koirobi Haldar
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Mona Bafadhel
- Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leena George
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Robert C Free
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Ivo Gut
- Centre for Genomic Regulation, Barcelona Institute for Science and Technology, 5CNAG-CRG Centre Nacional d'Anàlisi Genòmica, Barcelona, Spain
| | - Dave Singh
- Medicines Evaluation Unit, University Hospital of South Manchester, University of Manchester, Manchester, UK
| | - Vijay Mistry
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Marco R Oggioni
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Chris Brightling
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Michael R Barer
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
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16
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Microbiome as a tool and a target in the effort to address antimicrobial resistance. Proc Natl Acad Sci U S A 2019; 115:12902-12910. [PMID: 30559176 DOI: 10.1073/pnas.1717163115] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Reciprocal, intimate relationships between the human microbiome and the host immune system are shaped by past microbial encounters and prepare the host for future ones. Antibiotics and other antimicrobials leave their mark on both the microbiome and host immunity. Antimicrobials alter the structure of the microbiota, expand the host-specific pool of antimicrobial-resistance genes and organisms, degrade the protective effects of the microbiota against invasion by pathogens, and may impair vaccine efficacy. Through these effects on the microbiome they may affect immune responses. Vaccines that exert protective or therapeutic effects against pathogens may reduce the use of antimicrobials, the development and spread of antimicrobial resistance, and the harmful impacts of these drugs on the microbiome. Other strategies involving manipulation of the microbiome to deplete antibiotic-resistant organisms or to enhance immune responses to vaccines may prove valuable in addressing antimicrobial resistance as well. This article describes the intersections of immunity, microbiome and antimicrobial exposure, and the use of vaccines and other alternative strategies for the control and management of antimicrobial resistance.
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17
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18
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Lim MY, Cho Y, Rho M. Diverse Distribution of Resistomes in the Human and Environmental Microbiomes. Curr Genomics 2018; 19:701-711. [PMID: 30532649 PMCID: PMC6225452 DOI: 10.2174/1389202919666180911130845] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 04/14/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022] Open
Abstract
The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria. Such studies have revealed that the antibiotic resistance genes are located close to the mobility-associated genes, which promotes their dissemination. An increasing level of information on genomic sequences of resistome should expedite research on drug-resistance in our body and environment, thereby contributing to the development of public health policy. In this review, the high prevalence of antibiotic resistance genes and their exchange in the human and environmental microbiome is discussed with respect to the genomic contents. The relationships among diverse resistomes, related bacterial species, and the antibiotics are reviewed. In addition, recent advances in bioinformatics approaches to investigate such relationships are discussed.
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Affiliation(s)
- Mi Young Lim
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Youna Cho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
| | - Mina Rho
- 1Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do 55365, South Korea; 2Department of Computer Science and Engineering, Hanyang University, Seoul133-791, South Korea; 3Department of Biomedical Informatics, Hanyang University, Seoul133-791, South Korea
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19
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Abstract
OBJECTIVE Rapidly expanding insights into the human microbiome and health suggest that Western medicine is poised for significant evolution, or perhaps revolution-this while medicine continues on a trajectory from reductionism to a biopsychosocial (BPS) paradigm recognizing biological, psychological, and social influences on health. The apparent sensitivity of the microbiota to perturbations across BPS domains suggests that a broad and inclusive framework is needed to develop applicable knowledge in this emerging area. We outline an ecological framework of the human microbiome by extending the BPS concept to better incorporate environmental and human factors as members of a global, dynamic set of systems that interact over time. METHODS We conducted a selective literature review across disciplines to integrate microbiome research into a BPS framework. RESULTS The microbiome can be understood in terms of ecological systems encompassing BPS domains at four levels: (a) immediate (molecular, genetic, and neural processes), (b) proximal (physiology, emotion, social integration), (c) intermediate (built environments, behaviors, societal practices), and (d) distal (physical environments, attitudes, and broad cultural, economic, and political factors). The microbiota and host are thus understood in terms of their immediate interactions and the more distal physical and social arenas in which they participate. CONCLUSIONS A BPS ecological paradigm encourages replicable, generalizable, and interdisciplinary/transdisciplinary research and practices that take into account the vast influences on the human microbiome that may otherwise be overlooked or understood out of context. It also underscores the importance of sustainable bioenvironmental, psychological, and social systems that broadly support microbial, neural, and general health.
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20
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Hill EK, Li J. Current and future prospects for nanotechnology in animal production. J Anim Sci Biotechnol 2017; 8:26. [PMID: 28316783 PMCID: PMC5351054 DOI: 10.1186/s40104-017-0157-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 03/02/2017] [Indexed: 11/10/2022] Open
Abstract
Nanoparticles have been used as diagnostic and therapeutic agents in the human medical field for quite some time, though their application in veterinary medicine and animal production is still relatively new. Recently, production demands on the livestock industry have been centered around the use of antibiotics as growth promoters due to growing concern over microbial antibiotic resistance. With many countries reporting increased incidences of antibiotic-resistant bacteria, laws and regulations are being updated to end in-feed antibiotic use in the animal production industry. This sets the need for suitable alternatives to be established for inclusion in feed. Many reports have shown evidence that nanoparticles may be good candidates for animal growth promotion and antimicrobials. The current status and advancements of nanotechnological applications in animal production will be the focus of this review and the emerging roles of nanoparticles for nutrient delivery, biocidal agents, and tools in veterinary medicine and reproduction will be discussed. Additionally, influences on meat, egg, and milk quality will be reviewed.
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Affiliation(s)
- Emily K Hill
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong China.,Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Building #70, Guelph, ON N1G 2 W1 Canada
| | - Julang Li
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong China.,Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Building #70, Guelph, ON N1G 2 W1 Canada
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21
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Jin Y, Wu S, Zeng Z, Fu Z. Effects of environmental pollutants on gut microbiota. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 222:1-9. [PMID: 28086130 DOI: 10.1016/j.envpol.2016.11.045] [Citation(s) in RCA: 397] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 05/05/2023]
Abstract
Environmental pollutants have become an increasingly common health hazard in the last several decades. Recently, a number of studies have demonstrated the profound relationship between gut microbiota and our health. Gut microbiota are very sensitive to drugs, diet, and even environmental pollutants. In this review, we discuss the possible effects of environmental pollutants including antibiotics, heavy metals, persistent organic pollutants, pesticides, nanomaterials, and food additives on gut microbiota and their subsequent effects on health. We emphasize that gut microbiota are also essential for the toxicity evaluation of environmental pollution. In the future, more studies should focus on the relationship between environmental pollution, gut microbiota, and human health.
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Affiliation(s)
- Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Sisheng Wu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhaoyang Zeng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhengwei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China.
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