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Chen C, Li Y, Wu Z, Ruan Y, Long T, Wang X, Li W, Ren H, Liao X, Liu Y, Lian X, Sun J. Cat and dog feces as reservoirs of diverse novel antibiotic resistance genes. ENVIRONMENTAL RESEARCH 2024; 261:119690. [PMID: 39068967 DOI: 10.1016/j.envres.2024.119690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/21/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024]
Abstract
Companion animals have the potential to greatly enhance the physical and mental health of humans, thus leading to an increased focus on the interactions between humans and pets. Currently, the inappropriate and excessive utilization of antimicrobial agents has become prevalent in veterinary clinical practice for pets. This antibiotic contamination phenomenon has a profound impact on the enrichment of antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) in pets. However, the pet-associated resistome, especially the novel ARGs in pets, represents a relatively neglected area. In this study, we successfully constructed a total of 12 libraries using the functional metagenomics approach to assess the diversity of ARGs in pet cats and dogs from four pet hospitals. Through the integration of functional screening and high-throughput sequencing, a total of 122 antibiotic resistance determinants were identified, of which 15 were classified as putative novel ARGs originating from five classes. Functional assessment demonstrated that 6 novel ARGs including one β-lactam, two macrolides, two aminoglycosides, and one rifamycin (RIF), namely blaPF, ermPF, msrPF, aac(6')PF, aph(3')PF, and arrPF, exhibited functionally activity in conferring bacterial phenotypic resistance by increasing the minimum inhibitory concentrations (MICs) with a 4- to 128-fold. Genetic context analysis demonstrated that, with the exception of aac(6')PF and arrPF, the remaining four novel ARGs were found adjacent to mobile genetic elements (MGEs) including IS elements or transposases, which provided a prerequisite for horizontal transfer of these novel ARGs, thereby offering an explanation for their detection in diverse samples collected from various sampling sites. The current study has unveiled the significant role of cat and dog feces as one source of reservoirs of diverse novel ARGs, while also highlighting the potential adverse consequences of their further spread to medically significant pathogens and human commensal organisms.
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Affiliation(s)
- Caiping Chen
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Yuanyuan Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihong Wu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Yali Ruan
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Tengfei Long
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Xiran Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Wenjie Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Hao Ren
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoping Liao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China
| | - Yahong Liu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
| | - Xinlei Lian
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China.
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, China.
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2
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Gunarathne V, Phillips AJ, Zanoletti A, Rajapaksha AU, Vithanage M, Di Maria F, Pivato A, Korzeniewska E, Bontempi E. Environmental pitfalls and associated human health risks and ecological impacts from landfill leachate contaminants: Current evidence, recommended interventions and future directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169026. [PMID: 38056656 DOI: 10.1016/j.scitotenv.2023.169026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/17/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
The improper management of solid waste, particularly the dumping of untreated municipal solid waste, poses a growing global challenge in both developed and developing nations. The generation of leachate is one of the significant issues that arise from this practice, and it can have harmful impacts on both the environment and public health. This paper presents an overview of the primary waste types that generate landfill leachate and their characteristics. This includes examining the distribution of waste types in landfills globally and how they have changed over time, which can provide valuable insights into potential pollutants in a given area and their trends. With a lack of specific regulations and growing concerns regarding environmental and health impacts, the paper also focuses on emerging contaminants. Furthermore, the environmental and ecological impacts of leachate, along with associated health risks, are analyzed. The potential applications of landfill leachate, suggested interventions and future directions are also discussed in the manuscript. Finally, this work addresses future research directions in landfill leachate studies, with attention, for the first time to the potentialities that artificial intelligence can offer for landfill leachate management, studies, and applications.
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Affiliation(s)
- Viraj Gunarathne
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka; University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Ankur J Phillips
- Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Alessandra Zanoletti
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Anushka Upamali Rajapaksha
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka; Instrument Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
| | - Meththika Vithanage
- Ecosphere Resilience Research Centre, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, CO 10250, Sri Lanka
| | - Francesco Di Maria
- LAR5 Laboratory, Dipartimento di Ingegneria, University of Perugia, via G. Duranti 93, 06125 Perugia, Italy
| | - Alberto Pivato
- DICEA - Department of Civil, Environmental and Architectural Engineering, University of Padova, Via Marzolo 9, 35131 Padova, Italy
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, The Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-719 Olsztyn, Poland
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy.
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3
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Lin H, Peddada SD. Multigroup analysis of compositions of microbiomes with covariate adjustments and repeated measures. Nat Methods 2024; 21:83-91. [PMID: 38158428 PMCID: PMC10776411 DOI: 10.1038/s41592-023-02092-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/17/2023] [Indexed: 01/03/2024]
Abstract
Microbiome differential abundance analysis methods for two groups are well-established in the literature. However, many microbiome studies involve more than two groups, sometimes even ordered groups such as stages of a disease, and require different types of comparison. Standard pairwise comparisons are inefficient in terms of power and false discovery rates. In this Article, we propose a general framework, ANCOM-BC2, for performing a wide range of multigroup analyses with covariate adjustments and repeated measures. We illustrate our methodology through two real datasets. The first example explores the effects of aridity on the soil microbiome, and the second example investigates the effects of surgical interventions on the microbiome of patients with inflammatory bowel disease.
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Affiliation(s)
- Huang Lin
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park, NC, USA
- Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD, USA
| | - Shyamal Das Peddada
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park, NC, USA.
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4
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Chukwu KB, Abafe OA, Amoako DG, Essack SY, Abia ALK. Environmental concentrations of antibiotics, biocides, and heavy metals fail to induce phenotypic antimicrobial resistance in Escherichia coli. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165721. [PMID: 37482346 DOI: 10.1016/j.scitotenv.2023.165721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Most anthropogenically affected environments contain mixtures of pollutants from different sources. The impact of these pollutants is usually the combined effect of the individual polluting constituents. However, how these stressors contribute to the development of antimicrobial resistance in environmental microorganisms is poorly understood. Thus, a 30-day exposure experiment to environmental and sub-inhibitory concentrations of oxytetracycline, amoxicillin, zinc, copper, BAC (benzalkonium chloride) 10 and DADMAC (diallyldimethylammonium chloride) 12, was conducted using fully susceptible E. coli ATCC 25922 to ascertain any development of phenotypic or genotypic resistance. Furthermore, wild-type isolates were collected from the same aquatic environment as the stressors, analysed for phenotypic resistance using the disk diffusion method and genotypically through whole genome sequencing. Exposure to the various concentrations and combinations of the stressors did not trigger phenotypic resistance in the experimental bacteria. Furthermore, genotypic analysis of the WGS on the exposed isolates only found the macrolide resistance mdf(A) gene (also present in the control strain) and the disinfectant resistance gene sitABCD. With further analysis for single nucleotide variants (SNV), mutations were detected for 19 genes that encoded for oxidative stress, DNA repair, membrane proteins efflux systems, growth and persister formations except for the robA, a transcription protein subset of the ArcC/XylS family of proteins, which confer multidrug resistance in E. coli. This indicates that exposure to sub-inhibitory concentrations of antibiotics, heavy metals and biocide residues in the aquatic environmental concentrations of the stressors identified in the current study could not induce phenotypic or genotypic resistance but encoded for genes responsible for the development of persistence and tolerance in bacteria, which could be a precursor to the development of resistance in environmental bacteria.
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Affiliation(s)
- Kelechi B Chukwu
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ovokeroye A Abafe
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Residue Laboratory, Agricultural Research Council - Onderstepoort Veterinary Research Campus, Onderstepoort 0110, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Integrative Biology and Bioinformatics, University of Guelph, Ontario N1G 2W1, Canada
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Akebe L K Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Environmental Research Foundation, Westville 3630, Kwazulu-Natal, South Africa.
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5
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Venkatesan M, Fruci M, Verellen LA, Skarina T, Mesa N, Flick R, Pham C, Mahadevan R, Stogios PJ, Savchenko A. Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics. Nat Commun 2023; 14:4031. [PMID: 37419898 PMCID: PMC10328974 DOI: 10.1038/s41467-023-39778-7] [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: 01/16/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
The sulfonamides (sulfas) are the oldest class of antibacterial drugs and inhibit the bacterial dihydropteroate synthase (DHPS, encoded by folP), through chemical mimicry of its co-substrate p-aminobenzoic acid (pABA). Resistance to sulfa drugs is mediated either by mutations in folP or acquisition of sul genes, which code for sulfa-insensitive, divergent DHPS enzymes. While the molecular basis of resistance through folP mutations is well understood, the mechanisms mediating sul-based resistance have not been investigated in detail. Here, we determine crystal structures of the most common Sul enzyme types (Sul1, Sul2 and Sul3) in multiple ligand-bound states, revealing a substantial reorganization of their pABA-interaction region relative to the corresponding region of DHPS. We use biochemical and biophysical assays, mutational analysis, and in trans complementation of E. coli ΔfolP to show that a Phe-Gly sequence enables the Sul enzymes to discriminate against sulfas while retaining pABA binding and is necessary for broad resistance to sulfonamides. Experimental evolution of E. coli results in a strain harboring a sulfa-resistant DHPS variant that carries a Phe-Gly insertion in its active site, recapitulating this molecular mechanism. We also show that Sul enzymes possess increased active site conformational dynamics relative to DHPS, which could contribute to substrate discrimination. Our results reveal the molecular foundation for Sul-mediated drug resistance and facilitate the potential development of new sulfas less prone to resistance.
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Affiliation(s)
- Meenakshi Venkatesan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Michael Fruci
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Lou Ann Verellen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Nathalie Mesa
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3E2, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
- Center for Structural Biology of Infectious Diseases (CSBID), Calgary, AB, Canada.
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
- Center for Structural Biology of Infectious Diseases (CSBID), Calgary, AB, Canada.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Gschwind R, Ugarcina Perovic S, Weiss M, Petitjean M, Lao J, Coelho LP, Ruppé E. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics. Nucleic Acids Res 2023:7173762. [PMID: 37207327 DOI: 10.1093/nar/gkad384] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023] Open
Abstract
Metagenomics can be used to monitor the spread of antibiotic resistance genes (ARGs). ARGs found in databases such as ResFinder and CARD primarily originate from culturable and pathogenic bacteria, while ARGs from non-culturable and non-pathogenic bacteria remain understudied. Functional metagenomics is based on phenotypic gene selection and can identify ARGs from non-culturable bacteria with a potentially low identity shared with known ARGs. In 2016, the ResFinderFG v1.0 database was created to collect ARGs from functional metagenomics studies. Here, we present the second version of the database, ResFinderFG v2.0, which is available on the Center of Genomic Epidemiology web server (https://cge.food.dtu.dk/services/ResFinderFG/). It comprises 3913 ARGs identified by functional metagenomics from 50 carefully curated datasets. We assessed its potential to detect ARGs in comparison to other popular databases in gut, soil and water (marine + freshwater) Global Microbial Gene Catalogues (https://gmgc.embl.de). ResFinderFG v2.0 allowed for the detection of ARGs that were not detected using other databases. These included ARGs conferring resistance to beta-lactams, cycline, phenicol, glycopeptide/cycloserine and trimethoprim/sulfonamide. Thus, ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.
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Affiliation(s)
- Rémi Gschwind
- University of Paris Cité, INSERM UMR 1137 IAME, F-75018Paris, France
| | - Svetlana Ugarcina Perovic
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai200433, China
| | - Maja Weiss
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby 2800, Denmark
| | - Marie Petitjean
- University of Paris Cité, INSERM UMR 1137 IAME, F-75018Paris, France
| | - Julie Lao
- University of Paris Cité, INSERM UMR 1137 IAME, F-75018Paris, France
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai200433, China
| | - Etienne Ruppé
- University of Paris Cité, INSERM UMR 1137 IAME, F-75018Paris, France
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7
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Lin H, Peddada SD. Multi-group Analysis of Compositions of Microbiomes with Covariate Adjustments and Repeated Measures. RESEARCH SQUARE 2023:rs.3.rs-2778207. [PMID: 37205444 PMCID: PMC10187376 DOI: 10.21203/rs.3.rs-2778207/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microbiome differential abundance analysis methods for a pair of groups are well established in the literature. However, many microbiome studies involve multiple groups, sometimes even ordered groups, such as stages of a disease, and require different types of comparisons. Standard pairwise comparisons are not only inefficient in terms of power and false discovery rates, but they may not address the scientific question of interest. In this paper, we propose a general framework for performing a wide range of multi-group analyses with covariate adjustments and repeated measures. We demonstrate the effectiveness of our methodology through two real data sets. The first example explores the effects of aridity on the soil microbiome, and the second example investigates the effects of surgical interventions on the microbiome of IBD patients.
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Affiliation(s)
- Huang Lin
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park, NC, USA
| | - Shyamal Das Peddada
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park, NC, USA
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8
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Ren H, Lu Z, Sun R, Wang X, Zhong J, Su T, He Q, Liao X, Liu Y, Lian X, Sun J. Functional metagenomics reveals wildlife as natural reservoirs of novel β-lactamases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161505. [PMID: 36626997 DOI: 10.1016/j.scitotenv.2023.161505] [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: 10/25/2022] [Revised: 12/21/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
The antibiotic resistances in bacteria are believed to rapidly evolve over time in the anthropogenic environments which enriched with selection pressures. However, the knowledge regarding the development of antibiotic resistance in wildlife and their habitats is scarce. It is, therefore, of great interest and significance to unveil the yet-unknown antibiotic resistances in wildlife in accordance with One Health concept. To this end, we analyzed the samples taken from wildlife and surrounding environments using a functional metagenomics approach. By functional screening in combination with Illumina sequencing, a total of 32 candidate genes which encoding putative novel β-lactamase were identified. These putative β-lactamase were taxonomically assigned into bacteria of 23 genera from 7 phyla, where Proteobacteria, Actinobacteria and Firmicutes were dominant. The following functional assessment demonstrated that 4 novel β-lactamases, namely blaSSA, blaSSB1, blaSSB2 and blaSSD, were functionally active to confer the phenotypical resistance to bacteria by increasing MICs up to 128-fold. Further analysis indicated that the novel β-lactamases identified in the current study were able to hydrolyze a broad spectrum of β-lactams including cephalosporins, and they were genetically unique comparing with known β-lactamases. The plausible transmission of some novel β-lactamase genes was supported by our results as the same gene was detected in different samples from different sites. This study shed the light on the active role of wildlife and associated environments as natural reservoirs of novel β-lactamases, implying that the antibiotic resistances might evolve in absence of selection pressure and threaten public health once spread into clinically important pathogens.
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Affiliation(s)
- Hao Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Zhaoxiang Lu
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Ruanyang Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Xiran Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Jiahao Zhong
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Tiantian Su
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Qian He
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoping Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yahong Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xinlei Lian
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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Xin H, Gao M, Wang X, Qiu T, Guo Y, Zhang L. Animal farms are hot spots for airborne antimicrobial resistance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158050. [PMID: 35985594 DOI: 10.1016/j.scitotenv.2022.158050] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Animal farms are known reservoirs for environmental antimicrobial resistance (AMR). However, knowledge of AMR burden in the air around animal farms remains disproportionately limited. In this study, we characterized the airborne AMR based on the quantitative information of 30 antimicrobial resistance genes (ARGs), four mobile genetic elements (MGEs), and four human pathogenic bacteria (HPBs) involving four animal species from 20 farms. By comparing these genes with those in animal feces, the distinguishing features of airborne AMR were revealed, which included high enrichment of ARGs and their potential mobility to host HPBs. We found that depending on the antimicrobial class, the mean concentration of airborne ARGs in the animal farms ranged from 102 to 104 copies/m3 and was accompanied by a considerable intensity of MGEs and HPBs (approximately 103 copies/m3). Although significant correlations were observed between the ARGs and bacterial communities of air and fecal samples, the abundance of target genes was generally high in fine inhalable particles (PM2.5), with an enrichment ratio of up to 102 in swine and cattle farms. The potential transferability of airborne ARGs was universally strengthened, embodied by a pronounced co-occurrence of ARGs-MGEs in air compared with that in feces. Exposure analysis showed that animal farmworkers may inhale approximately 104 copies of human pathogenic bacteria-associated genera per day potentially carrying highly transferable ARGs, including multidrug resistant Staphylococcus aureus. Moreover, PM2.5 inhalation posed higher human daily intake burdens of some ARGs than those associated with drinking water intake. Overall, our findings highlight the severity of animal-related airborne AMR and the subsequent inhalation exposure, thus improving our understanding of the airborne flow of AMR genes from animals to humans. These findings could help develop strategies to mitigate the human exposure and dissemination of ARGs across different media.
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Affiliation(s)
- Huibo Xin
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing 100083, China; Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Liqiu Zhang
- Beijing Key Laboratory for Source Control Technology of Water Pollution, Engineering Research Center for Water Pollution Source Control and Eco-remediation, Beijing Forestry University, Beijing 100083, China.
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Molecular Characterization of Bacterial Isolates from Soil Samples and Evaluation of their Antibacterial Potential against MDRS. Molecules 2022; 27:molecules27196281. [PMID: 36234819 PMCID: PMC9573682 DOI: 10.3390/molecules27196281] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Some soil microbes, with their diverse inhabitance, biologically active metabolites, and endospore formation, gave them characteristic predominance and recognition among other microbial communities. The present study collected ten soil samples from green land, agricultural and marshy soil sites of Khyber Pakhtunkhwa, Pakistan. After culturing on described media, the bacterial isolates were identified through phenotypic, biochemical and phylogenetic analysis. Our phylogenetic analysis revealed three bacterial isolates, A6S7, A1S6, and A1S10, showing 99% nucleotides sequence similarity with Brevibacillus formosus, Bacillus Subtilis and Paenibacillus dendritiformis. The crude extract was prepared from bacterial isolates to assess the anti-bacterial potential against various targeted multidrug-resistant strains (MDRS), including Acinetobacter baumannii (ATCC 19606), Methicillin-resistant Staphylococcus aureus (MRSA) (BAA-1683), Klebsiella pneumoniae (ATCC 13883), Pseudomonas aeruginosa (BAA-2108), Staphylococcus aureus (ATCC 292013), Escherichia coli (ATCC25922) and Salmonella typhi (ATCC 14028). Our analysis revealed that all bacterial extracts possess activity against Gram-negative and Gram-positive bacteria at a concentration of 5 mg/mL, efficiently restricting the growth of E. coli compared with positive control ciprofloxacin. The study concluded that the identified species have the potential to produce antimicrobial compounds which can be used to control different microbial infections, especially MDRS. Moreover, the analysis of the bacterial extracts through GC-MS indicated the presence of different antimicrobial compounds such as propanoic acid, oxalic acid, phenol and hexadecanoic acid.
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11
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U.S. Consumer Attitudes toward Antibiotic Use in Livestock Production. SUSTAINABILITY 2022. [DOI: 10.3390/su14127035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Antimicrobial resistance, which decreases the efficacy of antibiotics and other antimicrobials, has led to concerns about the use of antibiotics in livestock production. Consumers play an important role in influencing producers’ decisions about the use of antimicrobials through their choices in the marketplace, which are driven by attitudes toward these practices. This study examines consumers’ levels of concern about (and acceptance of) the use of antibiotics in livestock production for four objectives: to treat, control, and prevent infections, and to promote growth. Results reveal that the majority of respondents were highly concerned about antibiotic use to promote growth in livestock production and considered this use to be unacceptable. Participants with higher objective knowledge of antibiotic resistance and antibiotic use in livestock production were more likely to accept antibiotic use to treat and control disease, but less likely to accept its use to prevent disease or to promote growth. Participants with high levels of trust in the livestock industry were more likely to accept antibiotic use to control and prevent infections and to be neutral about antibiotic use to promote growth in food animals. Respondents who believed that antibiotic use decreases animal welfare were more likely to be very concerned about antibiotic use to treat, prevent, and control disease, and less likely to accept antibiotic use to treat diseases in food animals. The study findings should be of interest to producers considering the adoption of sustainable technologies and production practices, food retailers making procurement decisions, and policymakers identifying policies that can alleviate antimicrobial resistance in the agri-food sector.
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12
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Abbassi MS, Badi S, Lengliz S, Mansouri R, Hammami S, Hynds P. Hiding in plain sight - Wildlife as a neglected reservoir and pathway for the spread of antimicrobial resistance: A narrative review. FEMS Microbiol Ecol 2022; 98:6568898. [DOI: 10.1093/femsec/fiac045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 04/12/2022] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Antimicrobial resistance represents a global health problem, with infections due to pathogenic antimicrobial resistant bacteria (ARB) predicted to be the most frequent cause of human mortality by 2050. The phenomenon of antimicrobial resistance has spread to and across all ecological niches, and particularly in livestock used for food production with antimicrobials consumed in high volumes. Similarly, hospitals and other healthcare facilities are recognized as significant “hotspots” of ARB and antimicrobial resistance genes (ARGs); however, over the past decade, new and previously overlooked ecological niches are emerging as hidden reservoirs of ARB/ARGs. Increasingly extensive and intensive industrial activities, degradation of natural environments, burgeoning food requirements, urbanization, and global climatic change have all dramatically affected the evolution and proliferation of ARB/ARGs, which now stand at extremely concerning ecological levels. While antimicrobial resistant bacteria and genes as they originate and emanate from livestock and human hosts have been extensively studied over the past 30 years, numerous ecological niches have received considerably less attention. In the current descriptive review, the authors have sought to highlight the importance of wildlife as sources/reservoirs, pathways and receptors of ARB/ARGs in the environment, thus paving the way for future primary research in these areas.
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Affiliation(s)
- Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie, Tunis, Tunisia
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche «Résistance aux antimicrobiens» 1007, Tunis, Tunisia
| | - Souhir Badi
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie, Tunis, Tunisia
| | - Sana Lengliz
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie, Tunis, Tunisia
| | - Riadh Mansouri
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie, Tunis, Tunisia
| | - Salah Hammami
- Université Manouba, IRESA, École Nationale de Médecine Vétérinaire de Sidi Thabet, Sidi Thabet 2020, Ariana, Tunisia
| | - Paul Hynds
- Environmental Sustainability and Health Institute (ESHI), Technological University Dublin, Grangegorman, Dublin 7, Dublin, Republic of Ireland
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13
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Characteristics changes on Applications of Antibiotics and Current Approaches to Enhance Productivity with Soil Microbiome. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The contamination of environmental sully with antibiotics is regarded as a major problem today and predictable to attain more recognition in near future. However, human intervention resulting in antibiotic consumption is being enhancing all around the world. Our review of literature revealed the role of microbiome in sully and how antibiotic resistant genes raised. The structure of antibiotics basically influenced by natural components such as biotic and abiotic push which shifts based on different soils. Therefore, management of microbiome in soil and their expression studies were distinctively revealed. The assessment of antibiotic resistance genes with help of next generation sequencing provided a clear comprehension on genome and transcriptome of the bacterial genes. Thus, interaction of microbiome with soil can also be well understood. The current findings in our study will guide every researcher to follow logical protocol in analyzing microbiota composition is covered as well and also to understand its metagenomic and sequenced with next-generation sequencer which helps to comprehend the diverse micro-flora present in soil and its operation. Finally, later progresses in bioinformatics computer program, flow of work, and applications for analyzing metagenomic information are put in a nutshell.
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Haenni M, Dagot C, Chesneau O, Bibbal D, Labanowski J, Vialette M, Bouchard D, Martin-Laurent F, Calsat L, Nazaret S, Petit F, Pourcher AM, Togola A, Bachelot M, Topp E, Hocquet D. Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes. ENVIRONMENT INTERNATIONAL 2022; 159:107047. [PMID: 34923370 DOI: 10.1016/j.envint.2021.107047] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Antimicrobial resistance (AMR) is a major global public health concern, shared by a large number of human and animal health actors. Within the framework of a One Health approach, actions should be implemented in the environmental realm, as well as the human and animal realms. The Government of France commissioned a report to provide policy and decision makers with an evidential basis for recommending or taking future actions to mitigate AMR in the environment. We first examined the mechanisms that underlie the emergence and persistence of antimicrobial resistance in the environment. This report drew up an inventory of the contamination of aquatic and terrestrial environments by AMR and antibiotics, anticipating that the findings will be representative of some other high-income countries. Effluents of wastewater treatment plants were identified as the major source of contamination on French territory, with spreading of organic waste products as a more diffuse and incidental contamination of aquatic environments. A limitation of this review is the heterogeneity of available data in space and time, as well as the lack of data for certain sources. Comparing the French Measured Environmental Concentrations (MECs) with predicted no effect concentrations (PNECs), fluoroquinolones and trimethoprim were identified as representing high and medium risk of favoring the selection of resistant bacteria in treated wastewater and in the most contaminated rivers. All other antibiotic molecules analyzed (erythromycin, clarithromycin, azithromycin, tetracycline) were at low risk of resistance selection in those environments. However, the heterogeneity of the data available impairs their full exploitation. Consequently, we listed indicators to survey AMR and antibiotics in the environment and recommended the harmonization of sampling strategies and endpoints for analyses. Finally, the objectives and methods used for the present work could comprise a useful example for how national authorities of countries sharing common socio-geographic characteristics with France could seek to better understand and define the environmental dimension of AMR in their particular settings.
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Affiliation(s)
- Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES (French Agency for Food, Environmental and Occupational Health & Safety) - Université de Lyon, Lyon, France
| | - Christophe Dagot
- Université of Limoges, RESINFIT, UMR INSERM 1092, CHU, F-87000 Limoges, France
| | - Olivier Chesneau
- Collection de l'Institut Pasteur (CIP), Microbiology Department, Institut Pasteur, Paris, France
| | - Delphine Bibbal
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Jérôme Labanowski
- Université de Poitiers, UMR CNRS 7285 IC2MP, ENSI Poitiers, Poitiers, France
| | | | - Damien Bouchard
- National Agency for Veterinary Medicinal Products, ANSES, Fougères, France
| | | | - Louisiane Calsat
- Risk Assessment Department (DER), ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Maisons-Alfort, France
| | - Sylvie Nazaret
- Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Fabienne Petit
- UNIROUEN, UNICAEN, CNRS, M2C, Normandie Université Rouen, France; Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris F-75005, France
| | | | | | - Morgane Bachelot
- ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Maisons-Alfort, France
| | - Edward Topp
- Agriculture and Agri-Food Canada, and University of Western Ontario, London, ON, Canada
| | - Didier Hocquet
- UMR Chronoenvironnement CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France; Hygiène Hospitalière, Centre Hospitalier Universitaire, 25030 Besançon, France.
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15
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Laskey A, Devenish J, Kang M, Savic M, Chmara J, Dan H, Lin M, Robertson J, Bessonov K, Gurnik S, Liu K, Nash JHE, Topp E, Guan J. Mobility of β-lactam resistance under ampicillin treatment in gut microbiota suffering from pre-disturbance. Microb Genom 2021; 7:000713. [PMID: 34882531 PMCID: PMC8767350 DOI: 10.1099/mgen.0.000713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to dissemination of antibiotic resistance genes (ARGs) in the gut microbiota. The gut microbiota often suffers from various disturbances. It is not clear whether and how disturbed microbiota may affect ARG mobility under antibiotic treatments. For proof of concept, in the presence or absence of streptomycin pre-treatment, mice were inoculated orally with a β-lactam-susceptible Salmonella enterica serovar Heidelberg clinical isolate (recipient) and a β-lactam resistant Escherichia coli O80:H26 isolate (donor) carrying a blaCMY-2 gene on an IncI2 plasmid. Immediately following inoculation, mice were treated with or without ampicillin in drinking water for 7 days. Faeces were sampled, donor, recipient and transconjugant were enumerated, blaCMY-2 abundance was determined by quantitative PCR, faecal microbial community composition was determined by 16S rRNA amplicon sequencing and cecal samples were observed histologically for evidence of inflammation. In faeces of mice that received streptomycin pre-treatment, the donor abundance remained high, and the abundance of S. Heidelberg transconjugant and the relative abundance of Enterobacteriaceae increased significantly during the ampicillin treatment. Co-blooming of the donor, transconjugant and commensal Enterobacteriaceae in the inflamed intestine promoted significantly (P<0.05) higher and possibly wider dissemination of the blaCMY-2 gene in the gut microbiota of mice that received the combination of streptomycin pre-treatment and ampicillin treatment (Str-Amp) compared to the other mice. Following cessation of the ampicillin treatment, faecal shedding of S. Heidelberg transconjugant persisted much longer from mice in the Str-Amp group compared to the other mice. In addition, only mice in the Str-Amp group shed a commensal E. coli O2:H6 transconjugant, which carries three copies of the blaCMY-2 gene, one on the IncI2 plasmid and two on the chromosome. The findings highlight the significance of pre-existing gut microbiota for ARG dissemination and persistence during and following antibiotic treatments of infectious diseases.
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Affiliation(s)
- Alexander Laskey
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Devenish
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mingsong Kang
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mirjana Savic
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Chmara
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Hanhong Dan
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Min Lin
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Simone Gurnik
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kira Liu
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - John H. E. Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Jiewen Guan
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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16
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Accurate acid dissociation constant (pK a) calculation for the sulfachloropyridazine and similar molecules. J Mol Model 2021; 27:233. [PMID: 34324066 DOI: 10.1007/s00894-021-04851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Accurate calculation of the acid dissociation constant (pKa) has fundamental importance for the description of molecular systems with pharmacological activities. The search for a more appropriate procedure for its determination is always welcome and has aroused increasing interest from the scientific community. In this sense, this work presents a computational study involving the combination of ten DFT functionals (M062X, M06L, B3LYP, BLYP, PBEPBE, BP86, LC-BLYP, SPBE, CAM-B3LYP, LC-PBEPBE) and HF method, eight basis set functions (6-311G, 6-311 + G, 6-311G(d,p), 6-311 + G(d,p), 6-311+ +G(d,p), 6-311(2d,2p), 6-311+ +G(2d,2p), and aug-cc-pVDZ), and three solvation models (SMD, PCM, and CPCM) for an accurate sulfachloropyridazine (SCR) pKa determination. It was found that the smallest deviation (0.02 unit of pKa) between the current study and experimental result was achieved with the BLYP/6-311 + G(d,p)/PCM combination. Therefore, this combination was extended to calculate the pKa of six SCR similar molecules selected through the eletroshape similarity method. For all these molecules, the difference between the obtained results and experimental data ranged between 0.14 and 0.69 units of pKa. This feature suggests that the obtained combination can determine pKa with experimental precision for complexes that are formed by sulfonamide functional group (SO2NHR). Graphical Abstract A computational study involving the combination of different levels of theory, basis sets and solvation models for an accurate sulfanamide pKa determination.
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17
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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18
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Wind L, Krometis LA, Hession WC, Pruden A. Cross-comparison of methods for quantifying antibiotic resistance in agricultural soils amended with dairy manure and compost. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:144321. [PMID: 33477102 DOI: 10.1016/j.scitotenv.2020.144321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Agricultural soils are often amended with livestock manure, making them a key reservoir of antibiotic resistance genes (ARGs). Given that soils are among the most microbially-diverse environments on the planet; effective characterization and quantification of the effects of manure-derived amendments on soil resistomes is a major challenge. This study examined the effects of dairy manure-derived amendments on agricultural soils via two strategies: quantification of anthropogenic ARG markers via qPCR and shotgun metagenomic resistome profiling; and these strategies were compared to a previously published antibiotic resistant fecal coliform dataset. Soil samples were collected throughout a 120 day complete block field experiment to compare the effects of amendment type on antibiotic resistance. Results of all three measurements were consistent with the hypothesis that the application of composted manure reduced antibiotic resistance in soil relative to the application of raw manure, although some differences were noted in comparing the patterns of the three measurements with time. Raw dairy manure-amended soils yielded high sul1 and tet(W) relative abundances on Day 0 (following amendment application), but significantly decreased to background levels by Day 67 (harvest) and Day 120 (study completion). Shotgun metagenomics similarly detected a decrease in the relative abundances of sulfonamide and tetracycline-associated ARGs over time in the raw manure- and compost-amended soils; however, these levels were significantly lower than those estimated by qPCR. Interestingly, although patterns of sulfonamide and tetracycline resistance among culturable fecal coliforms echoed those observed via qPCR and metagenomics; erythromycin resistant coliforms were directly recovered by culture in amended soils, but corresponding ARGs were not detected by qPCR or metagenomics. This study supports both composting and time restrictions as means of reducing the potential for antibiotic resistance in manure to spread via soil application. Results suggest some differences in finer conclusions drawn depending on which antibiotic resistance monitoring target is selected.
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Affiliation(s)
- Lauren Wind
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA.
| | - Leigh-Anne Krometis
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA
| | - W Cully Hession
- Department of Biological Systems Engineering, Virginia Tech, 155 Ag. Quad Lane, Seitz Hall RM 200, Blacksburg, VA, USA
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, 1145 Perry St, Durham Hall RM 403, Blacksburg, VA 24061, USA
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Willms IM, Grote M, Kocatürk M, Singhoff L, Kraft AA, Bolz SH, Nacke H. Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics. Antibiotics (Basel) 2021; 10:antibiotics10040378. [PMID: 33916668 PMCID: PMC8066302 DOI: 10.3390/antibiotics10040378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems.
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20
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Thakali A, MacRae JD. A review of chemical and microbial contamination in food: What are the threats to a circular food system? ENVIRONMENTAL RESEARCH 2021; 194:110635. [PMID: 33347866 DOI: 10.1016/j.envres.2020.110635] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
A circular food system is one in which food waste is processed to recover plant nutrients and returned to the soil to enable the production of more food, rather than being diverted to landfill or incineration. The approach may be used to reduce energy and water use in food production and contribute to the sustainability of the system. Anaerobic digestion and composting are common food waste treatment technologies used to stabilize waste and produce residual materials that can replenish the soil, thus contributing to a circular food system. This approach can only be deemed safe and feasible, however, if food waste is uncontaminated or any contaminants are destroyed during treatment. This review brings together information on several contaminant classes at different stages of the food supply chain, their possible sources, and their fates during composting and digestion. The main aim is to identify factors that could impede the transition towards a safe, reliable and efficient circular food system. We investigated heavy metals, halogenated organic compounds, foodborne pathogens and antibiotic resistance genes (ARGs) in the food system and their fates during digestion and composting. Production and processing stages were identified as major entry points for these classes of contaminants. Heavy metals and foodborne pathogens pose less risk in a circular system than halogenated organics or antibiotic resistance. Given the diversity of properties among halogenated organic compounds, there is conflicting evidence about their fate during treatment. There are relatively few studies on the fate of ARGs during treatment, and these have produced variable results, indicating a need for more research to clarify their fate in the final products. Repeated land application of contaminated food waste residuals can increase the risk of accumulation and jeopardize the safety of a circular food system. Thus, careful management of the system and research into the fate of the contaminants during treatment is needed.
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Affiliation(s)
- Astha Thakali
- Department of Civil and Environmental Engineering, University of Maine, 5711 Boardman Hall, Orono, ME, 04469, USA.
| | - Jean D MacRae
- Department of Civil and Environmental Engineering, University of Maine, 5711 Boardman Hall, Orono, ME, 04469, USA.
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21
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Zhang AN, Hou CJ, Negi M, Li LG, Zhang T. Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats. FEMS Microbiol Ecol 2020; 96:5849002. [PMID: 32472933 DOI: 10.1093/femsec/fiaa107] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/27/2020] [Indexed: 12/23/2022] Open
Abstract
Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method. Here, we constructed a comprehensive profile of the distribution of potential ARGs in bacterial tree of life and global habitats by investigating ARGs in 55 000 bacterial genomes, 16 000 bacterial plasmid sequences, 3000 bacterial integron sequences and 850 metagenomes using a standard pipeline. We found that >80% of all known ARGs are not carried by any plasmid or integron sequences. Among potential mobile ARGs, tetracycline and beta-lactam resistance genes (such as tetA, tetM and class A beta-lactamase gene) distribute in multiple pathogens across bacterial phyla, indicating their clinical relevance and importance. We showed that class 1 integrases (intI1) display a poor linear relationship with total ARGs in both non-human-associated and human-associated environments. Furthermore, both total ARGs and intI1 genes show little correlation with the degree of anthropogenicity. These observations highlight the need to differentiate ARGs of high clinical relevance. This profile is published on an online platform (ARGs-OSP, http://args-osp.herokuapp.com/) as a valuable resource for the most challenging topics in this field, i.e. the risk, evolution and emergence of ARGs.
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Affiliation(s)
- An Ni Zhang
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China.,Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Chen-Ju Hou
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Mishty Negi
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Li-Guan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China
| | - Tong Zhang
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China.,Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, China.,School of Public Health, The University of Hong Kong, Hong Kong, China
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22
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Imchen M, Moopantakath J, Kumavath R, Barh D, Tiwari S, Ghosh P, Azevedo V. Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance. Front Genet 2020; 11:563975. [PMID: 33240317 PMCID: PMC7677515 DOI: 10.3389/fgene.2020.563975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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23
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Chen S, Wang J, Feng H, Shen D, He S, Xu Y. Quantitative study on the fate of antibiotic emissions in China. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2020; 42:3471-3479. [PMID: 32419089 DOI: 10.1007/s10653-020-00563-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
China, the largest producer and user of antibiotics in the world, discharges excessive amounts of these substances into the environment, without prior treatment. This results in ubiquitous distribution of these substances, as well as increased levels of drug-resistant bacteria, that will eventually cause unimaginable consequences to the environment and to humans. However, most of the research on antibiotics has focused on residue analysis of single medium such as wastewater and landfills. There is paucity of research that systematically investigates the fate of antibiotics after excretion, and specifically of end-treatment processes. In this paper, the fate of antibiotic emissions is systematically calculated. The results show that human and livestock feces account for 57.6% and 42.6% of the discharge of medicinal antibiotics and veterinary antibiotics, respectively. Of these feces types, pig feces accounted for 98.7% of antibiotic residues in livestock feces. The above conclusions can be used to clarify the direction of the tracking and supervision of antibiotic residues and provide new ideas for the treatment of antibiotics, especially their terminal removal.
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Affiliation(s)
- Shuxin Chen
- Zhejiang Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Jing Wang
- Zhejiang Provincial Department of Ecology and Environment, Hangzhou, 310012, China
| | - Huajun Feng
- Zhejiang Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Dongsheng Shen
- Zhejiang Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Shichong He
- Zhejiang Provincial Department of Ecology and Environment, Hangzhou, 310012, China
| | - Yingfeng Xu
- Zhejiang Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China.
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24
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Lau CHF, Tien YC, Stedtfeld RD, Topp E. Impacts of multi-year field exposure of agricultural soil to macrolide antibiotics on the abundance of antibiotic resistance genes and selected mobile genetic elements. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138520. [PMID: 32330714 DOI: 10.1016/j.scitotenv.2020.138520] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
Exposure of environmental bacteria to antibiotics may be increasing the global resistome. Antibiotic residues are entrained into agricultural soil through the application of animal and human wastes, and irrigation with reclaimed water. The impact of a mixture of three macrolide antibiotics on the abundance of selected genes associated with antibiotic resistance and genetic mobility were determined in a long-term field experiment undertaken in London, Canada. Replicated plots received annual applications of a mixture of erythromycin, clarithromycin and azithromycin every spring since 2010. Each antibiotic was added directly to the soil at a concentration of either 0.1 or 10 mg kg soil-1 and all plots were cropped to soybeans. By means of qPCR, no gene targets were enriched in soil exposed to the 0.1 mg kg soil-1 dose compared to untreated control. In contrast, the relative abundance of several gene targets including int1, sul2 and mphE increased significantly with the annual exposure to the 10 mg kg soil-1 dose. By means of high-throughput qPCR, numerous gene targets associated with resistance to aminoglycosides, sulfonamides, trimethoprim, streptomycin, quaternary ammonium chemicals as well as mobile genetic elements (tnpA, IS26 and IS6100) were detected in soil exposed to 10 mg kg soil-1, but not the lower dose. Overall, exposure of soil to macrolide antibiotics increased the relative abundance of numerous gene targets associated with resistance to macrolides and other antibiotics, and mobile genetic elements. This occurred at an exposure dose that is unrealistically high, but did not occur at the lower more realistic exposure dose.
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Affiliation(s)
- Calvin Ho-Fung Lau
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Yuan-Ching Tien
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada; Department of Biology, University of Western Ontario, London, ON, Canada.
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25
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Laskey A, Ottenbrite M, Devenish J, Kang M, Savic M, Nadin-Davis S, Chmara J, Lin M, Robertson J, Bessonov K, Gurnik S, Liu K, Nash JHE, Scott A, Topp E, Guan J. Mobility of β-Lactam Resistance Under Bacterial Co-infection and Ampicillin Treatment in a Mouse Model. Front Microbiol 2020; 11:1591. [PMID: 32733428 PMCID: PMC7358583 DOI: 10.3389/fmicb.2020.01591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/17/2020] [Indexed: 01/21/2023] Open
Abstract
Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to the dissemination of antibiotic-resistance genes in the gut microbiota and the development of antibiotic-resistant bacterial infection, a significant threat to animal and public health. Food or water may be contaminated with multiple resistant bacteria, but animal models on gene transfer were mainly based on single-strain infections. In this study, we investigated the mobility of β-lactam resistance following infection with single- versus multi-strain of resistant bacteria under ampicillin treatment. We characterized three bacterial strains isolated from food-animal production systems, Escherichia coli O80:H26 and Salmonella enterica serovars Bredeney and Heidelberg. Each strain carries at least one conjugative plasmid that encodes a β-lactamase. We orally infected mice with each or all three bacterial strain(s) in the presence or absence of ampicillin treatment. We assessed plasmid transfer from the three donor bacteria to an introduced E. coli CV601gfp recipient in the mouse gut, and evaluated the impacts of the bacterial infection on gut microbiota and gut health. In the absence of ampicillin treatment, none of the donor or recipient bacteria established in the normal gut microbiota and plasmid transfer was not detected. In contrast, the ampicillin treatment disrupted the gut microbiota and enabled S. Bredeney and Heidelberg to colonize and transfer their plasmids to the E. coli CV601gfp recipient. E. coli O80:H26 on its own failed to colonize the mouse gut. However, during co-infection with the two Salmonella strains, E. coli O80:H26 colonized and transferred its plasmid to the E. coli CV601gfp recipient and a residential E. coli O2:H6 strain. The co-infection significantly increased plasmid transfer frequency, enhanced Proteobacteria expansion and resulted in inflammation in the mouse gut. Our findings suggest that single-strain infection models for evaluating in vivo gene transfer may underrepresent the consequences of multi-strain infections following the consumption of heavily contaminated food or water.
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Affiliation(s)
- Alexander Laskey
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Marie Ottenbrite
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Devenish
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mingsong Kang
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Mirjana Savic
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Susan Nadin-Davis
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Chmara
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Min Lin
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Simone Gurnik
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Kira Liu
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - John H. E. Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Andrew Scott
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Jiewen Guan
- Ottawa Laboratory, Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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26
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Abstract
Antibiotic resistance is mediated through several distinct mechanisms, most of which are relatively well understood and the clinical importance of which has long been recognized. Until very recently, neither of these statements was readily applicable to the class of resistance mechanism known as target protection, a phenomenon whereby a resistance protein physically associates with an antibiotic target to rescue it from antibiotic-mediated inhibition. In this Review, we summarize recent progress in understanding the nature and importance of target protection. In particular, we describe the molecular basis of the known target protection systems, emphasizing that target protection does not involve a single, uniform mechanism but is instead brought about in several mechanistically distinct ways.
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27
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Cunningham CJ, Kuyukina MS, Ivshina IB, Konev AI, Peshkur TA, Knapp CW. Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:1110-1124. [PMID: 32236187 DOI: 10.1039/c9em00606k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bioremediation represents a sustainable approach to remediating petroleum hydrocarbon contaminated soils. One aspect of sustainability includes the sourcing of nutrients used to stimulate hydrocarbon-degrading microbial populations. Organic nutrients such as animal manure and sewage sludge may be perceived as more sustainable than conventional inorganic fertilizers. However, organic nutrients often contain antibiotic residues and resistant bacteria (along with resistance genes and mobile genetic elements). This is further exacerbated since antibiotic resistant bacteria may become more abundant in contaminated soils due to co-selection pressures from pollutants such as metals and hydrocarbons. We review the issues surrounding bioremediation of petroleum-hydrocarbon contaminated soils, as an example, and consider the potential human-health risks from antibiotic resistant bacteria. While awareness is coming to light, the relationship between contaminated land and antibiotic resistance remains largely under-explored. The risk of horizontal gene transfer between soil microorganisms, commensal bacteria and/or human pathogens needs to be further elucidated, and the environmental triggers for gene transfer need to be better understood. Findings of antibiotic resistance from animal manures are emerging, but even fewer bioremediation studies using sewage sludge have made any reference to antibiotic resistance. Resistance mechanisms, including those to antibiotics, have been considered by some authors to be a positive trait associated with resilience in strains intended for bioremediation. Nevertheless, recognition of the potential risks associated with antibiotic resistant bacteria and genes in contaminated soils appears to be increasing and requires further investigation. Careful selection of bacterial candidates for bioremediation possessing minimal antibiotic resistance as well as pre-treatment of organic wastes to reduce selective pressures (e.g., antibiotic residues) are suggested to prevent environmental contamination with antibiotic-resistant bacteria and genes.
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Affiliation(s)
- Colin J Cunningham
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK
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28
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Böhm ME, Razavi M, Marathe NP, Flach CF, Larsson DGJ. Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities. MICROBIOME 2020; 8:41. [PMID: 32197644 PMCID: PMC7085159 DOI: 10.1186/s40168-020-00814-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/02/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after their transfer to pathogens could allow more effective measures to monitor and reduce spread, and facilitate genetics-based diagnostics. RESULTS We modified a functional metagenomics approach followed by in silico filtering of known resistance genes to discover novel, mobilised resistance genes in class 1 integrons in wastewater-impacted environments. We identified an integron-borne gene cassette encoding a protein that conveys high-level resistance against aminoglycosides with a garosamine moiety when expressed in E. coli. The gene is named gar (garosamine-specific aminoglycoside resistance) after its specificity. It contains none of the functional domains of known aminoglycoside modifying enzymes, but bears characteristics of a kinase. By searching public databases, we found that the gene occurs in three sequenced, multi-resistant clinical isolates (two Pseudomonas aeruginosa and one Luteimonas sp.) from Italy and China, respectively, as well as in two food-borne Salmonella enterica isolates from the USA. In all cases, gar has escaped discovery until now. CONCLUSION To the best of our knowledge, this is the first time a novel resistance gene, present in clinical isolates, has been discovered by exploring the environmental microbiome. The gar gene has spread horizontally to different species on at least three continents, further limiting treatment options for bacterial infections. Its specificity to garosamine-containing aminoglycosides may reduce the usefulness of the newest semisynthetic aminoglycoside plazomicin, which is designed to avoid common aminoglycoside resistance mechanisms. Since the gene appears to be not yet common in the clinics, the data presented here enables early surveillance and maybe even mitigation of its spread.
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Affiliation(s)
- Maria-Elisabeth Böhm
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Nachiket P. Marathe
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Institute of Marine Research (IMR), Bergen, Norway
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - D. G. Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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29
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Akbar N, Siddiqui R, Sagathevan K, Khan NA. Gut bacteria of animals living in polluted environments exhibit broad-spectrum antibacterial activities. Int Microbiol 2020; 23:511-526. [PMID: 32124096 DOI: 10.1007/s10123-020-00123-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 01/21/2020] [Accepted: 02/07/2020] [Indexed: 12/18/2022]
Abstract
Infectious diseases, in particular bacterial infections, are the leading cause of morbidity and mortality posing a global threat to human health. The emergence of antibiotic resistance has exacerbated the problem further. Hence, there is a need to search for novel sources of antibacterials. Herein, we explored gut bacteria of a variety of animals living in polluted environments for their antibacterial properties against multi-drug resistant pathogenic bacteria. A variety of species were procured including invertebrate species, Blaptica dubia (cockroach), Gromphadorhina portentosa (cockroach), Scylla serrata (crab), Grammostola rosea (tarantula), Scolopendra subspinipes (centipede) and vertebrate species including Varanus salvator (water monitor lizard), Malayopython reticulatus (python), Cuora amboinensis (tortoise), Oreochromis mossambicus (tilapia fish), Rattus rattus (rat), Gallus gallus domesticus (chicken) and Lithobates catesbeianus (frog). Gut bacteria of these animals were isolated and identified using microbiological, biochemical, analytical profiling index (API) and through molecluar identification using 16S rRNA sequencing. Bacterial conditioned media (CM) were prepared and tested against selected Gram-positive and Gram-negative pathogenic bacteria as well as human cells (HaCaT). The results revealed that CM exhibited significant broad-spectrum antibacterial activities. Upon heat inactivation, CM retained their antibacterial properties suggesting that this effect may be due to secondary metabolites or small peptides. CM showed minimal cytotoxicity against human cells. These findings suggest that gut bacteria of animals living in polluted environments produce broad-spectrum antibacterial molecule(s). The molecular identity of the active molecule(s) together with their mode of action is the subject of future studies which could lead to the rational development of novel antibacterial(s).
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Affiliation(s)
- Noor Akbar
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Ruqaiyyah Siddiqui
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, University City, 26666, Sharjah, United Arab Emirates
| | - K Sagathevan
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Naveed Ahmed Khan
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, University City, 26666, Sharjah, United Arab Emirates.
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30
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Lau CHF, DeJong EN, Dussault F, Carrillo C, Stogios PJ, Savchenko A, Topp E. A penicillin-binding protein that can promote advanced-generation cephalosporin resistance and genome adaptation in the opportunistic pathogen Pseudomonas aeruginosa. Int J Antimicrob Agents 2020; 55:105896. [PMID: 31927042 DOI: 10.1016/j.ijantimicag.2020.105896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/16/2019] [Accepted: 01/04/2020] [Indexed: 11/28/2022]
Abstract
A previous soil metagenomics study recovered a novel cephalosporin resistance determinant, pbpTET A6, for which the exact resistance mechanism was unclear. This study used a three-dimensional structure-guided mutagenesis approach to demonstrate that PBPTET A6 is likely to be a class A penicillin-binding protein (PBP), and that its ability to confer cephalosporin resistance is directly linked to the functional integrity of its transpeptidase (TP) catalytic core. Screening of a library of PBPTET A6 variants carrying randomly introduced point mutations revealed additional residue modifications that compromised resistance, all of which were proximal to the TP active site except one which was found in a 29-amino-acid-long superstructure (α6-α7 loop) absent in other class A PBP homologues. Based on the site-specific mutagenesis results, it is hypothesized that residue arginine-400 plays an important role in limiting the access of certain cephalosporin compounds to the enzymatic core of the TP domain of PBPTET A6. Using a combination of adaptive evolution assays and whole-genome sequencing, the potential impact of PBPTET A6 on promoting the development of resistance in the clinically significant opportunistic pathogen Pseudomonas aeruginosa was investigated. Under the selective pressure of serial ceftazidime exposures, the pbpTET A6-expressing P. aeruginosa population readily evolved by excluding a ~400-kbp chromosomal element to acquire additional resistance against cephalosporins, suggesting that PBPTET A6 has a catalytic effect on facilitating antibiotic-resistance-associated genome adaptation. Overall, the soil environment contains genes conferring resistance to critically important antibiotics by cryptic mechanisms. Understanding what impact anthropogenic activities might have on the abundance and evolution of these genes should be a priority.
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Affiliation(s)
- Calvin Ho-Fung Lau
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada; Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada.
| | - Erica N DeJong
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Forest Dussault
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Catherine Carrillo
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Center for Structural Genomics of Infectious Diseases
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Center for Structural Genomics of Infectious Diseases; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada; Department of Biology, University of Western Ontario, London, Ontario, Canada.
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31
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Mycobacterial HflX is a ribosome splitting factor that mediates antibiotic resistance. Proc Natl Acad Sci U S A 2019; 117:629-634. [PMID: 31871194 DOI: 10.1073/pnas.1906748117] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antibiotic resistance in bacteria is typically conferred by proteins that function as efflux pumps or enzymes that modify either the drug or the antibiotic target. Here we report an unusual mechanism of resistance to macrolide-lincosamide antibiotics mediated by mycobacterial HflX, a conserved ribosome-associated GTPase. We show that deletion of the hflX gene in the pathogenic Mycobacterium abscessus, as well as the nonpathogenic Mycobacterium smegmatis, results in hypersensitivity to the macrolide-lincosamide class of antibiotics. Importantly, the level of resistance provided by Mab_hflX is equivalent to that conferred by erm41, implying that hflX constitutes a significant resistance determinant in M. abscessus We demonstrate that mycobacterial HflX associates with the 50S ribosomal subunits in vivo and can dissociate purified 70S ribosomes in vitro, independent of GTP hydrolysis. The absence of HflX in a ΔMs_hflX strain also results in a significant accumulation of 70S ribosomes upon erythromycin exposure. Finally, a deletion of either the N-terminal or the C-terminal domain of HflX abrogates ribosome splitting and concomitantly abolishes the ability of mutant proteins to mediate antibiotic tolerance. Together, our results suggest a mechanism of macrolide-lincosamide resistance in which the mycobacterial HflX dissociates antibiotic-stalled ribosomes and rescues the bound mRNA. Given the widespread presence of hflX genes, we anticipate this as a generalized mechanism of macrolide resistance used by several bacteria.
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Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China. mSystems 2019; 4:4/6/e00206-19. [PMID: 31848308 PMCID: PMC6918024 DOI: 10.1128/msystems.00206-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry. To characterize the diversity and richness and explore the function and structure of swine gut microbiome and resistome in common pig-farming feedlots, we sampled and metagenomic sequenced the feces of pigs from four different industrialized feedlots located in four distant provinces across China. Surprisingly, more than half of the nonredundant genes (1,937,648, 54.3%) in the current catalogue were newly found compared with the previously published reference gene catalogue (RGC) of the pig gut microbiome. Additionally, 16 high-completeness draft genomes were obtained by analyzing the dominant species on each feedlot. Notably, seven of these species often appeared in the human body sites. Despite a smaller number of nonredundant genes, our study identified more antibiotic resistance genes than those available in the RGC. Tetracycline, aminoglycoside, and multidrug resistance genes accounted for nearly 70% of the relative abundance in the current catalogue. Slightly higher sharing ratios were shown between the industrialized feedlot pig gut microbiomes and human gut microbiomes than that between the RGC and human counterpart (14.7% versus 12.6% in genes and 94.1% versus 87.7% in functional groups, respectively). Furthermore, a remarkably high number of the antibiotic resistance proteins (n =141) were identified to be shared by the pig, human, and mouse resistome, indicating the potential for horizontal transfer of resistance genes. Of the antibiotic resistance proteins shared by pigs and humans, 50 proteins were related to tetracycline resistance, and 49 were related to aminoglycoside resistance. IMPORTANCE The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.
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Duan M, Gu J, Wang X, Li Y, Zhang R, Hu T, Zhou B. Factors that affect the occurrence and distribution of antibiotic resistance genes in soils from livestock and poultry farms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 180:114-122. [PMID: 31078018 DOI: 10.1016/j.ecoenv.2019.05.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/25/2019] [Accepted: 05/01/2019] [Indexed: 05/21/2023]
Abstract
Livestock manure is generally dumped directly onto open soil or used to enhance the soil fertility. However, there are growing concerns regarding the impact of these practices on the development and dissemination of antibiotic resistance genes (ARGs) in soil. In this study, we sampled soils treated with manure from 10 large-scale farms (pig, beef cattle, and chicken farms) and those from farmland without manure. The results showed that the abundance of ARGs was more than 2.62 times higher in the soil samples treated with livestock manure than the farmland soil without manure. The abundances of ARGs and intI1 in all samples were in the following order: pig farms > chicken farms > beef cattle farms. tetX, sul1, sul2, and tetG were the dominant ARGs in farm soil. The concentrations of tetracycline antibiotics and sulfonamide antibiotics were 0.15-4.76 mg/kg and 0-2.62 mg/kg, respectively, in the soils treated with manure, which were higher than those in farmland soils without manure. Redundancy analysis (P < 0.05) and network analysis (P < 0.01, R > 0.80) demonstrated that copper, zinc, actinomycetes, and tetracycline antibiotics were the main factors that affected the distribution of ARGs in soils treated with livestock manure.
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Affiliation(s)
- Manli Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; State Key Laboratory Base of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Yang Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710075, China
| | - Ranran Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Ting Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Beibei Zhou
- State Key Laboratory Base of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China
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Duval M, Cossart P. [A new mechanism of antibiotic resistance: ribosome recycling]. Med Sci (Paris) 2019; 35:613-615. [PMID: 31532368 DOI: 10.1051/medsci/2019117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mélodie Duval
- Département de biologie cellulaire et infection, Unité des interactions bactéries-cellules, Institut Pasteur, 25-28, rue du Docteur Roux, 75015 Paris, France. - Inserm, U604, F-75015 Paris, France. - INRA, unité sous contrat H2020, F-75015 Paris, France
| | - Pascale Cossart
- Département de biologie cellulaire et infection, Unité des interactions bactéries-cellules, Institut Pasteur, 25-28, rue du Docteur Roux, 75015 Paris, France. - Inserm, U604, F-75015 Paris, France. - INRA, unité sous contrat H2020, F-75015 Paris, France
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Bukowski M, Piwowarczyk R, Madry A, Zagorski-Przybylo R, Hydzik M, Wladyka B. Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus. Front Microbiol 2019; 10:805. [PMID: 31068910 PMCID: PMC6491766 DOI: 10.3389/fmicb.2019.00805] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/29/2019] [Indexed: 12/16/2022] Open
Abstract
The use of antibiotics on a mass scale, particularly in farming, and their release into the environment has led to a rapid emergence of resistant bacteria. Once emerged, resistance determinants are spread by horizontal gene transfer among strains of the same as well as disparate bacterial species. Their accumulation in free-living as well as livestock and community-associated strains results in the widespread multiple-drug resistance among clinically relevant species posing an increasingly pressing problem in healthcare. One of these clinically relevant species is Staphylococcus aureus, a common cause of hospital and community outbreaks. Among the rich diversity of mobile genetic elements regularly occurring in S. aureus such as phages, pathogenicity islands, and staphylococcal cassette chromosomes, plasmids are the major mean for dissemination of resistance determinants and virulence factors. Unfortunately, a vast number of whole-genome sequencing projects does not aim for complete sequence determination, which results in a disproportionately low number of known complete plasmid sequences. To address this problem we determined complete plasmid sequences derived from 18 poultry S. aureus strains and analyzed the prevalence of antibiotic and heavy metal resistance determinants, genes of virulence factors, as well as genetic elements relevant for their maintenance. Some of the plasmids have been reported before and are being found in clinical isolates of strains typical for humans or human ones of livestock origin. This shows that livestock-associated staphylococci are a significant reservoir of resistance determinants and virulence factors. Nevertheless, nearly half of the plasmids were unknown to date. In this group we found a potentially mobilizable plasmid pPA3 being a unique example of accumulation of resistance determinants and virulence factors likely stabilized by a presence of a toxin–antitoxin system.
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Affiliation(s)
- Michal Bukowski
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Rafal Piwowarczyk
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Madry
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Rafal Zagorski-Przybylo
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Marcin Hydzik
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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Cycoń M, Mrozik A, Piotrowska-Seget Z. Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity. Front Microbiol 2019; 10:338. [PMID: 30906284 PMCID: PMC6418018 DOI: 10.3389/fmicb.2019.00338] [Citation(s) in RCA: 369] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/08/2019] [Indexed: 01/11/2023] Open
Abstract
Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.
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Affiliation(s)
- Mariusz Cycoń
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine, Medical University of Silesia, Sosnowiec, Poland
| | - Agnieszka Mrozik
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Zofia Piotrowska-Seget
- Department of Microbiology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
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Willms IM, Kamran A, Aßmann NF, Krone D, Bolz SH, Fiedler F, Nacke H. Discovery of Novel Antibiotic Resistance Determinants in Forest and Grassland Soil Metagenomes. Front Microbiol 2019; 10:460. [PMID: 30899254 PMCID: PMC6416219 DOI: 10.3389/fmicb.2019.00460] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 02/21/2019] [Indexed: 01/06/2023] Open
Abstract
Soil represents a significant reservoir of antibiotic resistance genes (ARGs), which can potentially spread across distinct ecosystems and be acquired by pathogens threatening human as well as animal health. Currently, information on the identity and diversity of these genes, enabling anticipation of possible future resistance development in clinical environments and the livestock sector, is lacking. In this study, we applied functional metagenomics to discover novel sulfonamide as well as tetracycline resistance genes in soils derived from forest and grassland. Screening of soil metagenomic libraries revealed a total of eight so far unknown ARGs. The recovered genes originate from phylogenetically diverse soil bacteria (e.g., Actinobacteria, Chloroflexi, or Proteobacteria) and encode proteins with a minimum identity of 46% to other antibiotic resistance determinants. In particular forest soil ecosystems have so far been neglected in studies focusing on antibiotic resistance. Here, we detected for the first time non-mobile dihydropteroate synthase (DHPS) genes conferring resistance to sulfonamides in forest soil with no history of exposure to these synthetic drugs. In total, three sulfonamide resistant DHPSs, differing in taxonomic origin, were discovered in beech or pine forest soil. This indicates that sulfonamide resistance naturally occurs in forest-resident soil bacterial communities. Besides forest soil-derived sulfonamide resistance proteins, we also identified a DHPS affiliated to Chloroflexi in grassland soil. This enzyme and the other recovered DHPSs confer reduced susceptibility toward sulfamethazine, which is widely used in food animal production. With respect to tetracycline resistance, four efflux proteins affiliated to the major facilitator superfamily (MFS) were identified. Noteworthy, one of these proteins also conferred reduced susceptibility toward lincomycin.
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Affiliation(s)
- Inka Marie Willms
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Aysha Kamran
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Nils Frederik Aßmann
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Denis Krone
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Simon Henning Bolz
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Fabian Fiedler
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
| | - Heiko Nacke
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germany
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Ramakrishnan B, Venkateswarlu K, Sethunathan N, Megharaj M. Local applications but global implications: Can pesticides drive microorganisms to develop antimicrobial resistance? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:177-189. [PMID: 30445319 DOI: 10.1016/j.scitotenv.2018.11.041] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 05/07/2023]
Abstract
Pesticides are an important agricultural input, and the introduction of new active ingredients with increased efficiencies drives their higher production and consumption worldwide. Inappropriate application and storage of these chemicals often contaminate plant tissues, air, water, or soil environments. The presence of pesticides can lead to developing tolerance, resistance or persistence and even the capabilities to degrade them by the microbiomes of theses environments. The pesticide-degrading microorganisms gain and employ several mechanisms for attraction (chemotaxis), membrane transport systems, efflux pumps, enzymes and genetical make-up with plasmid and chromosome encoded catabolic genes for degradation. Even the evolution and the mechanisms of inheritance for pesticide-degradation as a functional trait in several microorganisms are beginning to be understood. Because of the commonalities in the microbial responses of sensing and uptake, and adaptation due to the selection pressures of pesticides and antimicrobial substances including antibiotics, the pesticide-degraders have higher chances of possessing antimicrobial resistance as a surplus functional trait. This review critically examines the probabilities of pesticide contamination of soil and foliage, the knowledge gaps in the regulation and storage of pesticide chemicals, and the human implications of pesticide-degrading microorganisms with antimicrobial resistance in the global strategy of 'One Health'.
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Affiliation(s)
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapur 515055, India
| | - Nambrattil Sethunathan
- Flat No. 103, Ushodaya Apartments, Sri Venkateswara Officers Colony, Ramakrishnapuram, Secunderabad 500056, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER) and Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), University of Newcastle, ATC Building, Callaghan, NSW 2308, Australia.
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Antibiotic resistance in grass and soil. Biochem Soc Trans 2019; 47:477-486. [DOI: 10.1042/bst20180552] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/21/2019] [Accepted: 01/28/2019] [Indexed: 12/25/2022]
Abstract
Abstract
Antibiotic resistance is currently one of the greatest threats to human health. The global overuse of antibiotics in human medicine and in agriculture has resulted in the proliferation and dissemination of a multitude of antibiotic resistance genes (ARGs). Despite a large proportion of antibiotics being used in agriculture, little is understood about how this may contribute to the overall antibiotic resistance crisis. The use of manure in agriculture is a traditional and widespread practice and is essential for returning nutrients to the soil; however, the impact of continuous manure application on the environmental microbiome and resistome is unknown. The use of antibiotics in animal husbandry in therapeutic and sub-therapeutic doses creates a selective pressure for ARGs in the gut microbiome of the animal, which is then excreted in the faeces. Therefore, the application of manure to agricultural land is a potential route for the transmission of antibiotic-resistant bacteria from livestock to crops, animals and humans. It is of vital importance to understand the mechanisms behind ARG enrichment and its maintenance both on the plant and within the soil microbiome to mitigate the spread of this resistance to animals and humans. Understanding this link between human health, animal health, plant health and the environment is crucial to inform implementation of new regulations and practice regarding antibiotic use in agriculture and manure application, aimed at ensuring the antibiotic resistance crisis is not aggravated.
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Abstract
Antibiotics have been widely used to treat bacterial infections and are also found in the environment. Bacteria have evolved various resistance mechanisms, allowing them to overcome antibiotic exposure and raising important health issues. Here, we report a bacterial antibiotic resistance mechanism, based on ribosome splitting and recycling, ensuring efficient translation even in presence of lincomycin and erythromycin, two antibiotics that block protein synthesis. This mechanism is mediated by a HflX-like protein, encoded by lmo0762 in Listeria monocytogenes, whose expression is tightly regulated by a transcriptional attenuation mechanism. This gene increases bacterial fitness in the environment. Our results raise the possibility that other antibiotic-induced resistance mechanisms remain to be discovered. To overcome the action of antibiotics, bacteria have evolved a variety of different strategies, such as drug modification, target mutation, and efflux pumps. Recently, we performed a genome-wide analysis of Listeria monocytogenes gene expression after growth in the presence of antibiotics, identifying genes that are up-regulated upon antibiotic treatment. One of them, lmo0762, is a homolog of hflX, which encodes a heat shock protein that rescues stalled ribosomes by separating their two subunits. To our knowledge, ribosome splitting has never been described as an antibiotic resistance mechanism. We thus investigated the role of lmo0762 in antibiotic resistance. First, we demonstrated that lmo0762 is an antibiotic resistance gene that confers protection against lincomycin and erythromycin, and that we renamed hflXr (hflX resistance). We show that hflXr expression is regulated by a transcription attenuation mechanism relying on the presence of alternative RNA structures and a small ORF encoding a 14 amino acid peptide containing the RLR motif, characteristic of macrolide resistance genes. We also provide evidence that HflXr is involved in ribosome recycling in presence of antibiotics. Interestingly, L. monocytogenes possesses another copy of hflX, lmo1296, that is not involved in antibiotic resistance. Phylogenetic analysis shows several events of hflXr duplication in prokaryotes and widespread presence of hflXr in Firmicutes. Overall, this study reveals the Listeria hflXr as the founding member of a family of antibiotic resistance genes. The resistance conferred by this gene is probably of importance in the environment and within microbial communities.
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Imchen M, Kumavath R, Barh D, Vaz A, Góes-Neto A, Tiwari S, Ghosh P, Wattam AR, Azevedo V. Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems. Sci Rep 2018; 8:11187. [PMID: 30046123 PMCID: PMC6060162 DOI: 10.1038/s41598-018-29521-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 07/13/2018] [Indexed: 12/17/2022] Open
Abstract
The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing (NGS) and compared their taxonomic and functional community structures to mangrove metagenomics samples from Brazil and Saudi Arabia. The most abundant phyla in the mangroves of all three countries was Proteobacteria, followed by Firmicutes and Bacteroidetes. A total of 1,942 genes were found to be common across all the mangrove sediments from each of the three countries. The mangrove resistome consistently showed high resistance to fluoroquinolone and acriflavine. A comparative study of the mangrove resistome with other ecosystems shows a higher frequency of heavy metal resistance in mangrove and terrestrial samples. Ocean samples had a higher abundance of drug resistance genes with fluoroquinolone and methicillin resistance genes being as high as 28.178% ± 3.619 and 10.776% ± 1.823. Genes involved in cobalt-zinc-cadmium resistance were higher in the mangrove (23.495% ± 4.701) and terrestrial (27.479% ± 4.605) ecosystems. Our comparative analysis of samples collected from a variety of habitats shows that genes involved in resistance to both heavy metals and antibiotics are ubiquitous, irrespective of the ecosystem examined.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya P.O, Kasaragod, Kerala, 671316, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya P.O, Kasaragod, Kerala, 671316, India.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India.,Division of Bioinformatics and Computational Genomics, NITTE University Center for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India.,Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Aline Vaz
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Preetam Ghosh
- Department of Computer Science Virginia Commonwealth University, Virginia, 23284, USA
| | - Alice R Wattam
- Biocomplexity Institute, Virginia Tech University, Blacksburg, Virginia, 24061, USA
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
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Manaia CM, Rocha J, Scaccia N, Marano R, Radu E, Biancullo F, Cerqueira F, Fortunato G, Iakovides IC, Zammit I, Kampouris I, Vaz-Moreira I, Nunes OC. Antibiotic resistance in wastewater treatment plants: Tackling the black box. ENVIRONMENT INTERNATIONAL 2018; 115:312-324. [PMID: 29626693 DOI: 10.1016/j.envint.2018.03.044] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/05/2018] [Accepted: 03/28/2018] [Indexed: 05/20/2023]
Abstract
Wastewater is among the most important reservoirs of antibiotic resistance in urban environments. The abundance of carbon sources and other nutrients, a variety of possible electron acceptors such as oxygen or nitrate, the presence of particles onto which bacteria can adsorb, or a fairly stable pH and temperature are examples of conditions favouring the remarkable diversity of microorganisms in this peculiar habitat. The wastewater microbiome brings together bacteria of environmental, human and animal origins, many harbouring antibiotic resistance genes (ARGs). Although numerous factors contribute, mostly in a complex interplay, for shaping this microbiome, the effect of specific potential selective pressures such as antimicrobial residues or metals, is supposedly determinant to dictate the fate of antibiotic resistant bacteria (ARB) and ARGs during wastewater treatment. This paper aims to enrich the discussion on the ecology of ARB&ARGs in urban wastewater treatment plants (UWTPs), intending to serve as a guide for wastewater engineers or other professionals, who may be interested in studying or optimizing the wastewater treatment for the removal of ARB&ARGs. Fitting this aim, the paper overviews and discusses: i) aspects of the complexity of the wastewater system and/or treatment that may affect the fate of ARB&ARGs; ii) methods that can be used to explore the resistome, meaning the whole ARB&ARGs, in wastewater habitats; and iii) some frequently asked questions for which are proposed addressing modes. The paper aims at contributing to explore how ARB&ARGs behave in UWTPs having in mind that each plant is a unique system that will probably need a specific procedure to maximize ARB&ARGs removal.
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Affiliation(s)
- Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal.
| | - Jaqueline Rocha
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Nazareno Scaccia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Roberto Marano
- Department of Agroecology and Plant Health, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel; Institute of Soil, Water, and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Elena Radu
- University of Technology Vienna, Institute for Water Quality and Resources Management, Karlsplatz 13/226, A-1040 Vienna, Austria; AGES - Austrian Agency for Health and Food Safety, Spargelfeldstraße 191, A-1220 Vienna, Austria
| | - Francesco Biancullo
- Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Adventech-Advanced Environmental Technologies, Centro Empresarial e Tecnológico, Rua de Fundões 151, 3700-121 São João da Madeira, Portugal
| | - Francisco Cerqueira
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034 Barcelona, Spain
| | - Gianuário Fortunato
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Iakovos C Iakovides
- NIREAS-International Water Research Center and Department of Civil and Environmental Engineering, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Ian Zammit
- Department of Civil Engineering, University of Salerno, SP24a, 84084 Fisciano, SA, Italy
| | - Ioannis Kampouris
- Institute for Hydrobiology, Technische Universität Dresden, 01217 Dresden, Germany
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal; LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
| | - Olga C Nunes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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Scott A, Tien YC, Drury CF, Reynolds WD, Topp E. Enrichment of antibiotic resistance genes in soil receiving composts derived from swine manure, yard wastes, or food wastes, and evidence for multiyear persistence of swine Clostridium spp. Can J Microbiol 2018; 64:201-208. [DOI: 10.1139/cjm-2017-0642] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of amendment with swine manure compost (SMC), yard waste compost (YWC), or food waste compost (FWC) on the abundance of antibiotic resistance genes in soil was evaluated. Following a commercial-scale application of the composts in a field experiment, soils were sampled periodically for a decade, and archived air-dried. Soil DNA was extracted and gene targets quantified by qPCR. Compared with untreated control soil, all 3 amendment types increased the abundance of gene targets for up to 4 years postapplication. The abundance of several gene targets was much higher in soil amended with SMC than in soil receiving either YWC or FWC. The gene target ermB remained higher in the SMC treatment for a decade postapplication. Clostridia were significantly more abundant in the SMC-amended soil throughout the decade following application. Eight percent of Clostridium spp. isolates from the SMC treatment carried ermB. Overall, addition of organic amendments to soils has the potential to increase the abundance of antibiotic resistance genes. Amendments of fecal origin, such as SMC, will in addition entrain bacteria carrying antibiotic resistance genes. Environmentally recalcitrant clostridia, and the antibiotic resistance genes that they carry, will persist for many years under field conditions following the application of SMC.
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Affiliation(s)
- Andrew Scott
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Yuan-Ching Tien
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Craig F. Drury
- Agriculture and Agri-Food Canada, 2585 County Road 20, Harrow, ON N0R 1G0, Canada
| | - W. Daniel Reynolds
- Agriculture and Agri-Food Canada, 2585 County Road 20, Harrow, ON N0R 1G0, Canada
| | - Edward Topp
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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Understanding the Proline-Centric Design of a Peptide-Mediated Macrolide Resistance Mechanism. Antimicrob Agents Chemother 2018; 62:AAC.02618-17. [PMID: 29437611 DOI: 10.1128/aac.02618-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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González-Plaza JJ, Šimatović A, Milaković M, Bielen A, Wichmann F, Udiković-Kolić N. Functional Repertoire of Antibiotic Resistance Genes in Antibiotic Manufacturing Effluents and Receiving Freshwater Sediments. Front Microbiol 2018; 8:2675. [PMID: 29387045 PMCID: PMC5776109 DOI: 10.3389/fmicb.2017.02675] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/21/2017] [Indexed: 11/21/2022] Open
Abstract
Environments polluted by direct discharges of effluents from antibiotic manufacturing are important reservoirs for antibiotic resistance genes (ARGs), which could potentially be transferred to human pathogens. However, our knowledge about the identity and diversity of ARGs in such polluted environments remains limited. We applied functional metagenomics to explore the resistome of two Croatian antibiotic manufacturing effluents and sediments collected upstream of and at the effluent discharge sites. Metagenomic libraries built from an azithromycin-production site were screened for resistance to macrolide antibiotics, whereas the libraries from a site producing veterinary antibiotics were screened for resistance to sulfonamides, tetracyclines, trimethoprim, and beta-lactams. Functional analysis of eight libraries identified a total of 82 unique, often clinically relevant ARGs, which were frequently found in clusters and flanked by mobile genetic elements. The majority of macrolide resistance genes identified from matrices exposed to high levels of macrolides were similar to known genes encoding ribosomal protection proteins, macrolide phosphotransferases, and transporters. Potentially novel macrolide resistance genes included one most similar to a 23S rRNA methyltransferase from Clostridium and another, derived from upstream unpolluted sediment, to a GTPase HflX from Emergencia. In libraries deriving from sediments exposed to lower levels of veterinary antibiotics, we found 8 potentially novel ARGs, including dihydrofolate reductases and beta-lactamases from classes A, B, and D. In addition, we detected 7 potentially novel ARGs in upstream sediment, including thymidylate synthases, dihydrofolate reductases, and class D beta-lactamase. Taken together, in addition to finding known gene types, we report the discovery of novel and diverse ARGs in antibiotic-polluted industrial effluents and sediments, providing a qualitative basis for monitoring the dispersal of ARGs from environmental hotspots such as discharge sites of pharmaceutical effluents.
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Affiliation(s)
- Juan J González-Plaza
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Šimatović
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
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Topp E. Agriculture and Agri-Food Canada's research program on antimicrobial resistance. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2017; 43:224-227. [PMID: 29770051 PMCID: PMC5764729 DOI: 10.14745/ccdr.v43i11a03] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A key strategy for attenuating the development of antimicrobial resistance (AMR) is ensuring judicious use of antimicrobials in human and veterinary medicine and in agriculture. Research on AMR in agriculture includes risk assessment, risk management, and identifying the role of agricultural practices in development of AMR. Risk assessment includes an impact assessment of antimicrobial use in livestock and on the environment; for example, many antimicrobials are excreted unchanged and thus reach the environment through manure application. This creates the potential for AMR transmission through the food processing chain and into agro-ecosystems receiving the agricultural waste. Risk management includes the assessment of cost-effective methods to keep animals healthy without the need for antimicrobial use, such as the use of vaccines, nutritional supplements and pre-, pro- or synbiotics and of waste management strategies to avoid AMR transmission. Currently, there is an important gap in understanding the degree of human exposure to AMR that is generated through agriculture, the burden of illness of AMR pathogens in human populations and the relationship between exposure and burden of illness. It is important that research on the agricultural, environmental and human medicine dimensions of AMR not be undertaken in silos, which is why the United Nations and countries around the world are working together within the One Health Framework that considers the inter-relatedness of humans, animals and the environment.
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Affiliation(s)
- E Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON
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Leung V, Szewczyk A, Chau J, Hosseinidoust Z, Groves L, Hawsawi H, Anany H, Griffiths MW, Ali MM, Filipe CDM. Long-Term Preservation of Bacteriophage Antimicrobials Using Sugar Glasses. ACS Biomater Sci Eng 2017; 4:3802-3808. [PMID: 33429601 DOI: 10.1021/acsbiomaterials.7b00468] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vincent Leung
- Department of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, Ontario, Canada L8S 4L7
| | - Alexandra Szewczyk
- Department of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, Ontario, Canada L8S 4L7
| | - Jacqueline Chau
- Department of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, Ontario, Canada L8S 4L7
| | - Zeinab Hosseinidoust
- Department of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, Ontario, Canada L8S 4L7
| | - Logan Groves
- Department of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, Ontario, Canada L8S 4L7
| | - Hajar Hawsawi
- Canadian Research Institute for Food Safety, 50 Stone Road East, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Hany Anany
- Canadian Research Institute for Food Safety, 50 Stone Road East, University of Guelph, Guelph, Ontario, Canada N1G 2W1
- Agriculture and Agri-Food Canada, Guelph Research and Development Center, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9
| | - Mansel W. Griffiths
- Canadian Research Institute for Food Safety, 50 Stone Road East, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - M. Monsur Ali
- Department of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, Ontario, Canada L8S 4L7
| | - Carlos D. M. Filipe
- Department of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, Ontario, Canada L8S 4L7
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Joseph FJRS, Iniyan AM, Vincent SGP. HR-LC-MS based analysis of two antibacterial metabolites from a marine sponge symbiont Streptomyces pharmamarensis ICN40. Microb Pathog 2017; 111:450-457. [PMID: 28935203 DOI: 10.1016/j.micpath.2017.09.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/29/2022]
Abstract
On the effort to screen antibiotics against Methicillin resistant Staphylococcus aureus (MRSA), an actinomycete strain which can produce bactericidal compound was isolated from a marine sponge of Kanyakumari Coast, India. Two anti-MRSA compounds (PVI401 and PVI402) were isolated from the fermentation plates of Streptomyces pharmamarensis ICN40. TLC bioautography analysis yielded two active spots with Rf value of 0.75 (PVI401) and 0.8 (PVI402) from the crude extract. Both the compounds were characterized by HR-LC-MS analysis. LC-MS based de-replication analysis found out the compound PVI401 with an exact mass of 376.09435 Da and PVI402 with an exact mass of 273.26795 Da were found to be unidentified. Antibacterial spectrum showed significant minimal inhibitory concentration as 0.5 μg/ml of PVI401 and 2 μg/ml of PVI402 against MRSA. The whole organism zebrafish safety evaluation exhibited the compound PVI402 is safe upto 1 mg/ml 40 μg/ml of PVI401 exhibited thrombosis in cardiac chamber and this compound exhibited 44 μg/ml of LC50 against HepG2 hepatic carcinoma cell line. Both the compounds may be identified further for its structural novelty and clinical studies.
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Affiliation(s)
- Francis-Joseph Rosemary Sharmila Joseph
- International Centre for Nanobiotechnology (ICN), Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, 629502 Kanyakumari District, TN, India
| | - Appadurai Muthamil Iniyan
- International Centre for Nanobiotechnology (ICN), Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, 629502 Kanyakumari District, TN, India
| | - Samuel Gnana Prakash Vincent
- International Centre for Nanobiotechnology (ICN), Centre for Marine Science and Technology (CMST), Manonmaniam Sundaranar University, Rajakkamangalam, 629502 Kanyakumari District, TN, India.
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Disassembly of the Staphylococcus aureus hibernating 100S ribosome by an evolutionarily conserved GTPase. Proc Natl Acad Sci U S A 2017; 114:E8165-E8173. [PMID: 28894000 DOI: 10.1073/pnas.1709588114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial hibernating 100S ribosome is a poorly understood form of the dimeric 70S particle that has been linked to pathogenesis, translational repression, starvation responses, and ribosome turnover. In the opportunistic pathogen Staphylococcus aureus and most other bacteria, hibernation-promoting factor (HPF) homodimerizes the 70S ribosomes to form a translationally silent 100S complex. Conversely, the 100S ribosomes dissociate into subunits and are presumably recycled for new rounds of translation. The regulation and disassembly of the 100S ribosome are largely unknown because the temporal abundance of the 100S ribosome varies considerably among different bacterial phyla. Here, we identify a universally conserved GTPase (HflX) as a bona fide dissociation factor of the S. aureus 100S ribosome. The expression levels hpf and hflX are coregulated by general stress and stringent responses in a temperature-dependent manner. While all tested guanosine analogs stimulate the splitting activity of HflX on the 70S ribosome, only GTP can completely dissociate the 100S ribosome. Our results reveal the antagonistic relationship of HPF and HflX and uncover the key regulators of 70S and 100S ribosome homeostasis that are intimately associated with bacterial survival.
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