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Zhang T, Han Y, Peng Y, Deng Z, Shi W, Xu X, Wu Y, Dong X. The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms. mSystems 2025:e0157124. [PMID: 40396743 DOI: 10.1128/msystems.01571-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Accepted: 04/23/2025] [Indexed: 05/22/2025] Open
Abstract
Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research. IMPORTANCE In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.
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Affiliation(s)
- Tianxueyu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, Shanghai, China
- State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
| | - Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, Zhejiang, China
- Ocean Research Center of Zhoushan, Zhejiang University, Zhoushan, Zhejiang, China
| | - Wenqing Shi
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University College of Ocean and Earth Science, Xiamen, Fujian, China
- RU Marine Symbioses, RD3 Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Schleswig-Holstein, Germany
| | - Xuewei Xu
- State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
| | - Yuehong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, Shanghai, China
- State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, Zhejiang, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, China
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Baek JW, Lim S, Park N, Song B, Kirtipal N, Nielsen J, Mardinoglu A, Shoaie S, Kim JI, Son JW, Koh A, Lee S. Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions. NPJ Biofilms Microbiomes 2025; 11:78. [PMID: 40360555 PMCID: PMC12075632 DOI: 10.1038/s41522-025-00705-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Accepted: 04/15/2025] [Indexed: 05/15/2025] Open
Abstract
In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.
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Grants
- 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699 National Research Foundation of Korea
- 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699 National Research Foundation of Korea
- 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699 National Research Foundation of Korea
- 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699 National Research Foundation of Korea
- 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699 National Research Foundation of Korea
- 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699 National Research Foundation of Korea
- HR22C141105 the Korea Health Industry Development Institute
- HR22C141105 the Korea Health Industry Development Institute
- HR22C141105 the Korea Health Industry Development Institute
- HR22C141105 the Korea Health Industry Development Institute
- HR22C141105 the Korea Health Industry Development Institute
- HR22C141105 the Korea Health Industry Development Institute
- 2024-ER2108-00, 2024-ER0608-00 Korea National Institute of Health
- 2024-ER2108-00, 2024-ER0608-00 Korea National Institute of Health
- 2024-ER2108-00, 2024-ER0608-00 Korea National Institute of Health
- 2024-ER2108-00, 2024-ER0608-00 Korea National Institute of Health
- 2024-ER2108-00, 2024-ER0608-00 Korea National Institute of Health
- 2024-ER2108-00, 2024-ER0608-00 Korea National Institute of Health
- 2024-ER2108-00, 2024-ER0608-00 Korea National Institute of Health
- GIST-MIT research Collaboration grant GIST Research Institute
- GIST-MIT research Collaboration grant GIST Research Institute
- GIST-MIT research Collaboration grant GIST Research Institute
- GIST-MIT research Collaboration grant GIST Research Institute
- GIST-MIT research Collaboration grant GIST Research Institute
- GIST-MIT research Collaboration grant GIST Research Institute
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Affiliation(s)
- Jae Woo Baek
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Songwon Lim
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Nayeon Park
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Byeongsop Song
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Nikhil Kirtipal
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Kemivägen 10, Chalmers University of Technology, Gothenburg, Sweden
- BioInnovation Institute, Copenhagen, Denmark
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Jae-Il Kim
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Jang Won Son
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ara Koh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Sunjae Lee
- Department of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea.
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Xin Y, Zhang J, Tang Q, Wei M, Zhu L, Zhao Y, Cui Y, Sun T, Wei Y, Richnow HH. Virus-host interactions driving the transfer of antibiotic resistance genes in a river-reservoir system under heavy rainfall. JOURNAL OF HAZARDOUS MATERIALS 2025; 494:138605. [PMID: 40381353 DOI: 10.1016/j.jhazmat.2025.138605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 04/12/2025] [Accepted: 05/12/2025] [Indexed: 05/20/2025]
Abstract
Global river systems are grappling with severe pollution from antibiotic resistance genes (ARGs), with river-reservoir (R-R) systems being a common feature in urban waterways. The intensified extreme rainfall events triggered by global climate change exacerbate the spread of ARGs posed by non-point source pollution and combined sewage overflows. This study employs a metagenomics approach to decipher the profile of ARGs and virus-host interactions driving their transfer under heavy rainfall in North Canal, Beijing, with extensive R-R systems. Results indicated that R-R systems contributed to ARGs reduction despite continuous discharge of treated wastewater into the North Canal. The ARGs assembly is predominantly governed by stochastic process, and heavy rainfall enhances the dispersal capability. Nonetheless, the deterministic process determined the assembly of both microbial and viral community. Heavy rainfall not only significantly increased the abundance and diversity of ARGs within the rivers with minimal change in the reservoir, but also promotes the horizontal gene transfer of ARGs with higher conjugative mobility. Although the species accumulation curves approached saturation, no viruses carrying ARGs were detected among the 23,835 non-redundant viral operational taxonomic units (vOTUs), and lytic phage-ARB interactions drove the ARGs reduction with higher VHRs, highlighting its contribution to the reduction of ARGs in R-R system after heavy rainfall.
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Affiliation(s)
- Yuan Xin
- Department of Emergency Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Junya Zhang
- State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qihe Tang
- State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Minghai Wei
- The Center for Water Ecology Management, Chinese Academy of Environmental Planning, Beijing 100041, China
| | - Liying Zhu
- State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhao
- State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunwei Cui
- State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Tongwen Sun
- Department of Emergency Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Yuansong Wei
- State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hans Hermann Richnow
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig 04318, Germany; Leibniz Institute for Tropospheric Research, Permoserstr. 15, Leipzig 04318, Germany
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Wang Y, Chen C, Zhou B, Zhang Y, Qin J, Huang J, Li X. Presence of high-risk ARGs with greater diversity and abundance in the rare resistome in wastewater across China. JOURNAL OF HAZARDOUS MATERIALS 2025; 488:137435. [PMID: 39899931 DOI: 10.1016/j.jhazmat.2025.137435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 01/10/2025] [Accepted: 01/27/2025] [Indexed: 02/05/2025]
Abstract
Antibiotic resistance genes (ARGs) are widely recognized as hazardous materials that pose risks to public health. The core resistome, with its low ARG diversity yet accounting for the majority of the total ARG abundance, dominating the profile of antibiotic resistance. In this study, nationwide wastewater surveillance in China using metagenomic sequencing also identified a core resistome of 117 ARGs that accounted for 69.6 % of the total abundance. The emphasis of the work was to examine the rare resistome that included 1503 ARGs outside the core resistome. The abundances of clinically relevant ARG types (e.g., β-lactams and quinolones) were significantly higher in the rare resistome compared to the core resistome. Human pathogen-related ARGs were much greater in subtype number (96 vs. 34) and significantly higher in abundance (67.0 % vs. 33.0 %) in the rare relative to the core resistome, indicating that the rare resistome was the major contributor to the human pathogen resistome. The majority of ARG types accounting for the highest proportions of the rare resistome were plasmid-originated (65.5 %-100 %). In addition, human pathogen-related ARGs also had a significantly higher proportion of plasmid sources than non-pathogen ARGs, further highlighting their importance in wastewater-based surveillance.
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Affiliation(s)
- Yue Wang
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Chaoqi Chen
- School of Resource and Environmental Sciences, Wuhan University, Wuhan 430079, PR China.
| | - Bo Zhou
- Weiming Environmental Molecular Diagnostics (Changshu) Inc., Changshu, Jiangsu Province 215500, PR China
| | - Yu Zhang
- Weiming Environmental Molecular Diagnostics (Changshu) Inc., Changshu, Jiangsu Province 215500, PR China
| | - Jun Qin
- Weiming Environmental Molecular Diagnostics (Changshu) Inc., Changshu, Jiangsu Province 215500, PR China
| | - Jianwen Huang
- Weiming Environmental Molecular Diagnostics (Guangdong) Inc., Foshan, Guangdong Province 528300, PR China
| | - Xiqing Li
- Laboratory of Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China; Weiming Environmental Molecular Diagnostics (Guangdong) Inc., Foshan, Guangdong Province 528300, PR China.
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5
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Farooq S, Talat A, Dhariwal A, Petersen FC, Khan AU. Transgenerational gut dysbiosis: Unveiling the dynamics of antibiotic resistance through mobile genetic elements from mothers to infants. Int J Antimicrob Agents 2025; 65:107458. [PMID: 39921114 DOI: 10.1016/j.ijantimicag.2025.107458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 01/04/2025] [Accepted: 01/29/2025] [Indexed: 02/10/2025]
Abstract
OBJECTIVES The initial microbial colonization of the gut is seeded by microbes transmitted from the mother's gut, skin, and vaginal tract. As the gut microbiome evolves, a few transmitted microbes persist throughout life. Understanding the impact of mother-to-neonate gut microbiome and antibiotic resistance genes (ARGs) transmission is crucial for establishing its role in infants' immunity against pathogens. METHODS This study primarily explores mother-neonate ARG transmission through 125 publicly available fecal metagenomes, isolated from eighteen mother-neonate pairs. RESULTS The core ARGs, detected in both mothers and their respective infants at all stages (birth, 1st, 2nd, 3rd, 4th, 8th and 12th months) included aminoglycosidases APH(3')-IIIa, Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin, β-lactamases CblA-1, CfxA2, multidrug resistance gene CRP, diaminopyrimidine resistance gene dfrF, fluoroquinolone-resistance gene emrR, macrolide; lincosamide; streptogramin resistance gene ErmB, ErmG, macrolide resistance gene Mef(En2), nucleosidase SAT-4, and tetracycline-resistance genes tet(O), tet(Q), and tet(W). Most of these infants and mothers were not administered any antibiotics. In infants, ARGs were predominantly carried by Bacillota, Pseudomonadota, and Actinomycetota, similar to the mothers. The dominant ARG-carrying opportunistic pathogens were Escherichia coli, Klebsiella, and Streptococcus, found across all infant cohorts. All the core ARGs were associated with mobile genetic elements, signifying the role of horizontal gene transfer(HGT). We detected 132 virulence determinants, mostly E. coli-specific, including pilus chaperones, general secretion pathway proteins, type III secretion system effectors, and heme-binding proteins. CONCLUSIONS Maternal-neonate transmission of ARGs along with possible nosocomial infections, mode of delivery, breastfeeding versus formula feeding, and gestation period, must be considered for mother-neonate health.
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Affiliation(s)
- Samiya Farooq
- Antimicrobial Resistance Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India; Bioinformatics and Computational Biology Centre of DBT Government of India, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Absar Talat
- Antimicrobial Resistance Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India; Bioinformatics and Computational Biology Centre of DBT Government of India, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | | | - Asad U Khan
- Antimicrobial Resistance Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India; Bioinformatics and Computational Biology Centre of DBT Government of India, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.
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Yu D, Wang T, Zhang L, Gao N, Huang Y, Zhang J, Yan J. Identification of body fluid sources based on microbiome antibiotic resistance genes using high-throughput qPCR. Forensic Sci Int Genet 2025; 77:103241. [PMID: 39983320 DOI: 10.1016/j.fsigen.2025.103241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 02/13/2025] [Accepted: 02/16/2025] [Indexed: 02/23/2025]
Abstract
Identifying the origin of body fluids is a critical step in forensic investigation. Recently, the development of high-throughput sequencing technology has led to the use of microbiomes for body fluid identification in forensic studies. However, high-throughput sequencing data are difficult to analyze, the sequencing protocol is complicated. An increasing number of studies have focused on antibiotic resistance genes (ARGs) in the human microbiome. The abundance and diversity of ARGs in different parts of the human body can be detected using quantitative polymerase chain reaction (qPCR). To date, no studies have inferred the sources of body fluids based on ARGs. Therefore, we attempted to use ARGs as a tool to infer the origin of body fluids. We assessed the abundance and diversity of 64 ARGs in blood, semen, saliva, vaginal secretions (VS), nasal secretions (NS), and fecal samples using high-throughput qPCR. The results showed that ARGs were more diverse in fecal samples, which was significantly higher than those of other sample types (P < 0.05). Principal coordinate analysis (PCoA) showed that the samples clustered mainly according to their type. We constructed a random forest classification model based on 64 ARGs with a prediction accuracy of 92.68 %. Next, we evaluated the importance of the features in the random forest model (mean decrease accuracy, MDA). Subsequently, we constructed prediction models for the top 40 and 20 ARGs after sorting genes with the highest MDA, and their prediction accuracies were both 92.68 %. The accuracy of the top 10 ARGs was 87.80 %. Notably, when only the top 10 characterized ARGs were used to construct models for saliva, semen, and VS samples, the prediction accuracy reached was 95.24 %. This shows that blood, semen, saliva, NS, VS, and fecal samples can be accurately identified using ARGs. Our results suggest that ARGs are promising markers for forensic body fluid identification.
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Affiliation(s)
- Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi 030600, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi 030600, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi 030600, China
| | - Niu Gao
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi 030600, China
| | - Yuqing Huang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi 030600, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China; Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi 030600, China.
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Sun J, Xie YG, Zhou H, Chen L, Qu YN, Cheng H, Chen Z, Hua ZS, Wang Y. Distribution patterns and ecological risks of antibiotic resistance genes in the Yap Trench. WATER RESEARCH 2025; 281:123589. [PMID: 40187144 DOI: 10.1016/j.watres.2025.123589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2024] [Revised: 03/16/2025] [Accepted: 03/31/2025] [Indexed: 04/07/2025]
Abstract
Antibiotic resistance genes (ARGs) are a global environmental concern, yet their vertical distribution in pristine marine ecosystems remains poorly understood. This study investigated the distribution of ARG distribution in both the water column and sediments of the Yap Trench, which reaches depths over 6500 m Results revealed significant variations in ARG diversity and abundance across depths and habitats. The deep-water (DW) zones exhibited the highest diversity (291-472 subtypes) and abundance (1.79 copies/cell), followed by upper-water (UW) zones (240-314 subtypes, 0.31 copies/cell), while sediments had the lowest diversity (72-236 subtypes) and abundance (0.03 copies/cell). The most prevalent resistance genes included those conferring resistance to multidrug, polymyxin, and beta-lactam in the Yap Trench. ARG distribution closely correlated with microbial hosts, including Pseudomonadota, Chloroflexota, Bacteroidota, and Planctomycetota. Risk assessment showed high-risk ARGs were most abundant in DW zones, with pathogenic groups capable of spreading multiple ARGs (e.g., macAB, mexDJKW, mdtE, muxC). This study provides a systematic understanding of the distribution patterns and potential risks of ARGs in the water column and sediments of pristine marine ecosystems, underscoring the penetration of antibiotic pollution into the deep ocean and offering new insights for marine pollution control strategies.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Lei Chen
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, PR China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, PR China.
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
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Zhao Y, Wang Y, Lu J, Zhu B, Li AD. Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities. Life (Basel) 2025; 15:547. [PMID: 40283102 PMCID: PMC12028981 DOI: 10.3390/life15040547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2025] [Revised: 03/24/2025] [Accepted: 03/25/2025] [Indexed: 04/29/2025] Open
Abstract
The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.
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Affiliation(s)
- Yunfei Zhao
- School of Public Health, Nanjing Medical University, Nanjing 211166, China; (Y.Z.); (Y.W.)
| | - Yixiao Wang
- School of Public Health, Nanjing Medical University, Nanjing 211166, China; (Y.Z.); (Y.W.)
| | - Jie Lu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Southeast University, Nanjing 210009, China;
| | - Baoli Zhu
- School of Public Health, Nanjing Medical University, Nanjing 211166, China; (Y.Z.); (Y.W.)
- Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
- Department of Occupational Disease Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - An-Dong Li
- School of Public Health, Nanjing Medical University, Nanjing 211166, China; (Y.Z.); (Y.W.)
- Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
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Raju NP, Ansari A, Patil G, Sheeraz MS, Kukade S, Kumar S, Kapley A, Qureshi A. Antibiotic Resistance Dissemination and Mapping in the Environment Through Surveillance of Wastewater. J Basic Microbiol 2025; 65:e2400330. [PMID: 39676299 DOI: 10.1002/jobm.202400330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 12/17/2024]
Abstract
Antibiotic resistance is one of the major health threat for humans, animals, and the environment, according to the World Health Organization (WHO) and the Global Antibiotic-Resistance Surveillance System (GLASS). In the last several years, wastewater/sewage has been identified as potential hotspots for the dissemination of antibiotic resistance and transfer of resistance genes. However, systematic approaches for mapping the antibiotic resistance situation in sewage are limited and underdeveloped. The present review has highlighted all possible perspectives by which the dynamics of ARBs/ARGs in the environment may be tracked, quantified and assessed spatio-temporally through surveillance of wastewater. Moreover, application of advanced methods like wastewater metagenomics for determining the community distribution of resistance at large has appeared to be promising. In addition, monitoring wastewater for antibiotic pollution at various levels, may serve as an early warning system and enable policymakers to take timely measures and build infrastructure to mitigate health crises. Thus, by understanding the alarming presence of antibiotic resistance in wastewater, effective action plans may be developed to address this global health challenge and its associated environmental risks.
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Affiliation(s)
- Neenu P Raju
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Aamir Ansari
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Gandhali Patil
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Mohammed Shahique Sheeraz
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Sushrut Kukade
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Shailendra Kumar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Asifa Qureshi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
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Ali S, Tariq MHA, Yaqoob M, Haq MU, Zahra R. Molecular epidemiology and characterization of antibiotic resistance of Pasteurella multocida isolated from livestock population of Punjab, Pakistan. Int J Vet Sci Med 2025; 13:1-12. [PMID: 40017904 PMCID: PMC11866652 DOI: 10.1080/23144599.2024.2437223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 11/23/2024] [Accepted: 11/28/2024] [Indexed: 03/01/2025] Open
Abstract
Haemorrhagic septicaemia (HS) is an acute and life-threatening infection of livestock population caused by Pasteurella multocida (P. multocida), responsible for huge mortality, morbidity and production losses. The increase in antibiotic resistance is a growing concern, posing a significant threat to animals and public health. There is limited data on P. multocida disease burden, serotypes, antibiotic susceptibility, and resistance gene profiles in Pakistan. In the current study, 1017 nasal swabs from haemorrhagic septicaemic cattle and buffaloes were collected to isolate P. multocida through microbiological and molecular methods. Susceptibility against commonly used antibiotics was performed and antibiotic resistance genes were evaluated. A prevalence rate of 7.57% was found, where buffaloes were more prone to infection (8.3%) as compared to cows (6.7%). Molecular and sequence analysis confirmed P. multocida isolates in 94.8% (73/77) of samples. Capsular typing revealed all isolates belong to serotype B. Antibiogram analysis showed that enrofloxacin 85.7% (66/77) and ceftiofur 56/77 (72.7%) were the most effective antibiotics. The highest resistance was observed against trimethoprim/sulfamethoxazole 54/77 (70.1%), followed by erythromycin 52/77 (67.5%). Most of the isolates (31.5% (23/73)) carried β-lactamase resistance genes (bla TEM n = 10, bla ROB-1 n = 6, bla OXA-2 n = 5, bla NDM n = 2) followed by trimethoprim/sulfamethoxazole (sul2) resistance genes (26% (19/73)). The current study indicates that HS is consistently circulating among the animal population in Punjab, Pakistan. The current scenario of higher resistance in P. multocida needs continuous surveillance of the infection and mass awareness programs about the non-prescribed and excessive use of antibiotics in the animal sector.
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Affiliation(s)
- Shahid Ali
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Muhammad Haseeb Ali Tariq
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Muhammad Yaqoob
- Khan Bahadar Choudry Mushtaq Ahmed College of Veterinary Sciences, Narowal, Punjab, Pakistan
| | - Mazhar Ul Haq
- Faculty of Veterinary and Animal Sciences, Department of Veterinary Biomedical Sciences, PMAS-Arid Agriculture University, Rawalpindi, Punjab, Pakistan
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
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11
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Zhao M, Zhang Y, Liu S, Wang F, Zhang P. Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut. BMC Microbiol 2025; 25:90. [PMID: 40000989 PMCID: PMC11853306 DOI: 10.1186/s12866-025-03823-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 02/12/2025] [Indexed: 02/27/2025] Open
Abstract
Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.
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Affiliation(s)
- Meiqi Zhao
- Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin, 300384, China
- The Third Central Hospital of Tianjin, Nankai University, Tianjin, 300170, China
| | - Yunlong Zhang
- Hospital of Stomatology, Tianjin Medical University, Tianjin, 300070, China
| | - Shuangqing Liu
- Department of Clinical Laboratory, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Fengmei Wang
- The Third Central Hospital of Tianjin, Nankai University, Tianjin, 300170, China
- Department of Organ Transplantation, Tianjin Key Laboratory of Organ Transplantation, Tianjin First Central Hospital, Nankai University, Tianjin, 300192, China
| | - Peng Zhang
- Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin, 300384, China.
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12
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Xu H, Zhu D, Zhong M, Li C, Wen C, Zhu S, Li Q, Luo X. Source-oriented risks of heavy metals and their effects on resistance genes in natural biofilms. JOURNAL OF HAZARDOUS MATERIALS 2025; 484:136735. [PMID: 39647330 DOI: 10.1016/j.jhazmat.2024.136735] [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: 09/05/2024] [Revised: 10/23/2024] [Accepted: 11/30/2024] [Indexed: 12/10/2024]
Abstract
Heavy metal (HM) introduction from various land-use patterns can be a major source of metal resistance genes (MRGs) entering river environments. This influx can trigger the occurrence of other resistomes, such as antibiotic resistance genes (ARGs), by improving co-resistant conjugative transfer. Biofilms, which form at water-solid interfaces, could serve as potential hotspots for HMs and resistance genes. However, the enrichment of HMs from various sources within biofilms and their effect on resistomes remain undocumented. This study aims to investigate the physicochemical properties of biofilm samples collected from the Heihui River, a tributary of the Lancang River, and to analyze the concentrations of nine HMs (As, Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) within these biofilms. The 16S rRNA gene and metagenomic high-throughput sequencing techniques were integrated to uncover the association between HM accumulation levels in biofilms and ecological and health risks, considering the presence of two resistance genes. Natural sources (Co, Cr), industrial (As, Cu, V), agricultural (Cd, Ni), and transportation activities (Pb, Zn) markedly contributed to HM presence within biofilms, with industrial activities posing higher noncarcinogenic and carcinogenic risks than other sources. The network-correlation analyses revealed higher levels of ARG-MRG coexistence in biofilms, with the ecological and health risk index of HMs in biofilms closely associated with the abundance of both resistance genes. Furthermore, the biofilm As concentration markedly affected the abundance and expression of ARGs and MRGs, with elevated As levels within biofilms significantly and positively influencing all four functional categories of MRGs. Water pH also indirectly impacted these functional types by modulating the ionic form of HMs within the biofilm matrix. Our findings underscore the significance of integrating biofilms into environmental management practices and standards for assessing environmental quality.
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Affiliation(s)
- Hansen Xu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China; Leshan Meteorological Bureau, Sichuan Province, Leshan 614000, China
| | - Dan Zhu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Mei Zhong
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Chunyan Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Chen Wen
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Shijun Zhu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Qi Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China
| | - Xia Luo
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming 650500, China; Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Kunming 650500, China.
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13
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Cao T, Guo Y, Lin L, Wang D, Liu Z, Zou X, Ke Y, Lv Z. Effect of folpet on hypoglycaemia, intestinal microbiota, and drug resistance genes in mice. BMC Microbiol 2025; 25:11. [PMID: 39789436 PMCID: PMC11715183 DOI: 10.1186/s12866-024-03725-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 12/20/2024] [Indexed: 01/12/2025] Open
Abstract
BACKGROUND Folpet is a nonspecific sulfonamide fungicide widely used to protect crops from mildew. However, the in vivo effects of folpet on glucose metabolism homeostasis, gut microbiota, and abundance of drug resistance genes remain unknown. The purpose of this study was to assess the effects of the pesticide, folpet, on glucose metabolism homeostasis, and folpet-induced changes in the intestinal microbiota and resistance genes in mice. METHODS Mice were orally administered folpet at 0, 1, 10, and 100 mg/kg body weight/day for 5 weeks. Blood sugar levels in mice were measured after 5 weeks of folpet administration. Metagenomic sequencing and drug resistance gene analyses were performed to explore changes in the abundance of gut microbiota members and drug resistance genes in mice after folpet administration. Correlation analysis was performed using metabolomics to explore the relationship between intestinal microbiota, drug resistance genes, and glucose metabolism. RESULTS Mice in the folpet group had significantly lower blood glucose levels than those in the control group. The abundance of Atopobium, Libanicoccus, Collinsella, and Parabacteroides in the intestinal microbiota of folpet-treated mice was significantly higher than that in the control group. However, the abundance of Mailhella, Bilophila, Roseburia, and Bacteroides were reduced in folpet-treated mice. Compared with the control group, the abundance of APH6-Ic and AAC6-Ie-APH2-Ia resistance genes in mice treated with folpet significantly increased. The abundance of tetQ, ermE, and BahA resistance genes was significantly reduced after folpet treatment. CONCLUSIONS Folpet is associated with changes in the abundance of gut microbiota in mice and may also affect the abundance of drug-resistance genes and the regulation of blood glucose levels.
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Affiliation(s)
- Tingting Cao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yajie Guo
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, China
| | - Liangqiang Lin
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Dan Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Zhiyang Liu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Xuan Zou
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yuebin Ke
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China.
| | - Ziquan Lv
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China.
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14
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Feng Y, Lu X, Zhao J, Li H, Xu J, Li Z, Wang M, Peng Y, Tian T, Yuan G, Zhang Y, Liu J, Zhang M, Zhu La ALT, Qu G, Mu Y, Guo W, Wu Y, Zhang Y, Wang D, Hu Y, Kan B. Regional antimicrobial resistance gene flow among the One Health sectors in China. MICROBIOME 2025; 13:3. [PMID: 39763003 PMCID: PMC11705761 DOI: 10.1186/s40168-024-01983-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 11/19/2024] [Indexed: 01/11/2025]
Abstract
BACKGROUND Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance. RESULTS In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance. CONCLUSIONS Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.
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Affiliation(s)
- Yuqing Feng
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Jiayong Zhao
- Institute of Infectious Disease Prevention and Control, Henan Center for Disease Control and Prevention, Zhengzhou, 450016, China
| | - Hongmin Li
- Dengfeng Center for Disease Control and Prevention, Dengfeng, Zhengzhou, 452470, China
| | - Jialiang Xu
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Zhenpeng Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Mengyu Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Yao Peng
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Tian Tian
- Dengfeng Center for Disease Control and Prevention, Dengfeng, Zhengzhou, 452470, China
| | - Gailing Yuan
- Dengfeng Center for Disease Control and Prevention, Dengfeng, Zhengzhou, 452470, China
| | - Yuan Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jiaqi Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Meihong Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - A La Teng Zhu La
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Geruo Qu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing, 100048, China
| | - Yujiao Mu
- Institute of Infectious Disease Prevention and Control, Henan Center for Disease Control and Prevention, Zhengzhou, 450016, China
| | - Wanshen Guo
- Institute of Infectious Disease Prevention and Control, Henan Center for Disease Control and Prevention, Zhengzhou, 450016, China
| | - Yongning Wu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Yuyu Zhang
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing, 100048, China.
| | - Dexiang Wang
- Dengfeng Center for Disease Control and Prevention, Dengfeng, Zhengzhou, 452470, China.
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Biao Kan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
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15
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Chu VT, Glascock A, Donnell D, Grabow C, Brown CE, Ward R, Love C, Kalantar KL, Cohen SE, Cannon C, Woodworth MH, Kelley CF, Celum C, Luetkemeyer AF, Langelier CR. Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome. Nat Med 2025; 31:207-217. [PMID: 39363100 PMCID: PMC11750720 DOI: 10.1038/s41591-024-03274-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 08/28/2024] [Indexed: 10/05/2024]
Abstract
Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections among men who have sex with men and transgender women. Although poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from the DoxyPEP trial, a randomized clinical trial comparing doxy-PEP use, a one-time doxycycline 200-mg dose taken after condomless sex (DP arm, n = 100), to standard of care (SOC arm, n = 50) among men who have sex with men and transgender women. From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data were analyzable from 127 samples derived from 89 participants, and RNA-seq data were analyzable from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time. The median number of doxycycline doses taken since enrollment by participants with DNA-seq data was zero (interquartile range (IQR): 0-7 doses) for the SOC arm and 42 (IQR: 27-64 doses) for the DP arm. Tetracycline ARGs were detected in all day-0 DNA-seq samples and in 85% of day-0 RNA-seq samples. The proportional mass of tetracycline ARGs in the resistome increased between day-0 and month-6 in DP participants from 46% to 51% in the metagenome (P = 2.3 × 10-2) and from 4% to 15% in the metatranscriptome (P = 4.5 × 10-6), but no statistically significant increases in other ARG classes were observed. Exposure to a higher number of doxycycline doses correlated with proportional enrichment of tetracycline ARGs in the metagenome (Spearman's ρ = 0.23, P = 9.0 × 10-3) and metatranscriptome (Spearman's ρ = 0.55, P = 3.7 × 10-8). Bacterial microbiome alpha diversity, beta diversity and total bacterial mass did not differ between day-0 and month-6 samples from DP participants when assessed by either DNA-seq or RNA-seq. In an abundance-based correlation analysis, we observed an increase over time in the strength of the correlation between tetracycline ARGs and specific bacterial taxa, including some common human pathogens. In sum, doxy-PEP use over a 6-month period was associated with an increase in the proportion of tetracycline ARGs comprising the gut resistome and an increase in the expression of tetracycline ARGs. At 6 months of doxy-PEP use, no residual differences were observed in alpha and beta diversity or taxonomic composition of the gut microbiome. As doxy-PEP is implemented as a public health strategy, further studies and population-level surveillance of doxycycline-resistant pathogens are needed to understand the implications of these findings. ClinicalTrials.gov registration number: NCT03980223 .
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Affiliation(s)
- Victoria T Chu
- Department of Pediatrics, Division of Infectious Diseases and Global Health, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | | | | | - Cole Grabow
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Clare E Brown
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ryan Ward
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Christina Love
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | | | - Stephanie E Cohen
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Department of Public Health, San Francisco, CA, USA
| | - Chase Cannon
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael H Woodworth
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Colleen F Kelley
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Connie Celum
- Departments of Global Health, Medicine and Epidemiology, University of Washington, Seattle, WA, USA
| | - Anne F Luetkemeyer
- Division of HIV, Infectious Diseases & Global Medicine, Zuckerberg San Francisco General, University of California, San Francisco, San Francisco, CA, USA
| | - Charles R Langelier
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
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16
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Niu X, Lin L, Zhang T, An X, Li Y, Yu Y, Hong M, Shi H, Ding L. Research on antibiotic resistance genes in wild and artificially bred green turtles (Chelonia mydas). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176716. [PMID: 39368512 DOI: 10.1016/j.scitotenv.2024.176716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/11/2024] [Accepted: 10/02/2024] [Indexed: 10/07/2024]
Abstract
Sea turtles, vital to marine ecosystems, face population decline. Artificial breeding is a recovery strategy, yet it risks introducing antibiotic resistance genes (ARGs) to wild populations and ecosystems. This study employed metagenomic techniques to compare the distribution characteristics of ARGs in the guts of wild and artificially bred green turtles (Chelonia mydas). The findings revealed that the total abundance of ARGs in C. mydas that have been artificially bred was significantly higher than that in wild individuals. Additionally, the abundance of mobile genetic elements (MGEs) co-occurring with ARGs in artificially bred C. mydas was significantly higher than in wild C. mydas. In the analysis of bacteria carrying ARGs, wild C. mydas exhibited greater bacterial diversity. Furthermore, in artificially bred C. mydas, we discovered 23 potential human pathogenic bacteria (HPB) that contain antibiotic resistance genes. In contrast, in wild C. mydas, only one type of HPB carrying an antibiotic resistance gene was found. The findings of this study not only enhance our understanding of the distribution and dissemination of ARGs within the gut microbial communities of C. mydas, but also provide vital information for assessing the potential impact of releasing artificially bred C. mydas on the spread of antibiotic resistance.
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Affiliation(s)
- Xin Niu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China
| | - Liu Lin
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China
| | - Ting Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China
| | - Xiaoyu An
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China
| | - Yupei Li
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China; Marine Protected Area Administration of Sansha City, Sansha 573199, China
| | - Yangfei Yu
- Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China; Marine Protected Area Administration of Sansha City, Sansha 573199, China
| | - Meiling Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China
| | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China; Hainan Sansha Provincial Observation and Research Station of Sea Turtle Ecology, Sansha 573199, China.
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17
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Jiao P, Zhou Y, Zhang X, Jian H, Zhang XX, Ma L. Mechanisms of horizontal gene transfer and viral contribution to the fate of intracellular and extracellular antibiotic resistance genes in anaerobic digestion supplemented with conductive materials under ammonia stress. WATER RESEARCH 2024; 267:122549. [PMID: 39368190 DOI: 10.1016/j.watres.2024.122549] [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: 07/22/2024] [Revised: 09/27/2024] [Accepted: 09/28/2024] [Indexed: 10/07/2024]
Abstract
The addition of conductive materials (CMs) is an effective strategy for mitigating ammonia inhibition during anaerobic digestion (AD). However, the introduction of CMs can result in increased antibiotic resistance genes (ARGs) pollution, potentially facilitated by enhanced horizontal gene transfer (HGT). The complex dynamics of intracellular and extracellular ARGs (iARGs/eARGs) and the mechanisms underlying their transfer, mediated by CMs, in ammonia-stressed AD systems remain unclear. In this study, we investigated the effects of three commonly used CMs-nano magnetite (Mag), nano zero-valent iron (nZVI), and granular activated carbon (GAC)-on the fate of iARGs and eARGs during the AD of waste activated sludge under ammonia stress. The results revealed an unexpected enrichment of iARGs by 1.5 %-10.9 % and a reduction of eARGs by 14.1 %-25.2 % in CM-supplemented AD. This discrepancy in the dynamics of iARGs and eARGs may be attributed to changes in microbial hosts and the horizontal transfer of ARGs. Notably, CMs activated prophages within antibiotic-resistant bacteria (ARB) and their symbiotic partners involved in vitamin B12 provision, leading to the lysis of ARB and the subsequent release of eARGs for transformation. Additionally, the abundance of potentially mobile ARGs, which co-occurred with mobile genetic elements, increased by 56.6 %-134.5 % with CM addition, highlighting an enhanced potential for the HGT of ARGs. Specifically, Mag appeared to promote both transformation and conjugation processes, while nZVI only promoted conjugation. Moreover, none of the three CMs had any discernible impact on transduction. GAC proved superior to both nano Mag and nZVI in controlling the enrichment of iARGs, reducing eARGs, and limiting HGTs simultaneously. Overall, these findings provide novel insights into the role of viruses and the mechanisms of ARG spread in CM-assisted AD, offering valuable information for developing strategies to mitigate ARG pollution in practical applications.
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Affiliation(s)
- Pengbo Jiao
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Ying Zhou
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Xingxing Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Liping Ma
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai, 200062, China.
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18
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Yang C, Yan S, Zhang B, Yao X, Mo J, Rehman F, Guo J. Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics. ENVIRONMENTAL RESEARCH 2024; 262:119808. [PMID: 39153565 DOI: 10.1016/j.envres.2024.119808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/03/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3--N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.
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Affiliation(s)
- Chuanmao Yang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Shiwei Yan
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Baihuan Zhang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Xiunan Yao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Jiezhang Mo
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou, China
| | - Fozia Rehman
- Interdisciplinary Research Center in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Pakistan
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China.
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19
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Su Z, Cui S, Wen D, Chen L. Metagenomic insights into resistome, mobilome and virulome in different fecal waste. ENVIRONMENTAL RESEARCH 2024; 262:119861. [PMID: 39208976 DOI: 10.1016/j.envres.2024.119861] [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: 07/16/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Fecal waste is a significant source of antimicrobial resistance (AMR) pollution and provides valuable insights into the AMR development in animal and human populations within the "One health" framework. Various genetic elements, including antibiotic resistance genes (ARGs), biocide and metal resistance genes (BMGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs), are crucial AMR risk determinants (ARDs). However, few studies focused on compositional characteristics of ARDs in different feces. Here, we analyzed 753 public metagenomes from human, pig, chicken, and cattle feces, revealing significant differences in ARD richness and abundance across fecal types, notably lowest in cattle samples. Tetracycline, multi-metal, and -biocide resistance genes were dominant resistome. A few core genes contributed to 25.6%-91.1% of gene abundance, and their correlations were stronger in cattle samples. Procrustes analysis showed that microbial composition had higher correlations with ARGs (M2 = 0.579) and BMGs (M2 = 0.519). Gammaproteobacteria was identified as major ARD-hosts especially in human and pig feces, and they mainly carried multi-resistance genes. MGEs exhibited direct positive effects on ARGs and BMGs, indirectly impacting VFGs. Utilizing random forest methods, we identified 42 indicator genes for tracking AMR pollution originating from fecal sources in the environments. This study offers new insights into understanding and controlling the AMR pollution of fecal waste from human and food animals.
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Affiliation(s)
- Zhiguo Su
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Saishi Cui
- Department of Epidemiology and Biostatistics, Dornsife School of Public Health, Drexel University, Philadelphia, PA 19104, USA
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Lyujun Chen
- School of Environment, Tsinghua University, Beijing 100084, China.
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20
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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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21
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Qing Y, Zou Z, Jiang G, Qin L, Liu K, Liu Z. A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli. Front Vet Sci 2024; 11:1442159. [PMID: 39606649 PMCID: PMC11600533 DOI: 10.3389/fvets.2024.1442159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 10/31/2024] [Indexed: 11/29/2024] Open
Abstract
Introduction Escherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance. Methods In this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity. Results Our analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), β-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with β-lactam and aminoglycoside ARGs being the most widespread. Discussion This study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and β-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.
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Affiliation(s)
- Yun Qing
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China
- College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
| | - Zhongai Zou
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, China
| | - Guolian Jiang
- College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
| | - Lingshi Qin
- College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
| | - Kehui Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China
| | - Zongbao Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China
- College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
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22
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Raviranga NGH, Ayinla M, Perera HA, Qi Y, Yan M, Ramström O. Antimicrobial Potency of Nor-Pyochelin Analogues and Their Cation Complexes against Multidrug-Resistant Pathogens. ACS Infect Dis 2024; 10:3842-3852. [PMID: 39469860 DOI: 10.1021/acsinfecdis.4c00421] [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: 10/30/2024]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa develops increasing resistance toward even the most potent antibiotics. Like other bacteria, the pathogen produces a number of virulence factors including metallophores, which constitute an important group. Pseudomonads produce the iron-chelating metallophore (siderophore) pyochelin, which, in addition to its iron-scavenging ability, is an effector for the transcriptional regulator PchR in its FeIII-bound form (ferripyochelin). In the present study, docking studies predicted a major ferripyochelin binding site in PchR, which prompted the exploration of nor-pyochelin analogues to produce tight binding to PchR, and thereby upregulation of the pyochelin metabolism. In addition, we investigated the effects of using the analogues to bind the antimicrobial cations GaIII and InIII. Selected analogues of nor-pyochelin were synthesized, and their GaIII- and InIII-based complexes were assessed for antimicrobial activity. The results indicate that the GaIII complexes inhibit the pathogens under iron-limited conditions, while the InIII-based systems are more effective in iron-rich media. Several of the GaIII complexes were shown to be highly effective against a multidrug-resistant P. aeruginosa clinical isolate, with minimum inhibitory concentrations (MICs) of ≤1 μg/mL. Similarly, two of the InIII-based systems were particularly effective against the isolate, with an MIC of 8 μg/mL. These results show high promise in comparison with other, traditionally potent antibiotics, as the compounds generally indicated low cytotoxicity toward mammalian cells. Preliminary mechanistic investigations using pseudomonal transposon mutants suggested that the inhibitory effects of the InIII-based systems could be due to acute iron deficiency as a result of InIII-bound bacterioferritin.
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Affiliation(s)
- N G Hasitha Raviranga
- Department of Chemistry, University of Massachusetts Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Mubarak Ayinla
- Department of Chemistry, University of Massachusetts Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Harini A Perera
- Department of Chemistry, University of Massachusetts Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Yunchuan Qi
- Department of Chemistry, University of Massachusetts Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Olof Ramström
- Department of Chemistry, University of Massachusetts Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE-39182 Kalmar, Sweden
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23
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Liao X, Hou L, Zhang L, Grossart HP, Liu K, Liu J, Chen Y, Liu Y, Hu A. Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135675. [PMID: 39216241 DOI: 10.1016/j.jhazmat.2024.135675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 07/20/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.
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Affiliation(s)
- Xin Liao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liyuan Hou
- Department of Civil and Environmental Engineering, Utah State University, Logan, UT 84322, United States; Utah Water Research Laboratory, 1600 Canyon Road, Logan, UT 84321, United States
| | - Lanping Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany; Institute of Biochemistry and Biology, Potsdam University, 14476 Potsdam, Germany
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Junzhi Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China.
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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24
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Tang A, Zhang J, Huang J, Deng Y, Wang D, Yu P, Zhao R, Wang Y, Chen Z, Zhang T, Li B. Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater. WATER RESEARCH 2024; 265:122253. [PMID: 39167968 DOI: 10.1016/j.watres.2024.122253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/31/2024] [Accepted: 08/10/2024] [Indexed: 08/23/2024]
Abstract
Viruses are the most abundant yet understudied members that may influence microbial metabolism in activated sludge treating antibiotic production wastewater. This study comprehensively investigated virome community characteristics under the selection pressure of nine types and different concentrations of antibiotics using a metagenomics approach. Of the 15,514 total viral operational taxonomic units (tOTUs) recovered, only 37.5 % were annotated. Antibiotics altered the original viral community structure in activated sludge. The proportion of some pathogenic viral families, including Herpesviridae_like, increased significantly in reactors treating erythromycin production wastewater. In total, 16.5 % of the tOTUs were associated with two or more hosts. tOTUs rarely carried antibiotic resistance genes (ARGs), and the ARG types in the tOTUs did not match the ARGs carried by the bacterial hosts. This suggests that transduction contributes little to the horizontal ARG transfer. Auxiliary metabolic genes (AMGs) were prevalent in tOTUs, and those involved in folate biosynthesis were particularly abundant, indicating their potential to mitigate antibiotic-induced host damage. This study provides comprehensive insights into the virome community in activated sludge treating antibiotic production wastewater and sheds light on the potential role of viral AMGs in mitigating antibiotic-induced stress.
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Affiliation(s)
- Aixi Tang
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jiayu Zhang
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Huang
- Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Renxin Zhao
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, China
| | - Zihan Chen
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Bing Li
- Key Laboratory of Microorganism Application and Risk Control, Ministry of Ecology and Environment, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
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25
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Souque C, González Ojeda I, Baym M. From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance. Annu Rev Microbiol 2024; 78:361-382. [PMID: 39141706 DOI: 10.1146/annurev-micro-041522-102707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Tackling the challenge created by antibiotic resistance requires understanding the mechanisms behind its evolution. Like any evolutionary process, the evolution of antimicrobial resistance (AMR) is driven by the underlying variation in a bacterial population and the selective pressures acting upon it. Importantly, both selection and variation will depend on the scale at which resistance evolution is considered (from evolution within a single patient to the host population level). While laboratory experiments have generated fundamental insights into the mechanisms underlying antibiotic resistance evolution, the technological advances in whole genome sequencing now allow us to probe antibiotic resistance evolution beyond the lab and directly record it in individual patients and host populations. Here we review the evolutionary forces driving antibiotic resistance at each of these scales, highlight gaps in our current understanding of AMR evolution, and discuss future steps toward evolution-guided interventions.
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Affiliation(s)
- Célia Souque
- Departments of Biomedical Informatics and Microbiology, Harvard Medical School, Boston, Massachusetts, USA; ,
| | - Indra González Ojeda
- Departments of Biomedical Informatics and Microbiology, Harvard Medical School, Boston, Massachusetts, USA; ,
| | - Michael Baym
- Departments of Biomedical Informatics and Microbiology, Harvard Medical School, Boston, Massachusetts, USA; ,
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Shang KM, Elsheikha HM, Ma H, Wei YJ, Zhao JX, Qin Y, Li JM, Zhao ZY, Zhang XX. Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 286:117186. [PMID: 39426111 DOI: 10.1016/j.ecoenv.2024.117186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 09/18/2024] [Accepted: 10/10/2024] [Indexed: 10/21/2024]
Abstract
The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance.
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Affiliation(s)
- Kai-Meng Shang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, PR China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - He Ma
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, PR China
| | - Yong-Jie Wei
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, PR China
| | - Ji-Xin Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, PR China
| | - Ya Qin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, PR China; College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, PR China
| | - Jian-Ming Li
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, Jilin Province, PR China; Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun, Jilin Province, PR China; Key Laboratory of Animal Production and Product Quality and Security, Ministry of Education, Ministry of National Education, Changchun, Jilin Province, PR China
| | - Zi-Yu Zhao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, PR China
| | - Xiao-Xuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, PR China.
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27
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Li J, Sun Z, Sun F, Lai Y, Yi X, Wang Z, Yuan J, Hu Y, Pan A, Pan XF, Zheng Y, Chen D. Gut antibiotic resistome during pregnancy associates with the risk of gestational diabetes mellitus: New evidence from a prospective nested case-control study. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135434. [PMID: 39146585 DOI: 10.1016/j.jhazmat.2024.135434] [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: 12/24/2023] [Revised: 07/24/2024] [Accepted: 08/04/2024] [Indexed: 08/17/2024]
Abstract
Antibiotic resistome has emerged as a global threat to public health. However, gestational antibiotic resistome and potential link with adverse pregnancy outcomes remains poorly understood. Our study reports for the first time an association between gut antibiotic resistome during early pregnancy and the risk of gestational diabetes mellitus (GDM) based on a prospective nested case-control cohort including 120 cases and 120 matched controls. A total of 214 antibiotic resistance gene (ARG) subtypes belonging to 17 ARG types were identified in > 10 % fecal samples collected during each trimester. The data revealed dynamic profiles of gut antibiotic resistome through pregnancy, and significant positive associations between selected features (i.e., ARG abundances and a GDM-ARG score which is a new feature characterizing the association between ARGs and GDM) of gut antibiotic resistome during early pregnancy and GDM risk as well as selected endogenous metabolites. The findings demonstrate ubiquitous presence of ARGs in pregnant women and suggest it could constitute an important risk factor for the development of GDM.
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Affiliation(s)
- Jing Li
- College of Environment and Climate, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China; School of Public Health, Health Science Center, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Zhonghan Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 200433, Shanghai, China
| | - Fengjiang Sun
- College of Environment and Climate, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yuwei Lai
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou 510631, Guangdong, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou 510631, Guangdong, China
| | - Jiaying Yuan
- Department of Science and Education, Shuangliu Maternal and Child Health Hospital, Chengdu 610200, Sichuan, China
| | - Yayi Hu
- Department of Gynecology and Obstetrics, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - An Pan
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Xiong-Fei Pan
- Shuangliu Institute of Women's and Children's Health, Shuangliu Maternal and Child Health Hospital, Chengdu 610041, Sichuan, China; Section of Epidemiology and Population Health & Department of Gynecology and Obstetrics, Ministry of Education Key Laboratory of Birth Defects and Related Diseases of Women and Children & National Medical Products Administration Key Laboratory for Technical Research on Drug Products In Vitro and In Vivo Correlation, West China Second University Hospital, Sichuan University, Shuangliu Maternal and Child Health Hospital, Chengdu 610041, Sichuan, China.
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 200433, Shanghai, China.
| | - Da Chen
- College of Environment and Climate, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, Guangdong, China.
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28
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Peruzzo A, Petrin S, Boscolo Anzoletti A, Mancin M, Di Cesare A, Sabatino R, Lavagnolo MC, Beggio G, Baggio G, Danesi P, Barco L, Losasso C. The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135567. [PMID: 39182301 DOI: 10.1016/j.jhazmat.2024.135567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/15/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024]
Abstract
In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.
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Affiliation(s)
- Arianna Peruzzo
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Italy; PhD National Programme in One Health Approaches to Infectious Diseases and Life Science Research, Departiment of Public Health, Experimental and Forensice Medicine, University of Pavia, Pavia 27100, Italy
| | - Sara Petrin
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Italy
| | - Aurora Boscolo Anzoletti
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Italy
| | - Marzia Mancin
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Italy
| | - Andrea Di Cesare
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Raffaella Sabatino
- National Research Council of Italy (CNR) - Water Research Institute (IRSA), Largo Tonolli 50, 28922 Verbania, Italy; National Biodiversity Future Center (NBFC), Piazza Marina 61, 90133 Palermo, Italy
| | - Maria Cristina Lavagnolo
- Department of Civil Environmental and Architectural Engineering, University of Padova, Lungargine Rovetta 8, 35100 Padova, Italy
| | - Giovanni Beggio
- Department of Civil Environmental and Architectural Engineering, University of Padova, Lungargine Rovetta 8, 35100 Padova, Italy
| | - Giulia Baggio
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Italy
| | - Patrizia Danesi
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Italy
| | - Lisa Barco
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Italy
| | - Carmen Losasso
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Italy.
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Pei Z, Liu Y, Zhao F, Wang H, Zhao J, Chen W, Lu W. Antibiotic Susceptibility Testing and Establishment of Tentative Species-Specific Microbiological Cut-off Values for Bifidobacteria Isolated from Chinese Population. Probiotics Antimicrob Proteins 2024; 16:1657-1672. [PMID: 37515711 DOI: 10.1007/s12602-023-10128-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2023] [Indexed: 07/31/2023]
Abstract
Bifidobacteria are commonly used as probiotics in the food industry. The resistance of Bifidobacterium species to antibiotics is closely linked to food safety. However, we still lack a system for the safety evaluation of antibiotic resistance in bifidobacteria, and genus-level microbiological cut-off values remain in use for the determination of phenotypic resistance of Bifidobacterium strains to a given antibiotic. Here, we collected a total of 422 gut-derived bifidobacterial strains isolated from Chinese population and identified their phenotypic resistance profiles against ampicillin, amoxicillin, ciprofloxacin, chloramphenicol, clindamycin, erythromycin, rifampicin, tetracycline, trimethoprim, and vancomycin. Different Bifidobacterium species were found to have varying tolerances to the same antibiotic; therefore, we further established species-specific cut-off values for bifidobacterial species to ten antibiotics. Species-specific rather than genus-specific cut-off values for species belonging to the same taxon were considered more suitable to determine the phenotypic resistance of a Bifidobacterium strain. Moreover, a comprehensive scanning of antibiotic resistance genes in all Bifidobacterium strains tested revealed that the existence of the tetracycline resistance gene tet(W) and the erythromycin/clindamycin resistance gene ErmX is closely related to host phenotypes. Our findings provide guidance and reference values at both phenotype and genotype levels for the safe application of bifidobacteria in the food industry and the development of probiotic resistance evaluation standards.
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Affiliation(s)
- Zhangming Pei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yufei Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Fang Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, People's Republic of China.
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30
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Jiang G, Liu K, Qing Y, Qin L, Zou Z, Liu Z. Global Trends of Antibiotic Resistance Genes in Staphylococcus aureus: A Comprehensive Genomic Analysis. Foodborne Pathog Dis 2024; 21:653-661. [PMID: 39052696 DOI: 10.1089/fpd.2024.0043] [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: 07/27/2024] Open
Abstract
Staphylococcus aureus (S. aureus) is a pathogen capable of causing severe diseases and exhibiting resistance to multiple antibiotics. However, there is a significant lack of comprehensive research on the global prevalence of its antibiotic resistance genes (ARGs). This study provided a comprehensive analysis of ARGs in S. aureus, using 113,842 S. aureus genome sequences from the National Center for Biotechnology Information database. The results revealed that a significant majority (84%) of these genomes harbored at least one ARG, with a total of 389,464 ARG sequences identified across 19 major types and 103 subtypes. These ARGs exhibited varied abundances and diversities, linked primarily to clinical cases worldwide. ARGs for fluoroquinolones, multidrug resistance, bacitracin, tetracyclines, beta-lactams, and aminoglycosides were notably abundant, ranging from 3.16 × 10-5 to 1.49 copies of ARG per million bp. Variations in the abundance and diversity of ARGs were observed between countries, with middle- and low-income countries showing higher gene abundance but lower diversity compared with high-income countries. Temporal analysis over 30 years showed a fluctuating decline in ARG abundance alongside an increase in diversity, suggesting evolving resistance mechanisms. The study also explored the role of mobile genetic elements in ARG dissemination, finding a substantial proportion of ARG subtypes associated with plasmids and insertion sequence elements, indicating their potential for spread across borders. The global distribution of mobile ARGs was further analyzed, revealing the extensive reach of certain ARGs across countries. This research provides valuable insights into the prevalence and dissemination of antibiotic resistance in S. aureus on a global scale, aiding in the development of effective monitoring and control strategies to combat ARGs in S. aureus and other pathogens.
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Affiliation(s)
- Guolian Jiang
- Ministry of Education, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Guilin, China
| | - Kehui Liu
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
| | - Yun Qing
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Lingshi Qin
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Zhongai Zou
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, China
| | - Zongbao Liu
- Ministry of Education, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
- College of Life Sciences, Guangxi Normal University, Guilin, China
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31
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Chi W, Zou Y, Qiu T, Shi W, Tang L, Xu M, Wu H, Luan X. Horizontal gene transfer plays a crucial role in the development of antibiotic resistance in an antibiotic-free shrimp farming system. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135150. [PMID: 38986416 DOI: 10.1016/j.jhazmat.2024.135150] [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: 05/08/2024] [Revised: 06/24/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
Antibiotic selective pressure in aquaculture systems often results in the antibiotic resistance genes (ARGs) proliferation. Nonetheless, a paucity of data exists concerning the mechanisms of ARGs development in aquaculture systems without the influences of antibiotics. This study utilized metagenomic approaches to elucidate the dynamics and transfer mechanisms of ARGs throughout the aquaculture of Pacific white shrimp. A marked change in the resistome was observed throughout the aquaculture without antibiotics. The total ARGs relative abundance increased from 0.05 to 0.33 by day 90 of cultivation, with even higher in mixed wastewater (0.44). Both bacterial communities and mobile genetic elements play pivotal roles in the development of ARGs. Metagenome-assembled genomes showed enrichment of environmentally intrinsic ARGs on chromosomes including macB and mdtK. The plasmid-mediated horizontal transfer was recognized as a principal factor contributing to the rise of ARGs, particularly for tetG and floR, and this led to an escalation of resistance risk, peaking at a risks core of 35.43 on day 90. This study demonstrates that horizontal gene transfer plays a crucial role in ARGs development without antibiotic pressure, which can provide a theoretical foundation for controlling ARGs proliferation in aquaculture systems.
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Affiliation(s)
- Wendan Chi
- Marine Science Research Institute of Shandong Province, Qingdao 266104, People's Republic of China; Qingdao Key Laboratory of Coastal Ecological Restoration and Security, Qingdao, Shandong, People's Republic of China
| | - Yan Zou
- Marine Science Research Institute of Shandong Province, Qingdao 266104, People's Republic of China
| | - Tianlong Qiu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
| | - Wen Shi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Liuqing Tang
- Marine Science Research Institute of Shandong Province, Qingdao 266104, People's Republic of China; Qingdao Key Laboratory of Coastal Ecological Restoration and Security, Qingdao, Shandong, People's Republic of China
| | - Mengxue Xu
- Marine Science Research Institute of Shandong Province, Qingdao 266104, People's Republic of China; Qingdao Key Laboratory of Coastal Ecological Restoration and Security, Qingdao, Shandong, People's Republic of China
| | - Haiyi Wu
- Marine Science Research Institute of Shandong Province, Qingdao 266104, People's Republic of China; Qingdao Key Laboratory of Coastal Ecological Restoration and Security, Qingdao, Shandong, People's Republic of China.
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100048, People's Republic of China.
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32
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Li W, Wang Y, Gao J, Wang A. Antimicrobial resistance and its risks evaluation in wetlands on the Qinghai-Tibetan Plateau. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116699. [PMID: 38981389 DOI: 10.1016/j.ecoenv.2024.116699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/11/2024]
Abstract
Amidst the global antimicrobial resistance (AMR) crisis, antibiotic resistance has permeated even the most remote environments. To understand the dissemination and evolution of AMR in minimally impacted ecosystems, the resistome and mobilome of wetlands across the Qinghai-Tibetan Plateau and its marginal regions were scrutinized using metagenomic sequencing techniques. The composition of wetland microbiomes exhibits significant variability, with dominant phyla including Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Notably, a substantial abundance of Antibiotic Resistance Genes (ARGs) and Mobile Genetic Elements (MGEs) was detected, encompassing 17 ARG types, 132 ARG subtypes, and 5 types of MGEs (Insertion Sequences, Insertions Sequences, Genomic Islands, Transposons, and Integrative Conjugative Elements). No significant variance was observed in the prevalence of resistome and mobilome across different wetland types (i.e., the Yellow River, other rivers, lakes, and marshes) (R=-0.5882, P=0.607). The co-occurrence of 74 ARG subtypes and 22 MGEs was identified, underscoring the pivotal role of MGEs in shaping ARG pools within the Qinghai-Tibetan Plateau wetlands. Metagenomic binning and analysis of assembled genomes (MAGs) revealed that 93 out of 206 MAGs harbored ARGs (45.15 %). Predominantly, Burkholderiales, Pseudomonadales, and Enterobacterales were identified as the primary hosts of these ARGs, many of which represent novel species. Notably, a substantial proportion of ARG-carrying MAGs also contained MGEs, reaffirming the significance of MGEs in AMR dissemination. Furthermore, utilizing the arg_ranker framework for risk assessment unveiled severe contamination of high-risk ARGs across most plateau wetlands. Moreover, some prevalent human pathogens were identified as potential hosts for these high-risk ARGs, posing substantial transmission risks. This study aims to investigate the prevalence of resistome and mobilome in wetlands, along with evaluating the risk posed by high-risk ARGs. Such insights are crucial for informing environmental protection strategies and facilitating the management of water resources on the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Weiwei Li
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Yanfang Wang
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Jianxin Gao
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China
| | - Ailan Wang
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, China.
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Lu N, Du Z, Chu F, Xiao R, Wu Z, Wang M, Jia R, Chu W. Tracking the impact of perfluoroalkyl acid emissions on antibiotic resistance gene profiles in receiving water by metagenomic analysis. WATER RESEARCH 2024; 261:121931. [PMID: 38924952 DOI: 10.1016/j.watres.2024.121931] [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: 02/01/2024] [Revised: 05/17/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
The ecological risks posed by perfluoroalkyl acids (PFAAs) to the aquatic environment have recently been of great concern. However, little information was available on the impact of PFAAs on antibiotic resistance genes (ARGs) profiles. In this study, the receiving river of the largest fluoropolymer production facility in China was selected to investigate the effects of PFAAs on ARGs profiles. The highest PFAAs concentration for water samples near the industrial effluent discharge point was 310.9 μg/L, which was thousands times of higher than the average concentration collected at upstream sites. Perfluorooctanoic acid accounted for more than 67.2 % of ∑PFAAs concentration in water samples collected at the downstream sites, followed by perfluorohexanoic acid (3.6 %-15.9 %). 145 ARG subtypes including high-risk ARGs were detected by metagenomic technology. The results indicated that the discharge of PFAA-containing effluents had a significant impact on the abundance and diversity of ARGs in receiving waters, and PFAAs and water quality parameters (e.g., pH, NH3N, CODMn, TP) could largely affect ARG profiles. Specifically, short-chain PFAAs had similar impacts on ARG profiles compared to the restricted long-chain PFAAs. This study confirmed the potential effects of PFAAs on ARGs in aquatic environment and provided more insights into the ecological risk raised by PFAAs.
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Affiliation(s)
- Nannan Lu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China
| | - Zhenqi Du
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China
| | - Fumin Chu
- Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China
| | - Rong Xiao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Zhengdi Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Mingquan Wang
- Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China
| | - Ruibao Jia
- Shandong Provincial Water Supply and Drainage Monitoring Centre, Jinan, 250101, China.
| | - Wenhai Chu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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34
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Wei X, Liang J, Ning T, Zhang C, Wang J, Tan L, Shen F. Response of soil microbial community structure and function to the sewage leakage: A case study of a 25-year-old cesspool. CHEMOSPHERE 2024; 363:142753. [PMID: 38971439 DOI: 10.1016/j.chemosphere.2024.142753] [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: 02/29/2024] [Revised: 06/07/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Providing many millions of rural households with decentralized sanitation facilities remains challenging. In undeveloped areas, cesspools have still been widely used due to technologically simple and low-cost. However, the influence of cesspools on the surrounding soil remains unclear. In this study, we investigated the influence of a 25-year-old household cesspool on soil physicochemical factors, microbial community composition and function, pathogens and antibiotic resistance genes (ARGs). Soil at the depth around the sewage liquid level (D70) was mostly disturbed where TOC, NO3-N and TP was increased to 16.8 g/kg, 18.2 mg/kg and 1.02 mg/kg respectively. Correspondingly, the element cycling genes of carbon fixation, methanotrophy, nitrogen fixation, ammonia oxidation, and nitrate reduction etc., were increased at D70. Notably, human derived pathogens such as Enterobacter, Salmonella, Pseudomonas aeruginosa, Klebsiella pneumoniae, Prevotella, and Vibrio were highly enriched by 5-10 folders in D70, indicating the potential health risk to human. Mantel tests suggested that EC, TP, pH, NH3-N and particularly NO3-N are important factors that influence the microbial community and element cycling genes in cesspool-affected soil. Overall, this study revealed the impact of household cesspool leakage on the surrounding soil and provided information for the selection and construction of basic sanitation facilities in poor regions.
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Affiliation(s)
- Xiaocheng Wei
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China; Key Laboratory of Rural Toilet and Sewage Treatment Technology, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China
| | - Jiayin Liang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China; Key Laboratory of Rural Toilet and Sewage Treatment Technology, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China
| | - Tianyang Ning
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China; Key Laboratory of Rural Toilet and Sewage Treatment Technology, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China
| | - Chunxue Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China; Key Laboratory of Rural Toilet and Sewage Treatment Technology, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China
| | - Jiarui Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China; Key Laboratory of Rural Toilet and Sewage Treatment Technology, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China
| | - Lu Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China; Key Laboratory of Rural Toilet and Sewage Treatment Technology, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China.
| | - Feng Shen
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China; Key Laboratory of Rural Toilet and Sewage Treatment Technology, Ministry of Agriculture and Rural Affairs, No. 31 Fukang Road, Nankai District, Tianjin 300191, China.
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Ge Z, Ai D, Ma Z, Li Y, Zhang J. Evolution and distribution of antibiotic resistance genes in submerged macrophytes and biofilm systems: From seasonal monitoring to mesocosm experiments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 367:121947. [PMID: 39068786 DOI: 10.1016/j.jenvman.2024.121947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/08/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
The aquatic ecosystem has been extensively investigated as a hotspot for the spread of antibiotic resistance genes (ARGs); yet, the evolution and distribution of ARGs profiles in submerged macrophytes biofilms and surrounding water remained unclear. In this study, the dynamic distribution and seasonal variations of microbial communities and ARGs profiles were investigated, alongside their assembly processes and mutual interactions. Bacitracin and multidrug resistance genes were predominant, constituting more than 60% of the total ARGs abundance. The deterministic processes (<65%), influenced by the physicochemical properties of the river environment, governed the assembly and composition of ARGs profiles, exhibiting significant seasonal variation. The peak diversity (21 types) and abundance (0.316 copy ratios) of ARGs were detected during the summer. Proteobacteria and Actinobacteria were the dominant bacterial phyla, accounting for 38.41-85.50% and 4.03-27.09% of the microbial community, respectively. Furthermore, Proteobacteria, especially genera such as Acinetobacter, Burkholderia, and Pseudomonas, with various resistance sequences, were the primary carriers of multiple ARGs. Notably, the genetic exchanges between biofilms and surrounding water facilitated the further propagation of high-risk ARGs, posing greater ecological risks. Redundancy analysis indicated that the total nitrogen and temperature in water determined the fate of pathogenic-resistant species. These findings provided theoretical support for the mitigation of ARGs contamination in aquatic environments.
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Affiliation(s)
- Zuhan Ge
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China; Shanghai Shifang Ecology and Landscape Co., Ltd, Shanghai, 200233, PR China
| | - Dan Ai
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China
| | - Zihang Ma
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China
| | - Yaguang Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China; Shanghai Shifang Ecology and Landscape Co., Ltd, Shanghai, 200233, PR China
| | - Jibiao Zhang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China; Shanghai Shifang Ecology and Landscape Co., Ltd, Shanghai, 200233, PR China.
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36
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Olanrewaju OS, Molale-Tom LG, Bezuidenhout CC. Genomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates. World J Microbiol Biotechnol 2024; 40:289. [PMID: 39102038 PMCID: PMC11300488 DOI: 10.1007/s11274-024-04098-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/27/2024] [Indexed: 08/06/2024]
Abstract
This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.
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Affiliation(s)
- Oluwaseyi Samuel Olanrewaju
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa.
| | - Lesego G Molale-Tom
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa.
| | - Cornelius C Bezuidenhout
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa
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Yin LZ, Luo XQ, Li JL, Liu Z, Duan L, Deng QQ, Chen C, Tang S, Li WJ, Wang P. Deciphering the pathogenic risks of microplastics as emerging particulate organic matter in aquatic ecosystem. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134728. [PMID: 38805824 DOI: 10.1016/j.jhazmat.2024.134728] [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: 02/19/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
Microplastics are accumulating rapidly in aquatic ecosystems, providing habitats for pathogens and vectors for antibiotic resistance genes (ARGs), potentially increasing pathogenic risks. However, few studies have considered microplastics as particulate organic matter (POM) to elucidate their pathogenic risks and underlying mechanisms. Here, we performed microcosm experiments with microplastics and natural POM (leaves, algae, soil), thoroughly investigating their distinct effects on the community compositions, functional profiles, opportunistic pathogens, and ARGs in Particle-Associated (PA) and Free-Living (FL) bacterial communities. We found that both microplastics and leaves have comparable impacts on microbial community structures and functions, enriching opportunistic pathogens and ARGs, which may pose potential environmental risks. These effects are likely driven by their influences on water properties, including dissolved organic carbon, nitrate, DO, and pH. However, microplastics uniquely promoted pathogens as keystone species and further amplified their capacity as hosts for ARGs, potentially posing a higher pathogenic risk than natural POM. Our research also emphasized the importance of considering both PA and FL bacteria when assessing microplastic impacts, as they exhibited different responses. Overall, our study elucidates the role and underlying mechanism of microplastics as an emerging POM in intensifying pathogenic risks of aquatic ecosystems in comparison with conventional natural POM.
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Affiliation(s)
- Ling-Zi Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology & School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; Bioscience and Biomedical Engineering Thrust, Systems Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong, China; Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiao-Qing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology & School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology & School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zetao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology & School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Li Duan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology & School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology & School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chen Chen
- State Environmental Protection Key Laboratory of Urban Ecological Environment Simulation and Protection, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Guangzhou 510655, China
| | - Shaojun Tang
- Bioscience and Biomedical Engineering Thrust, Systems Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, Guangdong, China; Division of Emerging Interdisciplinary Areas, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology & School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology & School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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38
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Yan W, Bai R, Zhang Q, Jiang Y, Chen G, Zhang Y, Wu Y, Guo X, Xiao Y, Zhao F. Metagenomic insights into ecological risk of antibiotic resistome and mobilome in riverine plastisphere under impact of urbanization. ENVIRONMENT INTERNATIONAL 2024; 190:108946. [PMID: 39151267 DOI: 10.1016/j.envint.2024.108946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/05/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
Microplastics (MPs) are of increasing concern due to their role as reservoirs for antibiotic resistance genes (ARGs) and pathogens. To date, few studies have explored the influence of anthropogenic activities on ARGs and mobile genetic elements (MGEs) within various riverine MPs, in comparison to their natural counterparts. Here an in-situ incubation was conducted along heavily anthropogenically-impacted Houxi River to characterize the geographical pattern of antibiotic resistome, mobilome and pathogens inhabiting MPs- and leaf-biofilms. The metagenomics result showed a clear urbanization-driven profile in the distribution of ARGs, MGEs and pathogens, with their abundances sharply increasing 4.77 to 19.90 times from sparsely to densely populated regions. The significant correlation between human fecal marker crAssphage and ARG (R2 = 0.67, P=0.003) indicated the influence of anthropogenic activity on ARG proliferation in plastisphere and natural leaf surfaces. And mantel tests and random forest analysis revealed the impact of 17 socio-environmental factors, e.g., population density, antibiotic concentrations, and pore volume of materials, on the dissemination of ARGs. Partial least squares-path modeling further unveiled that intensifying human activities not only directly boosted ARGs abundance but also exerted a comparable indirect impact on ARGs propagation. Furthermore, the polyvinylchloride plastisphere created a pathogen-friendly habitat, harboring higher abundances of ARGs and MGEs, while polylactic acid are not likely to serve as vectors for pathogens in river, with a lower resistome risk score than that in leaf-biofilms. This study highlights the diverse ecological risks associated with the dissemination of ARGs and pathogens in varied MPs, offering insights for the policymaking of usage and control of plastics within urbanization.
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Affiliation(s)
- Weifu Yan
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Rui Bai
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Qinghua Zhang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yuhao Jiang
- Academy of Forest Inventory and Planning, National Forestry and Grassland Administration, Beijing 100714, China
| | - Geng Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Yanru Zhang
- Fujian Key Laboratory of Pollution Control & Resource Reuse, College of Environmental and Resource Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Yicheng Wu
- Fujian Engineering and Research Center of Rural Sewage Treatment and Water Safety, Xiamen University of Technology, Xiamen 361024, China
| | - Xuetao Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yong Xiao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China.
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China.
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Liu CSC, Pandey R. Integrative genomics would strengthen AMR understanding through ONE health approach. Heliyon 2024; 10:e34719. [PMID: 39816336 PMCID: PMC11734142 DOI: 10.1016/j.heliyon.2024.e34719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 01/18/2025] Open
Abstract
Emergence of drug-induced antimicrobial resistance (AMR) forms a crippling health and economic crisis worldwide, causing high mortality from otherwise treatable diseases and infections. Next Generation Sequencing (NGS) has significantly augmented detection of culture independent microbes, potential AMR in pathogens and elucidation of mechanisms underlying it. Here, we review recent findings of AMR evolution in pathogens aided by integrated genomic investigation strategies inclusive of bacteria, virus, fungi and AMR alleles. While AMR monitoring is dominated by data from hospital-related infections, we review genomic surveillance of both biotic and abiotic components involved in global AMR emergence and persistence. Identification of pathogen-intrinsic as well as environmental and/or host factors through robust genomics/bioinformatics, along with monitoring of type and frequency of antibiotic usage will greatly facilitate prediction of regional and global patterns of AMR evolution. Genomics-enabled AMR prediction and surveillance will be crucial - in shaping health and economic policies within the One Health framework to combat this global concern.
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Affiliation(s)
- Chinky Shiu Chen Liu
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110007, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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40
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Bai X, Zhong H, Cui X, Wang T, Gu Y, Li M, Miao X, Li J, Lu L, Xu W, Li D, Sun J. Metagenomic profiling uncovers microbiota and antibiotic resistance patterns across human, chicken, pig fecal, and soil environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174734. [PMID: 39002589 DOI: 10.1016/j.scitotenv.2024.174734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
The ongoing and progressive evolution of antibiotic resistance presents escalating challenges for the clinical management and prevention of bacterial infections. Understanding the makeup of resistance genomes and accurately quantifying the current abundance of antibiotic resistance genes (ARGs) are crucial for assessing the threat of antimicrobial resistance (AMR) to public health. This comprehensive study investigated the distribution and diversity of bacterial community composition, ARGs, and virulence factors (VFs) across human, chicken, pig fecal, and soil microbiomes in various provinces of China. As a result, multidrug resistance was identified across all samples. Core ARGs primarily related to multidrug, MLS (Macrolides-Lincosamide-Streptogramins), and tetracycline resistance were characterized. A significant correlation between ARGs and bacterial taxa was observed, especially in soil samples. Probiotic strains such as Lactobacillus harbored ARGs, potentially contributing to the dissemination of antibiotic resistance. We screened subsets of ARGs from samples from different sources as indicators to assess the level of ARGs contamination in samples, with high accuracy. These results underline the complex relationship between microbial communities, resistance mechanisms, and environmental factors, emphasizing the importance of continued research and monitoring to better understand these dynamics.
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Affiliation(s)
- Xue Bai
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hang Zhong
- Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Xiang Cui
- Department of Clinical Animal Medicine, College of Animal Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China
| | - Yiren Gu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaomeng Miao
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Academy of Agricultural Sciences, Guiyang 550005, China
| | - Jing Li
- College of Agriculture, Kunming University, Kunming 650214, China
| | - Lizhi Lu
- National Center of Technology Innovation for Swine, Chongqing 402460, China
| | - Wenwu Xu
- National Center of Technology Innovation for Swine, Chongqing 402460, China.
| | - Diyan Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Jing Sun
- Chongqing Academy of Animal Sciences, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402461, China.
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Zhai J, Wang Y, Tang B, Zheng S, He S, Zhao W, Lin J, Li F, Bao Y, Lancuo Z, Liu C, Wang W. A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures. PeerJ 2024; 12:e17710. [PMID: 39006014 PMCID: PMC11243982 DOI: 10.7717/peerj.17710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.
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Affiliation(s)
- Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Sisi Zheng
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, China
| | - Jun Lin
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Feng Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Yuzi Bao
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, China
| | - Chuanfa Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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Vences-Guzmán MÁ, Jiménez-Rodríguez M, Lozano L, Rojas-Juárez S, Ramírez-Estudillo JA, Hernández-Vázquez ÁY, Pita-Ortiz IY, Ramírez-Ceballos KG, Medina-Medina S, Sohlenkamp C. A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes. Access Microbiol 2024; 6:000639.v3. [PMID: 39045243 PMCID: PMC11261729 DOI: 10.1099/acmi.0.000639.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 05/13/2024] [Indexed: 07/25/2024] Open
Abstract
Infectious endophthalmitis is a severe ophthalmic emergency. This infection can be caused by bacteria and fungi. For efficient treatment, the administration of antimicrobial drugs to which the microbes are susceptible is essential. The aim of this study was to identify micro-organisms in biopsies of Mexican endophthalmitis patients using metagenomic next-generation sequencing and determine which antibiotic resistance genes were present in the biopsy samples. In this prospective case study, 19 endophthalmitis patients were recruited. Samples of vitreous or aqueous humour were extracted for DNA extraction for metagenomic next-generation sequencing. Analysis of the sequencing results revealed the presence of a wide variety of bacteria in the biopsies. Resistome analysis showed that homologues of antibiotic resistance genes were present in several biopsy samples. Genes possibly conferring resistance to ceftazidime and vancomycin were detected in addition to various genes encoding efflux pumps. Our findings contrast with the widespread opinion that only one or a few bacterial strains are present in the infected tissues of endophthalmitis patients. These diverse communities might host many of the resistance genes that were detected, which can further complicate the infections.
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Affiliation(s)
| | | | - Luis Lozano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Sergio Rojas-Juárez
- Departamento de Retina, Fundación Hospital Nuestra Señora de la Luz IAP, Mexico City, Mexico
| | | | | | | | | | - Silvia Medina-Medina
- Departamento de Retina, Fundación Hospital Nuestra Señora de la Luz IAP, Mexico City, Mexico
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Wang S, Nie W, Gu Q, Wang X, Yang D, Li H, Wang P, Liao W, Huang J, Yuan Q, Zhou S, Ahmad I, Kotaro K, Chen G, Zhu B. Spread of antibiotic resistance genes in drinking water reservoirs: Insights from a deep metagenomic study using a curated database. WATER RESEARCH 2024; 256:121572. [PMID: 38621316 DOI: 10.1016/j.watres.2024.121572] [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: 01/05/2024] [Revised: 03/13/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
The exploration of antibiotic resistance genes (ARGs) in drinking water reservoirs is an emerging field. Using a curated database, we enhanced the ARG detection and conducted a comprehensive analysis using 2.2 Tb of deep metagenomic sequencing data to determine the distribution of ARGs across 16 drinking water reservoirs and associated environments. Our findings reveal a greater diversity of ARGs in sediments than in water, underscoring the importance of extensive background surveys. Crucial ARG carriers-specifically Acinetobacter, Pseudomonas, and Mycobacterium were identified in drinking water reservoirs. Extensive analysis of the data uncovered a considerable concern for drinking water safety, particularly in regions reliant on river sources. Mobile genetic elements have been found to contribute markedly to the propagation of ARGs. The results of this research suggest that the establishment of drinking water reservoirs for supplying raw water may be an effective strategy for alleviating the spread of water-mediated ARGs.
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Affiliation(s)
- Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| | - Qing Gu
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Xie Wang
- Southwest China Mountain Agricultural Environment Key Laboratory, Ministry of Agriculture and Rural Areas, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Shizishan Rd, Chengdu, 610066, China
| | - Danping Yang
- Observation and Research Station of Ecological Restoration for Chongqing Typical Mining Areas, Ministry of Natural Resources (Chongqing Institute of Geology and Mineral Resources), Chongqing, 401120. China
| | - Hongyu Li
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peihong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weixue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Huang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Quan Yuan
- School of Energy and Power Engineering, Xihua University, Chengdu, 610039, China
| | - Shengli Zhou
- Zhejiang Province Ecological and Environmental Monitoring Centre, Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Hangzhou, 310012, China
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Kiga Kotaro
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Gongyou Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Wang C, Mao Y, Zhang L, Wei H, Wang Z. Insight into environmental adaptability of antibiotic resistome from surface water to deep sediments in anthropogenic lakes by metagenomics. WATER RESEARCH 2024; 256:121583. [PMID: 38614031 DOI: 10.1016/j.watres.2024.121583] [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: 12/21/2023] [Revised: 03/06/2024] [Accepted: 04/06/2024] [Indexed: 04/15/2024]
Abstract
The escalating antibiotic resistance threatens the long-term global health. Lake sediment is a vital hotpot in transmitting antibiotic resistance genes (ARGs); however, their vertical distribution pattern and driving mechanisms in sediment cores remain unclear. This study first utilized metagenomics to reveal how resistome is distributed from surface water to 45 cm sediments in four representative lakes, central China. Significant vertical variations in ARG profiles were observed (R2 = 0.421, p < 0.001), with significant reductions in numbers, abundance, and Shannon index from the surface water to deep sediment (all p-values < 0.05). ARGs also has interconnections within the vertical profile of the lakes: twelve ARGs persistently exist all sites and depths, and shared ARGs (e.g., vanS and mexF) were assembled by diverse hosts at varying depths. The 0-18 cm sediment had the highest mobility and health risk of ARGs, followed by the 18-45 cm sediment and water. The drivers of ARGs transformed along the profile of lakes: microbial communities and mobile genetic elements (MGEs) dominated in water, whereas environmental variables gradually become the primary through regulating microbial communities and MGEs with increasing sediment depth. Interestingly, the stochastic process governed ARG assembly, while the stochasticity diminished under the mediation of Chloroflexi, Candidatus Bathyarcaeota and oxidation-reduction potential with increasing depth. Overall, we formulated a conceptual framework to elucidate the vertical environmental adaptability of resistome in anthropogenic lakes. This study shed on the resistance risks and their environmental adaptability from sediment cores, which could reinforce the governance of public health issues.
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Affiliation(s)
- Cong Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujie Mao
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huimin Wei
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430077, China.
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45
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Alessandri G, Rizzo SM, Mancabelli L, Fontana F, Longhi G, Turroni F, van Sinderen D, Ventura M. Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities. Microb Biotechnol 2024; 17:e14509. [PMID: 38878269 PMCID: PMC11179620 DOI: 10.1111/1751-7915.14509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/18/2024] Open
Abstract
The availability of microbial biobanks for the storage of individual gut microbiota members or their derived and artificially assembled consortia has become fundamental for in vitro investigation of the molecular mechanisms behind microbe-microbe and/or microbe-host interactions. However, to preserve bacterial viability, adequate storage and processing technologies are required. In this study, the effects on cell viability of seven different combinations of cryoprotective agents were evaluated by flow cytometry for 53 bacterial species representing key members of the human gut microbiota after one and 3 months of cryopreservation at -80°C. The obtained results highlighted that no universal cryoprotectant was identified capable of guaranteeing effective recovery of intact cells after cryopreservation for all tested bacteria. However, the presence of inulin or skimmed milk provided high levels of viability protection during cryoexposure. These results were further corroborated by cryopreserving 10 artificial gut microbiota produced through in vitro continuous fermentation system technology. Indeed, in this case, the inclusion of inulin or skimmed milk resulted in a high recovery of viable cells, while also allowing consistent and reliable preservation of the artificial gut microbiota biodiversity. Overall, these results suggest that, although the efficacy of various cryoprotective agents is species-specific, some cryoprotectants based on glycerol and the addition of inulin or skimmed milk are preferable to retain viability and biodiversity for both single bacterial species and artificial gut microbiota.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Leonardo Mancabelli
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
- Microbiome Research HubUniversity of ParmaParmaItaly
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
- Microbiome Research HubUniversity of ParmaParmaItaly
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of IrelandCorkIreland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental SustainabilityUniversity of ParmaParmaItaly
- Microbiome Research HubUniversity of ParmaParmaItaly
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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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Pei Y, Shum MHH, Liao Y, Leung VW, Gong YN, Smith DK, Yin X, Guan Y, Luo R, Zhang T, Lam TTY. ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences. MICROBIOME 2024; 12:84. [PMID: 38725076 PMCID: PMC11080312 DOI: 10.1186/s40168-024-01805-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identification of ARGs, particularly from high-throughput sequencing data of the specimens, is the state-of-the-art method for comprehensively monitoring their spread and evolution. Current computational methods to identify ARGs mainly rely on alignment-based sequence similarities with known ARGs. Such approaches are limited by choice of reference databases and may potentially miss novel ARGs. The similarity thresholds are usually simple and could not accommodate variations across different gene families and regions. It is also difficult to scale up when sequence data are increasing. RESULTS In this study, we developed ARGNet, a deep neural network that incorporates an unsupervised learning autoencoder model to identify ARGs and a multiclass classification convolutional neural network to classify ARGs that do not depend on sequence alignment. This approach enables a more efficient discovery of both known and novel ARGs. ARGNet accepts both amino acid and nucleotide sequences of variable lengths, from partial (30-50 aa; 100-150 nt) sequences to full-length protein or genes, allowing its application in both target sequencing and metagenomic sequencing. Our performance evaluation showed that ARGNet outperformed other deep learning models including DeepARG and HMD-ARG in most of the application scenarios especially quasi-negative test and the analysis of prediction consistency with phylogenetic tree. ARGNet has a reduced inference runtime by up to 57% relative to DeepARG. CONCLUSIONS ARGNet is flexible, efficient, and accurate at predicting a broad range of ARGs from the sequencing data. ARGNet is freely available at https://github.com/id-bioinfo/ARGNet , with an online service provided at https://ARGNet.hku.hk . Video Abstract.
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Grants
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- T21-705/20-N Hong Kong Research Grants Council's Theme-based Research Scheme
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727 Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province
- 31922087 National Natural Science Foundation of China's Excellent Young Scientists Fund (Hong Kong and Macau)
- Hong Kong Research Grants Council’s Theme-based Research Scheme
- Innovation and Technology Commission’s InnoHK funding (D24H), and the Government of Guangdong Province
- National Natural Science Foundation of China’s Excellent Young Scientists Fund (Hong Kong and Macau)
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Affiliation(s)
- Yao Pei
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Yunshi Liao
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
- Centre for Immunology & Infection (C2i), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
| | - Vivian W Leung
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Yu-Nong Gong
- Division of Biotechnology, Research Center of Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
| | - Xiaole Yin
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tong Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, China.
- Laboratory of Data Discovery for Health (D²4H), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
- Advanced Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, 518045, China.
- Centre for Immunology & Infection (C2i), Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
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48
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Xu Y, Tao M, Xu W, Xu L, Yue L, Cao X, Chen F, Wang Z. Nano-CeO 2 activates physical and chemical defenses of garlic (Allium sativum L.) for reducing antibiotic resistance genes in plant endosphere. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 276:116289. [PMID: 38570269 DOI: 10.1016/j.ecoenv.2024.116289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/05/2024]
Abstract
The transmission of manure- and wastewater-borne antibiotic-resistant bacteria (ARB) to plants contributes to the proliferation of antimicrobial resistance in agriculture, necessitating effective strategies for preventing the spread of antibiotic resistance genes (ARGs) from ARB in the environment to humans. Nanomaterials are potential candidates for efficiently controlling the dissemination of ARGs. The present study investigated the abundance of ARGs in hydroponically grown garlic (Allium sativum L.) following nano-CeO2 (nCeO2) application. Specifically, root exposure to nCeO2 (1, 2.5, 5, 10 mg L-1, 18 days) reduced ARG abundance in the endosphere of bulbs and leaves. The accumulation of ARGs (cat, tet, and aph(3')-Ia) in garlic bulbs decreased by 24.2-32.5 % after nCeO2 exposure at 10 mg L-1. Notably, the lignification extent of garlic stem-disc was enhanced by 10 mg L-1 nCeO2, thereby accelerating the formation of an apoplastic barrier to impede the upward transfer of ARG-harboring bacteria to garlic bulbs. Besides, nCeO2 upregulated the gene expression related to alliin biosynthesis and increased allicin content by 15.9-16.2 %, promoting a potent antimicrobial defense for reducing ARG-harboring bacteria. The potential exposure risks associated with ARGs and Ce were evaluated according to the estimated daily intake (EDI). The EDI of ARGs exhibited a decrease exceeding 95 %, while the EDI of Ce remained below the estimated oral reference dose. Consequently, through stimulating physical and chemical defenses, nCeO2 contributed to a reduced EDI of ARGs and Ce, highlighting its potential for controlling ARGs in plant endosphere within the framework of nano-enabled agrotechnology.
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Affiliation(s)
- Yinuo Xu
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Mengna Tao
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Wei Xu
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; School of Environment & Energy, South China University of Technology, Guangzhou 510006, China
| | - Lanqing Xu
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China.
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
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49
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Yu Z, Qiu D, Zhou T, Zeng L, Yan C. Biofilm enhances the interactive effects of microplastics and oxytetracycline on zebrafish intestine. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 270:106905. [PMID: 38569307 DOI: 10.1016/j.aquatox.2024.106905] [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: 12/06/2023] [Revised: 03/18/2024] [Accepted: 03/24/2024] [Indexed: 04/05/2024]
Abstract
The enhanced adsorption of pollutants on biofilm-developed microplastics has been proved in many studies, but the ecotoxicological effects of biofilm-developed microplastics on organisms are still unclear. In this study, adult zebrafish were exposed to original microplastics, biofilm-developed microplastics, original microplastics absorbed with oxytetracycline (OTC), and biofilm-developed microplastics absorbed with OTC for 30 days. The intestinal histological damage, intestinal biomarker response, gut microbiome and antibiotic resistance genes (ARGs) profile of zebrafish were measured to explore the roles of biofilm in the effects of microplastics. The results showed that biofilm-developed microplastics significantly increased the number of goblet cells in intestinal epithelium compared with the control group. The biofilm-developed microplastics also induced the oxidative response in the zebrafish intestines, and biofilm changed the response mode in the combined treatment with OTC. Additionally, the biofilm-developed microplastics caused intestinal microbiome dysbiosis, and induced the abundance of some pathogenic genera increasing by several times compared with the control group and the original microplastics treatments, regardless of OTC adsorption. Furthermore, the abundance of ARGs in biofilm-developed microplastics increased significantly compared with the control and the original microplastic treatments. This study emphasized the significant influence and unique role of biofilm in microplastic studies.
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Affiliation(s)
- Ziyue Yu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Donghua Qiu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liqing Zeng
- Department of Public Health and Medical Technology, Xiamen Medical College, Xiamen 361021, China
| | - Changzhou Yan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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50
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Makowska-Zawierucha N, Trzebny A, Zawierucha K, Manthapuri V, Bradley JA, Pruden A. Arctic plasmidome analysis reveals distinct relationships among associated antimicrobial resistance genes and virulence genes along anthropogenic gradients. GLOBAL CHANGE BIOLOGY 2024; 30:e17293. [PMID: 38687495 DOI: 10.1111/gcb.17293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/30/2024] [Accepted: 03/30/2024] [Indexed: 05/02/2024]
Abstract
Polar regions are relatively isolated from human activity and thus could offer insight into anthropogenic and ecological drivers of the spread of antibiotic resistance. Plasmids are of particular interest in this context given the central role that they are thought to play in the dissemination of antibiotic resistance genes (ARGs). However, plasmidomes are challenging to profile in environmental samples. The objective of this study was to compare various aspects of the plasmidome associated with glacial ice and adjacent aquatic environments across the high Arctic archipelago of Svalbard, representing a gradient of anthropogenic inputs and specific treated and untreated wastewater outflows to the sea. We accessed plasmidomes by applying enrichment cultures, plasmid isolation and shotgun Illumina sequencing of environmental samples. We examined the abundance and diversity of ARGs and other stress-response genes that might be co/cross-selected or co-transported in these environments, including biocide resistance genes (BRGs), metal resistance genes (MRGs), virulence genes (VGs) and integrons. We found striking differences between glacial ice and aquatic environments in terms of the ARGs carried by plasmids. We found a strong correlation between MRGs and ARGs in plasmids in the wastewaters and fjords. Alternatively, in glacial ice, VGs and BRGs genes were dominant, suggesting that glacial ice may be a repository of pathogenic strains. Moreover, ARGs were not found within the cassettes of integrons carried by the plasmids, which is suggestive of unique adaptive features of the microbial communities to their extreme environment. This study provides insight into the role of plasmids in facilitating bacterial adaptation to Arctic ecosystems as well as in shaping corresponding resistomes. Increasing human activity, warming of Arctic regions and associated increases in the meltwater run-off from glaciers could contribute to the release and spread of plasmid-related genes from Svalbard to the broader pool of ARGs in the Arctic Ocean.
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Affiliation(s)
- Nicoletta Makowska-Zawierucha
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Artur Trzebny
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Vineeth Manthapuri
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
| | - James A Bradley
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO, Marseille, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA
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