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Hackenberger D, Imtiaz H, Raphenya AR, Alcock BP, Poinar HN, Wright GD, McArthur AG. CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment. Appl Environ Microbiol 2025; 91:e0187624. [PMID: 40019273 PMCID: PMC11921354 DOI: 10.1128/aem.01876-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 02/06/2025] [Indexed: 03/01/2025] Open
Abstract
Better interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here, we describe the Comprehensive Antibiotic Resistance Probe Design Machine (CARPDM), a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and tested two separate probe sets: allCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database's protein homolog models (n = 4,661), and clinicalCARD, which focuses on a clinically relevant subset of resistance genes (n = 323). We demonstrate that allCARD increases the number of reads mapping to resistance genes by up to 594-fold. clinicalCARD performs similarly when clinically relevant genes are present, increasing the number of resistance-gene mapping reads by up to 598-fold. In parallel with this development, we have established a protocol to synthesize any probe set in-house, saving up to 350 dollars per reaction. Together, these probe sets, their associated design program CARPDM, and the protocol for in-house synthesis will democratize metagenomic resistome analyses, allowing researchers access to a cost-effective and efficient means to explore the antibiotic resistome.IMPORTANCEAntimicrobial resistance threatens to undermine all modern medicine and is driven by the spread of antimicrobial resistance genes among pathogens, environments, patients, and animals. DNA sequencing of complex samples, such as wastewater, shows considerable promise for tracking these genes and making risk assessments. However, these methods suffer from high costs and low detection limits, plus a requirement for frequent redesign due to the constantly evolving diversity of resistance genes. Building upon our Comprehensive Antibiotic Resistance Database, our research provides software for on-demand renewal, based on the latest knowledge of resistance gene diversity, of our novel bait-capture hybridization platform that simultaneously reduces cost and increases detection levels for DNA sequencing of complex samples. The significance of our research is in the development of new software tools, reagent synthesis protocols, and hybridization enrichment protocols to provide affordable, high-resolution metagenomics DNA sequencing, which we test using environmental and wastewater samples.
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Affiliation(s)
- Dirk Hackenberger
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Hamna Imtiaz
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R. Raphenya
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian P. Alcock
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Hendrik N. Poinar
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- McMaster Ancient DNA Center, McMaster University, Hamilton, Ontario, Canada
- Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Andrew G. McArthur
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Stankiewicz K, Bulanda K, Prajsnar J, Lenart-Boroń A. Impact of the Technical Snow Production Process on Bacterial Community Composition, Antibacterial Resistance Genes, and Antibiotic Input-A Dual Effect of the Inevitable. Int J Mol Sci 2025; 26:2771. [PMID: 40141411 PMCID: PMC11942910 DOI: 10.3390/ijms26062771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 03/15/2025] [Accepted: 03/17/2025] [Indexed: 03/28/2025] Open
Abstract
Although climate warming-induced snow cover reduction, as well as the development of ski tourism in hot and dry countries, is shifting industries toward the use of technical snowmaking, its use raises hydrological, health-related, and environmental concerns. This study was aimed at enhancing our current understanding of the impact of technical snowmaking on the environment and human health. Culturable bacteriological indicators of water quality (Escherichia coli, fecal enterococci, Salmonella, and Staphylococcus), the presence and concentration of antimicrobials, genes determining bacterial antibiotic resistance (ARGs), and next-generation sequencing-based bacterial community composition and diversity were examined from river water, technological reservoirs, and technical snow from five ski resorts. The number of culturable bacteria and prevalence of most ARGs decreased during snowmaking. The concentration of antimicrobial agents changed irregularly, e.g., ofloxacin and erythromycin dropped in the snowmaking process, while cefoxitin was quantified only in technical snow. The bacterial community composition and diversity were altered through the technical snowmaking process, resulting in the survivability of freezing temperatures or the presence of antimicrobial agents. Water storage in reservoirs prior to snowmaking allows us to reduce bacterial and ARG contaminants. Frequent and thorough cleaning of snowmaking devices may aid in reducing the negative impact snowmaking can have on the environment by reducing contaminant input and limiting the disturbance of the ecological balance.
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Affiliation(s)
- Klaudia Stankiewicz
- Department of Microbiology and Biomonitoring, Faculty of Agriculture and Economics, University of Agriculture in Kraków, Adam Mickiewicz Ave. 24/28, 30-059 Kraków, Poland;
| | - Klaudia Bulanda
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Kraków, 29 Listopada Ave. 46, 31-425 Kraków, Poland;
| | - Justyna Prajsnar
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str. 8, 30-239 Kraków, Poland;
| | - Anna Lenart-Boroń
- Department of Microbiology and Biomonitoring, Faculty of Agriculture and Economics, University of Agriculture in Kraków, Adam Mickiewicz Ave. 24/28, 30-059 Kraków, Poland;
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Shayan MNM, Onodera T, Hirano R, Kuroda K, Narihiro T, Nakaya Y, Satoh H. Effects of snowmelt runoff on bacterial communities and antimicrobial resistance gene concentrations in an urban river in a cold climate region. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2025; 32:7641-7650. [PMID: 40042701 DOI: 10.1007/s11356-025-36168-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 02/19/2025] [Indexed: 03/28/2025]
Abstract
Urban rivers are essential for human activities and ecosystems. Urban runoff is a major source of various pollutants in urban rivers. In this study, we investigated the effect of rainfall and snowmelt subsequently causing urban runoff in a cold climate region on bacterial community structures and antimicrobial resistance gene concentrations in an urban river in Sapporo city, Japan, which has an average snowfall of 4.8 m. Bacterial community structures of the river water were analyzed by next generation sequencing of bacterial 16S rRNA genes. The antimicrobial resistance genes, mphA and blaIMP, were determined using quantitative polymerase chain reaction. Rainfall and snowmelt increased the effluent discharge rate of treated wastewater, and river water depth. Rainfall and snowmelt also increased Escherichia coli concentrations by 4-20 folds in the river, probably because of combined sewer overflows, urban runoff, or increased effluent discharge rate of treated wastewater to the river. Urban runoff and the subsequent discharge of treated wastewater decreased the bacterial alpha diversity and increased the species evenness of bacteria. Bacterial beta diversity analysis showed that the discharge of treated wastewater caused by rainfall and snowmelt changed the structure and diversity of the bacterial community in the river. The concentrations of the antimicrobial resistance gene mphA were related to the discharge of treated wastewater. In contrast, the antimicrobial resistance gene blaIMP appeared to be present in the upstream pristine environment. Results of this study should be informative for challenge to reduce the antimicrobial resistance bacteria due to combined sewer overflows by wastewater management authorities.
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Affiliation(s)
- Mohomed N M Shayan
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo, 060-8628, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-Ku, Sapporo, 062-8517, Japan
| | - Takeshiro Onodera
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo, 060-8628, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-Ku, Sapporo, 062-8517, Japan
| | - Reiko Hirano
- Cellspect Co., Ltd, 1-10-82 Kitaiioka, Morioka, Iwate, 020-0857, Japan
| | - Kyohei Kuroda
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo, 060-8628, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-Ku, Sapporo, 062-8517, Japan
| | - Takashi Narihiro
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo, 060-8628, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-Ku, Sapporo, 062-8517, Japan
| | - Yuki Nakaya
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo, 060-8628, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Sapporo, 060-8628, Japan.
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Velazquez-Meza ME, Galarde-López M, Cornejo-Juárez P, Bobadilla-del-Valle M, Godoy-Lozano E, Aguilar-Vera E, Carrillo-Quiroz BA, Ponce de León-Garduño A, Velazquez Acosta C, Alpuche-Aranda CM. Bacterial Communities and Resistance and Virulence Genes in Hospital and Community Wastewater: Metagenomic Analysis. Int J Mol Sci 2025; 26:2051. [PMID: 40076673 PMCID: PMC11900532 DOI: 10.3390/ijms26052051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2025] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/14/2025] Open
Abstract
Metagenomic studies have made it possible to deepen the analysis of the abundance of bacterial populations that carry resistance and virulence determinants in the wastewater environment. In this study, a longitudinal collection of samples of community and hospital wastewater from August 2021 to September 2022 was obtained. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize the bacterial abundance, antimicrobial resistance genes (ARGs), plasmids, and virulence factor genes (VFGs) contained in the wastewater. The microbial composition of the community and hospital wastewater showed that the most abundant bacterial phyla detected in all samples were: Proteobacteria, Bacteroides, Firmicutes, Campylobacterota, and Actinobacteria. Seasonal differences in the relative abundances of species, ARGs, plasmids, and VFGs were observed. In this study, a total of 270 ARGs were detected, and it was found that the absolute abundance of ARGs only showed a 39% reduction in the treated wastewater. Furthermore, the ARGs detected in this study were found to encode resistance to antibiotics of the last choice. Our results showed that plasmids carrying resistance genes were more abundant in raw wastewater, and 60% more abundant in hospital wastewater compared to community wastewater. Several of the VFGs detected in this study encode for adhesion, motility, and biofilm formation, which likely allows bacteria to remain and persist in the wastewater environment and survive WWTP treatment systems, thus managing to escape into the environment via treated wastewater.
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Affiliation(s)
- Maria Elena Velazquez-Meza
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (E.G.-L.); (E.A.-V.); (B.A.C.-Q.)
| | - Miguel Galarde-López
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Cuajimalpa, Mexico City 05110, Mexico;
| | - Patricia Cornejo-Juárez
- Departamento de Infectología, Instituto Nacional de Cancerología, Tlalpan, Mexico City 14080, Mexico; (P.C.-J.); (C.V.A.)
| | - Miriam Bobadilla-del-Valle
- Laboratorio Nacional de Máxima Seguridad para el Estudio de Tuberculosis y Enfermedades Emergentes, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City 14080, Mexico; (M.B.-d.-V.); (A.P.d.L.-G.)
| | - Ernestina Godoy-Lozano
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (E.G.-L.); (E.A.-V.); (B.A.C.-Q.)
| | - Edgar Aguilar-Vera
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (E.G.-L.); (E.A.-V.); (B.A.C.-Q.)
| | - Berta Alicia Carrillo-Quiroz
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (E.G.-L.); (E.A.-V.); (B.A.C.-Q.)
| | - Alfredo Ponce de León-Garduño
- Laboratorio Nacional de Máxima Seguridad para el Estudio de Tuberculosis y Enfermedades Emergentes, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City 14080, Mexico; (M.B.-d.-V.); (A.P.d.L.-G.)
| | - Consuelo Velazquez Acosta
- Departamento de Infectología, Instituto Nacional de Cancerología, Tlalpan, Mexico City 14080, Mexico; (P.C.-J.); (C.V.A.)
| | - Celia Mercedes Alpuche-Aranda
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (E.G.-L.); (E.A.-V.); (B.A.C.-Q.)
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Monaco A, Caruso M, Bellantuono L, Cazzolla Gatti R, Fania A, Lacalamita A, La Rocca M, Maggipinto T, Pantaleo E, Tangaro S, Amoroso N, Bellotti R. Measuring water pollution effects on antimicrobial resistance through explainable artificial intelligence. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2025; 367:125620. [PMID: 39788180 DOI: 10.1016/j.envpol.2024.125620] [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: 08/06/2024] [Revised: 12/29/2024] [Accepted: 12/30/2024] [Indexed: 01/12/2025]
Abstract
Antimicrobial resistance refers to the ability of pathogens to develop resistance to drugs designed to eliminate them, making the infections they cause more difficult to treat and increasing the likelihood of disease diffusion and mortality. As such, antimicrobial resistance is considered as one of the most significant and universal challenges to both health and society, as well as the environment. In our research, we employ the explainable artificial intelligence paradigm to identify the factors that most affect the onset of antimicrobial resistance in diversified territorial contexts, which can vary widely from each other in terms of climatic, economic and social conditions. Specifically, we employ a large set of indicators identified through the One Health framework to predict, at the country level, mortality resulting from antimicrobial resistance related to Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Streptococcus pneumoniae. The analysis reveals the outstanding importance of indicators related to water accessibility and quality in determining mortality due to antimicrobial resistance to the considered pathogens across countries, providing perspective as a potential tool for decision support and monitoring.
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Affiliation(s)
- Alfonso Monaco
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Mario Caruso
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy
| | - Loredana Bellantuono
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy; Università degli Studi di Bari Aldo Moro, Dipartimento di Biomedicina Traslazionale e Neuroscienze (DiBraiN), Bari, 70124, Italy.
| | - Roberto Cazzolla Gatti
- Alma Mater Studiorum University of Bologna, Department of Biological Sciences, Geological and Environmental (BiGeA), Bologna, 40126, Italy
| | - Alessandro Fania
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Antonio Lacalamita
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Marianna La Rocca
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Tommaso Maggipinto
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Ester Pantaleo
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
| | - Sabina Tangaro
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy; Università degli Studi di Bari Aldo Moro, Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Bari, 70126, Italy
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy; Università degli Studi di Bari Aldo Moro, Dipartimento di Farmacia - Scienze del Farmaco, Bari, 70125, Italy
| | - Roberto Bellotti
- Università degli Studi di Bari Aldo Moro, Dipartimento Interateneo di Fisica M. Merlin, Bari, 70125, Italy; Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, 70125, Italy
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6
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Berteina-Raboin S. Comprehensive Overview of Antibacterial Drugs and Natural Antibacterial Compounds Found in Food Plants. Antibiotics (Basel) 2025; 14:185. [PMID: 40001427 PMCID: PMC11851795 DOI: 10.3390/antibiotics14020185] [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: 12/28/2024] [Revised: 02/04/2025] [Accepted: 02/08/2025] [Indexed: 02/27/2025] Open
Abstract
The aim of this review is to list the various natural sources of antimicrobials that are readily available. Indeed, many plant sources are known to have antibiotic properties, although it is not always clear which molecule is responsible for this activity. Many food supplements also have this therapeutic indication. We propose here to take stock of the scientific knowledge attesting or not to these indications for some food sources. An overview of the various antibiotic drugs commercially available will be provided. A structural indication of the natural molecules present in various plants and reported to contribute to their antibiotic power will be given. The plants mentioned in this review, which does not claim to be exhaustive, are referenced for fighting Gram-positive and/or Gram-negative bacteria. It is difficult to attribute activity to just one of these natural molecules, as it is likely to result from synergy within the plant. Similarly, chitosan is mentioned for its fungistatic and bacteriostatic properties. In this case, this polymeric compound derived from the chitin of marine organisms is referenced for its antibiofilm activity. It seems that, in the face of growing antibiotic resistance, it makes sense to keep high-performance synthetic antibiotics on hand to treat the difficult pathologies that require them. On the other hand, for minor infections, the use of better-tolerated natural sources is certainly sufficient. To achieve this, we need to take stock of common plant sources, available as food products or dietary supplements, which are known to be active in this field.
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Affiliation(s)
- Sabine Berteina-Raboin
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans, UMR-CNRS 7311, BP 6759, Rue de Chartres, CEDEX 2, 45067 Orleans, France
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7
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La Rosa MC, Maugeri A, Favara G, La Mastra C, Magnano San Lio R, Barchitta M, Agodi A. The Impact of Wastewater on Antimicrobial Resistance: A Scoping Review of Transmission Pathways and Contributing Factors. Antibiotics (Basel) 2025; 14:131. [PMID: 40001375 PMCID: PMC11851908 DOI: 10.3390/antibiotics14020131] [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: 12/17/2024] [Revised: 01/16/2025] [Accepted: 01/24/2025] [Indexed: 02/27/2025] Open
Abstract
BACKGROUND/OBJECTIVES Antimicrobial resistance (AMR) is a global issue driven by the overuse of antibiotics in healthcare, agriculture, and veterinary settings. Wastewater and treatment plants (WWTPs) act as reservoirs for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). The One Health approach emphasizes the interconnectedness of human, animal, and environmental health in addressing AMR. This scoping review analyzes wastewater's role in the AMR spread, identifies influencing factors, and highlights research gaps to guide interventions. METHODS This scoping review followed the PRISMA-ScR guidelines. A comprehensive literature search was conducted across the PubMed and Web of Science databases for articles published up to June 2024, supplemented by manual reference checks. The review focused on wastewater as a source of AMR, including hospital effluents, industrial and urban sewage, and agricultural runoff. Screening and selection were independently performed by two reviewers, with conflicts resolved by a third. RESULTS Of 3367 studies identified, 70 met the inclusion criteria. The findings indicated that antibiotic residues, heavy metals, and microbial interactions in wastewater are key drivers of AMR development. Although WWTPs aim to reduce contaminants, they often create conditions conducive to horizontal gene transfer, amplifying resistance. Promising interventions, such as advanced treatment methods and regulatory measures, exist but require further research and implementation. CONCLUSIONS Wastewater plays a pivotal role in AMR dissemination. Targeted interventions in wastewater management are essential to mitigate AMR risks. Future studies should prioritize understanding AMR dynamics in wastewater ecosystems and evaluating scalable mitigation strategies to support global health efforts.
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Affiliation(s)
| | | | | | | | | | | | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (M.C.L.R.); (A.M.); (G.F.); (C.L.M.); (R.M.S.L.); (M.B.)
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8
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Mendoza-Guido B, Rivera-Montero L, Barrantes K, Chacon L. Plasmid and integron-associated antibiotic resistance in Escherichia coli isolated from domestic wastewater treatment plants. FEMS Microbiol Lett 2025; 372:fnaf041. [PMID: 40246693 DOI: 10.1093/femsle/fnaf041] [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: 02/07/2025] [Revised: 03/17/2025] [Accepted: 04/14/2025] [Indexed: 04/19/2025] Open
Abstract
The rapid dissemination of antibiotic resistance genes (ARGs) represents a significant global threat, with wastewater treatment plants (WWTPs) playing an important role as reservoirs and propagation hubs. In this study, we performed whole-genome sequencing and bioinformatic analyses on eight multidrug-resistant Escherichia coli isolates previously obtained from domestic WWTPs in Costa Rica. We identified 61 ARGs (23 unique), with 40 located on plasmids, and 21 on chromosomal sequences, seven of which were within integrons. Several ARGs were associated with resistance to clinically and veterinary important antibiotics, including sulfamethoxazole/trimethoprim, beta-lactams, and tetracyclines. One hundred twenty-one virulence-associated genes (29 unique) were detected, with 16 located on plasmids. Notably, the presence of virulence factors such as ompT and hlyF genes alongside ARGs on plasmids underscores the transmissible pathogenic potential of WWTP-associated E. coli strains. These findings highlight the role of small domestic WWTPs in disseminating pathogenic and multidrug-resistant bacteria and their mobile genetic elements, emphasizing the need for further research to understand how these discharges impact aquatic environments.
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Affiliation(s)
- Bradd Mendoza-Guido
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José 11501, Costa Rica
- Programa de Doctorado en Ciencias, Universidad de Costa Rica, San José 11501, Costa Rica
| | - Luis Rivera-Montero
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José 11501, Costa Rica
| | - Kenia Barrantes
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José 11501, Costa Rica
- Doctorado en Ciencias Naturales para el Desarrollo (DOCINADE), Instituto Tecnológico de Costa Rica, Universidad Nacional and Universidad Estatal a Distancia, San José 474-2050, Costa Rica
| | - Luz Chacon
- Instituto de Investigaciones en Salud (INISA), Universidad de Costa Rica, San José 11501, Costa Rica
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9
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Doyle C, Wall K, Fanning S, McMahon BJ. Making sense of sentinels: wildlife as the One Health bridge for environmental antimicrobial resistance surveillance. J Appl Microbiol 2025; 136:lxaf017. [PMID: 39805713 DOI: 10.1093/jambio/lxaf017] [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: 09/02/2024] [Revised: 10/25/2024] [Accepted: 01/12/2025] [Indexed: 01/16/2025]
Abstract
Antimicrobial resistance (AMR), arising from decades of imprudent anthropogenic use of antimicrobials in healthcare and agriculture, is considered one of the greatest One Health crises facing healthcare globally. Antimicrobial pollutants released from human-associated sources are intensifying resistance evolution in the environment. Due to various ecological factors, wildlife interact with these polluted ecosystems, acquiring resistant bacteria and genes. Although wildlife are recognized reservoirs and disseminators of AMR in the environment, current AMR surveillance systems still primarily focus on clinical and agricultural settings, neglecting this environmental dimension. Wildlife can serve as valuable sentinels of AMR in the environment, reflecting ecosystem health, and the effectiveness of mitigation strategies. This review explores knowledge gaps surrounding the ecological factors influencing AMR acquisition and dissemination in wildlife, and highlights limitations in current surveillance systems and policy instruments that do not sufficiently address the environmental component of AMR. We discuss the underutilized opportunity of using wildlife as sentinel species in a holistic, One Health-centred AMR surveillance system. By better integrating wildlife into systematic AMR surveillance and policy, and leveraging advances in high-throughput technologies, we can track and predict resistance evolution, assess the ecological impacts, and better understand the complex dynamics of environmental transmission of AMR across ecosystems.
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Affiliation(s)
- Caoimhe Doyle
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Katie Wall
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Barry J McMahon
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
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10
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McCorison CB, Kim T, Donato JJ, LaPara TM. Proximity-Ligation Metagenomic Sequence Analysis Reveals That the Antibiotic Resistome Makes Significant Transitions During Municipal Wastewater Treatment. Environ Microbiol 2025; 27:e70036. [PMID: 39797441 PMCID: PMC11724201 DOI: 10.1111/1462-2920.70036] [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: 07/08/2024] [Revised: 11/20/2024] [Accepted: 12/20/2024] [Indexed: 01/13/2025]
Abstract
Shotgun and proximity-ligation metagenomic sequencing were used to generate thousands of metagenome assembled genomes (MAGs) from the untreated wastewater, activated sludge bioreactors, and anaerobic digesters from two full-scale municipal wastewater treatment facilities. Analysis of the antibiotic resistance genes (ARGs) in the pool of contigs from the shotgun metagenomic sequences revealed significantly different relative abundances and types of ARGs in the untreated wastewaster compared to the activated sludge bioreactors or the anaerobic digesters (p < 0.05). In contrast, these results were statistically similar when comparing the ARGs in the pool of MAGs, suggesting that proximity-ligation metagenomic sequencing is particularly useful for pairing ARGs with their hosts but less adept at discerning quantitative differences in ARG types and relative abundances. For example, numerous MAGs of the genera Acinetobacter, Enterococcus, Klebsiella and Pseudomonas were identified in the untreated wastewater, many of which harboured plasmid-borne and/or chromosomal-borne ARGs; none of these MAGs, however, were detected in the activated sludge bioreactors or anaerobic digesters. In conclusion, this research demonstrates that the antibiotic resistome undergoes significant transitions in both the relative abundance and the host organisms during the municipal wastewater treatment process.
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Affiliation(s)
| | - Taegyu Kim
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Justin J. Donato
- Department of ChemistryUniversity of St. ThomasSt. PaulMinnesotaUSA
| | - Timothy M. LaPara
- Department of Civil, Environmental, and Geo‐EngineeringUniversity of MinnesotaMinneapolisMinnesotaUSA
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11
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Herrera-Muñoz J, Ibáñez M, Calzadilla W, Cabrera-Reina A, García V, Salazar-González R, Hernández F, Campos-Mañas M, Miralles-Cuevas S. Assessment of contaminants of emerging concern and antibiotic resistance genes in the Mapocho River (Chile): A comprehensive study on water quality and municipal wastewater impact. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176198. [PMID: 39278476 DOI: 10.1016/j.scitotenv.2024.176198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/08/2024] [Accepted: 09/09/2024] [Indexed: 09/18/2024]
Abstract
The primary objective of this study was to evaluate the persistence and elimination of Contaminants of Emerging Concern (CECs) in municipal wastewater treatment plants (MWWTPs) and their presence in the Mapocho River within the metropolitan area of Santiago, Chile. The use of advanced analytical techniques, based on liquid chromatography coupled to both low and high-resolution mass spectrometry, allowed a comprehensive overview on the presence of CECs in samples. Additionally, a preliminary assessment of the microbiological aspects aimed to determine the presence of indicator microorganisms of fecal contamination, such as Escherichia coli and total coliforms was conducted. Furthermore, a qualitative assessment of Antibiotic Resistant Genes (ARGs) was performed. No CECs were detected upstream to the MWWTPs. However, the results from various wastewater samples (influent, secondary, and tertiary effluents) revealed significant diversity, with 73 CECs detected alongside prevalent ARGs including sulI, sulfII, qnrB, and blaTEM. The presence of CECs and ARGs downstream of the MWWTP in the Mapocho River was mainly attributed to effluent discharge. On the other hand, typical values for a healthy river and a MWWTP with a final disinfection stage were found in terms of fecal contamination. Consequently, the imperative for developing tertiary or quaternary treatments capable of degrading CECs and ARGs to minimize environmental impact is underscored. These findings hold public health significance, offering insights into potential risks and influencing future legislative measures in Chile.
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Affiliation(s)
- José Herrera-Muñoz
- Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Casilla 40, Correo 33, Santiago, Chile; Grupo de Investigación de Análisis, Tratamiento, Electroquímica, Recuperación y Reúso de Agua (WATER(b)), Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile; Instituto Universitario de Investigación y Desarrollo Tecnológico (IDT), Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Santiago, Chile
| | - María Ibáñez
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain
| | - Wendy Calzadilla
- Grupo de Investigación de Análisis, Tratamiento, Electroquímica, Recuperación y Reúso de Agua (WATER(b)), Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile
| | - Alejandro Cabrera-Reina
- Instituto Universitario de Investigación y Desarrollo Tecnológico (IDT), Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Santiago, Chile
| | - Verónica García
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile, Alameda 3363, Estación Central, Santiago, Chile; Centro de Estudio en Ciencia y Tecnología de los Alimentos (CECTA-USACH), Obispo Manuel Umaña 050, Estación Central, Santiago, Chile
| | - Ricardo Salazar-González
- Grupo de Investigación de Análisis, Tratamiento, Electroquímica, Recuperación y Reúso de Agua (WATER(b)), Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile.
| | - Félix Hernández
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain
| | - Marina Campos-Mañas
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain
| | - Sara Miralles-Cuevas
- Instituto Universitario de Investigación y Desarrollo Tecnológico (IDT), Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Santiago, Chile.
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12
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Mendoza-Guido B, Barrantes K, Rodríguez C, Rojas-Jimenez K, Arias-Andres M. The Impact of Urban Pollution on Plasmid-Mediated Resistance Acquisition in Enterobacteria from a Tropical River. Antibiotics (Basel) 2024; 13:1089. [PMID: 39596782 PMCID: PMC11591392 DOI: 10.3390/antibiotics13111089] [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: 10/03/2024] [Revised: 11/07/2024] [Accepted: 11/11/2024] [Indexed: 11/29/2024] Open
Abstract
Background: The exposure of environmental bacteria to contaminants in aquatic ecosystems accelerates the dissemination of antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Methods: In this study, we sampled three locations along a contamination gradient of a polluted river, focusing on isolating Enterobacteria from the surface waters to investigate the relationship between urban pollution and antibiotic resistance. The genomes of 15 isolates (5 per site) were sequenced to identify plasmid-borne ARGs and their association with resistance phenotypes. Results: Isolates from the site with the highest contamination (Site 3) showeda larger number of ARGs, plasmids, and resistance phenotypes. Notably, one of the isolates analyzed, E. coli A231-12, exhibited phenotypic resistance to seven antibiotics, presumably conferred by a single plasmid carrying 12 ARGs. Comparative analysis of this plasmid revealed its close evolutionary relationship with another IncH plasmid hosted by Salmonella enterica, underscoring its high ARG burden in the aquatic environment. Other plasmids identified in our isolates carried sul and dfrA genes, conferring resistance to trimethoprim/sulfamethoxazole, a commonly prescribed antibiotic combination in clinical settings. Conclusions: These results highlight the critical need to expand research on the link between pollution and plasmid-mediated antimicrobial resistance in aquatic ecosystems, which can act as reservoirs of ARGs.
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Affiliation(s)
- Bradd Mendoza-Guido
- Instituto de Investigaciones en Salud, Universidad de Costa Rica, San José P.O. Box 11501-2060, Costa Rica; (B.M.-G.); (K.B.)
| | - Kenia Barrantes
- Instituto de Investigaciones en Salud, Universidad de Costa Rica, San José P.O. Box 11501-2060, Costa Rica; (B.M.-G.); (K.B.)
- Programa de Doctorado en Ciencias Naturales para el Desarrollo, Universidad Estatal a Distancia, San José P.O. Box 474-2050, Costa Rica
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José P.O. Box 11501-2060, Costa Rica;
| | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, San José P.O. Box 11501-2060, Costa Rica
| | - Maria Arias-Andres
- Instituto Regional de Estudios en Sustancias Tóxicas, Universidad Nacional de Costa Rica, Heredia P.O. Box 86-3000, Costa Rica
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13
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Ariani IK, Aydin S, Yangin-Gomec C. Assessment of antibiotics removal and transformation products by Eichhornia crassipes-assisted biomass in a UASB reactor treating pharmaceutical effluents. BIOFOULING 2024; 40:915-931. [PMID: 39564881 DOI: 10.1080/08927014.2024.2429554] [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: 02/07/2024] [Revised: 10/28/2024] [Accepted: 11/06/2024] [Indexed: 11/21/2024]
Abstract
The dried roots of an aquatic plant (Eichhornia crassipes commonly known as water hyacinth) were included in the biomass of an upflow anaerobic sludge bed (UASB) reactor to evaluate the improvement effect on treating antibiotic-containing synthetic pharmaceutical effluent. The removals of three different antibiotics, namely erythromycin (ERY), tetracycline (TET) and sulfamethoxazole (SMX), were investigated using the unacclimatized inoculum during the startup period. Then, about 2.5% E. crassipes (w/w of volatile solids) was added to biomass during the last month of operation. Almost complete removal of each antibiotic was achieved, with efficiencies up to 99% (with initial ERY, TET and SMX of 200, 75 and 230 mg L-1, respectively) regardless of E. crassipes addition. The presence of transformation products (TPs) of selected antibiotics was also investigated and ERY showed a higher potential to transform into its metabolites than SMX and TET. With the studied amount of E. crassipes, no positive impact against TPs formation was observed.
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Affiliation(s)
| | - Sevcan Aydin
- Division of Biotechnology, Biology Department, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Cigdem Yangin-Gomec
- Department of Environmental Engineering, Istanbul Technical University, Istanbul, Turkey
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14
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Ransirini AM, Elżbieta MS, Joanna G, Bartosz K, Wojciech T, Agnieszka B, Magdalena U. Fertilizing drug resistance: Dissemination of antibiotic resistance genes in soil and plant bacteria under bovine and swine slurry fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174476. [PMID: 38969119 DOI: 10.1016/j.scitotenv.2024.174476] [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: 03/12/2024] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
The increasing global demand for food production emphasizes the use of organic animal fertilizers, such as manure and slurry, to support sustainable agricultural practices. However, recent studies highlight concerns about antibiotic resistance determinants in animal excrements, posing a potential risk of spreading antibiotic resistance genes (ARGs) in agricultural soil and, consequently, in food products. This study examines the dissemination of ARGs within the soil and plant-associated microbiomes in cherry radish following the application of swine and bovine slurry. In a 45-day pot experiment, slurry-amended soil, rhizospheric bacteria, and endophytic bacteria in radish roots and leaves were sampled and analyzed for 21 ARGs belonging to 7 Antibiotic Resistance Phenotypes (ARPs). The study also assessed slurry's impact on soil microbiome functional diversity, enzymatic activity, physicochemical soil parameters, and the concentration of 22 selected antimicrobials in soil and plant tissues. Tetracyclines and β-lactams were the most frequently identified ARGs in bovine and swine slurry, aligning with similar studies worldwide. Swine slurry showed a higher prevalence of ARGs in soil and plant-associated bacteria, particularly TET genes, reflecting pig antibiotic treatments. The persistent dominance of TET genes across slurry, soil, and plant microbiomes highlights significant influence of slurry application on gene occurrence in plant bacteria. The presence of ARGs in edible plant parts underscores health risks associated with raw vegetable consumption. Time-dependent dynamics of ARG occurrence highlighted their persistent presence throughout the experiment duration, influenced by the environmental factors and antibiotic residuals. Notably, ciprofloxacin, which was the only one antimicrobial detected in fertilized soil, significantly impacted bovine-amended variants. Soil salinity modifications induced by slurry application correlated with changes in ARG occurrence. Overall, the research underscores the complex relationships between agricultural practices, microbial activity, and antibiotic resistance dissemination, emphasizing the need for a more sustainable and health-conscious farming approaches.
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Affiliation(s)
- Attanayake Mudiyanselage Ransirini
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Mierzejewska-Sinner Elżbieta
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Giebułtowicz Joanna
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Pharmaceutical and Biomedical Analysis, Banacha 1, 02-097 Warsaw, Poland
| | - Kózka Bartosz
- Medical University of Warsaw, Faculty of Pharmacy, Department of Drug Chemistry, Pharmaceutical and Biomedical Analysis, Banacha 1, 02-097 Warsaw, Poland
| | - Tołoczko Wojciech
- Department of Physical Geography, Faculty of Geography, University of Lodz, Prez. Gabriela Narutowicza 88, 90-139, Lodz, Poland
| | - Bednarek Agnieszka
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland
| | - Urbaniak Magdalena
- University of Lodz, Faculty of Biology and Environmental Protection, UNESCO Chair on Ecohydrology and Applied Ecology, Banacha 12/16, 90-237 Lodz, Poland.
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15
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Haque A, Chowdhury A, Islam Bhuiyan MN, Bhowmik B, Afrin S, Sarkar R, Haque MM. Molecular characterization, antibiotic resistant pattern and biofilm forming potentiality of bacterial community associated with Ompok pabda fish farming in southwestern Bangladesh. Microb Pathog 2024; 194:106818. [PMID: 39047804 DOI: 10.1016/j.micpath.2024.106818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Ompok pabda is gaining popularity in the aquaculture industry due to its increasing demand; however research on microbial diversity and antibiotic susceptibility remains limited. The present study was designed to identify the bacterial pathogens commonly found in the pabda farming system with their biofilm forming potential and antibiotic susceptibility. Different bacterial strains were isolated from water, sediments and gut, gill of pabda fish and the isolates were identified based on their morphological traits, biochemical and molecular analysis. Antibiotic susceptibilities, antibiotic resistance gene determination and biofilm formation capabilities were evaluated by disc diffusion method, PCR amplification and Microtiter plate (MTP) assay, respectively. The respective isolates of gill and gut of pabda aquaculture and their environments were: Exiguobacterium spp. (25 %), Enterococcus spp. (20 %), Bacillus spp. (10 %), Acinetobacter spp. (10 %), Enterobacter spp. (10 %), Aeromonas spp. (10 %), Lactococcus spp. (5 %), Klebsiella spp. (5 %) and Kurthia spp. (5 %). Antibiotic resistance frequencies were found to be relatively high, especially for trimethoprim (95 %), sulfafurazole (75 %), ampicillin (60 %), amoxicillin-clavulanic acid (55 %), and cephradine (50 %). 30 % isolates were categorized as DR bacteria followed by 30 % isolates were MDR bacteria and 40 % were classified as XDR bacteria. Moreover, 4 antibiotic resistant genes were detected with sul1 (30 %), dfrA1 (10 %), tetC (40 %), and qnrA (5 %) of isolates. Based on the microtiter plate method, 20 %, 25 %, and 30 % of isolates were found to produce strong, moderate, and weak biofilms, respectively. The findings suggest that biofilm forming bacterial strains found in O. pabda fish farm may be a potential source of numerous antibiotic-resistant bacteria. The study sheds new light on antibiotic resistance genes, which are typically inherited by bacteria and play an important role in developing effective treatments or control strategies.
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Affiliation(s)
- Afrina Haque
- Department of Zoology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Abhijit Chowdhury
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh; Central Analytical & Research Facilities (CARF), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh.
| | - Mohammad Nazrul Islam Bhuiyan
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Banasree Bhowmik
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Sadia Afrin
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Rajib Sarkar
- Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Md Mansurul Haque
- Department of Zoology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
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16
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Saccà ML, Resci I, Cilia G. Phenotypic and genotypic antimicrobial resistance patterns in honey bee (Apis mellifera L.) bacterial symbionts. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-34598-8. [PMID: 39098972 DOI: 10.1007/s11356-024-34598-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/29/2024] [Indexed: 08/06/2024]
Abstract
Antimicrobial resistance (AMR) is a major global public health problem. Nevertheless, the knowledge of the factors driving the spread of resistance among environmental microorganisms is limited, and few studies have been performed worldwide. Honey bees (Apis mellifera L.) have long been considered bioindicators of environmental pollution and more recently also of AMR. In this study, 53 bacterial strains isolated from the body surface of honey bees at three ontogenetic stages, collected from ten different geographic locations, were tested for their phenotypic and genotypic resistance to eight classes of the most widely used antimicrobials in human and veterinary medicine. Results showed that 83% of the strains were resistant to at least one antimicrobial and 62% were multidrug-resistant bacteria, with a prevalence of resistance to nalidixic acid, cefotaxime, and aztreonam. A high percentage of isolates harbouring at least one antimicrobial gene was also observed (85%). The gene encoding resistance to colistin mcr-1 was the most abundant, followed by those for tetracycline tetM and tetC. Geographical features influenced the distribution of these traits more than bacterial species or bee stage, supporting the use of honey bee colonies and their associated bacteria as indicators to monitor environmental resistance. This approach can improve the scientific understanding of this global threat by increasing data collection capacity.
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Affiliation(s)
- Maria Ludovica Saccà
- Research Centre for Agriculture and Environment (CREA-AA), Council for Agricultural Research and Economics, Via Di Corticella 133, 40128, Bologna, Italy.
| | - Ilaria Resci
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Giovanni Cilia
- Research Centre for Agriculture and Environment (CREA-AA), Council for Agricultural Research and Economics, Via Di Corticella 133, 40128, Bologna, Italy
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17
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Galarde-López M, Velazquez-Meza ME, Godoy-Lozano EE, Carrillo-Quiroz BA, Cornejo-Juárez P, Sassoé-González A, Ponce-de-León A, Saturno-Hernández P, Alpuche-Aranda CM. Presence and Persistence of ESKAPEE Bacteria before and after Hospital Wastewater Treatment. Microorganisms 2024; 12:1231. [PMID: 38930614 PMCID: PMC11206169 DOI: 10.3390/microorganisms12061231] [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: 05/22/2024] [Revised: 06/02/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The metagenomic surveillance of antimicrobial resistance in wastewater has been suggested as a methodological tool to characterize the distribution, status, and trends of antibiotic-resistant bacteria. In this study, a cross-sectional collection of samples of hospital-associated raw and treated wastewater were obtained from February to March 2020. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize bacterial abundance and antimicrobial resistance gene analysis. The main bacterial phyla found in all the samples were as follows: Proteobacteria, Bacteroides, Firmicutes, and Actinobacteria. At the species level, ESKAPEE bacteria such as E. coli relative abundance decreased between raw and treated wastewater, but S. aureus, A. baumannii, and P. aeruginosa increased, as did the persistence of K. pneumoniae in both raw and treated wastewater. A total of 172 different ARGs were detected; blaOXA, blaVEB, blaKPC, blaGES, mphE, mef, erm, msrE, AAC(6'), ant(3″), aadS, lnu, PBP-2, dfrA, vanA-G, tet, and sul were found at the highest abundance and persistence. This study demonstrates the ability of ESKAPEE bacteria to survive tertiary treatment processes of hospital wastewater, as well as the persistence of clinically important antimicrobial resistance genes that are spreading in the environment.
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Affiliation(s)
- Miguel Galarde-López
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| | - Maria Elena Velazquez-Meza
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| | - Elizabeth Ernestina Godoy-Lozano
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| | - Berta Alicia Carrillo-Quiroz
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
| | - Patricia Cornejo-Juárez
- Departamento de Infectología, Instituto Nacional de Cancerología, Tlalpan, Mexico City 14080, Mexico;
| | - Alejandro Sassoé-González
- Unidad de Inteligencia Epidemiológica, Hospital Regional de Alta Especialidad de Ixtapaluca, Ixtapaluca 56530, Mexico;
| | - Alfredo Ponce-de-León
- Laboratorio Nacional de Máxima Seguridad para el Estudio de Tuberculosis y Enfermedades Emergentes, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City 14080, Mexico;
| | - Pedro Saturno-Hernández
- Centro de Investigación en Evaluación de Encuestas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico;
| | - Celia Mercedes Alpuche-Aranda
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Morelos 62100, Mexico; (M.G.-L.); (E.E.G.-L.); (B.A.C.-Q.)
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18
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Pourrostami Niavol K, Bordoloi A, Suri R. An overview of the occurrence, impact of process parameters, and the fate of antibiotic resistance genes during anaerobic digestion processes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:41745-41774. [PMID: 38853230 PMCID: PMC11219439 DOI: 10.1007/s11356-024-33844-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Antibiotic resistance genes (ARGs) have emerged as a significant global health threat, contributing to fatalities worldwide. Wastewater treatment plants (WWTPs) and livestock farms serve as primary reservoirs for these genes due to the limited efficacy of existing treatment methods and microbial adaptation to environmental stressors. Anaerobic digestion (AD) stands as a prevalent biological treatment for managing sewage sludge and manure in these settings. Given the agricultural utility of AD digestate as biofertilizers, understanding ARGs' fate within AD processes is essential to devise effective mitigation strategies. However, understanding the impact of various factors on ARGs occurrence, dissemination, and fate remains limited. This review article explores various AD treatment parameters and correlates to various resistance mechanisms and hotspots of ARGs in the environment. It further evaluates the dissemination and occurrence of ARGs in AD feedstocks and provides a comprehensive understanding of the fate of ARGs in AD systems. This review explores the influence of key AD parameters such as feedstock properties, pretreatments, additives, and operational strategies on ARGs. Results show that properties such as high solid content and optimum co-digestion ratios can enhance ARG removal, while the presence of heavy metals, microplastics, and antibiotics could elevate ARG abundance. Also, operational enhancements, such as employing two-stage digestion, have shown promise in improving ARG removal. However, certain pretreatment methods, like thermal hydrolysis, may exhibit a rebounding effect on ARG levels. Overall, this review systematically addresses current challenges and offers future perspectives associated with the fate of ARGs in AD systems.
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Affiliation(s)
- Kasra Pourrostami Niavol
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA
| | - Achinta Bordoloi
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA
| | - Rominder Suri
- Department of Civil and Environmental Engineering, Temple University, Philadelphia, PA, 19122, USA.
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19
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Daw Elbait G, Daou M, Abuoudah M, Elmekawy A, Hasan SW, Everett DB, Alsafar H, Henschel A, Yousef AF. Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater. PLoS One 2024; 19:e0298325. [PMID: 38578803 PMCID: PMC10997137 DOI: 10.1371/journal.pone.0298325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/18/2024] [Indexed: 04/07/2024] Open
Abstract
Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.
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Affiliation(s)
- Gihan Daw Elbait
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mariane Daou
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Miral Abuoudah
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed Elmekawy
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Shadi W. Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Chemical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Dean B. Everett
- Department of Pathology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Infection Research Unit, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Emirates Bio-research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed F. Yousef
- Department of Biological Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Membranes and Advanced Water Technology (CMAT), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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20
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Li Z, Guo X, Liu B, Huang T, Liu R, Liu X. Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants. WATER RESEARCH 2024; 253:121289. [PMID: 38341975 DOI: 10.1016/j.watres.2024.121289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.
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Affiliation(s)
- Zong Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China
| | - Xiaoxiao Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China
| | - Bingxin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Huang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China.
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Binzhou Institute of Technology, Binzhou 256212, China.
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21
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Begmatov S, Beletsky AV, Dorofeev AG, Pimenov NV, Mardanov AV, Ravin NV. Metagenomic insights into the wastewater resistome before and after purification at large‑scale wastewater treatment plants in the Moscow city. Sci Rep 2024; 14:6349. [PMID: 38491069 PMCID: PMC10942971 DOI: 10.1038/s41598-024-56870-0] [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: 10/26/2023] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
Wastewater treatment plants (WWTPs) are considered to be hotspots for the spread of antibiotic resistance genes (ARGs). We performed a metagenomic analysis of the raw wastewater, activated sludge and treated wastewater from two large WWTPs responsible for the treatment of urban wastewater in Moscow, Russia. In untreated wastewater, several hundred ARGs that could confer resistance to most commonly used classes of antibiotics were found. WWTPs employed a nitrification/denitrification or an anaerobic/anoxic/oxic process and enabled efficient removal of organic matter, nitrogen and phosphorus, as well as fecal microbiota. The resistome constituted about 0.05% of the whole metagenome, and after water treatment its share decreased by 3-4 times. The resistomes were dominated by ARGs encoding resistance to beta-lactams, macrolides, aminoglycosides, tetracyclines, quaternary ammonium compounds, and sulfonamides. ARGs for macrolides and tetracyclines were removed more efficiently than beta-lactamases, especially ampC, the most abundant ARG in the treated effluent. The removal efficiency of particular ARGs was impacted by the treatment technology. Metagenome-assembled genomes of multidrug-resistant strains were assembled both for the influent and the treated effluent. Ccomparison of resistomes from WWTPs in Moscow and around the world suggested that the abundance and content of ARGs depend on social, economic, medical, and environmental factors.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071.
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Alexander G Dorofeev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Nikolai V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33‑2, Moscow, Russia, 119071.
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22
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Fayaz T, Renuka N, Ratha SK. Antibiotic occurrence, environmental risks, and their removal from aquatic environments using microalgae: Advances and future perspectives. CHEMOSPHERE 2024; 349:140822. [PMID: 38042426 DOI: 10.1016/j.chemosphere.2023.140822] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/14/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Antibiotic pollution has caused a continuous increase in the development of antibiotic-resistant bacteria and antibiotic-resistant genes (ARGs) in aquatic environments worldwide. Algae-based bioremediation technology is a promising eco-friendly means to remove antibiotics and highly resistant ARGs, and the generated biomass can be utilized to produce value-added products of industrial significance. This review discussed the prevalence of antibiotics and ARGs in aquatic environments and their environmental risks to non-target organisms. The potential of various microalgal species for antibiotic and ARG removal, their mechanisms, strategies for enhanced removal, and future directions were reviewed. Antibiotics can be degraded into non-toxic compounds in microalgal cells through the action of extracellular polymeric substances, glutathione-S-transferase, and cytochrome P450; however, antibiotic stress can alter microalgal gene expression and growth. This review also deciphered the effect of antibiotic stress on microalgal physiology, biomass production, and biochemical composition that can impact their commercial applications.
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Affiliation(s)
- Tufail Fayaz
- Algal Biotechnology Laboratory, Department of Botany, Central University of Punjab, Bathinda, 151401, India
| | - Nirmal Renuka
- Algal Biotechnology Laboratory, Department of Botany, Central University of Punjab, Bathinda, 151401, India.
| | - Sachitra Kumar Ratha
- Algology Laboratory, CSIR-National Botanical Research Institute, Lucknow, 226001, India
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23
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Perez-Bou L, Gonzalez-Martinez A, Gonzalez-Lopez J, Correa-Galeote D. Promising bioprocesses for the efficient removal of antibiotics and antibiotic-resistance genes from urban and hospital wastewaters: Potentialities of aerobic granular systems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123115. [PMID: 38086508 DOI: 10.1016/j.envpol.2023.123115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/07/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
The use, overuse, and improper use of antibiotics have resulted in higher levels of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs), which have profoundly disturbed the equilibrium of the environment. Furthermore, once antibiotic agents are excreted in urine and feces, these substances often can reach wastewater treatment plants (WWTPs), in which improper treatments have been highlighted as the main reason for stronger dissemination of antibiotics, ARB, and ARGs to the receiving bodies. Hence, achieving better antibiotic removal capacities in WWTPs is proposed as an adequate approach to limit the spread of antibiotics, ARB, and ARGs into the environment. In this review, we highlight hospital wastewater (WW) as a critical hotspot for the dissemination of antibiotic resistance due to its high level of antibiotics and pathogens. Hence, monitoring the composition and structure of the bacterial communities related to hospital WW is a key factor in controlling the spread of ARGs. In addition, we discuss the advantages and drawbacks of the current biological WW treatments regarding the antibiotic-resistance phenomenon. Widely used conventional activated sludge technology has proved to be ineffective in mitigating the dissemination of ARB and ARGs to the environment. However, aerobic granular sludge (AGS) technology is a promising technology-with broad adaptability and excellent performance-that could successfully reduce antibiotics, ARB, and ARGs in the generated effluents. We also outline the main operational parameters involved in mitigating antibiotics, ARB, and ARGs in WWTPs. In this regard, WW operation under long hydraulic and solid retention times allows better removal of antibiotics, ARB, and ARGs independently of the WW technology employed. Finally, we address the current knowledge of the adsorption and degradation of antibiotics and their importance in removing ARB and ARGs. Notably, AGS can enhance the removal of antibiotics, ARB, and ARGs due to the complex microbial metabolism within the granular biomass.
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Affiliation(s)
- Lizandra Perez-Bou
- Microbiology Department, Faculty of Pharmacy, University of Granada, Granada, Andalucía, Spain; Microbiology and Environmental Technology Section, Institute of Water Research, University of Granada, Granada, Andalucía, Spain; Microbial Biotechnology Group, Microbiology and Virology Department, Faculty of Biology, University of Havana, Cuba
| | - Alejandro Gonzalez-Martinez
- Microbiology Department, Faculty of Pharmacy, University of Granada, Granada, Andalucía, Spain; Microbiology and Environmental Technology Section, Institute of Water Research, University of Granada, Granada, Andalucía, Spain
| | - Jesus Gonzalez-Lopez
- Microbiology Department, Faculty of Pharmacy, University of Granada, Granada, Andalucía, Spain; Microbiology and Environmental Technology Section, Institute of Water Research, University of Granada, Granada, Andalucía, Spain
| | - David Correa-Galeote
- Microbiology Department, Faculty of Pharmacy, University of Granada, Granada, Andalucía, Spain; Microbiology and Environmental Technology Section, Institute of Water Research, University of Granada, Granada, Andalucía, Spain.
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24
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Gorecki A, Ostapczuk P, Dziewit L. Diversity of antibiotic resistance gene variants at subsequent stages of the wastewater treatment process revealed by a metagenomic analysis of PCR amplicons. Front Genet 2024; 14:1334646. [PMID: 38274111 PMCID: PMC10808613 DOI: 10.3389/fgene.2023.1334646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Wastewater treatment plants have been recognised as point sources of various antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) which are considered recently emerging biological contaminants. So far, culture-based and molecular-based methods have been successfully applied to monitor antimicrobial resistance (AMR) in WWTPs. However, the methods applied do not permit the comprehensive identification of the true diversity of ARGs. In this study we applied next-generation sequencing for a metagenomic analysis of PCR amplicons of ARGs from the subsequent stages of the analysed WWTP. The presence of 14 genes conferring resistance to different antibiotic families was screened by PCR. In the next step, three genes were selected for detailed analysis of changes of the profile of ARG variants along the process. A relative abundance of 79 variants was analysed. The highest diversity was revealed in the ermF gene, with 52 variants. The relative abundance of some variants changed along the purification process, and some ARG variants might be present in novel hosts for which they were currently unassigned. Additionally, we identified a pool of novel ARG variants present in the studied WWTP. Overall, the results obtained indicated that the applied method is sufficient for analysing ARG variant diversity.
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Affiliation(s)
- Adrian Gorecki
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warsaw, Poland
| | - Piotr Ostapczuk
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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25
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Ochman H, Quandt EM, Gottell N, Gilbert JA. Examining the taxonomic distribution of tetracycline resistance in a wastewater plant. SUSTAINABLE MICROBIOLOGY 2024; 1:qvad003. [PMID: 38317688 PMCID: PMC10840452 DOI: 10.1093/sumbio/qvad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
Microbial communities serve as reservoirs of antibiotic resistance genes (ARGs) and facilitate the dissemination of these genes to bacteria that infect humans. Relatively little is known about the taxonomic distribution of bacteria harboring ARGs in these reservoirs and the avenues of transmission due to the technical hurdles associated with characterizing the contents of complex microbial populations and the assignment of genes to particular genomes. Focusing on the array of tetracycline resistance (Tcr) genes in the primary and secondary phases of wastewater treatment, 17 of the 22 assayed Tcr genes were detected in at least one sample. We then applied emulsion, paired isolation, and concatenation PCR (epicPCR) to link tetracycline resistance genes to specific bacterial hosts. Whereas Tcr genes tend to vary in their distributions among bacterial taxa according to their modes of action, there were numerous instances in which a particular Tcr gene was associated with a host that was distantly related to all other bacteria bearing the same gene, including several hosts not previously identified. Tcr genes are far less host-restricted than previously assumed, indicating that complex microbial communities serve as settings where ARGs are spread among divergent bacterial phyla.
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Affiliation(s)
- Howard Ochman
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, United States
| | - Erik M Quandt
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, United States
| | - Neil Gottell
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
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26
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Costa BF, Zarei-Baygi A, Md Iskander S, Smith AL. Antibiotic resistance genes fate during food waste management - Comparison between thermal treatment, hyperthermophilic composting, and anaerobic membrane bioreactor. BIORESOURCE TECHNOLOGY 2023; 388:129771. [PMID: 37739184 DOI: 10.1016/j.biortech.2023.129771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
The fate of eight different antibiotic resistance genes (ARGs) in food waste (sul1, sul2, tetO, tetW, ermF, ermB, ampC, oxa-1), intI1, and rpoB were monitored during thermal treatment (pyrolysis and incineration), hyperthermophilic composting, and anaerobic membrane bioreactor (AnMBR) treatment. ARGs in food waste ranged from 2.9 × 106 to 3.5 × 109 copies/kg with ampC being the least abundant and sul1 being the most abundant. Thermal treatment achieved removal below detection limits of all ARGs. Only two ARGs (sul1 and ampC) persisted in hyperthermophilic composting. While all genes except for ermB decreased in the AnMBR effluent relative to the food waste feed, sul1 remained at relatively high abundance. Biosolids on the contrary, accumulated tetO, ampC and sul2 in all tested operating conditions. Thermal treatment, despite limited resource recovery, provides the most effective mitigation of ARG risk in food waste.
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Affiliation(s)
- Bianca F Costa
- Astani Department of Civil and Environmental Engineering, University of Southern California, 920 Downey Way, Los Angeles, CA 90089, USA
| | - Ali Zarei-Baygi
- Astani Department of Civil and Environmental Engineering, University of Southern California, 920 Downey Way, Los Angeles, CA 90089, USA
| | - Syeed Md Iskander
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, 1410 14(th) Ave N, Fargo, ND 58102, USA
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 920 Downey Way, Los Angeles, CA 90089, USA.
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27
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K S, Vasanthrao R, Chattopadhyay I. Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance. Folia Microbiol (Praha) 2023; 68:657-675. [PMID: 37589876 DOI: 10.1007/s12223-023-01083-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.
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Affiliation(s)
- Suganya K
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Ramavath Vasanthrao
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India
| | - Indranil Chattopadhyay
- Department of Biotechnology, School of Life Sciences, Central University of Tamil Nadu, Thiruvarur, 610101, India.
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28
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Carrillo MP, Sevilla M, Casado M, Piña B, Pastor López E, Matamoros V, Vila-Costa M, Barata C. Impact of the antibiotic doxycycline on the D. magna reproduction, associated microbiome and antibiotic resistance genes in treated wastewater conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122188. [PMID: 37442322 DOI: 10.1016/j.envpol.2023.122188] [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: 02/09/2023] [Revised: 06/02/2023] [Accepted: 07/11/2023] [Indexed: 07/15/2023]
Abstract
Wastewater Treatment Plant (WWTP) effluents are important sources of antibiotics, antibiotic resistance genes (ARGs) and resistant bacteria that threaten aquatic biota and human heath. Antibiotic effects on host-associated microbiomes, spread of ARGs and the consequences for host health are still poorly described. This study investigated changes of the Daphnia magna associated microbiome exposed to the recalcitrant antibiotic doxycycline under artificial reconstituted lab water media (lab water) and treated wastewater media. D. magna individual juveniles were exposed for 10 days to treated wastewater with and without doxycycline, and similarly in lab water. We analysed 16 S rRNA gene sequences to assess changes in community structure, monitored Daphnia offspring production and quantified ARGs abundances by qPCR from both Daphnia and water (before and after the exposure). Results showed that doxycycline and media (lab water or wastewater) had a significant effect modulating Daphnia-associated microbiome composition and one of the most discriminant taxa was Enterococcus spp. Moreover, in lab water, doxycycline reduced the presence of Limnohabitans sp., which are dominant bacteria of the D. magna-associated microbiome and impaired Daphnia reproduction. Contrarily, treated wastewater increased diversity and richness of Daphnia-associated microbiome and promoted fecundity. In addition, the detected ARG genes in both lab water and treated wastewater medium included the qnrS1, sul1, and blaTEM, and the integron-related intI1 gene. The treated wastewater contained about 10 times more ARGs than lab water alone. Furthermore, there was an increase of sul1 in Daphnia cultured in treated wastewater compared to lab water. In addition, there were signs of a higher biodegradation of doxycycline by microbiomes of treated wastewater in comparison to lab water. Thus, results suggest that Daphnia-associated microbiomes are influenced by their environment, and that bacterial communities present in treated wastewater are better suited to cope with the effects of antibiotics.
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Affiliation(s)
- Maria Paula Carrillo
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Marina Sevilla
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Marta Casado
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Benjamin Piña
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Edward Pastor López
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Victor Matamoros
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Maria Vila-Costa
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Carlos Barata
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain.
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29
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Li R, Ling B, Zeng J, Wang X, Yang N, Fan L, Guo G, Li X, Yan F, Zheng J. A nosocomial Pseudomonas aeruginosa ST3495 isolated from a wild Burmese python (Python bivittatus) with suppurative pneumonia and bacteremia in Hainan, China. Braz J Microbiol 2023; 54:2403-2412. [PMID: 37344655 PMCID: PMC10484839 DOI: 10.1007/s42770-023-01038-7] [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: 11/17/2022] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
Pseudomonas aeruginosa is a common infectious agent associated with respiratory diseases in boas and pythons, however, the histopathology, resistance and virulence are yet described for this species. In this study, we investigated a dying Burmese python rescued from tropical rainforest in Hainan. Clinical signs were open-mouthed breathing, abnormal shedding and anorexia. Abundant yellow mucopurulent secretions were observed in highly ectatic segmental bronchi by postmortem. Histopathological lesions included systemic pneumonia, enteritis, nephritis and carditis. P. aeruginosa was the only species isolated from heart blood, kidney, trachea and lung. The phenotype analysis demonstrated that the isolates had strong biofilm, and were sensitive to amikacin, spectinomycin, ciprofloxacin, norfloxacin and polymyxin B, moreover, the LD50 of the most virulent isolate was 2.22×105 cfu/mL in a zebrafish model. Molecular epidemiological analysis revealed that the isolates belonged to sequence type 3495, the common gene patterns were toxA + exoSYT + phzIM + plcHN in virulence and catB + blaTEM + ant (3'')-I+ tetA in resistance. This study highlights that P. aeruginosa should be worth more attention in wildlife conservation and raise the public awareness for the cross infection and cross spread between animals and human.
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Affiliation(s)
- Roushan Li
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
- School of Animal Science and Technology, Hainan University, Haikou, 570228, China
| | - Bo Ling
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Jifeng Zeng
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
- School of Animal Science and Technology, Hainan University, Haikou, 570228, China
- One health institute, Hainan university, Haikou, 570228, China
| | - Xin Wang
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Nuo Yang
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Lixia Fan
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Guiying Guo
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
- School of Science, Hainan University, Haikou, 570228, China
| | - Xuesong Li
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
- One health institute, Hainan university, Haikou, 570228, China
| | - Fei Yan
- Biological and Chemical Engineering College, Panzhihua University, Panzhihua, 617000, China
| | - Jiping Zheng
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China.
- One health institute, Hainan university, Haikou, 570228, China.
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30
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Kneis D, Lemay-St-Denis C, Cellier-Goetghebeur S, Elena AX, Berendonk TU, Pelletier JN, Heß S. Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene. THE ISME JOURNAL 2023; 17:1455-1466. [PMID: 37369703 PMCID: PMC10432401 DOI: 10.1038/s41396-023-01460-7] [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: 01/05/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high level TMP resistance (dfrB10 to dfrB21), the prevalence of dfrB is still unknown due to underreporting, heterogeneity of the analyzed genetic material in terms of isolation sources, and limited bioinformatic processing. In this study, we explored a coherent set of shotgun metagenomic sequences to quantitatively estimate the abundance of dfrB gene variants in aquatic environments. Specifically, we scanned sequences originating from influents and effluents of municipal sewage treatment plants as well as river-borne microbiomes. Our analyses reveal an increased prevalence of dfrB1, dfrB2, dfrB3, dfrB4, dfrB5, and dfrB7 in wastewater microbiomes as compared to freshwater. These gene variants were frequently found in genomic neighborship with other resistance genes, transposable elements, and integrons, indicating their mobility. By contrast, the relative abundances of the more recently discovered variants dfrB9, dfrB10, and dfrB13 were significantly higher in freshwater than in wastewater microbiomes. Moreover, their direct neighborship with other resistance genes or markers of mobile genetic elements was significantly less likely. Our findings suggest that natural freshwater communities form a major reservoir of the recently discovered dfrB gene variants. Their proliferation and mobilization in response to the exposure of freshwater communities to selective TMP concentrations may promote the prevalence of high-level TMP resistance and thus limit the future effectiveness of antimicrobial therapies.
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Affiliation(s)
- David Kneis
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany.
| | - Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Stella Cellier-Goetghebeur
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Alan X Elena
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany
| | | | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
- Chemistry Department, University of Montréal, Montréal, QC, H2V 0B3, Canada
| | - Stefanie Heß
- TU Dresden, Institute of Microbiology, 01062, Dresden, Germany
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31
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Wang J, Xu S, Zhao K, Song G, Zhao S, Liu R. Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162772. [PMID: 36933744 DOI: 10.1016/j.scitotenv.2023.162772] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/14/2023] [Accepted: 03/06/2023] [Indexed: 05/06/2023]
Abstract
Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.
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Affiliation(s)
- Jiaqi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Yangze Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Xu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Kai Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ge Song
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunan Zhao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruiping Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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32
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Grudlewska-Buda K, Bauza-Kaszewska J, Wiktorczyk-Kapischke N, Budzyńska A, Gospodarek-Komkowska E, Skowron K. Antibiotic Resistance in Selected Emerging Bacterial Foodborne Pathogens-An Issue of Concern? Antibiotics (Basel) 2023; 12:antibiotics12050880. [PMID: 37237783 DOI: 10.3390/antibiotics12050880] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Antibiotic resistance (AR) and multidrug resistance (MDR) have been confirmed for all major foodborne pathogens: Campylobacter spp., Salmonella spp., Escherichia coli and Listeria monocytogenes. Of great concern to scientists and physicians are also reports of antibiotic-resistant emerging food pathogens-microorganisms that have not previously been linked to food contamination or were considered epidemiologically insignificant. Since the properties of foodborne pathogens are not always sufficiently recognized, the consequences of the infections are often not easily predictable, and the control of their activity is difficult. The bacteria most commonly identified as emerging foodborne pathogens include Aliarcobacter spp., Aeromonas spp., Cronobacter spp., Vibrio spp., Clostridioides difficile, Escherichia coli, Mycobacterium paratuberculosis, Salmonella enterica, Streptocccus suis, Campylobacter jejuni, Helicobacter pylori, Listeria monocytogenes and Yersinia enterocolitica. The results of our analysis confirm antibiotic resistance and multidrug resistance among the mentioned species. Among the antibiotics whose effectiveness is steadily declining due to expanding resistance among bacteria isolated from food are β-lactams, sulfonamides, tetracyclines and fluoroquinolones. Continuous and thorough monitoring of strains isolated from food is necessary to characterize the existing mechanisms of resistance. In our opinion, this review shows the scale of the problem of microbes related to health, which should not be underestimated.
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Affiliation(s)
- Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Justyna Bauza-Kaszewska
- Department of Microbiology and Food Technology, Bydgoszcz University of Science and Technology, 85-029 Bydgoszcz, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Anna Budzyńska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
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Klair D, Dobhal S, Ahmad A, Hassan ZU, Uyeda J, Silva J, Wang KH, Kim S, Alvarez AM, Arif M. Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms. Front Microbiol 2023; 14:1039292. [PMID: 36876060 PMCID: PMC9981659 DOI: 10.3389/fmicb.2023.1039292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/16/2023] [Indexed: 02/19/2023] Open
Abstract
Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and storage tank water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3-V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phylum in the stream source and associated water samples from wetland taro fields. Cyanobacteria was also a dominant phylum in samples from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. In contrast, Oxford Nanopore MinION was a better choice for microbe classification at the genus and species levels as indicated by samples sequenced for full length 16S rRNA. No reliable taxonomic classification results were obtained while using shotgun metagenome data. In functional analyzes, only 12% of the genes were shared by two consortia and 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Full descriptions of microbial communities and their functions are essential for the development of better water management strategies aimed to produce safer fresh produce and to protect plant, animal, human and environmental health. Quantitative comparisons illustrated the importance of selecting the appropriate analytical method depending on the level of taxonomic delineation sought in each microbiome.
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Affiliation(s)
- Diksha Klair
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Amjad Ahmad
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Zohaib Ul Hassan
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
- Department of Bio-Medical Measurement, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jensen Uyeda
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Joshua Silva
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Koon-Hui Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Seil Kim
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
- Department of Bio-Medical Measurement, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Anne M. Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
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Zhao F, Wang B, Huang K, Yin J, Ren X, Wang Z, Zhang XX. Correlations among Antibiotic Resistance Genes, Mobile Genetic Elements and Microbial Communities in Municipal Sewage Treatment Plants Revealed by High-Throughput Sequencing. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3593. [PMID: 36834289 PMCID: PMC9965123 DOI: 10.3390/ijerph20043593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Municipal sewage treatment plants (MSTPs) are environmental pools for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which is cause for growing environmental-health concerns. In this study, the effects of different wastewater treatment processes on microbial antibiotic resistance in four MSTPs were investigated. PCR, q-PCR, and molecular cloning integrally indicated that the tetracycline resistance (tet) genes significantly reduced after activated-sludge treatment. Illumina high-throughput sequencing revealed that the broad-spectrum profile of ARGs and mobile element genes (MGEs) were also greatly decreased by one order of magnitude via activated sludge treatment and were closely associated with each other. Correlations between ARGs and bacterial communities showed that potential ARB, such as Acinetobacter, Bacteroides, and Cloaibacterium, were removed by the activated-sludge process. Sedimentation processes cannot significantly affect the bacterial structure, resulting in the relative abundance of ARGs, MGEs, and ARB in second-clarifier effluent water being similar to activated sludge. A comprehensive study of ARGs associated with MGEs and bacterial structure might be technologically guided for activated sludge design and operation in the MSTPs, to purposefully control ARGs carried by pathogenic hosts and mobility.
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Affiliation(s)
- Fuzheng Zhao
- Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou Jiaotong University, Lanzhou 730070, China
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Bo Wang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Jinbao Yin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xuechang Ren
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Zhu Wang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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35
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Zhao B, van Bodegom PM, Trimbos KB. Antibiotic Resistance Genes in Interconnected Surface Waters as Affected by Agricultural Activities. Biomolecules 2023; 13:biom13020231. [PMID: 36830600 PMCID: PMC9953135 DOI: 10.3390/biom13020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 01/27/2023] Open
Abstract
Pastures have become one of the most important sources of antibiotic resistance genes (ARGs) pollution, bringing risks to human health through the environment and the food that is grown there. Another significant source of food production is greenhouse horticulture, which is typically located near pastures. Through waterways, pasture-originated ARGs may transfer to the food in greenhouses. However, how these pasture-originated ARGs spread to nearby waterways and greenhouses has been much less investigated, while this may pose risks to humans through agricultural products. We analyzed 29 ARGs related to the most used antibiotics in livestock in the Netherlands at 16 locations in an agricultural area, representing pastures, greenhouses and lakes. We found that ARGs were prevalent in all surface waters surrounding pastures and greenhouses and showed a similar composition, with sulfonamide ARGs being dominant. This indicates that both pastures and greenhouses cause antibiotic resistance pressures on neighboring waters. However, lower pressures were found in relatively larger and isolated lakes, suggesting that a larger water body or a non-agricultural green buffer zone could help reducing ARG impacts from agricultural areas. We also observed a positive relationship between the concentrations of the class 1 integron (intl1 gene)-used as a proxy for horizontal gene transfer-and ARG concentration and composition. This supports that horizontal gene transfer might play a role in dispersing ARGs through landscapes. In contrast, none of the measured four abiotic factors (phosphate, nitrate, pH and dissolved oxygen) showed any impact on ARG concentrations. ARGs from different classes co-occurred, suggesting simultaneous use of different antibiotics. Our findings help to understand the spatial patterns of ARGs, specifically the impacts of ARGs from pastures and greenhouses on each other and on nearby waterways. In this way, this study guides management aiming at reducing ARGs' risk to human health from agricultural products.
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36
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Navarro A, Sanseverino I, Cappelli F, Lahm A, Niegowska M, Fabbri M, Paracchini V, Petrillo M, Skejo H, Valsecchi S, Pedraccini R, Guglielmetti S, Frattini S, Villani G, Lettieri T. Study of antibiotic resistance in freshwater ecosystems with low anthropogenic impact. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159378. [PMID: 36272475 DOI: 10.1016/j.scitotenv.2022.159378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
This study aimed to investigate the bacterial diversity and the background level of antibiotic resistance in two freshwater ecosystems with low anthropogenic impact in order to evaluate the presence of natural antimicrobial resistance in these areas and its potential to spread downstream. Water samples from a pre-Alpine and an Apennine river (Variola and Tiber, respectively) were collected in three different sampling campaigns and bacterial diversity was assessed by 16S sequencing, while the presence of bacteria resistant to five antibiotics was screened using a culturable approach. Overall bacterial load was higher in the Tiber River compared with the Variola River. Furthermore, the study revealed the presence of resistant bacteria, especially the Tiber River showed, for each sampling, the presence of resistance to all antibiotics tested, while for the Variola River, the detected resistance was variable, comprising two or more antibiotics. Screening of two resistance genes on a total of one hundred eighteen bacterial isolates from the two rivers showed that blaTEM, conferring resistance to β-lactam antibiotics, was dominant and present in ~58 % of isolates compared to only ~9 % for mefA/E conferring resistance to macrolides. Moreover, β-lactam resistance was detected in various isolates showing also resistance to additional antibiotics such as macrolides, aminoglycosides and tetracyclines. These observations would suggest the presence of co-resistant bacteria even in non-anthropogenic environments and this resistance may spread from the environment to humans and/or animals.
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Affiliation(s)
- Anna Navarro
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Isabella Sanseverino
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Francesca Cappelli
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy; Water Research Institute IRSA-CNR, Via del Mulino 19, Brugherio 20861, MB, Italy
| | - Armin Lahm
- Bioinformatic project support, P.za S.M. Liberatrice 18, 00153 Roma, Italy
| | - Magdalena Niegowska
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Marco Fabbri
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Valentina Paracchini
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | | | - Helle Skejo
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Sara Valsecchi
- Water Research Institute IRSA-CNR, Via del Mulino 19, Brugherio 20861, MB, Italy
| | | | | | | | - Gabriella Villani
- Energy and Sustainable Economic Development (ENEA), Via E. Fermi 2749, 21027 Ispra, VA, Italy
| | - Teresa Lettieri
- European Commission Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, VA, Italy.
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37
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Depta J, Niedźwiedzka-Rystwej P. The Phenomenon of Antibiotic Resistance in the Polar Regions: An Overview of the Global Problem. Infect Drug Resist 2023; 16:1979-1995. [PMID: 37034396 PMCID: PMC10081531 DOI: 10.2147/idr.s369023] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/02/2022] [Indexed: 04/11/2023] Open
Abstract
The increasing prevalence of antibiotic resistance is a global problem in human and animal health. This leads to a reduction in the therapeutic effectiveness of the measures used so far and to the limitation of treatment options, which may pose a threat to human health and life. The problem of phenomenon of antibiotic resistance affects more and more the polar regions. This is due to the increase in tourist traffic and the number of people staying at research stations, unmodernised sewage systems in inhabited areas, as well as the migration of animals or the movement of microplastics, which may contain resistant bacteria. Research shows that the presence of antibiotic resistance genes is more dominant in zones of human and wildlife influence than in remote areas. In a polluted environment, there is evidence of a direct correlation between human activity and the spread and survival of antibiotic-resistant bacteria. Attention should be paid to the presence of resistance to synthetic and semi-synthetic antibiotics in the polar regions, which is likely to be correlated with human presence and activity, and possible steps to be taken. We need to understand many more aspects of this, such as bacterial epigenetics and environmental stress, in order to develop effective strategies for minimizing the spread of antibiotic resistance genes. Studying the diversity and abundance of antibiotic resistance genes in regions with less anthropogenic activity could provide insight into the diversity of primary genes and explain the historical evolution of antibiotic resistance.
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Affiliation(s)
- Julia Depta
- Institute of Biology, University of Szczecin, Szczecin, 71-412, Poland
| | - Paulina Niedźwiedzka-Rystwej
- Institute of Biology, University of Szczecin, Szczecin, 71-412, Poland
- Correspondence: Paulina Niedźwiedzka-Rystwej, Institute of Biology, University of Szczecin, Szczecin, 71-412, Poland, Tel +48 91 444 15 15, Email
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38
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Clark JR, Terwilliger A, Avadhanula V, Tisza M, Cormier J, Javornik-Cregeen S, Ross MC, Hoffman KL, Troisi C, Hanson B, Petrosino J, Balliew J, Piedra PA, Rios J, Deegan J, Bauer C, Wu F, Mena KD, Boerwinkle E, Maresso AW. Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program. Front Public Health 2023; 11:1137881. [PMID: 37026145 PMCID: PMC10070845 DOI: 10.3389/fpubh.2023.1137881] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 04/08/2023] Open
Abstract
Molecular analysis of public wastewater has great potential as a harbinger for community health and health threats. Long-used to monitor the presence of enteric viruses, in particular polio, recent successes of wastewater as a reliable lead indicator for trends in SARS-CoV-2 levels and hospital admissions has generated optimism and emerging evidence that similar science can be applied to other pathogens of pandemic potential (PPPs), especially respiratory viruses and their variants of concern (VOC). However, there are substantial challenges associated with implementation of this ideal, namely that multiple and distinct fields of inquiry must be bridged and coordinated. These include engineering, molecular sciences, temporal-geospatial analytics, epidemiology and medical, and governmental and public health messaging, all of which present their own caveats. Here, we outline a framework for an integrated, state-wide, end-to-end human pathogen monitoring program using wastewater to track viral PPPs.
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Affiliation(s)
- Justin R. Clark
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Austen Terwilliger
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Michael Tisza
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Juwan Cormier
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Sara Javornik-Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Matthew Clayton Ross
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - Catherine Troisi
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Blake Hanson
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Center for Infectious Diseases, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Alkek Center for Metagenomics and Microbiome Research, CMMR, Baylor College of Medicine, Houston, TX, United States
| | - John Balliew
- El Paso Water Utility, El Paso, TX, United States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Pediatrics Department, Baylor College of Medicine, Houston, TX, United States
| | - Janelle Rios
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Jennifer Deegan
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Cici Bauer
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Department of Biostatistics and Data Science, UTHealth School of Public Health, Houston, TX, United States
| | - Fuqing Wu
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Kristina D. Mena
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
| | - Eric Boerwinkle
- UTHealth Houston School of Public Health, Houston, TX, United States
- Texas Epidemic Public Health Institute (TEPHI), UTHealth Houston, Houston, TX, United States
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, Houston, TX, United States
| | - Anthony W. Maresso
- TAILOR Labs, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- Anthony W. Maresso
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Batista MPB, Cavalcante FS, Alves Cassini ST, Pinto Schuenck R. Diversity of bacteria carrying antibiotic resistance genes in hospital raw sewage in Southeastern Brazil. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 87:239-250. [PMID: 36640035 DOI: 10.2166/wst.2022.427] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In recent decades, antibiotic-resistant bacteria (ARB) emerged and spread among humans and animals worldwide. In this study, we evaluated the presence of ARB and antibiotic resistance genes (ARGs) in the raw sewage of two hospitals in Brazil. Sewage aliquots were inoculated in a selective medium with antibiotics. Bacterial identification was performed by MALDI-TOF and ARGs were assessed by polymerase chain reaction (PCR). A total of 208 strains from both hospitals were isolated (H1 = 117; H2 = 91). A wide variety of Enterobacterales and non-Enterobacterales species were isolated and most of them were Enterobacter spp. (13.0%), Proteus mirabilis (10.1%), and Klebsiella pneumoniae (9.6%). blaTEM and blaKPC were the most frequent β-lactamase-encoding genes and the predominant macrolide resistance genes were mph(A) and mel. Many species had the three tetracycline resistance genes (tetD, tetM, tetA) and strB was the prevalent aminoglycoside resistance gene. Two Staphylococcus haemolyticus strains had the mecA gene. Quinolone, colistin, and vancomycin resistance genes were not found. This study showed that hospital raw sewage is a great ARB and ARG disseminator. Strict monitoring of hospital sewage treatment is needed to avoid the spread of these genes among bacteria in the environment.
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Affiliation(s)
| | | | | | - Ricardo Pinto Schuenck
- Department of Pathology, Health Sciences Center, Federal University of Espírito Santo, Vitória, Brazil E-mail:
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Selvarajan R, Obize C, Sibanda T, Abia ALK, Long H. Evolution and Emergence of Antibiotic Resistance in Given Ecosystems: Possible Strategies for Addressing the Challenge of Antibiotic Resistance. Antibiotics (Basel) 2022; 12:28. [PMID: 36671228 PMCID: PMC9855083 DOI: 10.3390/antibiotics12010028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR.
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Affiliation(s)
- Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Chinedu Obize
- Centre d’étude de la Forêt, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Timothy Sibanda
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Akebe Luther King Abia
- Department of Microbiology, Venda University, Thohoyando 1950, South Africa
- Environmental Research Foundation, Westville 3630, South Africa
| | - Haijun Long
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
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Cellier-Goetghebeur S, Lafontaine K, Lemay-St-Denis C, Tsamo P, Bonneau-Burke A, Copp JN, Pelletier JN. Discovery of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases in Diverse Environmental Settings Suggests an Evolutionary Advantage Unrelated to Antibiotic Resistance. Antibiotics (Basel) 2022; 11:1768. [PMID: 36551425 PMCID: PMC9774602 DOI: 10.3390/antibiotics11121768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
Type B dihydrofolate reductases (DfrB) are intrinsically highly resistant to the widely used antibiotic trimethoprim, posing a threat to global public health. The ten known DfrB family members have been strongly associated with genetic material related to the application of antibiotics. Several dfrB genes were associated with multidrug resistance contexts and mobile genetic elements, integrated both in chromosomes and plasmids. However, little is known regarding their presence in other environments. Here, we investigated the presence of dfrB beyond the traditional areas of enquiry by conducting metagenomic database searches from environmental settings where antibiotics are not prevalent. Thirty putative DfrB homologues that share 62 to 95% identity with characterized DfrB were identified. Expression of ten representative homologues verified trimethoprim resistance in all and dihydrofolate reductase activity in most. Contrary to samples associated with the use of antibiotics, the newly identified dfrB were rarely associated with mobile genetic elements or antibiotic resistance genes. Instead, association with metabolic enzymes was observed, suggesting an evolutionary advantage unrelated to antibiotic resistance. Our results are consistent with the hypothesis that multiple dfrB exist in diverse environments from which dfrB were mobilized into the clinically relevant resistome. Our observations reinforce the need to closely monitor their progression.
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Affiliation(s)
- Stella Cellier-Goetghebeur
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Kiana Lafontaine
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Claudèle Lemay-St-Denis
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Princesse Tsamo
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
| | - Alexis Bonneau-Burke
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
| | - Janine N. Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joelle N. Pelletier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
- The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC H3A 0B8, Canada
- Chemistry Department, Université de Montréal, Montréal, QC H2V 0B3, Canada
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Wei X, Huang Z, Jiang L, Li Y, Zhang X, Leng Y, Jiang C. Charting the landscape of the environmental exposome. IMETA 2022; 1:e50. [PMID: 38867899 PMCID: PMC10989948 DOI: 10.1002/imt2.50] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/13/2022] [Accepted: 07/30/2022] [Indexed: 06/14/2024]
Abstract
The exposome depicts the total exposures in the lifetime of an organism. Human exposome comprises exposures from environmental and humanistic sources. Biological, chemical, and physical environmental exposures pose potential health threats, especially to susceptible populations. Although still in its nascent stage, we are beginning to recognize the vast and dynamic nature of the exposome. In this review, we systematically summarize the biological and chemical environmental exposomes in three broad environmental matrices-air, soil, and water; each contains several distinct subcategories, along with a brief introduction to the physical exposome. Disease-related environmental exposures are highlighted, and humans are also a major source of disease-related biological exposures. We further discuss the interactions between biological, chemical, and physical exposomes. Finally, we propose a list of outstanding challenges under the exposome research framework that need to be addressed to move the field forward. Taken together, we present a detailed landscape of environmental exposome to prime researchers to join this exciting new field.
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Affiliation(s)
- Xin Wei
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Zinuo Huang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Liuyiqi Jiang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Yueer Li
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
| | - Xinyue Zhang
- Department of GeneticsStanford UniversityStanfordCaliforniaUSA
| | - Yuxin Leng
- Department of Intensive Care UnitPeking University Third HospitalBeijingChina
| | - Chao Jiang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouZhejiangChina
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangChina
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43
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Rumky J, Kruglova A, Repo E. Fate of antibiotic resistance genes (ARGs) in wastewater treatment plant: Preliminary study on identification before and after ultrasonication. ENVIRONMENTAL RESEARCH 2022; 215:114281. [PMID: 36096165 DOI: 10.1016/j.envres.2022.114281] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
This study collected sludge samples from four different sections of a local wastewater treatment plant in Mikkeli, Finland, for antibiotic resistance genes (ARGs) analysis. Here, we examine the seven representative ARGs in sludge, encoding erythromycin (ermB), tetracycline (tetA, tetC, tetQ, tetW) and sulphonamide (sul1) to check abundance before and after ultrasonication. The class 1 integron (intl1) was also observed as an indicator of antibiotic resistance and horizontal gene transmission. The pre-treatment condition included 10 min of ultrasonication (US) for the sludge sample before freeze-drying. The droplet digital PCR system was used to assess the ARGs from the samples, and it was found that ARGs were not effectively eliminated by pre-treatment. After ultrasonication, tetA, tetC and tetQ did not show any variation but tetW showed 20 copies/ng of lower abundance in digested sludge than raw sludge, and a similar abundance was found in dewatered sludge. For MBR sludge, only ermB showed 1000 copies/ng higher abundance compared to the raw sample and surprisingly it did not show the presence of any other types of ARG. This study provides an overview of the appearance of ARGs in regional municipal sludge for further research reflection.
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Affiliation(s)
- Jannatul Rumky
- Department of Separation Science, LUT University, Sammonkatu 12, FI-50130, Mikkeli, Finland.
| | - Antonina Kruglova
- Department of Built Environment, Aalto University, Tietotie 1E, 15200, Espoo, Finland
| | - Eveliina Repo
- Department of Separation Science, LUT University, Sammonkatu 12, FI-50130, Mikkeli, Finland
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He H, Choi Y, Wu SJ, Fang X, Anderson AK, Liou SY, Roberts MC, Lee Y, Dodd MC. Application of Nucleotide-Based Kinetic Modeling Approaches to Predict Antibiotic Resistance Gene Degradation during UV- and Chlorine-Based Wastewater Disinfection Processes: From Bench- to Full-Scale. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15141-15155. [PMID: 36098629 DOI: 10.1021/acs.est.2c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study investigated antibiotic resistance gene (ARG) degradation kinetics in wastewaters during bench- and full-scale treatment with UV light and chlorine─with the latter maintained as free available chlorine (FAC) in low-ammonia wastewater and converted into monochloramine (NH2Cl) in high-ammonia wastewater. Twenty-three 142-1509 bp segments (i.e., amplicons) of seven ARGs (blt, mecA, vanA, tet(A), ampC, blaNDM, blaKPC) and the 16S rRNA gene from antibiotic resistant bacteria (ARB) strains Bacillus subtilis, Staphylococcus aureus, Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were monitored as disinfection targets by qPCR. Rate constants for ARG and 16S rRNA gene amplicon degradation by UV, FAC, and NH2Cl were measured in phosphate buffer and used to expand and validate several recently developed approaches to predict DNA segment degradation rate constants based solely on their nucleotide contents, which were then applied to model ARG degradation during bench-scale treatment in buffer and wastewater matrixes. Kinetics of extracellular and intracellular ARG degradation by UV and FAC were well predicted up to ∼1-2-log10 elimination, although with decreasing accuracy at higher levels for intracellular genes, while NH2Cl yielded minimal degradation under all conditions (agreeing with predictions). ARB inactivation kinetics varied substantially across strains, with intracellular gene degradation lagging cell inactivation in each case. ARG degradation levels observed during full-scale disinfection at two wastewater treatment facilities were consistent with bench-scale measurements and predictions, where UV provided ∼1-log10 ARG degradation, and chlorination of high-ammonia wastewater (dominated by NH2Cl) yielded minimal ARG degradation.
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Affiliation(s)
- Huan He
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, Washington 98195, United States
| | - Yegyun Choi
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sean J Wu
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, Washington 98195, United States
| | - Xuzhi Fang
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, Washington 98195, United States
| | - Annika K Anderson
- Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Sin-Yi Liou
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, Washington 98195, United States
| | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Michael C Dodd
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, Washington 98195, United States
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45
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Sanz C, Casadoi M, Tadic Đ, Pastor-López EJ, Navarro-Martin L, Parera J, Tugues J, Ortiz CA, Bayona JM, Piña B. Impact of organic soil amendments in antibiotic levels, antibiotic resistance gene loads, and microbiome composition in corn fields and crops. ENVIRONMENTAL RESEARCH 2022; 214:113760. [PMID: 35753374 DOI: 10.1016/j.envres.2022.113760] [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: 02/25/2022] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
The potential spreading of antibiotic resistance genes (ARG) into agricultural fields and crops represent a fundamental limitation on the use of organic fertilization in food production systems. We present here a study of the effect of spreading four types of organic soil amendments (raw pig slurry, liquid and solid fractions, and a digested derivative) on demonstrative plots in two consecutive productive cycles of corn harvest (Zea mays), using a mineral fertilizer as a control, following the application of organic amendments at 32-62 T per ha (150 kg total N/ha) and allowing 5-8 months between fertilization and harvest. A combination of qPCR and high-throughput 16S rDNA sequencing methods showed a small, but significant impact of the fertilizers in both ARG loads and microbiomes in soil samples, particularly after the second harvesting cycle. The slurry solid fraction showed the largest impact on both ARG loads and microbiome variation, whereas its digestion derivatives showed a much smaller impact. Soil samples with the highest ARG loads also presented increased levels of tetracyclines, indicating a potential dual hazard by ARG and antibiotic residues linked to some organic amendments. Unlike soils, no accumulation of ARG or antibiotics was observed in corn leaves (used as fodder) or grains, and no grain sample reached detection limits for neither parameter. These results support the use of organic soil amendments in corn crops, while proposing the reduction of the loads of ARGs and antibiotics from the fertilizers to greatly reduce their potential risk.
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Affiliation(s)
- Claudia Sanz
- IDAEA-CSIC, Jordi Girona, 18. E-08034, Barcelona, Spain
| | - Marta Casadoi
- IDAEA-CSIC, Jordi Girona, 18. E-08034, Barcelona, Spain
| | - Đorde Tadic
- IDAEA-CSIC, Jordi Girona, 18. E-08034, Barcelona, Spain
| | | | | | - Joan Parera
- DACC, Departament d'Acció Climàtica, Alimentació i Agenda Rural, Generalitat de Catalunya, Gran Via de les Corts Catalanes, 612-614, E-08007, Barcelona, Spain
| | - Jordi Tugues
- DACC, Departament d'Acció Climàtica, Alimentació i Agenda Rural, Generalitat de Catalunya, Gran Via de les Corts Catalanes, 612-614, E-08007, Barcelona, Spain
| | - Carlos A Ortiz
- DACC, Departament d'Acció Climàtica, Alimentació i Agenda Rural, Generalitat de Catalunya, Gran Via de les Corts Catalanes, 612-614, E-08007, Barcelona, Spain
| | | | - Benjamin Piña
- IDAEA-CSIC, Jordi Girona, 18. E-08034, Barcelona, Spain.
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Waśko I, Kozińska A, Kotlarska E, Baraniak A. Clinically Relevant β-Lactam Resistance Genes in Wastewater Treatment Plants. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192113829. [PMID: 36360709 PMCID: PMC9657204 DOI: 10.3390/ijerph192113829] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 05/17/2023]
Abstract
Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health's concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lactams, the most widely used antibiotics. Therefore, this paper aimed to present the available research data for ARGs in WWTPs that confer resistance to β-lactam antibiotics, with a particular emphasis on clinically important life-threatening mechanisms of resistance, including extended-spectrum β-lactamases (ESBLs) and carbapenemases (KPC, NDM).
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Affiliation(s)
- Izabela Waśko
- Department of Biomedical Research, National Medicines Institute, Chelmska 30/34, 00-725 Warsaw, Poland
- Correspondence: ; Tel.: +48-228-410-623
| | - Aleksandra Kozińska
- Department of Biomedical Research, National Medicines Institute, Chelmska 30/34, 00-725 Warsaw, Poland
| | - Ewa Kotlarska
- Genetics and Marine Biotechnology Department, Institute of Oceanology of the Polish Academy of Sciences, Powstancow Warszawy 55, 81-712 Sopot, Poland
| | - Anna Baraniak
- Department of Biomedical Research, National Medicines Institute, Chelmska 30/34, 00-725 Warsaw, Poland
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Liu L, Zhang Y, Chen H, Teng Y. Fate of resistome components and characteristics of microbial communities in constructed wetlands and their receiving river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157226. [PMID: 35809723 DOI: 10.1016/j.scitotenv.2022.157226] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Currently, most researches focus on that constructed wetlands (CWs) achieve desirable removal of antibiotics, antibiotic resistance genes (ARGs) and human pathogens. However, few studies have assessed the fate of resistome components, especially the behavior and cooccurrence of ARGs, mobile genetic elements (MGEs) and virulence factors (VFs). Therefore, characteristics of microbial communities (MCs) in CWs and their receiving rivers also deserve attention. These factors are critical to water ecological security. This study used two CWs to explore the fate of resistome components and characteristics of MCs in the CWs and their receiving river. Eleven samples were collected from the two CWs and their receiving river. High-throughput profiles of ARGs and microbial taxa in the samples were characterized. 31 ARG types consisting of 400 subtypes with total relative abundance 42.63-84.94× /Gb of sequence were detected in CWs, and 62.07-88.08× /Gb of sequence in river, evidencing that ARG pollution covered CWs and the river, and implying huge potential risks from ARGs. MGEs and VFs were detected, and tnpA, IS91 and intI1 were the three dominant MGEs, while Flagella. Type IV pili and peritrichous flagella were main VFs. Both CWs can remove ARGs, MGEs and VFs efficiently. However, some ARGs were difficult to remove, such as sul1 and sul2, and certain ARGs remained in the effluent of the CWs. The co-occurrence of ARGs, MGEs, and VFs implies the risk of antibiotic resistance and dissemination of ARGs. Eighty-five types of human pathogen were detected in the river samples, particularly Pseudomonas aeruginosa, Bordetella bronchiseptica, Aeromonas hydrophila and Helicobacter pylori. Correlation analysis indicated that MCs had significant effects on the profiles of ARGs in the water environment. This study reveals potential risks of the reuse of reclaimed water, and illustrates the removal ability of ARGs and related elements by CWs. This study will be helpful for monitoring and managing resistomes in water environments.
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Affiliation(s)
- Linmei Liu
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yuxin Zhang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Haiyang Chen
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yanguo Teng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China.
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48
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Kraemer SA, Barbosa da Costa N, Oliva A, Huot Y, Walsh DA. A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use. Front Microbiol 2022; 13:995418. [PMID: 36338036 PMCID: PMC9629221 DOI: 10.3389/fmicb.2022.995418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome – the diversity of ARGs – under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.
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Affiliation(s)
- Susanne A. Kraemer
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Department of Biology, Concordia University, Montreal, QC, Canada
- *Correspondence: Susanne A. Kraemer,
| | | | - Anais Oliva
- Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Yannick Huot
- Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - David A. Walsh
- Department of Biology, Concordia University, Montreal, QC, Canada
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de Nies L, Busi SB, Kunath BJ, May P, Wilmes P. Mobilome-driven segregation of the resistome in biological wastewater treatment. eLife 2022; 11:81196. [PMID: 36111782 PMCID: PMC9643006 DOI: 10.7554/elife.81196] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/15/2022] [Indexed: 12/05/2022] Open
Abstract
Biological wastewater treatment plants (BWWTP) are considered to be hotspots for the evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of 15 AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS and sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both. Combined and timepoint-specific analyses of gene, transcript and protein abundances further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, and here MGEs also contributed differentially to the dissemination of the corresponding ARGs. Collectively our findings pave the way toward understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.
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Affiliation(s)
- Laura de Nies
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg
| | | | | | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg
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Li S, Ondon BS, Ho SH, Jiang J, Li F. Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156544. [PMID: 35679932 DOI: 10.1016/j.scitotenv.2022.156544] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
This study aims to discuss the following: (1) occurrence and proliferation of antibiotic resistance in wastewater treatment plants (WWTPs); (2) factors influencing antibiotic resistance bacteria and genes in WWTPs; (3) tools to assess antibiotic resistance in WWTPs; (4) environmental contamination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from WWTPs; (5) effects of ARB and ARGs from WWTPs on human health; and (6) treatment strategies. In general, resistant and multi-resistant bacteria, including Enterobacteriaceae, Pseudomonas aeruginosa, and Escherichia coli, exist in various processes of WWTPs. The existence of ARB and ARGs results from the high concentration of antibiotics in wastewater, which promote selective pressures on the local bacteria present in WWTPs. Thus, improving wastewater treatment technology and avoiding the misuse of antibiotics is critical to overcoming the threat of proliferation of ARBs and ARGs. Numerous factors can affect the development of ARB and ARGs in WWTPs. Abiotic factors can affect the bacterial community dynamics, thereby, affecting the applicability of ARB during the wastewater treatment process. Furthermore, the organic loads and other nutrients influence bacterial survival and growth. Specifically, molecular methods for the rapid characterization and detection of ARBs or their genes comprise DNA sequencing, real-time PCR, simple and multiplex PCR, and hybridization-based technologies, including micro- and macro-arrays. The reuse of effluent from WWTPs for irrigation is an efficient method to overcome water scarcity. However, there are also some potential environmental risks associated with this practice, such as increase in the levels of antibiotic resistance in the soil microbiome. Human mortality rates may significantly increase, as ARB can lead to resistance among several types of antibiotics or longer treatment times. Some treatment technologies, such as anaerobic and aerobic treatment, coagulation, membrane bioreactors, and disinfection processes, are considered potential techniques to restrict antibiotic resistance in the environment.
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Affiliation(s)
- Shengnan Li
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Brim Stevy Ondon
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Jiwei Jiang
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Fengxiang Li
- Key Laboratory of Pollution Processes and Environmental Criteria of the Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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