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Pathogens, Virulence and Resistance Genes Surveillance with Metagenomics Can Pre-empt Dissemination and Escalation of Untreatable Infections: A Systematic Review and Meta-analyses

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Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN
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A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species
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Effect of temperature on removal of antibiotic resistance genes by anaerobic digestion of activated sludge revealed by metagenomic approach
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Free-living bacteria and potential bacterial pathogens in sewage treatment plants
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Parasitic contamination in wastewater and sludge samples in Tunisia using three different detection techniques
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Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant
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Detection of Pathogenic Viruses in the Ambient Air in Seoul, Korea
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Nanobodies®: New ammunition to battle viruses
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Metagenomic analysis reveals the effects of long-term antibiotic pressure on sludge anaerobic digestion and antimicrobial resistance risk
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Sulphur-based autotrophic denitrification of wastewater obtained following graphite production: Long-term performance, microbial communities involved, and functional gene analysis
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The negative impact of antibiotic resistance
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Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease 2019: a cross-sectional study
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Metagenomic datasets of air samples collected during episodes of severe smoke-haze in Malaysia
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Environmental resistome risks of wastewaters and aquatic environments deciphered by shotgun metagenomic assembly
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Selective concentration for ciprofloxacin resistance in Escherichia coli grown in complex aquatic bacterial biofilms
inferredcites →https://doi.org/10.1016/j.envint.2019.03.056openalex-snapshot
Integrated aquaculture contributes to the transfer of mcr-1 between animals and humans via the aquaculture supply chain
inferredcites →https://doi.org/10.1016/j.envint.2019.05.036openalex-snapshot
Metagenomic and metatranscriptomic analyses reveal activity and hosts of antibiotic resistance genes in activated sludge
inferredcites →https://doi.org/10.1016/j.envint.2019.105008openalex-snapshot
Developmental dynamics of antibiotic resistome in aerobic biofilm microbiota treating wastewater under stepwise increasing tigecycline concentrations
inferredcites →https://doi.org/10.1016/j.envint.2019.105270openalex-snapshot
Exploration of the antibiotic resistome in a wastewater treatment plant by a nine-year longitudinal metagenomic study
inferredcites →https://doi.org/10.1016/j.envint.2019.105449openalex-snapshot
Metagenomic insights into the profile of antibiotic resistomes in a large drinking water reservoir
inferredcites →https://doi.org/10.1016/j.envint.2020.105538openalex-snapshot
Characterization and source identification of antibiotic resistance genes in the sediments of an interconnected river-lake system
inferredcites →https://doi.org/10.1016/j.envint.2020.105667openalex-snapshot
Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes
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Metagenomic insights into differences in environmental resistome profiles between integrated and monoculture aquaculture farms in China
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A metagenomic analysis framework for characterization of antibiotic resistomes in river environment: Application to an urban river in Beijing
inferredcites →https://doi.org/10.1016/j.envpol.2020.113913openalex-snapshot
Occurrence of carbapenemase-producing Enterobacteriaceae in a Portuguese river: blaNDM, blaKPC and blaGES among the detected genes
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Deep-amplicon sequencing (DAS) analysis to determine the presence of pathogenic Helicobacter species in wastewater reused for irrigation
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Metagenomic study focusing on antibiotic resistance genes from the sediments of River Yamuna
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Biochemical and functional characterization of a novel thermoacidophilic, heat and halo-ionic liquids tolerant endo-β-1,4-glucanase from saline-alkaline lake soil microbial metagenomic DNA
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Multiple identification of most important waterborne protozoa in surface water used for irrigation purposes by 18S rRNA amplicon-based metagenomics
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Metagenomic analysis of viruses, bacteria and protozoa in irrigation water
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DNA adenine methylation and bacterial pathogenesis
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Fate of pathogenic microorganisms and indicators in secondary activated sludge wastewater treatment plants
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Dissemination of antibiotic resistance genes and human pathogenic bacteria from a pig feedlot to the surrounding stream and agricultural soils
inferredcites →https://doi.org/10.1016/j.jhazmat.2020.123170openalex-snapshot
Metagenomic and network analyses decipher profiles and co-occurrence patterns of antibiotic resistome and bacterial taxa in the reclaimed wastewater distribution system
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DNA adenine methylation modulates pathogenicity of Klebsiella pneumoniae genotype K1
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Concentration and detection of SARS coronavirus in sewage from Xiao Tang Shan Hospital and the 309th Hospital
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Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance
inferredcites →https://doi.org/10.1016/j.scitotenv.2018.07.213openalex-snapshot
Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city
inferredcites →https://doi.org/10.1016/j.scitotenv.2018.11.302openalex-snapshot
Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments
inferredcites →https://doi.org/10.1016/j.scitotenv.2018.12.264openalex-snapshot
Evaluation of the possible persistence of potential human pathogenic bacteria in olive orchards irrigated with treated urban wastewater
inferredcites →https://doi.org/10.1016/j.scitotenv.2019.135395openalex-snapshot
Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics
inferredcites →https://doi.org/10.1016/j.watres.2016.11.056openalex-snapshot
Identification of new bacteria harboring qnrS and aac(6′)-Ib/cr and mutations possibly involved in fluoroquinolone resistance in raw sewage and activated sludge samples from a full-scale WWTP
inferredcites →https://doi.org/10.1016/j.watres.2017.01.014openalex-snapshot
Diversity of DNA viruses in effluents of membrane bioreactors in Traverse City, MI (USA) and La Grande Motte (France)
inferredcites →https://doi.org/10.1016/j.watres.2017.07.060openalex-snapshot
Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics
inferredcites →https://doi.org/10.1016/j.watres.2017.09.063openalex-snapshot
Viral diversity and abundance in polluted waters in Kampala, Uganda
inferredcites →https://doi.org/10.1016/j.watres.2018.12.069openalex-snapshot
New insights into antibiotic resistome in drinking water and management perspectives: A metagenomic based study of small-sized microbes
inferredcites →https://doi.org/10.1016/j.watres.2019.06.073openalex-snapshot
Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities
inferredcites →https://doi.org/10.1016/j.watres.2019.06.075openalex-snapshot
Spatial ecology of a wastewater network defines the antibiotic resistance genes in downstream receiving waters
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Exposure to Animal Feces and Human Health: A Systematic Review and Proposed Research Priorities
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Interconnected microbiomes and resistomes in low-income human habitats
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Patterns of protist diversity associated with raw sewage in New York City
inferredcites →https://doi.org/10.1038/s41467-018-08103-yopenalex-snapshot
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community
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Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
inferredcites →https://doi.org/10.1038/s41564-018-0190-yopenalex-snapshot
Host-linked soil viral ecology along a permafrost thaw gradient
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Deciphering bacterial epigenomes using modern sequencing technologies
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Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease
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Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi
inferredcites →https://doi.org/10.1038/s41598-019-40171-yopenalex-snapshot
Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India
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Visualizing Speech-Generated Oral Fluid Droplets with Laser Light Scattering
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Olive orchard microbiome: characterisation of bacterial communities in soil-plant compartments and their comparison between sustainable and conventional soil management systems
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ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database
inferredcites →https://doi.org/10.1093/cid/civ1013openalex-snapshot
Global, Regional, and National Estimates of Rotavirus Mortality in Children <5 Years of Age, 2000–2013
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Metagenomic profiles of antibiotic resistance genes in paddy soils from South China
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The MG-RAST metagenomics database and portal in 2015
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Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains
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SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics
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Global evolutionary epidemiology and resistome dynamics of Citrobacter species , Enterobacter hormaechei , Klebsiella variicola , and Proteeae clones
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Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: advances and applications
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Production Practices as Risk Factors in Microbial Food Safety of Fresh and Fresh‐Cut Produce
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Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing
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Comparative study of sequence aligners for detecting antibiotic resistance in bacterial metagenomes
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Deciphering the role of the capsule of Klebsiella pneumoniae during pathogenesis: A cautionary tale
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The Expression of Antibiotic Resistance Methyltransferase Correlates with mRNA Stability Independently of Ribosome Stalling
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inferredcites →https://doi.org/10.1186/s40168-019-0710-xopenalex-snapshot
Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes
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Frequency of Bacterial Species Associated with Nosocomial Infection among Health Care Personnel in Nigeria
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Agriculture and food animals as a source of antimicrobial-resistant bacteria
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Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment
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Emerging Mechanisms of Antimicrobial Resistance in Bacteria and Fungi: Advances in the Era of Genomics
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Resistance Mutations in gyrA and parC are Common in Escherichia Communities of both Fluoroquinolone-Polluted and Uncontaminated Aquatic Environments
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Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System
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Culture-Dependent and Culture-Independent Characterization of the Olive Xylem Microbiota: Effect of Sap Extraction Methods
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Review of Antibiotic Resistance in the Indian Ocean Commission: A Human and Animal Health Issue
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Marine Plastics from Norwegian West Coast Carry Potentially Virulent Fish Pathogens and Opportunistic Human Pathogens Harboring New Variants of Antibiotic Resistance Genes
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes
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Methods for the Behavioral, Educational, and Social Sciences: An R package
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Hepatitis E Virus Methyltransferase Inhibits Type I Interferon Induction by Targeting RIG-I
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Cryptosporidiosis in HIV/AIDS Patients in Kenya: Clinical Features, Epidemiology, Molecular Characterization and Antibody Responses
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Risk Assessment for Giardia in Environmental Samples
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Statistical Analysis of Metagenomics Data
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Prevalence of parasites in soil samples in Tehran public places
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Resistome diversity in cattle and the environment decreases during beef production
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A brief introduction to mixed effects modelling and multi-model inference in ecology

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41598-025-28692-1openalex-snapshot
Evaluation of bacterial bioaerosols and their relationship with environmental factors in the air of the wastewater treatment plant of industrial
inferred← citeshttps://doi.org/10.3390/greenhealth2030025openalex-snapshot
Climate-Sensitive Microbial Water Quality and Household Water Security in Saharan and Sahelian Africa
inferred← citeshttps://doi.org/10.3390/pr10091832openalex-snapshot
The Role of Conventional Methods and Artificial Intelligence in the Wastewater Treatment: A Comprehensive Review
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.