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Zhang Z, Li Q, He F, Wang Z, Zhu C, Tu J, Li H, Yi L, Deng Y, Fu S. Sewage surveillance revealed the seasonality and prevalence of respiratory syncytial virus and its implications for seasonal immunization strategy in low and middle-income regions of China. WATER RESEARCH 2025; 270:122828. [PMID: 39608158 DOI: 10.1016/j.watres.2024.122828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 10/28/2024] [Accepted: 11/19/2024] [Indexed: 11/30/2024]
Abstract
Respiratory syncytial virus (RSV) represents a significant global health threat, with a disproportionately high disease burden in low and middle-income regions (LMIRs). Estimating the prevalence of RSV infection at the community levels remains a huge challenge, particularly in LMIRs where clinical data are scarce. In this study, we first detected RSV RNA in the fecal samples from 300 patients to understand the fecal shedding patterns of RSV. Meanwhile, we conducted sewage surveillance of RSV in four geographically distinct LMIRs in China from April 2023 to June 2024. Real-time reverse transcription quantitative Polymerase Chain Reaction (RT-qPCR) was employed to monitor the dynamics of sewage RSV concentration in a typical sewershed from Yingkou, Xi'an, Nanchang, and Nanning, respectively. Subsequent amplicon sequencing was conducted to understand the genotype and mutations of sewage RSV. Through RT-qPCR, we observed two RSV epidemics that lasted from late April to May and October to February in both Yingkou and Xi'an. For Nanchang, only one RSV epidemic was observed which emerged from September to February. Notably, in Nanning, a prolonged RSV epidemic was observed from August to April, suggesting RSV vaccination in Nanning faced more challenges. Amplicon sequencing revealed that sewage RSV found in four LMIRs is genetically distinct, highlighting the need for local initiatives for wastewater monitoring of RSV. This study filled the gaps in previous assessment of suitability of RSV vaccination in LMIRs based on clinical surveillance, demonstrating the effectiveness of wastewater surveillance in guiding public health interventions.
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Affiliation(s)
- Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, PR China
| | - Qingxiang Li
- Clinical Laboratory, The Third Hospital of Nanchang, Nanchang 330009, PR China
| | - Fenglan He
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Centre for Disease Control and Prevention, Nanchang 330038, PR China
| | - Zengguo Wang
- Department of Clinical Laboratory, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, No. 69, Xijuyuan Lane, Xi'an 710003, PR China
| | - Chulong Zhu
- Clinical Laboratory, The Third Hospital of Nanchang, Nanchang 330009, PR China
| | - Junling Tu
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Centre for Disease Control and Prevention, Nanchang 330038, PR China
| | - Haifeng Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, PR China
| | - Liu Yi
- The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Centre for Disease Control and Prevention, Nanchang 330038, PR China
| | - Yao Deng
- Clinical Laboratory, The Third Hospital of Nanchang, Nanchang 330009, PR China
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an 710069, PR China; The Collaboration Unit for State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Centre for Disease Control and Prevention, Nanchang 330038, PR China.
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Cheshomi N, Alum A, Smith MF, Lim ES, Conroy-Ben O, Abbaszadegan M. Viral concentration method biases in the detection of viral profiles in wastewater. Appl Environ Microbiol 2025; 91:e0133924. [PMID: 39641602 PMCID: PMC11784009 DOI: 10.1128/aem.01339-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 10/31/2024] [Indexed: 12/07/2024] Open
Abstract
Viral detection methodologies used for wastewater-based epidemiology (WBE) studies have a broad range of efficacies. The complex matrix and low viral particle load in wastewater emphasize the importance of the concentration method. This study focused on comparing three commonly used virus concentration methods: polyethylene glycol precipitation (PEG), immuno-magnetic nanoparticles (IMNP), and electronegative membrane filtration (EMF). Influent and effluent wastewater samples were processed by the methods and analyzed by DNA/RNA quantification and sequencing for the detection of human viruses. SARS-COV-2, Astrovirus, and Hepatitis C virus were detected by all the methods in both sample types. PEG precipitation resulted in the detection of 20 types of viruses in influent and 16 types in effluent samples. The corresponding number of virus types detected was 21 and 11 for IMNP, and 16 and 8 for EMF. Certain viruses were unique to only one concentration method. For example, PEG detected three types of viruses in influent and six types in effluent compared to IMNP, which detected seven types in influent and one type in effluent samples. However, the EMF method appeared to be the least effective, detecting three types in influent and none in effluent samples. Rotavirus was detected in influent sample using IMNP method, whereas EMF and PEG methods failed to yield a similar outcome. Consequently, the potential false negative results pose a risk to the credibility of WBE applications. Therefore, implementation of a proper concentration technique is critical to minimize method biases and ensure accurate viral profiling in WBE studies.IMPORTANCEIn recent years, significant research efforts have been focused on the development of viral detection methodology for wastewater-based epidemiology studies, showing a range of variability in detection efficacies. A proper methodology is essential for an appropriate evaluation of disease prevalence and community health in such studies and necessitates designing a concentration method based on the target pathogenic virus. There remains a need for comparative performance evaluations of methods in the context of detection efficiencies. This study highlights the significant impact of sample matrix, viral structure, and nucleic acid composition on the efficacy of viral concentration methods. Assessing WBE techniques to ensure accurate detection and understanding of viral presence within wastewater samples is critical for revealing viral profiles in municipality wastewater samples.
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Affiliation(s)
- Naeema Cheshomi
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
- Water and Environmental Technology Center, Arizona State University, Tempe, Arizona, USA
| | - Absar Alum
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
- Water and Environmental Technology Center, Arizona State University, Tempe, Arizona, USA
| | - Matthew F. Smith
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Otakuye Conroy-Ben
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - Morteza Abbaszadegan
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
- Water and Environmental Technology Center, Arizona State University, Tempe, Arizona, USA
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Poghosyan A, Hakobyan S, Avagyan H, Avetisyan A, Bayramyan N, Hakobyan L, Abroyan L, Davtyan A, Poghosyan D, Baghdasaryan B, Arakelova E, Karalova E, Karalyan Z. The role of gastropods in African swine fever virus ecology. Virol J 2024; 21:180. [PMID: 39113041 PMCID: PMC11308590 DOI: 10.1186/s12985-024-02444-5] [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: 05/27/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The spread of the African swine fever virus (ASF virus) genotype ii in the Eurasian region has been very successful and often inexplicable. The virus spreads rapidly and persists in areas with wild boar populations, but areas without feral pig populations are also affected. The virus has shown the ability to survive for a long time in the environment without a population of susceptible hosts, both pigs and Ornithodoros soft ticks. Published data indicated that ASF viruses persist significantly longer in an environment with some freshwater snails (especially Pomacea bridgesii, Tarebia granifera, Asolene spixii, Melanoides tuberculate, and Physa fontinalis), compared to freshwater without snails. Data obtained in this study suggest that gastropods theoretically can be the hosts of the ASF virus. Also, we have proven the possibility of long-term existence of an infectious virus when infected in vitro.
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Affiliation(s)
- Arpine Poghosyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Sona Hakobyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Hranush Avagyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
- Experimental Laboratory of Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Aida Avetisyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
- Experimental Laboratory of Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Nane Bayramyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Lina Hakobyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Liana Abroyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Aram Davtyan
- A.B. Nalbandyan Institute of Chemical Physics, NAS RA, Yerevan, Armenia
| | - Davit Poghosyan
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Biology NAS RA, Yerevan, Armenia
| | - Bagrat Baghdasaryan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Elina Arakelova
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Elena Karalova
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
- Experimental Laboratory of Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Zaven Karalyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia.
- Yerevan State Medical University after M. Heratsi, Yerevan, Armenia.
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Zeng H, Wang Y, Zhao Z, Zhu D, Xia H, Wei Y, Kuang P, An D, Chen K, Li R, Lei Y, Sun G. Travertine deposition rather than tourism activity is the primary contributor to the microplastic risks in alpine karst lakes. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135192. [PMID: 39002479 DOI: 10.1016/j.jhazmat.2024.135192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/15/2024]
Abstract
Microplastics (MPs) are emerging as anthropogenic vectors to form plastisphere, facilitating microbiome colonization and pathogenic dissemination, thus contributing to environmental and health crises across various ecosystems. However, a knowledge gap persists regarding MPs risks and their driving factors in certain unique and vulnerable ecosystems, such as Karst travertine lakes, some of which are renowned World Natural Heritage Sites under ever-increasing tourism pressure. We hypothesized that tourism activities serve as the most important factor of MPs pollution, whereas intrinsic features, including travertine deposition can exacerbate potential environmental risks. Thus, metagenomic approaches were employed to investigate the geographical distribution of the microbiome, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their combined environmental risks in Jiuzhaigou and Huanglong, two famous tourism destinations in Southwest China. The plastisphere risks were higher in Huanglong, contradicting our hypothesis that Jiuzhaigou would face more crucial antibiotic risks due to its higher tourist activities. Specifically, the levels of Lipopolysaccharide Lewis and fosD increased by sevenfold and 20-fold, respectively, from upstream to downstream in Huanglong, whereas in Jiuzhaigou, no significant accrual was observed. Structural equation modeling results showed that travertine deposition was the primary contributor to MPs risks in alpine karstic lakes. Our findings suggest that tourism has low impact on MPs risks, possibly because of proper management, and that travertine deposition might act as an MPs hotspot, emphasizing the importance of considering the unique aspects of travertine lakes in mitigating MPs pollution and promoting the sustainable development of World Natural Heritage Sites.
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Affiliation(s)
- Hanyong Zeng
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijin Wang
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Zhen Zhao
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Dalin Zhu
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Hongxia Xia
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Yihua Wei
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Peigang Kuang
- Jiuzhaigou Nature Reserve Administration Bureau, Jiuzhaigou 623402, China
| | - Dejun An
- Huanglong Nature Reserve Administration Bureau, Songpan 623300, China
| | - Ke Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Ruilong Li
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Yanbao Lei
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Geng Sun
- China-Croatia "Belt and Road" Joint Laboratory on Biodiversity and Ecosystem Services, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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5
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Spatz S, Afonso CL. Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases. Vet Sci 2024; 11:239. [PMID: 38921986 PMCID: PMC11209166 DOI: 10.3390/vetsci11060239] [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: 04/16/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with a slow transition from research to routine use. While longer turnaround times and higher costs were once concerns, these issues are currently being addressed by automation, better chemistries, improved sequencing platforms, better databases, and automated bioinformatics analysis. However, many technical options and steps, each producing highly variable outcomes, have reduced the technology's operational value, discouraging its implementation in diagnostic labs. We present a case for utilizing non-targeted RNA sequencing (NT-RNA-seq) as an ideal metagenomics method for the detection of infectious disease-causing agents in humans and animals. Additionally, to create operational value, we propose to identify best practices for the "core" of steps that are invariably shared among many human and veterinary protocols. Reference materials, sequencing procedures, and bioinformatics standards should accelerate the validation processes necessary for the widespread adoption of this technology. Best practices could be determined through "implementation research" by a consortium of interested institutions working on common samples.
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Affiliation(s)
- Stephen Spatz
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA;
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Xiao R, Hu Y, Wang Y, Li J, Guo C, Bai J, Zhang L, Zhang K, Jorquera MA, Acuña JJ, Pan W. Pathogen profile of Baiyangdian Lake sediments using metagenomic analysis and their correlation with environmental factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169628. [PMID: 38159771 DOI: 10.1016/j.scitotenv.2023.169628] [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: 10/13/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Increasing concerns about public health and safety after covid-19 have raised pathogen studies, especially in aquatic environments. However, the extent to how different location and human activities affect geographic occurrence and distribution of pathogens in response to agricultural pollution, boat tourism disturbances and municipal wastewater inflow in a degraded lake remains unclear. Since the surrounding residents depend on the lake for their livelihood, understanding the pathogens reserved in lake sediment and the regulation possibility by environmental factors are challenges with far-reaching significance. Results showed that 187 pathogens were concurrently shared by the nine sediment samples, with Salmonella enterica and Pseudomonas aeruginosa being the most abundant. The similar composition of the pathogens suggests that lake sediment may act as reservoirs of generalist pathogens which may pose infection risk to a wide range of host species. Of the four virulence factors (VFs) types analyzed, offensive VFs were dominant (>46 % on average) in all samples, with dominant subtypes including adherence, secretion systems and toxins. Notably, the lake sediments under the impact of agricultural use (g1) showed significantly higher diversity and abundance of pathogen species and VFs than those under the impact of boat tourism (g2) and/or municipal wastewater inflow with reed marshes filtration (g3). From the co-occurrence networks, pathogens and pesticides, aggregate fractions, EC, pH, phosphatase have strong correlations. Strong positive correlations between pathogens and diazinon in g1 and ppDDT in g2 and g3 suggest higher pesticide-pathogen co-exposure risk. These findings highlight the need to explore pathogen - environmental factor interaction mechanisms in the human-impacted water environments where the control of pathogen invasion by environmental factors may accessible.
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Affiliation(s)
- Rong Xiao
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China.
| | - Yanping Hu
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Yaping Wang
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Junming Li
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Congling Guo
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Ling Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Kegang Zhang
- Department of Environmental Science and Engineering, North China Electric Power University, Baoding 071003, China
| | - Milko A Jorquera
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco 01145, Chile
| | - Jacquelinne J Acuña
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco 01145, Chile
| | - Wenbin Pan
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
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Shen L, Zhang Z, Wang R, Wu S, Wang Y, Fu S. Metatranscriptomic data mining together with microfluidic card uncovered the potential pathogens and seasonal RNA viral ecology in a drinking water source. J Appl Microbiol 2024; 135:lxad310. [PMID: 38130237 DOI: 10.1093/jambio/lxad310] [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: 07/20/2023] [Revised: 10/26/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
AIMS Despite metatranscriptomics becoming an emerging tool for pathogen surveillance, very little is known about the feasibility of this approach for understanding the fate of human-derived pathogens in drinking water sources. METHODS AND RESULTS We conducted multiplexed microfluidic cards and metatranscriptomic sequencing of the drinking water source in a border city of North Korea in four seasons. Microfluidic card detected norovirus, hepatitis B virus (HBV), enterovirus, and Vibrio cholerae in the water. Phylogenetic analyses showed that environmental-derived sequences from norovirus GII.17, genotype C of HBV, and coxsackievirus A6 (CA6) were genetically related to the local clinical isolates. Meanwhile, metatranscriptomic assembly suggested that several bacterial pathogens, including Acinetobacter johnsonii and V. cholerae might be prevalent in the studied region. Metatranscriptomic analysis recovered 349 species-level groups with substantial viral diversity without detection of norovirus, HBV, and CA6. Seasonally distinct virus communities were also found. Specifically, 126, 73, 126, and 457 types of viruses were identified in spring, summer, autumn, and winter, respectively. The viromes were dominated by the Pisuviricota phylum, including members from Marnaviridae, Dicistroviridae, Luteoviridae, Potyviridae, Picornaviridae, Astroviridae, and Picobirnaviridae families. Further phylogenetic analyses of RNA (Ribonucleic Acid)-dependent RNA polymerase (RdRp) sequences showed a diverse set of picorna-like viruses associated with shellfish, of which several novel picorna-like viruses were also identified. Additionally, potential animal pathogens, including infectious bronchitis virus, Bat dicibavirus, Bat nodavirus, Bat picornavirus 2, infectious bursal disease virus, and Macrobrachium rosenbergii nodavirus were also identified. CONCLUSIONS Our data illustrate the divergence between microfluidic cards and metatranscriptomics, highlighting that the combination of both methods facilitates the source tracking of human viruses in challenging settings without sufficient clinical surveillance.
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Affiliation(s)
- Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Rui Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China
| | - Shuang Wu
- College of Food Technology and Sciences, Shanghai Ocean University, Shanghai 200093, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yongjie Wang
- College of Food Technology and Sciences, Shanghai Ocean University, Shanghai 200093, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai 200093, China
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
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8
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Sokoloski KJ, Holm RH, Smith M, Ford EE, Rouchka EC, Smith T. What is the functional reach of wastewater surveillance for respiratory viruses, pathogenic viruses of concern, and bacterial antibiotic resistance genes of interest? Hum Genomics 2023; 17:114. [PMID: 38105239 PMCID: PMC10726489 DOI: 10.1186/s40246-023-00563-8] [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: 05/12/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Despite a clear appreciation of the impact of human pathogens on community health, efforts to understand pathogen dynamics within populations often follow a narrow-targeted approach and rely on the deployment of specific molecular probes for quantitative detection or rely on clinical detection and reporting. MAIN TEXT Genomic analysis of wastewater samples for the broad detection of viruses, bacteria, fungi, and antibiotic resistance genes of interest/concern is inherently difficult, and while deep sequencing of wastewater provides a wealth of information, a robust and cooperative foundation is needed to support healthier communities. In addition to furthering the capacity of high-throughput sequencing wastewater-based epidemiology to detect human pathogens in an unbiased and agnostic manner, it is critical that collaborative networks among public health agencies, researchers, and community stakeholders be fostered to prepare communities for future public health emergencies or for the next pandemic. A more inclusive public health infrastructure must be built for better data reporting where there is a global human health risk burden. CONCLUSIONS As wastewater platforms continue to be developed and refined, high-throughput sequencing of human pathogens in wastewater samples will emerge as a gold standard for understanding community health.
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Affiliation(s)
- Kevin J Sokoloski
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
- Center for Predictive Medicine for Biodefense and Emerging Infectious Disease, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
| | - Rochelle H Holm
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY, 40202, USA.
| | - Melissa Smith
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, 580 S. Preston St., Louisville, KY, 40202, USA
| | - Easton E Ford
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, 580 S. Preston St., Louisville, KY, 40202, USA
- KY INBRE Bioinformatics Core, University of Louisville, 522 E. Gray St., Louisville, KY, 40202, USA
| | - Ted Smith
- Christina Lee Brown Envirome Institute, School of Medicine, University of Louisville, 302 E. Muhammad Ali Blvd., Louisville, KY, 40202, USA
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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Zhang M, Liu J, Hu N, Fang Q, Zhang D, Qiang Z, Pan X. Cascade capture, oxidization and inactivation for removing multi-species pollutants, antimicrobial resistance and pathogenicity from hospital wastewater. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131730. [PMID: 37269564 DOI: 10.1016/j.jhazmat.2023.131730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/29/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
As reservoirs of pathogens, antimicrobial resistant microorganisms and a wide variety of pollutants, hospital wastewaters (HWWs) need to be effectively treated before discharge. This study employed the functionalized colloidal microbubble technology as one-step fast HWW treatment. Inorganic coagulant (monomeric Fe(III)-coagulant or polymeric Al(III)-coagulant) and ozone were used as surface-decorator and gaseous core modifier, respectively. The Fe(III)- or Al(III)-modified colloidal gas (or, ozone) microbubbles (Fe(III)-CCGMBs, Fe(III)-CCOMBs, Al(III)-CCGMBs and Al(III)-CCOMBs) were constructed. Within 3 min, CCOMBs decreased CODCr and fecal coliform concentration to the levels meeting the national discharge standard for medical organization. Regrowth of bacteria was inhibited and biodegradability of organics was increased after the simultaneous oxidation and cell-inactivation process. The metagenomics analysis further reveals that Al(III)-CCOMBs performed best in capturing the virulence genes, antibiotic resistance genes and their potential hosts. The horizontal transfer of those harmful genes could be effectively hampered thanks to the removal of mobile genetic elements. Interestingly, the virulence factors of adherence, micronutrient uptake/acquisition and phase invasion could facilitate the interface-dominated capture. Featured as cascade processes of capture, oxidation and inactivation in the one-step operation, the robust Al(III)-CCOMB treatment is recommended for the HWW treatment and the protection of downstream aquatic environment.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiayuan Liu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Na Hu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qunkai Fang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
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Schaeffer J, Desdouits M, Besnard A, Le Guyader FS. Looking into sewage: how far can metagenomics help to detect human enteric viruses? Front Microbiol 2023; 14:1161674. [PMID: 37180249 PMCID: PMC10166864 DOI: 10.3389/fmicb.2023.1161674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
The impact of human sewage on environmental and food contamination constitutes an important safety issue. Indeed, human sewage reflects the microbiome of the local population, and a variety of human viruses can be detected in wastewater samples. Being able to describe the diversity of viruses present in sewage will provide information on the health of the surrounding population health and will help to prevent further transmission. Metagenomic developments, allowing the description of all the different genomes present in a sample, are very promising tools for virome analysis. However, looking for human enteric viruses with short RNA genomes which are present at low concentrations is challenging. In this study we demonstrate the benefits of performing technical replicates to improve viral identification by increasing contig length, and the set-up of quality criteria to increase confidence in results. Our approach was able to effectively identify some virus sequences and successfully describe the viral diversity. The method yielded full genomes either for norovirus, enterovirus and rotavirus, even if, for these segmented genomes, combining genes remain a difficult issue. Developing reliable viromic methods is important as wastewater sample analysis provides an important tool to prevent further virus transmission by raising alerts in case of viral outbreaks or emergence.
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Affiliation(s)
| | | | | | - Françoise S. Le Guyader
- Ifremer, Laboratoire de Microbiologie, U. Microbiologie Aliment Santé et Environnement, Nantes, France
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Fu S, Wang R, Xu Z, Zhou H, Qiu Z, Shen L, Yang Q. Metagenomic sequencing combined with flow cytometry facilitated a novel microbial risk assessment framework for bacterial pathogens in municipal wastewater without cultivation. IMETA 2023; 2:e77. [PMID: 38868349 PMCID: PMC10989823 DOI: 10.1002/imt2.77] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 06/14/2024]
Abstract
A workflow that combined metagenomic sequencing with flow cytometry was developed. The absolute abundance of pathogens was accurately estimated in mock communities and real samples. Metagenome-assembled genomes binned from metagenomic data set is robust in phylogenetic analysis and virulence profiling.
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Affiliation(s)
- Songzhe Fu
- Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of EducationDalian Ocean UniversityDalianChina
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of EducationNorthwest UniversityXi'anChina
| | - Rui Wang
- Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of EducationDalian Ocean UniversityDalianChina
| | - Zheng Xu
- Shenzhen Yantian District People's HospitalShenzhenChina
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Huiwen Zhou
- College of Life Science and HealthNortheastern UniversityShenyangChina
| | - Zhiguang Qiu
- School of Environment and Energy, Shenzhen Graduate SchoolPeking UniversityShenzhenChina
| | - Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of EducationNorthwest UniversityXi'anChina
| | - Qian Yang
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityGentBelgium
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