1
|
Shafiq M, Guo X, Wang M, Bilal H, Xin L, Yuan Y, Yao F, Sheikh TMM, Khan MN, Jiao X. Integrative metagenomic dissection of last-resort antibiotic resistance genes and mobile genetic elements in hospital wastewaters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174930. [PMID: 39067608 DOI: 10.1016/j.scitotenv.2024.174930] [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: 04/21/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024]
Abstract
Hospital wastewater is a critical source of antimicrobial resistance (AMR), which facilitates the proliferation and spread of clinically significant antimicrobial resistance genes (ARGs) and pathogenic bacteria. This study utilized metagenomic approaches, including advanced binning techniques, such as MetaBAT2, MaxBin2, and CONCOCT, which offer significant improvements in accuracy and completeness over traditional binning methods. These methods were used to comprehensively assess the dynamics and composition of resistomes and mobilomes in untreated wastewater samples taken from two general hospitals and one cancer hospital. This study revealed a diverse bacterial landscape, largely consisting of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with notable variations in microbial composition among hospitals. Analysis of the top 15 genera showed unique microbial pattern distribution in each hospital: Aeromonas was predominant in 1stHWTS (49.39 %), Acidovorax in the CAHWTS at 16.85 %, and Escherichia and Bacteroides in the 2ndHWTS at 11.44 % and 11.33 %, respectively. A total of 114 pathogenic bacteria were identified, with drug-resistant Aeromonas caviae and Escherichia coli being the most prevalent. The study identified 34 types and 1660 subtypes of ARGs, including important last-resort antibiotic resistance genes (LARGs), such as blaNDM, mcr, and tet(X). Using metagenomic binning, this study uncovered distinct patterns of host-resistance associations, particularly with Proteobacteria and Firmicutes. Network analysis highlighted the complex interactions among ARGs, mobile genetic elements (MGEs), and bacterial species, all contributing to the dissemination of AMR. These findings emphasize the intricate nature of AMR in hospital wastewater and the influence of hospital-specific factors on microbial resistance patterns. This study provides support for implementing integrated management strategies, including robust surveillance, advanced wastewater treatment, and strict antibiotic stewardship, to control the dissemination of AMR. Understanding the interplay among bacterial communities, ARGs, and MGEs is important for developing effective public health measures against AMR.
Collapse
Affiliation(s)
- Muhammad Shafiq
- Research Institute of Clinical Pharmacy, Department of Pharmacology, Shantou University Medical College, Shantou 515041, China; Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Xiaoling Guo
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Meimei Wang
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Hazrat Bilal
- Jiangxi Key Laboratory of Oncology, Jiangxi Cancer Hospital, The Second Affiliated Hospital of Nanchang Medical College, Jiangxi Cancer Institute, Nanchang, Jiangxi 330029, PR China
| | - Li Xin
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Fen Yao
- Research Institute of Clinical Pharmacy, Department of Pharmacology, Shantou University Medical College, Shantou 515041, China
| | | | - Muhammad Nadeem Khan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China.
| |
Collapse
|
2
|
Romero-Rodríguez A, Ruíz-Villafán B, Sánchez S, Paredes-Sabja D. Is there a role for intestinal sporobiota in the antimicrobial resistance crisis? Microbiol Res 2024; 288:127870. [PMID: 39173554 DOI: 10.1016/j.micres.2024.127870] [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: 06/04/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/24/2024]
Abstract
Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.
Collapse
Affiliation(s)
- A Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México 04510, Mexico.
| | - B Ruíz-Villafán
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - S Sánchez
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - D Paredes-Sabja
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
3
|
Zhang D, Calmanovici B, Marican H, Reisser J, Summers S. The assembly and ecological roles of biofilms attached to plastic debris of Ashmore reef. MARINE POLLUTION BULLETIN 2024; 205:116651. [PMID: 38917500 DOI: 10.1016/j.marpolbul.2024.116651] [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: 03/25/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Plastic pollution in the ocean is a global environmental hazard aggravated by poor management of plastic waste and growth of annual plastic consumption. Microbial communities colonizing the plastic's surface, the plastisphere, has gained global interest resulting in numerous efforts to characterize the plastisphere. However, there are insufficient studies deciphering the underlying metabolic processes governing the function of the plastisphere and the plastic they reside upon. Here, we collected plastic and seawater samples from Ashmore Reef in Australia to examine the planktonic microbes and plastic associated biofilm (PAB) to investigate the ecological impact, pathogenic potential, and plastic degradation capabilities of PAB in Ashmore Reef, as well as the role and impact of bacteriophages on PAB. Using high-throughput metagenomic sequencing, we demonstrated distinct microbial communities between seawater and PAB. Similar numbers of pathogenic bacteria were found in both sample types, yet plastic and seawater select for different pathogen populations. Virulence Factor analysis further illustrated stronger pathogenic potential in PAB, highlighting the pathogenicity of environmental PAB. Furthermore, functional analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed xenobiotic degradation and fatty acid degradation to be enriched in PABs. In addition, construction of metagenome-assembled genomes (MAG) and functional analysis further demonstrated the presence of a complete Polyethylene (PE) degradation pathway in multiple Proteobacteria MAGs, especially in Rhodobacteriaceae sp. Additionally, we identified viral population presence in PAB, revealing the key role of bacteriophages in shaping these communities within the PAB. Our result provides a comprehensive overview of the various ecological processes shaping microbial community on marine plastic debris.
Collapse
Affiliation(s)
- Dong Zhang
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Tropical Marine Science Institute, St. John's Island National Marine Laboratory, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Bruna Calmanovici
- UWA Oceans Institute, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Hana Marican
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 117456, Singapore
| | - Julia Reisser
- UWA Oceans Institute, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Stephen Summers
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Tropical Marine Science Institute, St. John's Island National Marine Laboratory, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore.
| |
Collapse
|
4
|
Tian L, Fang G, Li G, Li L, Zhang T, Mao Y. Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human. MICROBIOME 2024; 12:107. [PMID: 38877573 PMCID: PMC11179227 DOI: 10.1186/s40168-024-01824-x] [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: 10/06/2023] [Accepted: 04/26/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health. RESULTS The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer. CONCLUSIONS The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.
Collapse
Affiliation(s)
- Li Tian
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China
| | - Guimei Fang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China
| | - Guijie Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China
| | - Liguan Li
- The University of Hong Kong Shenzhen Institute of Research and Innovation, HKU SIRI, Shenzhen, Guangdong, 518057, China
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Zhang
- The University of Hong Kong Shenzhen Institute of Research and Innovation, HKU SIRI, Shenzhen, Guangdong, 518057, China
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China.
| |
Collapse
|
5
|
Robins K, O'Donnell G, Neumann A, Schmidt W, Hart A, Graham DW. Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172348. [PMID: 38614353 DOI: 10.1016/j.scitotenv.2024.172348] [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: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.
Collapse
Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Anke Neumann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wiebke Schmidt
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Alwyn Hart
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| |
Collapse
|
6
|
Xu X, Jiang H, Lu Q, Wang S. Pre-exposure of Triclosan compromise tetracycline-derived antibiotic resistance in methanogenic digestion microbiome. BIORESOURCE TECHNOLOGY 2024; 401:130758. [PMID: 38692374 DOI: 10.1016/j.biortech.2024.130758] [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: 02/17/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
Triclosan (TCS) and tetracycline (TC) are commonly detected antibacterial agents in sewage and environment matrices. Nonetheless, the impact of sequential exposure to TCS and TC on the methanogenic digestion microbiome remains unknown. In this study, TCS was shown to reduce COD removal efficiency to 69.8%, but alleviated the inhibitive effect of consequent TC-amendment on the digestion microbiome. Interestingly, TCS pre-exposure resulted in abundance increase of acetotrophic Methanosaeta to 2.68%, being 2.91 folds higher than that without TCS amendment. Microbial network analyses showed that TCS pre-exposure caused microorganisms to establish a co-ecological relationship against TC disturbance. Further analyses of total antibiotic resistance genes (ARGs) showed the TCS-derived compromise of TC-induced ARGs enrichment in digestion microbiomes, e.g., 238.2% and 152.1% ARGs increase upon TC addition in digestion microbiomes without and with TCS pre-exposure, respectively. This study provides new insights into the impact of antibacterial agents on the methanogenic digestion microbiome.
Collapse
Affiliation(s)
- Xiangping Xu
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Haihong Jiang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
| |
Collapse
|
7
|
Bombaywala S, Bajaj A, Dafale NA. Deterministic effect of oxygen level variation on shaping antibiotic resistome. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133047. [PMID: 38000281 DOI: 10.1016/j.jhazmat.2023.133047] [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: 08/28/2023] [Revised: 10/23/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023]
Abstract
An increase in acquisition of antibiotic resistance genes (ARGs) by pathogens under antibiotic selective pressure poses public health threats. Sub-inhibitory antibiotics induce bacteria to generate reactive oxygen species (ROS) dependent on dissolved oxygen (DO) levels, while molecular connection between ROS-mediated ARG emergence through DNA damage and metabolic changes remains elusive. Thus, the study investigates antibiotic resistome dynamics, microbiome shift, and pathogen distribution in hyperoxic (5-7 mg L-1), normoxic (2-4 mg L-1), and hypoxic (0.5-1 mg L-1) conditions using lab-scale bioreactor. Composite inoculums in the reactor were designed to represent comprehensive microbial community and AR profile from selected activated sludge. RT-qPCR and metagenomic analysis showed an increase in ARG count (100.98 ppm) with enrichment of multidrug efflux pumps (acrAB, mexAB) in hyperoxic condition. Conversely, total ARGs decreased (0.11 ppm) under hypoxic condition marked by a major decline in int1 abundance. Prevalence of global priority pathogens increased in hyperoxic (22.5%), compared to hypoxic (0.9%) wherein major decrease were observed in Pseudomonas, Shigella, and Borrelia. The study observed an increase in superoxide dismutase (sodA, sodB), DNA repair genes (nfo, polA, recA, recB), and ROS (10.4 µmol L-1) in adapted biomass with spiked antibiotics. This suggests oxidative damage that facilitates stress-induced mutagenesis providing evidence for observed hyperoxic enrichment of ARGs. Moreover, predominance of catalase (katE, katG) likely limit oxidative damage that deplete ARG breeding in hypoxic condition. The study proposes a link between oxygen levels and AR development that offers insights into mitigation and intervention of AR by controlling oxygen-related stress and strategic selection of bacterial communities.
Collapse
Affiliation(s)
- Sakina Bombaywala
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abhay Bajaj
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-Indian Institute of Toxicology Research, 31 Mahatma Gandhi Marg, Lucknow 226001, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
8
|
Jiang C, Zhao Z, Zhu D, Pan X, Yang Y. Rare resistome rather than core resistome exhibited higher diversity and risk along the Yangtze River. WATER RESEARCH 2024; 249:120911. [PMID: 38039820 DOI: 10.1016/j.watres.2023.120911] [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: 08/03/2023] [Revised: 11/09/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
As important freshwater ecosystems, the occurrence and distribution of antibiotic resistance genes (ARGs) in rivers are relevant to public health. However, studies investigating ARGs of different environmental media in river ecosystems are limited. In this study, we analyzed the ARGs of microbes in free-living setting, particle-associated setting, sediment and bank soil of the Yangtze River using metagenomics. Twenty-six ARGs were found in all samples regardless of media (core resistome) with a diversity of 8.6 %-34.7 %, accounting for 22.7 %-89.2 % of the relative abundance of the overall ARGs. The core resistome of the Yangtze River was dominated by multidrug resistance genes consisting mainly of efflux pumps and bacitracin resistance genes. The rare resistome was dominated by multidrug, sulfonamide, and aminoglycoside resistance genes. The core resistome was more prevalent in chromosomes, implying that these ARGs with low diversity and high relative abundance may be intrinsic to microbes in the Yangtze River. The rare resistome was more prevalent in plasmids, suggesting these ARGs with high diversity and low relative abundance were acquired under environmental stresses and had transfer potential. Additionally, we found that core and rare resistome were mainly carried by specific bacteria. Noteworthily, twenty-two ARGs of high clinical concern were identified in rare resistome, especially aac(6')-I, sul1, and tetM, which were plasmid-borne and hosted by clinically relevant pathogens. Both core and rare resistome hosts showed the highest niche breadths in particle-associated setting compared to other media, and particle-associated setting could provide more stable and ideal conditions for resistome hosts to survive. This study elucidated the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.
Collapse
Affiliation(s)
- Chunxia Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China
| | - Zelong Zhao
- Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Key Lab of Germplasm Improvement and Fine Seed Breeding of Marine Aquatic Animals, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiong Pan
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430014, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China.
| |
Collapse
|
9
|
Gholipour S, Shamsizadeh Z, Halabowski D, Gwenzi W, Nikaeen M. Combating antibiotic resistance using wastewater surveillance: Significance, applications, challenges, and future directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168056. [PMID: 37914125 DOI: 10.1016/j.scitotenv.2023.168056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023]
Abstract
The global increase of antibiotic resistance (AR) and resistant infections call for effective surveillance methods for understanding and mitigating (re)-emerging public health risks. Wastewater surveillance (WS) of antibiotic resistance is an emerging, but currently under-utilized decision-support tool in public health systems. Recent years have witnessed an increase in evidence linking antibiotic resistance in wastewaters to that of the community. To date, very few comprehensive reviews exist on the application of WS to understand AR and resistant infections in population. Current and emerging AR detection methods, and their merits and limitations are discussed. Wastewater surveillance has several merits relative to individual testing, including; (1) low per capita testing cost, (2) high spatial coverage, (3) low requirement for diagnostic equipment, and (4) detection of health threats ahead of real outbreaks. The applications of WS as an early warning system and decision support tool to understand and mitigate AR are discussed. Wastewater surveillance could be a tool of choice in low-income settings lacking resources and diagnostic facilities for individual testing. To demonstrate the utility of WS, empirical evidence from field case studies is presented. However, constraints still exist, including; (1) lack of standardized protocols, (2) the clinical utility and sensitivity of WS-based data, (3) uncertainties in relating WS data to pathogenic and virulent bacteria, and (4) whether or not AR in stools and ultimately wastewater represent the complete human resistome. Finally, further prospects are presented, include knowledge gaps on; (1) development of low-cost biosensors for AR, (2) development of WS protocols (sampling, processing, interpretation), (3) further pilot scale studies to understand the opportunities and limits of WS, and (4) development of computer-based analytical tools to facilitate rapid data collection, visualization and interpretation. Therefore, the present paper discusses the principles, opportunities, and constraints of wastewater surveillance applications to understand AR and safeguard public health.
Collapse
Affiliation(s)
- Sahar Gholipour
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zahra Shamsizadeh
- Department of Environmental Health Engineering, School of Health, Larestan University of Medical Sciences, Larestan, Iran
| | - Dariusz Halabowski
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Ecology and Vertebrate Zoology, Lodz, Poland
| | - Willis Gwenzi
- Universität Kassel, Fachbereich Ökologische Agrarwissenschaften Fachgebiet Grünlandwissenschaft und Nachwachsende Rohstoffe, Steinstr. 19, 37249 Witzenhausen, Germany; Leibniz-Institut für Agrartechnik und Bioökonomie e.V. Max-Eyth-Allee 100, D-14469 Potsdam, Germany.
| | - Mahnaz Nikaeen
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran; Environment Research Center, Research Institute for Primordial Prevention of Non-Communicable Diseases, Isfahan University of Medical Sciences, Isfahan, Iran.
| |
Collapse
|
10
|
Wang M, Masoudi A, Wang C, Wu C, Zhang Z, Zhao X, Liu Y, Yu Z, Liu J. Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management. ENVIRONMENT INTERNATIONAL 2024; 183:108357. [PMID: 38056093 DOI: 10.1016/j.envint.2023.108357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/08/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023]
Abstract
There has been increasing interest in the role of human activities in disseminating antibiotic-resistance genes (ARGs) in aquatic ecosystems. However, the influence of pollutant accumulation on anthropogenic pollutant-ARG synergistic actions is limited. This study explored the association of net cages with the propagation of anthropogenic pollutants and their consequences for influencing the enrichment of ARGs using high-throughput metagenomic sequencing. We showed that net cages could substantially impact the ecology of freshwater systems by enhancing i) ARG diversity and the tendency for ARG-horizontal gene transfer and ii) the overlap of mobile genetic elements (MGEs) with biocide-metal resistance genes (BMRGs) and ARGs. These findings suggested that the cotransfer of these three genetic determinants would be favored in net cage plots and that nonantibiotic factors such as metal(loid)s, particularly iron (Fe), displayed robust selective pressures on ARGs exerted by the net cage. The resistome risk scores of net cage sediments and biofilms were higher than those from off-net cage plots, indicating that the net cage-origin antibiotic resistome should be of great concern. The combination of deterministic and stochastic processes acting on bacterial communities could explain the higher ARG variations in cage plots (8.2%) than in off-cage plots (3.4%). Moreover, MGEs and pollutants together explained 43.3% of the total variation in ARG communities, which was higher than that of off-cage plots (8.8%), considering pollutants, environmental variables, MGEs, and assembly processes. These findings will inform the development of policies and guidelines to more effectively limit the spread of antimicrobial resistance and achieve the goal of sustainability in freshwater systems in urban areas.
Collapse
Affiliation(s)
- Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Changhao Wu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Ze Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Xin Zhao
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Yuanjie Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry, and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| |
Collapse
|
11
|
Zheng Q, Li L, Yin X, Che Y, Zhang T. Is ICE hot? A genomic comparative study reveals integrative and conjugative elements as "hot" vectors for the dissemination of antibiotic resistance genes. mSystems 2023; 8:e0017823. [PMID: 38032189 PMCID: PMC10734551 DOI: 10.1128/msystems.00178-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/14/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Different from other extensively studied mobile genetic elements (MGEs) whose discoveries were initiated decades ago (1950s-1980s), integrative and conjugative elements (ICEs), a diverse array of more recently identified elements that were formally termed in 2002, have aroused increasing concern for their crucial contribution to the dissemination of antibiotic resistance genes (ARGs). However, the comprehensive understanding on ICEs' ARG profile across the bacterial tree of life is still blurred. Through a genomic study by comparison with two key MGEs, we, for the first time, systematically investigated the ARG profile as well as the host range of ICEs and also explored the MGE-specific potential to facilitate ARG propagation across phylogenetic barriers. These findings could serve as a theoretical foundation for risk assessment of ARGs mediated by distinct MGEs and further to optimize therapeutic strategies aimed at restraining antibiotic resistance crises.
Collapse
Affiliation(s)
- Qi Zheng
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| | - Liguan Li
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| | - Xiaole Yin
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| | - You Che
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| | - Tong Zhang
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research,The University of Hong Kong, Hong Kong, China
| |
Collapse
|
12
|
Bombaywala S, Dafale NA. Mapping the spread and mobility of antibiotic resistance in wastewater due to COVID-19 surge. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:121734-121747. [PMID: 37955733 DOI: 10.1007/s11356-023-30932-8] [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: 06/28/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
Large amounts of antibiotics have been discharged into wastewater during the COVID-19 pandemic due to overuse and misuse of antibiotics to treat patients. Wastewater-based surveillance can be used as an early warning for antibiotic resistance (AR) emergence. The present study analyzed municipal wastewater corresponding to the major pandemic waves (WW1, WW2, and WW3) in India along with hospital wastewater (Ho) taken as a benchmark for AR. Commonly prescribed antibiotics during a pandemic, azithromycin and cefixime residues, were found in the range of 2.1-2.6 μg/L in Ho and WW2. Total residual antibiotic concentration was less in WW2; however, the total antibiotic resistance gene (ARG) count was 1065.6 ppm compared to 85.2 ppm in Ho. Metagenome and RT-qPCR analysis indicated a positive correlation between antibiotics and non-corresponding ARGs (blaOXA, aadA, cat, aph3, and ere), where 7.2-7.5% was carried by plasmid in the bacterial community of WW1 and WW2. Moreover, as the abundance of the dfrA and int1 genes varied most among municipal wastewater, they can be suggested as AR markers for the pandemic. The common pathogens Streptococcus, Escherichia, Shigella, and Aeromonas were putative ARG hosts in metagenome-assembled genomes. The ARG profile and antibiotic levels varied between municipal wastewaters but were fairly similar for WW2 and Ho, suggesting the impact of the pandemic in shaping the resistome pattern. The study provides insights into the resistome dynamic, AR markers, and host-ARG association in wastewater during the COVID-19 surge. Continued surveillance and identification of intervention points for AR beyond the pandemic are essential to curbing the environmental spread of ARGs in the near future.
Collapse
Affiliation(s)
- Sakina Bombaywala
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 4400 20, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
13
|
Xu L, Kasprzyk-Hordern B. Assessment of the stability of antimicrobials and resistance genes during short- and long-term storage condition: accounting for uncertainties in bioanalytical workflows. Anal Bioanal Chem 2023; 415:6027-6038. [PMID: 37526655 PMCID: PMC10556160 DOI: 10.1007/s00216-023-04874-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/30/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Unravelling complexities in antimicrobial agent-microbe interactions in the context of antimicrobial resistance (AMR) requires robust analytical workflows accounting for all uncertainties. Temporal storage of wastewater samples under refrigerated or frozen conditions prior to chemical and biological analysis is widely used to facilitate laboratory routine but may affect stability of analytes over time. Yet, little knowledge exists regarding stability of biological and chemical determinants in environmental samples, which hampers validity of research outputs. This study examines, for the first time, the stability of 32 antimicrobials (AAs) including commonly used classes of antibiotics and their representative metabolites and variation of 5 antibiotic resistance genes (ARGs) (ermB, sul1, tetW, blaCTX-M, qnrS), as well as intI1 and 16S rRNA genes in a reference wastewater sample stored under freezing condition for up to 1 year. Ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) and quantitative PCR (qPCR) techniques were adopted to measure concentration of AAs and ARGs, respectively. Results suggested that parent compounds are less affected by freezing storage compared to the metabolites. β-Lactams, clindamycin, and N-desmethyl clindamycin are the most-affected compounds which were poorly recovered (34-67%) from the starting concentration. By contrast, sulfonamides, macrolides, quinolones, and azoles are generally stable under freezing condition. No consistent differences were observed in gene copies between fresh and frozen samples, and ermB and tetW showed the highest variabilities at 30% under freezing condition. Overall, this study adds to the current knowledge on environmental AMR monitoring and emphasises the need for standardised protocols for AMR monitoring in the wastewater samples.
Collapse
Affiliation(s)
- Like Xu
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Barbara Kasprzyk-Hordern
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Institute for Sustainability, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Water and Innovation Research Centre, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| |
Collapse
|
14
|
Dwiyanto J, Huët MAL, Hussain MH, Su TT, Tan JBL, Toh KY, Lee JWJ, Rahman S, Chong CW. Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia. NPJ Biofilms Microbiomes 2023; 9:55. [PMID: 37573460 PMCID: PMC10423249 DOI: 10.1038/s41522-023-00425-0] [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: 12/27/2022] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
The prevalence of antibiotic-resistant bacteria in Southeast Asia is a significant concern, yet there is limited research on the gut resistome and its correlation with lifestyle and environmental factors in the region. This study aimed to profile the gut resistome of 200 individuals in Malaysia using shotgun metagenomic sequencing and investigate its association with questionnaire data comprising demographic and lifestyle variables. A total of 1038 antibiotic resistance genes from 26 classes were detected with a mean carriage rate of 1.74 ± 1.18 gene copies per cell per person. Correlation analysis identified 14 environmental factors, including hygiene habits, health parameters, and intestinal colonization, that were significantly associated with the resistome (adjusted multivariate PERMANOVA, p < 0.05). Notably, individuals with positive yeast cultures exhibited a reduced copy number of 15 antibiotic resistance genes. Network analysis highlighted Escherichia coli as a major resistome network hub, with a positive correlation to 36 antibiotic-resistance genes. Our findings suggest that E. coli may play a pivotal role in shaping the resistome dynamics in Segamat, Malaysia, and its abundance is strongly associated with the community's health and lifestyle habits. Furthermore, the presence of yeast appears to be associated with the suppression of antibiotic-resistance genes.
Collapse
Affiliation(s)
- J Dwiyanto
- AMILI, Singapore, 118261, Singapore.
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - M A L Huët
- Faculty of Science, University of Mauritius, Reduit, 80837, Mauritius
| | - M H Hussain
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - T T Su
- South East Asia Community Observatory, Segamat, 85000, Malaysia
| | - J B L Tan
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - K Y Toh
- AMILI, Singapore, 118261, Singapore
| | - J W J Lee
- AMILI, Singapore, 118261, Singapore
- Department of Medicine, National University Hospital, Singapore, 119228, Singapore
| | - S Rahman
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
- Tropical Medicine and Biology Platform, Monash University Malaysia, Bandar Sunway, 47500, Malaysia
| | - C W Chong
- AMILI, Singapore, 118261, Singapore.
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Malaysia.
| |
Collapse
|
15
|
Zeng J, Pan Y, Hu R, Liu F, Gu H, Ding J, Liu S, Liu S, Yang X, Peng Y, Tian Y, He Q, Wu Y, Yan Q, Shu L, He Z, Wang C. The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131974. [PMID: 37406521 DOI: 10.1016/j.jhazmat.2023.131974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.
Collapse
Affiliation(s)
- Jiaxiong Zeng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Jijuan Ding
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN, USA
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510530, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| |
Collapse
|
16
|
Behling AH, Wilson BC, Ho D, Virta M, O'Sullivan JM, Vatanen T. Addressing antibiotic resistance: computational answers to a biological problem? Curr Opin Microbiol 2023; 74:102305. [PMID: 37031568 DOI: 10.1016/j.mib.2023.102305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023]
Abstract
The increasing prevalence of infections caused by antibiotic-resistant bacteria is a global healthcare crisis. Understanding the spread of resistance is predicated on the surveillance of antibiotic resistance genes within an environment. Bioinformatics and artificial intelligence (AI) methods applied to metagenomic sequencing data offer the capacity to detect known and infer yet-unknown resistance mechanisms, and predict future outbreaks of antibiotic-resistant infections. Machine learning methods, in particular, could revive the waning antibiotic discovery pipeline by helping to predict the molecular structure and function of antibiotic resistance compounds, and optimising their interactions with target proteins. Consequently, AI has the capacity to play a central role in guiding antibiotic stewardship and future clinical decision-making around antibiotic resistance.
Collapse
Affiliation(s)
- Anna H Behling
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Brooke C Wilson
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Daniel Ho
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Justin M O'Sullivan
- Liggins Institute, University of Auckland, Auckland, New Zealand; The Maurice Wilkins Centre, The University of Auckland, Private Bag 92019, Auckland, New Zealand; Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, New South Wales, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton SO16 6YD, United Kingdom; Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore.
| | - Tommi Vatanen
- Liggins Institute, University of Auckland, Auckland, New Zealand; Department of Microbiology, University of Helsinki, Helsinki, Finland; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
17
|
Li Y, Shi X, Zuo Y, Li T, Liu L, Shen Z, Shen J, Zhang R, Wang S. Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes. Microbiol Spectr 2022; 10:e0229722. [PMID: 36287061 PMCID: PMC9769626 DOI: 10.1128/spectrum.02297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 01/06/2023] Open
Abstract
Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 104-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.
Collapse
Affiliation(s)
- Yiming Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaomin Shi
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Zuo
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Tian Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lu Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhangqi Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Shaolin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
18
|
Harrington A, Vo V, Papp K, Tillett RL, Chang CL, Baker H, Shen S, Amei A, Lockett C, Gerrity D, Oh EC. Urban monitoring of antimicrobial resistance during a COVID-19 surge through wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158577. [PMID: 36087661 PMCID: PMC9450474 DOI: 10.1016/j.scitotenv.2022.158577] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/25/2022] [Accepted: 09/03/2022] [Indexed: 05/31/2023]
Abstract
During the early phase of the COVID-19 pandemic, infected patients presented with symptoms similar to bacterial pneumonias and were treated with antibiotics before confirmation of a bacterial or fungal co-infection. We reasoned that wastewater surveillance could reveal potential relationships between reduced antimicrobial stewardship, specifically misprescribing antibiotics to treat viral infections, and the occurrence of antimicrobial resistance (AMR) in an urban community. Here, we analyzed microbial communities and AMR profiles in sewage samples from a wastewater treatment plant (WWTP) and a community shelter in Las Vegas, Nevada during a COVID-19 surge in December 2020. Using a respiratory pathogen and AMR enrichment next-generation sequencing panel, we identified four major phyla in the wastewater, including Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria. Consistent with antibiotics that were reportedly used to treat COVID-19 infections (e.g., fluoroquinolones and beta-lactams), we also measured a significant spike in corresponding AMR genes in the wastewater samples. AMR genes associated with colistin resistance (mcr genes) were also identified exclusively at the WWTP, suggesting that multidrug resistant bacterial infections were being treated during this time. We next compared the Las Vegas sewage data to local 2018-2019 antibiograms, which are antimicrobial susceptibility profile reports about common clinical pathogens. Similar to the discovery of higher levels of beta-lactamase resistance genes in sewage during 2020, beta-lactam antibiotics accounted for 51 ± 3 % of reported antibiotics used in antimicrobial susceptibility tests of 2018-2019 clinical isolates. Our data highlight how wastewater-based epidemiology (WBE) can be leveraged to complement more traditional surveillance efforts by providing community-level data to help identify current and emerging AMR threats.
Collapse
Affiliation(s)
- Anthony Harrington
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Van Vo
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Katerina Papp
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Ching-Lan Chang
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Hayley Baker
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Shirley Shen
- Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Amei Amei
- Department of Mathematical Sciences, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | | | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Edwin C Oh
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Department of Internal Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
| |
Collapse
|
19
|
Yang CX, He ZW, Liu WZ, Wang AJ, Wang L, Liu J, Liu BL, Ren NQ, Yu SP, Guo ZC. Chronic effects of benzalkonium chlorides on short chain fatty acids and methane production in semi-continuous anaerobic digestion of waste activated sludge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157619. [PMID: 35901877 DOI: 10.1016/j.scitotenv.2022.157619] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
As an emerging pollutant, benzalkonium chlorides (BACs) potentially enriched in waste activated sludge (WAS). However, the microbial response mechanism under chronic effects of BACs on acidogenesis and methanogenesis in anaerobic digestion (AD) has not been clearly disclosed. This study investigated the AD (by-)products and microbial evolution under low to high BACs concentrations from bioreactor startup to steady running. It was found that BACs can lead to an increase of WAS hydrolysis and fermentation, but a disturbance to acidogenic bacteria also occurred at low BACs concentration. A noticeable inhibition to methanogenesis occurred when BAC concentration was up to 15 mg/g TSS. Metagenomic analysis revealed the key genes involved in acetic acid (HAc) biosynthesis (i.e. phosphate acetyltransferase, PTA), β-oxidation pathway (acetyl-CoA C-acetyltransferase) and propionic acid (HPr) conversion was slightly promoted compared with control. Furthermore, BACs inhibited the acetotrophic methanogenesis (i.e. acetyl-CoA synthetase), especially BAC concentration was up to 15 mg/g TSS, thereby enhanced short chain fatty acids (SCFAs) accumulation. Overall, chronic stimulation of functional microorganisms with increasing concentrations of BACs impact WAS fermentation.
Collapse
Affiliation(s)
- Chun-Xue Yang
- Heilongjiang Province Key Laboratory of Cold Region Wetland Ecology and Environment Research, School of Geography and Tourism, Harbin University, Harbin, 150086, China; National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zhang-Wei He
- Shanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Wen-Zong Liu
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China.
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, Shenzhen Key Laboratory of Organic Pollution Prevention and Control, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Ling Wang
- School of Environmental & Municipal Engineering, Qingdao University of Technology, Qingdao, 266520, China
| | - Jia Liu
- Heilongjiang Province Key Laboratory of Cold Region Wetland Ecology and Environment Research, School of Geography and Tourism, Harbin University, Harbin, 150086, China
| | - Bao-Ling Liu
- Heilongjiang Province Key Laboratory of Cold Region Wetland Ecology and Environment Research, School of Geography and Tourism, Harbin University, Harbin, 150086, China
| | - Nan-Qi Ren
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Shao-Peng Yu
- Heilongjiang Province Key Laboratory of Cold Region Wetland Ecology and Environment Research, School of Geography and Tourism, Harbin University, Harbin, 150086, China
| | - Ze-Chong Guo
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| |
Collapse
|
20
|
Wang J, Pan R, Dong P, Liu S, Chen Q, Borthwick AGL, Sun L, Xu N, Ni J. Supercarriers of antibiotic resistome in a world's large river. MICROBIOME 2022; 10:111. [PMID: 35897057 PMCID: PMC9331799 DOI: 10.1186/s40168-022-01294-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/15/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Antibiotic resistome has been found to strongly interact with the core microbiota in the human gut, yet little is known about how antibiotic resistance genes (ARGs) correlate with certain microbes in large rivers that are regarded as "terrestrial gut." RESULTS By creating the integral pattern for ARGs and antibiotic-resistant microbes in water and sediment along a 4300-km continuum of the Yangtze River, we found that human pathogen bacteria (HPB) share 13.4% and 5.9% of the ARG hosts in water and sediment but contribute 64% and 46% to the total number of planktonic and sedimentary ARGs, respectively. Moreover, the planktonic HPB harbored 79 ARG combinations that are dominated by "natural" supercarriers (e.g., Rheinheimera texasensis and Noviherbaspirillum sp. Root189) in river basins. CONCLUSIONS We confirmed that terrestrial HPB are the major ARG hosts in the river, rather than conventional supercarriers (e.g., Enterococcus spp. and other fecal indicator bacteria) that prevail in the human gut. The discovery of HPB as natural supercarriers in a world's large river not only interprets the inconsistency between the spatial dissimilarities in ARGs and their hosts, but also highlights the top priority of controlling terrestrial HPB in the future ARG-related risk management of riverine ecosystems globally. Video Abstract.
Collapse
Affiliation(s)
- Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
| | - Rui Pan
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
| | - Peiyan Dong
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
| | - Shufeng Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Alistair G L Borthwick
- Institute of Infrastructure and Environment, School of Engineering, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JL, UK
- School of Engineering, Computing and Mathematics, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
| | - Liyu Sun
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China
| | - Nan Xu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, People's Republic of China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing, 100871, People's Republic of China.
| |
Collapse
|