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Lu Y, Wu J, Li J, Du Z, Zhang C, Chai Y, Jin Z, Li Z, Meng J, Zhuang H, Ping L, Wong MH, Zheng G, Shan S. Investigation of high-risk antibiotic resistance bacteria and their associated antibiotic resistance genes in different agricultural soils with biogas slurry from China. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134775. [PMID: 38824772 DOI: 10.1016/j.jhazmat.2024.134775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
High-risk antibiotic-resistant bacteria (ARB) and their accompanying antibiotic resistance genes (ARGs) seriously threaten public health. As a crucial medium for ARB and ARGs spread, soils with biogas slurry have been widely investigated. However, few studies focused on high-risk multi-drug resistant bacteria (MDRB) and their associated ARGs. This study examined ARB distribution in different agricultural soils with biogas slurry across 12 districts in China. It identified high-risk MDRB in various soil backgrounds, elucidating their resistance and spread mechanism. The findings revealed that diverse cultured ARB were enriched in soils with biogas slurry, especially soil ciprofloxacin ARB, which were enriched (>2.5 times) in 68.4 % of sampling sites. Four high-risk MDRB isolated from Hebei, Zhejiang, Shanxi, and Gansu districts were identified as severe or opportunistic pathogens, which carried abundant mobile genetic elements (MGEs) and 14 known high risk ARGs, including aac(3)-IId, aac(6')-Ib3, aph(6)-Id, aac(6')-Ib3, aadA1, blaOXA-10, blaTEM-1B, dfrA12, dfrA14, cmlA1, sul1, floR, tet(M) and tet(L). The antibiotics accumulation, diverse ARGs and MGEs enrichment, and proliferation of pathogenic bacteria could be potential driving factors of their occurrence and spread. Therefore, the coexistence of the high-risk MDRB and ARGs combined with the associated MGEs in soils with biogas slurry should be further investigated to develop technology and policy for reducing their negative influences on the effectiveness of clinical antibiotics.
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Affiliation(s)
- Yi Lu
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China.
| | - Junhui Wu
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Jiwei Li
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Zailin Du
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Changai Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Yanjun Chai
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Zewen Jin
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Zichuan Li
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Jun Meng
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Haifeng Zhuang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Lifeng Ping
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Ming Hung Wong
- Consortium on Health, Environment, Education, and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong SAR, China
| | - Guanyu Zheng
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, China.
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Checcucci A, Buscaroli E, Modesto M, Luise D, Blasioli S, Scarafile D, Di Vito M, Bugli F, Trevisi P, Braschi I, Mattarelli P. The swine waste resistome: Spreading and transfer of antibiotic resistance genes in Escherichia coli strains and the associated microbial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116774. [PMID: 39053184 DOI: 10.1016/j.ecoenv.2024.116774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/18/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The overuse of antimicrobials in livestock farming has led to the development of resistant bacteria and the spread of antibiotic-resistant genes (ARGs) among animals. When manure containing these antibiotics is applied to agricultural fields, it creates a selective pressure that promotes the acquisition of ARGs by bacteria, primarily through horizontal gene transfer. Most research on ARGs focuses on their role in clinical antibiotic resistance and their transfer from environmental sources to bacteria associated with humans, such as Escherichia coli. The study investigates the spread of antibiotic-resistant genes (ARGs) through class 1 integrons in 27 Escherichia coli strains from pig manure. It focuses on six common ARGs (ermB, cmlA, floR, qnrS, tetA, and TEM) and the class 1 integron gene, assessing their prevalence in manure samples from three pig farms. The study found correlations and anticorrelations among these genes, indicating a predisposition of the integron in spreading certain ARGs. Specifically, cmlA and tetA genes were positively correlated with each other and negatively with int1, suggesting they are not transferred via Int1. Farm B had the highest int1 counts and a higher abundance of the TEM gene, but lower levels of cmlA and tetA genes. The results underscore the complexity of predicting ARG spread in agricultural environments and the associated health risks to humans through the food chain. The study's results offer valuable insights into the antibiotic-resistant genes (ARGs) profile in swine livestock, potentially aiding in the development of methods to trace ARGs in the environment.
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Affiliation(s)
- Alice Checcucci
- Dipartimento di Scienze e Tecnologie Agrarie, Ambientali e Forestali (DAGRI), Università degli Studi di Firenze, Florence, Italy
| | - Enrico Buscaroli
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy.
| | - Monica Modesto
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy.
| | - Diana Luise
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Sonia Blasioli
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Donatella Scarafile
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Maura Di Vito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesca Bugli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy; Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Paolo Trevisi
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Ilaria Braschi
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
| | - Paola Mattarelli
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università di Bologna, Bologna, Italy
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3
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Ali I, Naz B, Liu Z, Chen J, Yang Z, Attia K, Ayub N, Ali I, Mohammed AA, Faisal S, Sun L, Xiao S, Chen S. Interplay among manures, vegetable types, and tetracycline resistance genes in rhizosphere microbiome. Front Microbiol 2024; 15:1392789. [PMID: 39011147 PMCID: PMC11246966 DOI: 10.3389/fmicb.2024.1392789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/03/2024] [Indexed: 07/17/2024] Open
Abstract
The rapid global emergence of antibiotic resistance genes (ARGs) is a substantial public health concern. Livestock manure serves as a key reservoir for tetracycline resistance genes (TRGs), serving as a means of their transmission to soil and vegetables upon utilization as a fertilizer, consequently posing a risk to human health. The dynamics and transfer of TRGs among microorganisms in vegetables and fauna are being investigated. However, the impact of different vegetable species on acquisition of TRGs from various manure sources remains unclear. This study investigated the rhizospheres of three vegetables (carrots, tomatoes, and cucumbers) grown with chicken, sheep, and pig manure to assess TRGs and bacterial community compositions via qPCR and high-throughput sequencing techniques. Our findings revealed that tomatoes exhibited the highest accumulation of TRGs, followed by cucumbers and carrots. Pig manure resulted in the highest TRG levels, compared to chicken and sheep manure, in that order. Bacterial community analyses revealed distinct effects of manure sources and the selective behavior of individual vegetable species in shaping bacterial communities, explaining 12.2% of TRG variation. Firmicutes had a positive correlation with most TRGs and the intl1 gene among the dominant phyla. Notably, both the types of vegetables and manures significantly influenced the abundance of the intl1 gene and soil properties, exhibiting strong correlations with TRGs and elucidating 30% and 17.7% of TRG variance, respectively. Our study delineated vegetables accumulating TRGs from manure-amended soils, resulting in significant risk to human health. Moreover, we elucidated the pivotal roles of bacterial communities, soil characteristics, and the intl1 gene in TRG fate and dissemination. These insights emphasize the need for integrated strategies to reduce selection pressure and disrupt TRG transmission routes, ultimately curbing the transmission of tetracycline resistance genes to vegetables.
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Affiliation(s)
- Izhar Ali
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Beenish Naz
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ziyang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agroecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Jingwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agroecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Zi Yang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Kotb Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nasir Ayub
- Korean Environmental Microorganism Resource Center, Department of Integrative Biotechnology, Sungkyuankwan University, Seoul, Republic of Korea
| | - Ikram Ali
- Center for Chinese Herbal Medicine Drug Development, Hong Kong Baptist University, Kowloon Tong, China
| | - Arif Ahmed Mohammed
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shah Faisal
- Department of Environmental Engineering, School of Architecture and Civil Engineering, Chengdu University, Chengdu, China
| | - Likun Sun
- College of Animal Sciences, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Sa Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agroecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Shuyan Chen
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
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Long TF, Zhou SY, Huang ZL, Li G, Zhong Q, Zhang XJ, Li YY, Chen CP, Xia LJ, Wei R, Wan L, Gao A, Ren H, Liao XP, Liu YH, Chen L, Sun J. Innovative Delivery System Combining CRISPR-Cas12f for Combatting Antimicrobial Resistance in Gram-Negative Bacteria. ACS Synth Biol 2024; 13:1831-1841. [PMID: 38863339 DOI: 10.1021/acssynbio.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Antimicrobial resistance poses a significant global challenge, demanding innovative approaches, such as the CRISPR-Cas-mediated resistance plasmid or gene-curing system, to effectively combat this urgent crisis. To enable successful curing of antimicrobial genes or plasmids through CRISPR-Cas technology, the development of an efficient broad-host-range delivery system is paramount. In this study, we have successfully designed and constructed a novel functional gene delivery plasmid, pQ-mini, utilizing the backbone of a broad-host-range Inc.Q plasmid. Moreover, we have integrated the CRISPR-Cas12f system into the pQ-mini plasmid to enable gene-curing in broad-host of bacteria. Our findings demonstrate that pQ-mini facilitates the highly efficient transfer of genetic elements to diverse bacteria, particularly in various species in the order of Enterobacterales, exhibiting a broader host range and superior conjugation efficiency compared to the commonly used pMB1-like plasmid. Notably, pQ-mini effectively delivers the CRISPR-Cas12f system to antimicrobial-resistant strains, resulting in remarkable curing efficiencies for plasmid-borne mcr-1 or blaKPC genes that are comparable to those achieved by the previously reported pCasCure system. In conclusion, our study successfully establishes and optimizes pQ-mini as a broad-host-range functional gene delivery vector. Furthermore, in combination with the CRISPR-Cas system, pQ-mini demonstrates its potential for broad-host delivery, highlighting its promising role as a novel antimicrobial tool against the growing threat of antimicrobial resistance.
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Affiliation(s)
- Teng-Fei Long
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Shi-Ying Zhou
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Zi-Lei Huang
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Gong Li
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Qin 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Xiao-Jing Zhang
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Yuan-Yuan Li
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Cai-Ping Chen
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Li-Juan Xia
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ran Wei
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Lei Wan
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ang Gao
- 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Xiao-Ping 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ya-Hong 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Liang Chen
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14214, United States
| | - 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, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
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Stehling EG, Sellera FP, de Almeida OGG, Gonzalez IHL, Ramos PL, da Rosa-Garzon NG, von Zeska Kress MR, Cabral H, Furlan JPR. Genomic features and comparative analysis of a multidrug-resistant Acinetobacter bereziniae strain infecting an animal: a novel emerging one health pathogen? World J Microbiol Biotechnol 2024; 40:63. [PMID: 38190002 DOI: 10.1007/s11274-023-03867-y] [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: 08/20/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
Abstract
Acinetobacter bereziniae has recently gained medical notoriety due to its emergence as a multidrug resistance and healthcare-associated pathogen. In this study, we report the whole-genome characterization of an A. bereziniae strain (A321) recovered from an infected semiaquatic turtle, as well as a comparative analysis of A. bereziniae strains circulating at the human-animal-environment interface. Strain A321 displayed a multidrug resistance profile to medically important antimicrobials, which was supported by a wide resistome. The novel Tn5393m transposon and a qnrB19-bearing ColE1-like plasmid were identified in A321 strain. Novel OXA-229-like β-lactamases were detected and expression of OXA-931 demonstrated a 2-64-fold increase in the minimum inhibitory concentration for β-lactam agents. Comparative genomic analysis revealed that most A. bereziniae strains did not carry any antimicrobial resistance genes (ARGs); however, some strains from China, Brazil, and India harbored six or more ARGs. Furthermore, A. bereziniae strains harbored conserved virulence genes. These results add valuable information regarding the spread of ARGs and mobile genetic elements that could be shared not only between A. bereziniae but also by other bacteria of clinical interest. This study also demonstrates that A. bereziniae can spill over from anthropogenic sources into natural environments and subsequently be transmitted to non-human hosts, making this a potential One Health bacteria that require close surveillance.
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Affiliation(s)
- Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Otávio Guilherme Gonçalves de Almeida
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Irys Hany Lima Gonzalez
- Coordination of Wild Fauna, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Coordination of Wild Fauna, Secretary of Environment, Infrastructure and Logistics, São Paulo, Brazil
| | - Nathália Gonsales da Rosa-Garzon
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Marcia Regina von Zeska Kress
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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7
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Tang L, Pan Z, Li X, Li J, Meng J. Antibiotics resistance removal from piggery wastewater by an integrated anaerobic-aerobic biofilm reactor: Efficiency and mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167031. [PMID: 37714352 DOI: 10.1016/j.scitotenv.2023.167031] [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: 08/15/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/17/2023]
Abstract
Antibiotic resistance residual in piggery wastewater poses serious threat to environment and human health. Biological treatment process is commonly installed to remove nutrient from piggery wastewater and also effective in removing antibiotics to varying degrees. But the specific pathways and mechanisms involved in the removal of antibiotic resistance are not yet well-understood. An integrated anaerobic-aerobic biofilm reactor (IAOBR) has been demonstrated efficient in removing conventional nutrients. It is here shown that the IAOBR effectively removed 79.0% of Sulfonamides, 55.7% of Tetracyclines and 53.6% of Quinones. Antibiotic resistance bacteria (ARB) were simultaneously inactivated by ~0.5 logs. Antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were decreased by 0.51 logs and 0.42 logs, respectively. The antibiotics were mainly removed through aerobic compartments of the IAOBR. The mass loss of antibiotics in the reactor was achieved by biodegradation and adsorption, accounting for 52.1% and 47.9%, respectively. An obvious accumulation of ARGs was observed in the activated sludge. The potential host of ARGs was analyzed via microbial community and network. Partial least squares-structural equation model and correlation analysis revealed that the enrichment of ARGs was positively affected by MGEs, followed by bacterial community and ARBs, but the effect of antibiotics on ARGs was negative. Outcomes of this study provide valuable insights into the mechanisms of antibiotic resistance removal in biological treatment processes.
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Affiliation(s)
- Lianggang Tang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhen Pan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xuan Li
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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Bagra K, Bellanger X, Merlin C, Singh G, Berendonk TU, Klümper U. Environmental stress increases the invasion success of antimicrobial resistant bacteria in river microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166661. [PMID: 37652387 DOI: 10.1016/j.scitotenv.2023.166661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
Environmental microbiomes are constantly exposed to invasion events through foreign, antibiotic resistant bacteria that were enriched in the anthropic sphere. However, the biotic and abiotic factors, as well as the natural barriers that determine the invasion success of these invader bacteria into the environmental microbiomes are poorly understood. A great example of such invasion events are river microbial communities constantly exposed to resistant bacteria originating from wastewater effluents. Here, we aim at gaining comprehensive insights into the key factors that determine their invasion success with a particular focus on the effects of environmental stressors, regularly co-released in wastewater effluents. Understanding invasion dynamics of resistant bacteria is crucial for limiting the environmental spread of antibiotic resistance. To achieve this, we grew natural microbial biofilms on glass slides in rivers for one month. The biofilms were then transferred to laboratory, recirculating flume systems and exposed to a single pulse of a model resistant invader bacterium (Escherichia coli) either in presence or absence of stress induced by Cu2+. The invasion dynamics of E. coli into the biofilms were then monitored for 14 days. Despite an initially successful introduction of E. coli into the biofilms, independent of the imposed stress, over time the invader perished in absence of stress. However, under stress the invading strain successfully established and proliferated in the biofilms. Noteworthy, the increased establishment success of the invader coincided with a loss in microbial community diversity under stress conditions, likely due to additional niche space becoming available for the invader.
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Affiliation(s)
- Kenyum Bagra
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany; Department of Civil Engineering, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Xavier Bellanger
- Université de Lorraine, CNRS, LCPME, UMR 7564, Villers-lès-Nancy, France
| | - Christophe Merlin
- Université de Lorraine, CNRS, LCPME, UMR 7564, Villers-lès-Nancy, France
| | - Gargi Singh
- Department of Civil Engineering, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Thomas U Berendonk
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - Uli Klümper
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany.
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Li J, Yang Z, Zhu Q, Zhong G, Liu J. Biodegradation of soil agrochemical contamination mitigates the direct horizontal transfer risk of antibiotic resistance genes to crops. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166454. [PMID: 37607639 DOI: 10.1016/j.scitotenv.2023.166454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
Microorganisms can drive a substrate-specific biodegradation process to mitigate soil contamination resulting from extensive agrochemical usage. However, microorganisms with high metabolic efficiency are capable of adapting to the co-occurrence of non-substrate contaminants in the soil (particularly antibiotics). Therefore, the utilization of active microorganisms for biodegradation raises concerns regarding the potential risk of antibiotic resistance development. Here, the horizontal transfer risk of antibiotic-resistance genes (ARGs) in the soil-plant biota was assessed during biodegradation by the newly isolated Proteus terrae ZQ02 (which shortened the half-life of fungicide chlorothalonil from 9.24 d to 2.35 d when exposed to tetracycline). Based on metagenomic analyses, the distribution of ARGs and mobile genetic elements (MGEs) was profiled. The ARGs shared with ∼118 core genes and mostly accumulated in the rhizosphere and maize roots. After ZQ02 was inoculated, the core genes of ARGs reduced significantly in roots. In addition, the Pseudomonas and Proteus genera were identified as the dominant microbial hosts of ARGs and MGEs after ZQ02 adoption. The richness of major ARG hosts increased in soil but barely changed in the roots, which contributed to the mitigation of hosts-mediated ARGs transfer from soil to maize. Finally, the risk of ARGs has been assessed. Compared with the regular planting system, the number of risky ARGs declined from 220 (occupied 4.77 % of the total ARGs) to 143 (occupied 2.67 %) after biodegradation. Among these, 23 out of 25 high-risk genes were aggregated in the soil whereas only 2 genes were identified in roots, which further verified the low antibiotic resistance risk for crop after biodegradation. In a nutshell, this work highlights the critical advantage of ZQ02-based biodegradation that alleviating the ARGs transfer risks from soil to crop, which offers deeper insights into the versatility and feasibility of bioremediation techniques in sustainable agriculture.
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Affiliation(s)
- Jinhong Li
- National Key Laboratory of Green Pesticide, Guangzhou, P.R. China; Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, P.R. China; Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, Guangzhou, P.R. China
| | - Zhengyi Yang
- National Key Laboratory of Green Pesticide, Guangzhou, P.R. China; Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, P.R. China; Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, Guangzhou, P.R. China
| | - Qi Zhu
- National Key Laboratory of Green Pesticide, Guangzhou, P.R. China; Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, P.R. China; Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, Guangzhou, P.R. China
| | - Guohua Zhong
- National Key Laboratory of Green Pesticide, Guangzhou, P.R. China; Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, P.R. China; Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, Guangzhou, P.R. China
| | - Jie Liu
- National Key Laboratory of Green Pesticide, Guangzhou, P.R. China; Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture and Rural Affairs, Guangzhou, P.R. China; Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, Guangzhou, P.R. China.
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10
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Tran TT, Cole M, Tomas E, Scott A, Topp E. Potential selection and maintenance of manure-originated multi-drug resistant plasmids at sub-clinical concentrations for tetracycline family antibiotics. Can J Microbiol 2023; 69:339-350. [PMID: 37267627 DOI: 10.1139/cjm-2022-0240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The goal of this study was to (a) determine the minimum selection concentrations of tetracycline family antibiotics necessary to maintain plasmids carrying tetracycline-resistant genes and (b) correlate these results to environmental hotspot concentrations reported in previous studies. This study used two plasmids (pT295A and pT413A) originating from dairy manure in a surrogate Escherichia coli host CV601. The minimum selection concentrations of antibiotics tested in nutrient-rich medium were determined as follows: 0.1 mg/L for oxytetracycline, 0.45 mg/L for chlortetracycline, and 0.13-0.25 mg/L for tetracycline. Mixing oxytetracycline and chlortetracycline had minimum selection concentration values increased 2-fold compared to those in single antibiotic tests. Minimum selection concentrations found in this study were lower than reported environmental hotspot concentrations, suggesting that tetracycline family antibiotics were likely to be the driver for the selection and maintenance of these plasmids. Relatively high plasmid loss rates (>90%) were observed when culturing a strain carrying a tetracycline-resistant plasmid in antibiotic-free nutrient-rich and nutrient-defined media. Overall, results suggested that these plasmids can be maintained at concentrations environmentally relevant in wastewater treatment plants, sewage, manure, and manured soil; however, they are unstable and easily lost in the absence of antibiotics.
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Affiliation(s)
- Tam T Tran
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON N6A 3K7, Canada
| | - Marlena Cole
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St, London, ON N5V 4T3, Canada
| | - Emily Tomas
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St, London, ON N5V 4T3, Canada
| | - Andrew Scott
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St, London, ON N5V 4T3, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford St, London, ON N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond St, London, ON N6A 3K7, Canada
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11
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Kneis D, Lemay-St-Denis C, Cellier-Goetghebeur S, Elena AX, Berendonk TU, Pelletier JN, Heß S. Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene. THE ISME JOURNAL 2023; 17:1455-1466. [PMID: 37369703 PMCID: PMC10432401 DOI: 10.1038/s41396-023-01460-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high level TMP resistance (dfrB10 to dfrB21), the prevalence of dfrB is still unknown due to underreporting, heterogeneity of the analyzed genetic material in terms of isolation sources, and limited bioinformatic processing. In this study, we explored a coherent set of shotgun metagenomic sequences to quantitatively estimate the abundance of dfrB gene variants in aquatic environments. Specifically, we scanned sequences originating from influents and effluents of municipal sewage treatment plants as well as river-borne microbiomes. Our analyses reveal an increased prevalence of dfrB1, dfrB2, dfrB3, dfrB4, dfrB5, and dfrB7 in wastewater microbiomes as compared to freshwater. These gene variants were frequently found in genomic neighborship with other resistance genes, transposable elements, and integrons, indicating their mobility. By contrast, the relative abundances of the more recently discovered variants dfrB9, dfrB10, and dfrB13 were significantly higher in freshwater than in wastewater microbiomes. Moreover, their direct neighborship with other resistance genes or markers of mobile genetic elements was significantly less likely. Our findings suggest that natural freshwater communities form a major reservoir of the recently discovered dfrB gene variants. Their proliferation and mobilization in response to the exposure of freshwater communities to selective TMP concentrations may promote the prevalence of high-level TMP resistance and thus limit the future effectiveness of antimicrobial therapies.
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Affiliation(s)
- David Kneis
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany.
| | - Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Stella Cellier-Goetghebeur
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Alan X Elena
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany
| | | | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
- Chemistry Department, University of Montréal, Montréal, QC, H2V 0B3, Canada
| | - Stefanie Heß
- TU Dresden, Institute of Microbiology, 01062, Dresden, Germany
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Alam M, Bano N, Upadhyay TK, Binsuwaidan R, Alshammari N, Sharangi AB, Kaushal RS, Saeed M. Enzymatic Activity and Horizontal Gene Transfer of Heavy Metals and Antibiotic Resistant Proteus vulgaris from Hospital Wastewater: An Insight. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:3399137. [PMID: 36523753 PMCID: PMC9747306 DOI: 10.1155/2022/3399137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/28/2022] [Accepted: 11/16/2022] [Indexed: 09/28/2023]
Abstract
Globally, the issue of microbial resistance to medicines and heavy metals is getting worse. There are few reports or data available for Proteus vulgaris (P. vulgaris), particularly in India. This investigation intends to reveal the bacteria's ability to transmit genes and their level of resistance as well. The wastewater samples were taken from several hospitals in Lucknow City, India, and examined for the presence of Gram-negative bacteria that were resistant to antibiotics and heavy metals. The microbial population count in different hospital wastewaters decreases with increasing concentrations of metal and antibiotics. Among all the examined metals, Ni and Zn had the highest viable counts, whereas Hg, Cd, and Co had the lowest viable counts. Penicillin, ampicillin, and amoxicillin, among the antibiotics, demonstrated higher viable counts, whereas tetracycline and erythromycin exhibited lower viable counts. The MIC values for the P. vulgaris isolates tested ranged from 50 to 16,00 μg/ml for each metal tested. The multiple metal resistance (MMR) index, which ranged from 0.04 to 0.50, showed diverse heavy metal resistance patterns in all P. vulgaris isolates (in the case of 2-7 metals in various combinations). All of the tested isolates had methicillin resistance, whereas the least number of isolates had ofloxacin, gentamycin, or neomycin resistance. The P. vulgaris isolates displayed multidrug resistance patterns (2-12 drugs) in various antibiotic combinations. The MAR indexes were shown to be between (0.02-0.7). From the total isolates, 98%, 84%, and 80% had urease, gelatinase, and amylase activity, whereas 68% and 56% displayed protease and beta-lactamase activity. Plasmids were present in all the selected resistant isolates and varied in size from 42.5 to 57.0 kb and molecular weight from 27.2 to 37.0 MD. The transmission of the antibiotic/metal resistance genes was evaluated between a total of 7 pairs of isolates. A higher transfer frequency (4.4 × 10-1) was observed among antibiotics, although a lower transfer frequency (1.0 × 10-2) was observed against metals in both the media from the entire site tested. According to exponential decay, the population of hospital wastewater declined in the following order across all sites: Site II > Site IV > Site III > Site I for antibiotics and site IV > site II > site I >site III for metal. Different metal and antibiotic concentrations have varying effects on the population. The metal-tolerant P. vulgaris from hospital wastewater was studied in the current study had multiple distinct patterns of antibiotic resistance. It could provide cutting-edge methods for treating infectious diseases, which are essential for managing and assessing the risks associated with hospital wastewater, especially in the case of P. vulgaris.
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Affiliation(s)
- Manzar Alam
- Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Nilofer Bano
- Department of Bioengineering, Integral University, Lucknow 226026, Uttar Pradesh, India
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara 391760, Gujarat, India
| | - Reem Binsuwaidan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia
| | - Amit Baran Sharangi
- Department of Plantation Spices Medicinal and Aromatic Crops, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur 741252, West Bengal, India
| | - Radhey Shyam Kaushal
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara 391760, Gujarat, India
| | - Mohd Saeed
- Department of Biology, College of Science, University of Ha'il, Ha'il, P.O. Box 2440, Saudi Arabia
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13
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Guo T, Li Z, Shao Y, Fu Y, Zhang W, Shao Y, Zhu Y. Effects of Oxytetracycline/Lead Pollution Alone and in the Combined Form on Antibiotic Resistance Genes, Mobile Genetic Elements, and Microbial Communities in the Soil. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:15619. [PMID: 36497692 PMCID: PMC9737759 DOI: 10.3390/ijerph192315619] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The application of livestock manure is the leading cause of antibiotic and heavy metal pollution in agricultural soil. However, the effects of oxytetracycline (OTC) and lead (Pb) pollution in the single or combined form on antibiotic resistance genes (ARGs) in the soil need to be further studied. This study was planned to investigate the effects of OTC and Pb application on ARGs, mobile genetic elements (MGEs), and bacterial abundance in the soil. The relative abundance of ARGs and MGEs increased by 0.31-fold and 0.03-fold after the addition of 80 mg kg-1 Pb to the soil, and by 0.49-fold and 0.03-fold after the addition of 160 mg kg-1 Pb. In addition, under the premise of the existence of OTC, the inhibitory effect of a low concentration of Pb on ARG is stronger than that of a high concentration of Pb, resulting in a lower abundance of ARGs. The abundance of ARGs and MGEs increased by 0.11-fold and 0.17-fold after the addition of OTC (30 mg kg-1) to the soil at a Pb concentration of 80 mg kg-1 and by 0.18-fold and 0.04-fold at a Pb concentration of 160 mg kg-1. The addition of OTC and Pb in the soil also decreased the many bacterial communities such as Bacteroidetes, Proteobacteria, Acidobacteria, and Firmicutes. Redundancy analysis (RDA) showed that organic matter content and pH were positively correlated with the abundance of ARGs and MGEs. At the same time, electrical conductivity (EC) had a negative correlation with the abundance of ARGs and MGEs in the soil. Intl1 was significantly associated with tetB, sul1, tetQ, sul2, and sul3. Network analysis illustrated that Actinobacteria, Bacteroidetes, and Proteobacteria were the main host bacteria causing changes in the abundance of ARGs and MGEs, and they were also predominant phylum in the culture environment. This conclusion can provide a reference for the related research of ARGs in soil.
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Affiliation(s)
- Tengfei Guo
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Zhaoyi Li
- Shandong Nuclear and Radiation Safety Monitoring Center, Jinan 250117, China
| | - Yanqiu Shao
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Yanli Fu
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Weiyi Zhang
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Yingying Shao
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Ying Zhu
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
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Cui G, Liu Z, Xu W, Gao Y, Yang S, Grossart HP, Li M, Luo Z. Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China). THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155784. [PMID: 35537512 DOI: 10.1016/j.scitotenv.2022.155784] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 06/14/2023]
Abstract
In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.
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Affiliation(s)
- Guojie Cui
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen 518060, China; Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Zongbao Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yuanhao Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin 16775, Germany; Institute of Biochemistry and Biology, Postdam University, Potsdam 14469, Germany
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
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15
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Molecular Characterization of pBOq-IncQ and pBOq-95LK Plasmids of Escherichia coli BOq 01, a New Isolated Strain from Poultry Farming, Involved in Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10081509. [PMID: 35893567 PMCID: PMC9331969 DOI: 10.3390/microorganisms10081509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
The increase in antimicrobial resistance has raised questions about how to use these drugs safely, especially in veterinary medicine, animal nutrition, and agriculture. Escherichia coli is an important human and animal pathogen that frequently contains plasmids carrying antibiotic resistance genes. Extra chromosomal elements are required for various functions or conditions in microorganisms. Several phage-like plasmids have been identified, which are important in antibiotic resistance. In this work, the molecular characterization of the pBOq-IncQ (4.5 kb) and pBOq-95LK (95 kb) plasmids found in the E. coli strain BOq 01, a multidrug resistant bacteria isolated from a poultry farm, are considered. Plasmid pBOq-IncQ belongs to the incQ incompatibility plasmid family and is involved in sulfonamide resistance. Plasmid pBOq-95LK is a lytic phage-like plasmid that is involved in the lysis of the E. coli BOq 01 strain and carries a bleomycin resistance gene and a strain cured of this plasmid shows bleomycin sensitivity. Induction of the lytic cycle indicates that this phage-like plasmid is an active phage. This type of plasmid has been reported to acquire genes such as mcr-1, which codes for colistin resistance and bacterial persistence and is a significant public health threat. A genome comparison, a pangenomic and phylogenomic analysis with other phage-like plasmids reported in the literature were performed to understand better the evolution of this kind of plasmid in bacteria and its potential importance in antibiotic resistance.
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Qin X, Zhai L, Khoshnevisan B, Pan J, Liu H. Restriction of biosolids returning to land: Fate of antibiotic resistance genes in soils after long-term biosolids application. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 301:119029. [PMID: 35217140 DOI: 10.1016/j.envpol.2022.119029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/15/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Although the utilization of biosolids in agricultural lands is widely considered as an effective way to improve resource reuse, the presence of antibiotic resistance genes (ARGs) severely restricts biosolids returning to fields. A 12-year long-term experiment with different biosolids application rates (from 0 to 36 t ha-1 yr-1) was conducted to study the effect of biosolids application on shaping ARGs in soil. Biosolids application significantly increased ARGs abundance in the soil, except for MBS treatment (9 t ha-1 yr-1 biosolids application). The abundance of ARGs in soil did not increase linearly with the dose of biosolids applied, but they were significantly (P < 0.05) positively correlated. A total of 173 subtypes were detected, among them mobile genetic elements (MGEs), aminoglycoside, and multidrug resistance genes were the most dominant types. Except for MBS treatment, most of the ARGs detected were enriched in amended soils after long-term continuous biosolids application. Specifically, tetPA, sul1, mefA, and IS6100 were highly enriched in all amended soils. In addition, biosolids application increased soil nutrients and heavy metals, and changed the soil microbial community, all of which affected ARGs formation. But MGEs may be a greater factor for shaping ARGs profiles than soil properties. Overall, controlling the rate of biosolid application is the key to reducing the accumulation and horizontal transfer of ARGs in soils.
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Affiliation(s)
- Xuechao Qin
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Limei Zhai
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Benyamin Khoshnevisan
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Denmark
| | - Junting Pan
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Hongbin Liu
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
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Werner KA, Poehlein A, Schneider D, El-Said K, Wöhrmann M, Linkert I, Hübner T, Brüggemann N, Prost K, Daniel R, Grohmann E. Thermophilic Composting of Human Feces: Development of Bacterial Community Composition and Antimicrobial Resistance Gene Pool. Front Microbiol 2022; 13:824834. [PMID: 35250940 PMCID: PMC8895236 DOI: 10.3389/fmicb.2022.824834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 01/01/2023] Open
Abstract
In times of climate change, practicing sustainable, climate-resilient, and productive agriculture is of primordial importance. Compost from different resources, now treated as wastes, could be one form of sustainable fertilizer creating a resilience of agriculture to the adverse effects of climate change. However, the safety of the produced compost regarding human pathogens, pharmaceuticals, and related resistance genes must be considered. We have assessed the effect of thermophilic composting of dry toilet contents, green cuttings, and straw, with and without biochar, on fecal indicators, the bacterial community, and antibiotic resistance genes (ARGs). Mature compost samples were analyzed regarding fecal indicator organisms, revealing low levels of Escherichia coli that are in line with German regulations for fertilizers. However, one finding of Salmonella spp. exceeded the threshold value. Cultivation of bacteria from the mature compost resulted in 200 isolates with 36.5% of biosafety level 2 (BSL-2) species. The majority is known as opportunistic pathogens that likewise occur in different environments. A quarter of the isolated BSL-2 strains exhibited multiresistance to different classes of antibiotics. Molecular analysis of total DNA before and after composting revealed changes in bacterial community composition and ARGs. 16S rRNA gene amplicon sequencing showed a decline of the two most abundant phyla Proteobacteria (start: 36-48%, end: 27-30%) and Firmicutes (start: 13-33%, end: 12-16%), whereas the abundance of Chloroflexi, Gemmatimonadetes, and Planctomycetes rose. Groups containing many human pathogens decreased during composting, like Pseudomonadales, Bacilli with Bacillus spp., or Staphylococcaceae and Enterococcaceae. Gene-specific PCR showed a decline in the number of detectable ARGs from 15 before to 8 after composting. The results reveal the importance of sufficiently high temperatures lasting for a sufficiently long period during the thermophilic phase of composting for reducing Salmonella to levels matching the criteria for fertilizers. However, most severe human pathogens that were targeted by isolation conditions were not detected. Cultivation-independent analyses also indicated a decline in bacterial orders comprising many pathogenic bacteria, as well as a decrease in ARGs. In summary, thermophilic composting could be a promising approach for producing hygienically safe organic fertilizer from ecological sanitation.
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Affiliation(s)
- Katharina A. Werner
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Dominik Schneider
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Khaliel El-Said
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
| | - Michael Wöhrmann
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
| | - Isabel Linkert
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
| | - Tobias Hübner
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research GmbH - UFZ, Leipzig, Germany
| | - Nicolas Brüggemann
- Institute of Bio- and Geosciences Agrosphere (IBG-3), Forschungszentrum Jülich, Jülich, Germany
| | - Katharina Prost
- Institute of Bio- and Geosciences Agrosphere (IBG-3), Forschungszentrum Jülich, Jülich, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Elisabeth Grohmann
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
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Zakharchenko N, Anisimov S, Dyadishchev I, Ponomarenko S, Khramov R. Effect of light-converting coatings on the growth of Sarepta mustard (Brassica juncea L.) plants colonized by associative microorganisms. BIO WEB OF CONFERENCES 2022. [DOI: 10.1051/bioconf/20224201024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effect of colonization by beneficial associative microorganisms Pseudomonas putida KT 2442 and Rhodococcus erythropolis X5 on the growth of Sarepta mustard (Brassica juncea L.) under a covering light-converting material containing organic photoluminophore, in vitro and in vivo, was investigated. The combined use of microbial colonization and photoluminophore coating led to stimulation of plant growth much stronger (2.4 times more) than separately only photoluminophoric coating (1.3 times) or colonization (2.1 times). These data indicate that when covering materials with photoluminophores are used in agrobiotechnologies, luminescent red light (610-730 nm) induces an increase in biochemical processes not only in plants, but also in microorganisms that supply plants with growth regulators and other useful metabolites. The data obtained are relevant for further study of the photobiological mechanisms of interactions between the plant-microorganism system in agrobiotechnologies.
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Wang Z, Li H, Zhang J, Wang X, Zhang Y, Wang H. Identification of a novel plasmid-mediated tigecycline resistance-related gene, tet(Y), in Acinetobacter baumannii. J Antimicrob Chemother 2021; 77:58-68. [PMID: 34634801 DOI: 10.1093/jac/dkab375] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To characterize a novel plasmid-mediated tigecycline resistance-related gene, tet(Y), in a clinical Acinetobacter baumannii isolate from China. METHODS The tet(Y)-encoded tigecycline-resistant A. baumannii 2016GDAB1 was screened through antimicrobial susceptibility testing and WGS. The function of tet(Y) was verified by complementation of tet(Y). The plasmid transferability and stability were detected via plasmid conjugation and in vitro bacterial passaging. The 3D structure of Tet(Y) was predicted and docked using tFold and AutoDock Vina. RESULTS The tigecycline-resistant A. baumannii 2016GDAB1 was isolated from bronchoalveolar lavage fluid of a patient with hospital-acquired pneumonia. However, this strain did not harbour any common tigecycline resistance genes, determinants or mutations. 2016GDAB1 belongs to the non-epidemic clone ST355 (Oxford scheme), which has been mainly reported in animals. The tet(Y) gene was located on a 72 156 bp plasmid and genomic environment analysis revealed that Tn5393 may play a role in tet(Y) transmission, whereas phylogenetic analysis indicated the origin of tet(Y) as from Aeromonas. Overexpression of tet(Y) resulted in a 2- to 4-fold increase in tigecycline MIC. Introduction of the tet(Y)-harbouring plasmid p2016GDAB1 via electroporation resulted in a 16-fold increase in tigecycline MIC but failed to transfer into the tigecycline-susceptible A. baumannii recipient via conjugation. Isolates carrying the tet(Y) gene were vulnerable to tigecycline pressure and exhibited decreased susceptibility to tigecycline. A tet(Y)-carrying plasmid was stably maintained in the host strains. CONCLUSIONS This study identified the tigecycline resistance-related gene tet(Y) in A. baumannii. This gene conferred an increased tigecycline MIC and the transposable element Tn5393 may play a role in its transmission across isolates.
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Affiliation(s)
- Zhiren Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Henan Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Jiangang Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Xiaojuan Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yawei Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
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20
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Mohammadi-Aragh MK, Stokes CE. Assessing Class 1 Integron Presence in Poultry Litter Amended with Wood Biochar and Wood Vinegar. Curr Microbiol 2021; 78:3733-3740. [PMID: 34459936 DOI: 10.1007/s00284-021-02640-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 08/20/2021] [Indexed: 11/26/2022]
Abstract
Class 1 integrons are mobile genetic elements that facilitate the spread of antibiotic resistance genes among bacteria. The use of prophylactic antibiotics has resulted in the rise of antibiotic resistance genes accumulating in a wide range of settings, including poultry houses and the agricultural fields where poultry litter is applied as a fertilizer. Biochar and wood vinegar are forest products wastes that have generated increasing attention as additives to agricultural soils. The objectives of this study were to observe the prevalence of class 1 integrons in poultry litter blended with biochar and wood vinegar over time and to verify a modified class 1 integron screening assay. Poultry litter blends were sampled and screened for class 1 integrons using polymerase chain reaction, and 80 products, 79 of which showed positive, were sent for DNA sequencing. The GenBank® BLAST database was used to verify the presence of the class 1 integron-integrase gene (intI1). There was no change in prevalence over time in poultry litter blends. Out of 79 PCR products that were intI1 positive, 78 showed at least 95% sequence identity to intI1 encoding bacteria and 64 showed at least 97% sequence identity. This indicates that this method was effective for conducting baseline surveillance of class 1 integrons in poultry litter and poultry litter-blended biochar and/or wood vinegar. Most significantly, class 1 integron prevalence did not decrease over time, further supporting the recalcitrance of these elements and the need for improved monitoring systems.
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Affiliation(s)
- Maryam K Mohammadi-Aragh
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, MS, USA.
| | - C Elizabeth Stokes
- Department of Sustainable Bioproducts, Mississippi State University, Starkville, MS, USA
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21
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Luo L, Payne M, Kaur S, Hu D, Cheney L, Octavia S, Wang Q, Tanaka MM, Sintchenko V, Lan R. Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing. Microb Genom 2021; 7. [PMID: 34292145 PMCID: PMC8477392 DOI: 10.1099/mgen.0.000605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.
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Affiliation(s)
- Lijuan Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Dalong Hu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Liam Cheney
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sophie Octavia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, New South Wales, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Westmead Hospital, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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22
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On-Farm Anaerobic Digestion of Dairy Manure Reduces the Abundance of Antibiotic Resistance-Associated Gene Targets and the Potential for Plasmid Transfer. Appl Environ Microbiol 2021; 87:e0298020. [PMID: 33931422 DOI: 10.1128/aem.02980-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The present study investigated the impact of on-farm anaerobic digestion on the abundance of enteric bacteria, antibiotic resistance-associated gene targets, and the horizontal transfer potential of extended-spectrum β-lactamase (ESBL) genes. Samples of raw and digested manure were obtained from six commercial dairy farms in Ontario, Canada. Digestion significantly abated populations of viable coliforms in all six farms. Conjugative transfer of plasmids carrying β-lactamase genes from manure bacteria enriched overnight with buffered peptone containing 4 mg/liter cefotaxime into a β-lactam-sensitive green fluorescent protein (GFP)-labeled Escherichia coli recipient strain was evaluated in patch matings. Digestion significantly decreased the frequency of the horizontal transfer of ESBL genes. Twenty-five transconjugants were sequenced, revealing six distinct plasmids, ranging in size from 40 to 180 kb. A variety of ESBL genes were identified: blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaPER-1. blaCTX-M-15 was the most prevalent ESBL gene detected on plasmids harbored by transconjugants. Various mobile genetic elements were found located proximal to resistance genes. Ten gene targets, including sul1, str(A), str(B), erm(B), erm(F), intI1, aadA, incW, blaPSE, and blaOXA-20, were quantified by quantitative PCR on a subset of 18 raw and 18 digested samples. Most targets were significantly more abundant in raw manure; however, erm(B) and erm(F) targets were more abundant in digested samples. Overall, on-farm digestion of dairy manure abated coliform bacteria, a number of antibiotic resistance-associated gene targets, and the potential for in vitro conjugation of plasmids conferring resistance to extended-spectrum β-lactams and other classes of antibiotics into E. coli CV601. IMPORTANCE Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied. Recommending the widespread implementation of the practice should be founded on understanding the impact of this treatment on various endpoints of human health concern. Although lab-scale anaerobic treatments have shown potential for reducing the abundance of antibiotic resistance genes, there are very few data from commercial farms. Anaerobic digestion of manure on six dairy farms efficiently abated coliform bacteria, E. coli, and a majority of antibiotic resistance-associated gene targets. In addition, the conjugation potential of plasmids carrying ESBL genes into introduced E. coli strain CV601 was reduced. Overall, anaerobic digestion abated coliform bacteria, the genes that they carry, and the potential for ESBL-carrying plasmid transfer.
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Dungan RS, Bjorneberg DL. Antimicrobial Resistance in Escherichia coli and Enterococcal Isolates From Irrigation Return Flows in a High-Desert Watershed. Front Microbiol 2021; 12:660697. [PMID: 34054760 PMCID: PMC8149595 DOI: 10.3389/fmicb.2021.660697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/13/2021] [Indexed: 11/25/2022] Open
Abstract
Irrigation return flows (IRFs) collect surface runoff and subsurface drainage, causing them to have elevated contaminant and bacterial levels, and making them a potential source of pollutants. The purpose of this study was to determine antimicrobial susceptibility among Escherichia coli and enterococcal isolates that were collected from IRFs in a south-central Idaho watershed. Environmental isolates can be a potentially important source of antimicrobial resistance (AMR) and IRFs may be one way resistance genes are transported out of agroecosystems. Water samples were collected from nine IRFs and one background site (canal water from Snake River) on a biweekly basis during 2018. Escherichia coli and enterococci were enumerated via a most probable number (MPN) technique, then subsamples were plated on selective media to obtain isolates. Isolates of E. coli (187) or enterococci (185) were tested for antimicrobial susceptibility using Sensititre broth microdilution plates. For E. coli, 13% (25/187) of isolates were resistant to tetracycline, with fewer numbers being resistant to 13 other antimicrobials, with none resistant to gentamicin. While 75% (141/187) of the E. coli isolates were pan-susceptible, 12 multidrug resistance (MDR) patterns with 17 isolates exhibiting resistance to up to seven drug classes (10 antimicrobials). For the enterococcal species, only 9% (16/185) of isolates were pan-susceptible and the single highest resistance was to lincomycin (138/185; 75%) followed by nitrofurantoin (56/185; 30%) and quinupristin/dalfopristin (34/185; 18%). In addition, 13 enterococcal isolates belonging to Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus, and Enterococcus thailandicus, were determined to be MDR to up to six different antimicrobial drug classes. None of the enterococcal isolates were resistant to gentamycin, linezolid, tigecycline, and vancomycin.
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Affiliation(s)
- Robert S Dungan
- Northwest Irrigation and Soils Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Kimberly, ID, United States
| | - David L Bjorneberg
- Northwest Irrigation and Soils Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Kimberly, ID, United States
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Pollution by Antibiotics and Antimicrobial Resistance in LiveStock and Poultry Manure in China, and Countermeasures. Antibiotics (Basel) 2021; 10:antibiotics10050539. [PMID: 34066587 PMCID: PMC8148549 DOI: 10.3390/antibiotics10050539] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 01/18/2023] Open
Abstract
The demand for animal protein has increased considerably worldwide, especially in China, where large numbers of livestock and poultry are produced. Antibiotics have been widely applied to promote growth and prevent diseases. However, the overuse of antibiotics in animal feed has caused serious environmental and health risks, especially the wide spread of antimicrobial resistance (AMR), which seriously affects animal and human health, food safety, ecosystems, and the sustainable future development of animal protein production. Unfortunately, AMR has already become a worldwide challenge, so international cooperation is becoming more important for combatting it. China’s efforts and determination to restrict antibiotic usage through law enforcement and effective management are of significance. In this review, we address the pollution problems of antibiotics; in particular, the AMR in water, soil, and plants caused by livestock and poultry manure in China. The negative impact of widespread and intensive use of antibiotics in livestock production is discussed. To reduce and mitigate AMR problems, we emphasize in this review the development of antibiotic substitutes for the era of antibiotic prohibition.
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Law A, Solano O, Brown CJ, Hunter SS, Fagnan M, Top EM, Stalder T. Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria. Front Microbiol 2021; 12:606409. [PMID: 33967971 PMCID: PMC8098119 DOI: 10.3389/fmicb.2021.606409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/09/2021] [Indexed: 12/05/2022] Open
Abstract
Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3-6 antibiotic resistance genes (ARG) conferring resistance to 2-4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.
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Affiliation(s)
- Aaron Law
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Olubunmi Solano
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Celeste J. Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Samuel S. Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
- UC-Davis Genome Center, Davis, CA, United States
| | - Matt Fagnan
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Eva M. Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
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26
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Pulami D, Schauss T, Eisenberg T, Wilharm G, Blom J, Goesmann A, Kämpfer P, Glaeser SP. Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants. FEMS Microbiol Ecol 2021; 96:5896450. [PMID: 32832994 DOI: 10.1093/femsec/fiaa176] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/20/2020] [Indexed: 12/19/2022] Open
Abstract
Studies considering environmental multidrug-resistant Acinetobacter spp. are scarce. The application of manure on agricultural fields is one source of multidrug-resistant bacteria from livestock into the environment. Here, Acinetobacter spp. were quantified by quantitative polymerase chain reaction in manure applied to biogas plants and in the output of the anaerobic digestion, and Acinetobacter spp. isolated from those samples were comprehensively characterized. The concentration of Acinetobacter 16S ribosomal ribonucleic acid (rRNA) gene copies per g fresh weight was in range of 106-108 in manure and decreased (partially significantly) to a still high concentration (105-106) in digestates. 16S rRNA, gyrB-rpoB and blaOXA51-like gene sequencing identified 17 different Acinetobacter spp., including six A. baumannii strains. Multilocus sequence typing showed no close relation of the six strains with globally relevant clonal complexes; however, they represented five novel sequence types. Comparative genomics and physiological tests gave an explanation how Acinetobacter could survive the anaerobic biogas process and indicated copper resistance and the presence of intrinsic beta-lactamases, efflux-pump and virulence genes. However, the A. baumannii strains lacked acquired resistance against carbapenems, colistin and quinolones. This study provided a detailed characterization of Acinetobacter spp. including A. baumannii released via manure through mesophilic or thermophilic biogas plants into the environment.
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Affiliation(s)
- Dipen Pulami
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Thorsten Schauss
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), D-35392 Giessen, Germany; Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, D-35392, Giessen, Germany
| | - Gottfried Wilharm
- Project Group P2, Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, D-35392 Giessen, Germany
| | - Alexander Goesmann
- Institute for Bioinformatics and Systems Biology, D-35392 Giessen, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, D-35392 Giessen, Germany
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Hill D, Morra MJ, Stalder T, Jechalke S, Top E, Pollard AT, Popova I. Dairy manure as a potential source of crop nutrients and environmental contaminants. J Environ Sci (China) 2021; 100:117-130. [PMID: 33279025 DOI: 10.1016/j.jes.2020.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 06/12/2023]
Abstract
Although animal manure is applied to agricultural fields for its nutrient value, it may also contain potential contaminants. To determine the variability in such contaminants as well as in valuable nutrients, nine uncomposted manure samples from Idaho dairies collected during 2.5 years were analyzed for macro- and micro-nutrients, hormones, phytoestrogens, antibiotics, veterinary drugs, antibiotic resistance genes, and genetic elements involved in the spread of antibiotic resistance. Total N ranged from 6.8 to 30.7 (C:N of 10 to 21), P from 2.4 to 9.0, and K from 10.2 to 47.7 g/kg manure. Zn (103 - 348 mg/kg) was more abundant than Cu (56 - 127 mg/kg) in all samples. Phytoestrogens were the most prevalent contaminants detected, with concentrations fluctuating over time, reflecting animal diets. This is the first study to document the presence of flunixin, a non-steroidal anti-inflammatory drug, in solid stacked manure from regular dairy operations. Monensin was the most frequently detected antibiotic. Progesterones and sulfonamides were regularly detected. We also investigated the relative abundance of several types of plasmids involved in the spread of antibiotic resistance in clinical settings. Plasmids belonging to the IncI, IncP, and IncQ1 incompatibility groups were found in almost all manure samples. IncQ1 plasmids, class 1 integrons, and sulfonamide resistance genes were the most widespread and abundant genetic element surveyed, emphasizing their potential role in the spread of antibiotic resistance. The benefits associated with amending agricultural soils with dairy manure must be carefully weighed against the potential negative consequences of any manure contaminants.
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Affiliation(s)
- Danika Hill
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | - Matthew J Morra
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | | | - Sven Jechalke
- Justus Liebig University Giessen, Institute for Phytopathology, 35392 Gießen, Germany
| | - Eva Top
- Department of Biology, University of Idaho, ID 83844-3051, USA
| | - Anne T Pollard
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | - Inna Popova
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA.
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Shintani M, Nour E, Elsayed T, Blau K, Wall I, Jechalke S, Spröer C, Bunk B, Overmann J, Smalla K. Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology. Front Microbiol 2020; 11:590776. [PMID: 33329469 PMCID: PMC7728920 DOI: 10.3389/fmicb.2020.590776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022] Open
Abstract
IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn501, IS1071, Tn402, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn501-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.
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Affiliation(s)
- Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Japan.,Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan.,Green Energy Research Division, Research Institute of Green Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Eman Nour
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Tarek Elsayed
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Khald Blau
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Inessa Wall
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Sven Jechalke
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Cathrin Spröer
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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Oliveira ÉMD, Beltrão EMB, Scavuzzi AML, Barros JF, Lopes ACS. High plasmid variability, and the presence of IncFIB, IncQ, IncA/C, IncHI1B, and IncL/M in clinical isolates of Klebsiella pneumoniae with bla KPC and bla NDM from patients at a public hospital in Brazil. Rev Soc Bras Med Trop 2020; 53:e20200397. [PMID: 33111914 PMCID: PMC7580274 DOI: 10.1590/0037-8682-0397-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Antibiotic resistance in carbapenemase-producing Klebsiella
pneumoniae is acquired and disseminated mainly by plasmids.
Therefore, we aimed to investigate the occurrence of carbapenemase genes,
analyze the genetic diversity by ERIC-PCR, and examine the most common
plasmid incompatibility groups (Incs) in clinical isolates of K.
pneumoniae from colonization and infection in patients from a
hospital in Brazil. METHODS Twenty-seven isolates of carbapenem-resistant K. pneumoniae
were selected and screened for the presence of carbapenemase genes and Incs
by PCR, followed by amplicon sequencing. RESULTS The blaKPC and blaNDM genes were detected in 24 (88.8 %) and 16 (59.2 %) of the
isolates, respectively. Thirteen isolates (48.1 %) were positive for both
genes. The IncFIB (92.6 %) and IncQ (88.8 %) were the most frequent
plasmids, followed by IncA/C, IncHI1B, and IncL/M, indicating that plasmid
variability existed in these isolates. To our knowledge, this is the first
report of IncHI1B in Brazil. We found eight isolates with clonal
relationship distributed in different sectors of the hospital. CONCLUSIONS The accumulation of resistance determinants, the variability of plasmid
Incs, and the clonal dissemination detected in K.
pneumoniae isolates demonstrate their potential for infection,
colonization, and the dissemination of different resistance genes and
plasmids.
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Affiliation(s)
- Érica Maria de Oliveira
- Universidade Federal de Pernambuco, Centro de Ciências Médicas, Área de Medicina Tropical, Recife, PE, Brasil
| | | | | | | | - Ana Catarina Souza Lopes
- Universidade Federal de Pernambuco, Centro de Ciências Médicas, Área de Medicina Tropical, Recife, PE, Brasil
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Berbers B, Ceyssens PJ, Bogaerts P, Vanneste K, Roosens NHC, Marchal K, De Keersmaecker SCJ. Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination. Antibiotics (Basel) 2020; 9:E503. [PMID: 32796589 PMCID: PMC7460218 DOI: 10.3390/antibiotics9080503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR. Next-generation sequencing (NGS) technologies are ideal for the detection of AMR genes; however, reliable reconstruction of plasmids is still a challenge due to large repetitive regions. This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads (Oxford Nanopore Technologies) and a combination of both (hybrid). Furthermore, the added value of conjugation of a plasmid to a known host was evaluated. As a case study, an isolate harboring a large, low-copy mcr-1-carrying plasmid (>200 kb) was used. Hybrid assemblies of NGS data obtained from whole-genome DNA extractions of the original isolates resulted in the most complete reconstruction of plasmids. The optimal workflow was successfully applied to multidrug-resistant Salmonella Kentucky isolates, where the transfer of an ESBL-gene-containing fragment from a plasmid to the chromosome was detected. This study highlights a strategy including wet and dry lab parameters that allows accurate plasmid reconstruction, which will contribute to an improved monitoring of circulating plasmids and the assessment of their risk of transfer.
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Affiliation(s)
- Bas Berbers
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium;
| | | | - Pierre Bogaerts
- National Reference Center for Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, 5530 Yvoir, Belgium;
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria 0083, South Africa
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32
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Checcucci A, Trevisi P, Luise D, Modesto M, Blasioli S, Braschi I, Mattarelli P. Exploring the Animal Waste Resistome: The Spread of Antimicrobial Resistance Genes Through the Use of Livestock Manure. Front Microbiol 2020; 11:1416. [PMID: 32793126 PMCID: PMC7387501 DOI: 10.3389/fmicb.2020.01416] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance is a public health problem of growing concern. Animal manure application to soil is considered to be a main cause of the propagation and dissemination of antibiotic residues, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) in the soil-water system. In recent decades, studies on the impact of antibiotic-contaminated manure on soil microbiomes have increased exponentially, in particular for taxonomical diversity and ARGs’ diffusion. Antibiotic resistance genes are often located on mobile genetic elements (MGEs). Horizontal transfer of MGEs toward a broad range of bacteria (pathogens and human commensals included) has been identified as the main cause for their persistence and dissemination. Chemical and bio-sanitizing treatments reduce the antibiotic load and ARB. Nevertheless, effects of these treatments on the persistence of resistance genes must be carefully considered. This review analyzed the most recent research on antibiotic and ARG environmental dissemination conveyed by livestock waste. Strategies to control ARG dissemination and antibiotic persistence were reviewed with the aim to identify methods for monitoring DNA transferability and environmental conditions promoting such diffusion.
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Affiliation(s)
- Alice Checcucci
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Paolo Trevisi
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Diana Luise
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Monica Modesto
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Sonia Blasioli
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Ilaria Braschi
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy
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33
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Pu Q, Zhao LX, Li YT, Su JQ. Manure fertilization increase antibiotic resistance in soils from typical greenhouse vegetable production bases, China. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122267. [PMID: 32062545 DOI: 10.1016/j.jhazmat.2020.122267] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 05/21/2023]
Abstract
A large quantity of manure is applied in greenhouse vegetable production (GVP) soils, while manure fertilization often leads to the proliferation of antibiotic resistance genes (ARGs) in soils. However, comprehensive study on the effects of different types of manure on ARGs in GVP soils remains unknown, and the baseline level of ARGs in GVP soil is poorly quantified. This study conducted a comprehensive survey of ARGs in GVP soils using high-throughput quantitative PCR. We found elevated ARG diversity and absolute abundance in fertilized soil, whereas no significant difference in soil ARGs amended with different types of manure. Redundancy analysis indicated that the change of bacterial community compositions and environmental factors contributed partially to the shift in ARG profiles. Bipartite network analysis indicated that one ARG was detected in non-manured soils, while 50 ARGs and 4 mobile gene elements were exclusively detected in fertilized soils, suggesting introduction of ARGs from manure into soils largely explained the increased ARG diversity in fertilized soil. By comparison of ARG absolute abundance between manured and non-manured soil, we estimated the typical level of ARG absolute abundance in non-manured soil, which provided the first rough baseline level of ARGs to assess ARG contamination in GVP soils.
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Affiliation(s)
- Qiang Pu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Li-Xia Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yong-Tao Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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34
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Lu W, Wang M, Wu J, Jiang Q, Jin J, Jin Q, Yang W, Chen J, Wang Y, Xiao M. Spread of chloramphenicol and tetracycline resistance genes by plasmid mobilization in agricultural soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:113998. [PMID: 31991360 DOI: 10.1016/j.envpol.2020.113998] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Spread of antibiotic resistance genes (ARGs) poses a worldwide threat to public health and food safety. However, ARG spread by plasmid mobilization, a broad host range transfer system, in agricultural soil has received little attention. Here, we investigated the spread of chloramphenicol resistance gene (CRG) and tetracycline resistance gene (TRG) in agricultural soil by mobilization of pSUP106 under different conditions, including different concentrations of nutrients, temperatures, soil depths, rhizosphere soils, and soil types. The number of resistant bacteria isolated in non-sterilized soil from the experiments was approximately 104 to 107 per gram of soil, belonging to 5-10 species from four genera, including nonpathogen, opportunistic pathogen, pathogen bacteria, and gram-positive and gram-negative bacteria, depending on the experiment conditions. In sterilized soil, higher levels of nutrients and higher temperatures promoted plasmid mobilization and ARG expression. Topsoil and deep soil might not support the spread of antibiotic resistance, while ARG dissemination by plasmid mobilization was better supported by maize rhizosphere and loam soils. All these factors might change bacterial growth and the activity of bacteria and lead to the above influence. Introduction of only the donor and helper, or the donor alone also resulted in the transfer of ARGs and large numbers of antibiotic resistant bacteria (ARB), indicating that some indigenous bacteria contain the elements necessary for plasmid mobilization. Our results showed that plasmid mobilization facilitated dissemination of ARGs and ARB in soil, which led to the disturbance of indigenous bacterial communities. It is important to clear ARG dissemination routes and inhibit the spread of ARGs.
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Affiliation(s)
- Wenwei Lu
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Min Wang
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Jianqiang Wu
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Qiuyan Jiang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jieren Jin
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qing Jin
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wenwu Yang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jun Chen
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yujing Wang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ming Xiao
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, 200240, China.
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35
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Liu C, Chen Y, Li X, Zhang Y, Ye J, Huang H, Zhu C. Temporal effects of repeated application of biogas slurry on soil antibiotic resistance genes and their potential bacterial hosts. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113652. [PMID: 31818620 DOI: 10.1016/j.envpol.2019.113652] [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: 04/27/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Biogas slurry, a liquid end product of animal manure fermentation, is widely used as fertilizer in crop fields. Land application may introduce antibiotics and related resistance genes from livestock production into agricultural soil. Nevertheless, changes in antimicrobial resistance in soil where biogas slurry has been repeatedly applied are not fully understood. In the present study, 13 veterinary antibiotics were analyzed in soils that were repeatedly sprayed with biogas slurry, and simultaneously, temporal changes in antibiotic resistance genes (ARGs) and bacterial community composition were investigated using a real-time quantitative PCR assay and MiSeq sequencing. Long-term repeated application of biogas slurry did not result in excessive accumulation of antibiotic residuals in the soil but increased the abundance of ARGs and facilitated ARG transfer among potential hosts. Although the quantitative PCR assay showed a decreasing trend for the relative abundance of ARGs over time, a relevance network analysis revealed highly complex bacteria-ARG co-occurrence after long-term application, which implied that repeated application might intensify horizontal gene transfer (HGT) of ARGs among different bacterial hosts in soil. The increased relative abundance of the intl1 gene supported the shift in ARG-bacteria co-occurrence. Furthermore, ordination analysis showed that the distributions of antibiotic resistance bacteria (ARB) and ARGs were closely related to application duration than to the influence of antibiotic residuals in the biogas slurry-treated soil environment. Additionally, natural level of ARG abundance in untreated soils indirectly suggested the presence/absence of antibiotics was not a key determinant causing the spread of antimicrobial resistance. This study provides improved insight into the effects of long-term repeated application of biogas slurry on the shift in ARG abundances and bacteria-ARG co-occurrence in soils, highlighting the need to focus on the influence of changed soil environment on the ARG transfer.
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Affiliation(s)
- Chong Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongxing Chen
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaohua Li
- Rural Energy & Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Yanrong Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Ye
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongkun Huang
- Rural Energy & Environment Agency, Ministry of Agriculture and Rural Affairs, Beijing, 100125, China
| | - Changxiong Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Blau K, Jechalke S, Smalla K. Detection, Isolation, and Characterization of Plasmids in the Environment. Methods Mol Biol 2020; 2075:39-60. [PMID: 31584153 DOI: 10.1007/978-1-4939-9877-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Plasmids play a major role in the bacterial adaptation to changing and stressful environmental conditions caused by antibiotics, heavy metals, and disinfectants. However, the investigation of the ecology and diversity of environmental plasmids is challenging due to their typically low abundance in soil bacterial communities and the low cultivability of their hosts. Here we discuss the potentials and limitations of cultivation-dependent and cultivation-independent approaches for detecting and quantifying plasmids in total community DNA from environmental samples. Protocols for PCR-based detection of plasmid-specific sequences in total community DNA are presented. Furthermore, protocols to obtain and characterize plasmids either from isolates (endogenous plasmid isolation) or by capturing into a recipient strain by biparental and triparental mating will be provided.
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Affiliation(s)
- Khald Blau
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Sven Jechalke
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany.
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Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria. Nat Commun 2019; 10:5809. [PMID: 31863068 PMCID: PMC6925257 DOI: 10.1038/s41467-019-13709-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/21/2019] [Indexed: 01/07/2023] Open
Abstract
Transmissible plasmids spread genes encoding antibiotic resistance and other traits to new bacterial species. Here we report that laboratory populations of Escherichia coli with a newly acquired IncQ plasmid often evolve 'satellite plasmids' with deletions of accessory genes and genes required for plasmid replication. Satellite plasmids are molecular parasites: their presence reduces the copy number of the full-length plasmid on which they rely for their continued replication. Cells with satellite plasmids gain an immediate fitness advantage from reducing burdensome expression of accessory genes. Yet, they maintain copies of these genes and the complete plasmid, which potentially enables them to benefit from and transmit the traits they encode in the future. Evolution of satellite plasmids is transient. Cells that entirely lose accessory gene function or plasmid mobility dominate in the long run. Satellite plasmids also evolve in Snodgrassella alvi colonizing the honey bee gut, suggesting that this mechanism may broadly contribute to the importance of IncQ plasmids as agents of bacterial gene transfer in nature.
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González-Plaza JJ, Blau K, Milaković M, Jurina T, Smalla K, Udiković-Kolić N. Antibiotic-manufacturing sites are hot-spots for the release and spread of antibiotic resistance genes and mobile genetic elements in receiving aquatic environments. ENVIRONMENT INTERNATIONAL 2019; 130:104735. [PMID: 31260930 DOI: 10.1016/j.envint.2019.04.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 05/24/2023]
Abstract
High antibiotic releases from manufacturing facilities have been identified as a risk factor for antibiotic resistance development in bacterial pathogens. However, the role of antibiotic pollution in selection and transferability of antibiotic resistance genes (ARGs) is still limited. In this study, we analyzed effluents from azithromycin-synthesis and veterinary-drug formulation facilities as well as sediments from receiving river and creek taken at the effluent discharge sites, upstream and downstream of discharge. Culturing showed that the effluent discharge significantly increased the proportion of antibiotic resistant bacteria in exposed sediments compared to the upstream ones. Quantitative real-time PCR revealed that effluents from both industries contained high and similar relative abundances of resistance genes [sul1, sul2, qacE/qacEΔ1, tet(A)], class 1 integrons (intI1) and IncP-1 plasmids (korB). Consequently, these genes significantly increased in relative abundances in receiving sediments, with more pronounced effects being observed for river than for creek sediments due to lower background levels of the investigated genes in the river. In addition, effluent discharge considerably increased transfer frequencies of captured ARGs from exposed sediments into Escherichia coli CV601 recipient as shown by biparental mating experiments. Most plasmids exogenously captured from effluent and polluted sediments belonged to the broad host range IncP-1ε plasmid group, conferred multiple antibiotic resistance and harbored class 1 integrons. Discharge of pharmaceutical waste from antibiotic manufacturing sites thus poses a risk for development and dissemination of multi-resistant bacteria, including pathogens.
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Affiliation(s)
| | - Khald Blau
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tamara Jurina
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
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Dionisio F, Zilhão R, Gama JA. Interactions between plasmids and other mobile genetic elements affect their transmission and persistence. Plasmid 2019; 102:29-36. [DOI: 10.1016/j.plasmid.2019.01.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 10/27/2022]
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Wu J, Su Y, Deng Y, Guo Z, Cheng C, Ma H, Liu G, Xu L, Feng J. Spatial and temporal variation of antibiotic resistance in marine fish cage-culture area of Guangdong, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 246:463-471. [PMID: 30583154 DOI: 10.1016/j.envpol.2018.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/20/2018] [Accepted: 12/09/2018] [Indexed: 06/09/2023]
Abstract
The rapid emergence and dissemination of antibiotic resistance poses a threat to human health and to the marine environment. We have investigated the abundance and diversity of antibiotic resistance genes (ARGs) and of antibiotic-resistant bacteria (ARB), during the seedling period, rearing period, and harvesting period in seven marine fish cage-culture areas in Guangdong. Spatial and temporal variations of AGRs and ARB were also analyzed. Culture-based methods and quantitative PCR were used to detect ARB and ARGs. Bacterial resistance rates were no significantly different within farming periods. The proportion of antibiotic-resistant bacteria was extremely low (average on 1.15%), except for oxytetracycline-resistant bacteria (average on 34.15%). Vibrio was the most common ARB. Sul1, tetB, and ermB, had the highest relative abundance. The abundance of ARGs in the harvesting period was significant highest. The total abundance of ARGs was highest at Raoping and lowest at Dayawan and Liusha. Most ARGs were associated with opportunistic pathogens. The environmental factors effecting ARB and ARGs are complex, and no key factors were identified. This study provides a theoretical basis for assessing the harmfulness of ARGs and ARB to food safety and human health.
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Affiliation(s)
- Jinjun Wu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China; College of Aqua-life Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Youlu Su
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Zhixun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Changhong Cheng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Hongling Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Guangfeng Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Liwen Xu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
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Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes. mBio 2019; 10:mBio.02899-18. [PMID: 30808697 PMCID: PMC6391923 DOI: 10.1128/mbio.02899-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Naturally occurring plasmids constitute a major category of mobile genetic elements responsible for harboring and transferring genes important in survival and fitness. A targeted evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We developed a model system to optimize plasmid DNA isolation procedures targeted to groundwater samples which are typically characterized by low cell density (and likely variations in the plasmid size and copy numbers). The optimized method resulted in successful identification of several hundred circular plasmids, including some large plasmids (11 plasmids more than 50 kb in size, with the largest being 1.7 Mb in size). Several interesting observations were made from the analysis of plasmid DNA isolated in this study. The plasmid pool (plasmidome) was more conserved than the corresponding microbiome distribution (16S rRNA based). The circular plasmids were diverse as represented by the presence of seven plasmid incompatibility groups. The genes carried on these groundwater plasmids were highly enriched in metal resistance. Results from this study confirmed that traits such as metal, antibiotic, and phage resistance along with toxin-antitoxin systems are encoded on abundant circular plasmids, all of which could confer novel and advantageous traits to their hosts. This study confirms the ecological role of the plasmidome in maintaining the latent capacity of a microbiome, enabling rapid adaptation to environmental stresses.IMPORTANCE Plasmidomes have been typically studied in environments abundant in bacteria, and this is the first study to explore plasmids from an environment characterized by low cell density. We specifically target groundwater, a significant source of water for human/agriculture use. We used samples from a well-studied site and identified hundreds of circular plasmids, including one of the largest sizes reported in plasmidome studies. The striking similarity of the plasmid-borne ORFs in terms of taxonomical and functional classifications across several samples suggests a conserved plasmid pool, in contrast to the observed variability in the 16S rRNA-based microbiome distribution. Additionally, the stress response to environmental factors has stronger conservation via plasmid-borne genes as marked by abundance of metal resistance genes. Last, identification of novel and diverse plasmids enriches the existing plasmid database(s) and serves as a paradigm to increase the repertoire of biological parts that are available for modifying novel environmental strains.
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Liu Y, Cui E, Neal AL, Zhang X, Li Z, Xiao Y, Du Z, Gao F, Fan X, Hu C. Reducing water use by alternate-furrow irrigation with livestock wastewater reduces antibiotic resistance gene abundance in the rhizosphere but not in the non-rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:12-24. [PMID: 30107302 PMCID: PMC6234105 DOI: 10.1016/j.scitotenv.2018.08.101] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 08/07/2018] [Indexed: 05/08/2023]
Abstract
Livestock wastewater is rich in nutrients but may contain antibiotics and antibiotic resistance genes (ARGs). Their discharge to watercourses or soil may result in proliferation of ARGs. Irrigation with wastewater appears to be the most feasible option of disposing of it. One efficient irrigation technology used in arid regions is alternate-furrow irrigation (AFI) by alternately drying part of the plant roots for a prolonged period to physiologically reduce transpiration without compromising yield. However, the extent to which AFI with wastewater influences the concentration of antibiotics and spread of ARGs in soil is poorly understood. The purpose of this paper is to investigate how AFI using swine wastewater alters antibiotic kinetics and ARGs abundance under different irrigation rates, using pepper as the model plant. We examined three AFI treatments using 50%, 65% and 80% of the amount of water employed in sufficient conventional furrow irrigation. Each treatment had a groundwater irrigation control. The results showed that antibiotic concentrations and relative ARGs abundance in the top 20 cm of soil did not increase with the irrigation amount, although they were higher than those in the groundwater-irrigated soils. The relative ARGs abundance in the soil was modulated by irrigation amount and reducing the irrigation amount in AFI reduced ARGs dispersion only in rhizosphere. When the soil moisture was close to field capacity, ARGs were more abundant in rhizosphere than in non-rhizosphere, possibly because the rhizosphere is rich in microbes and increasing antibiotic concentrations due to an increase in irrigation rate favors antibiotic-resistant microbiome in competing for substrates. These, however, were not mirrored in the relative ARGs abundance in the roots. These results have important implications as it revealed that reducing the input of antibiotics and ARGs into soil with AFI does not necessarily reduce ARGs proliferation.
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Affiliation(s)
- Yuan Liu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Erping Cui
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Andrew L Neal
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Xiaoxian Zhang
- Department of Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Zhongyang Li
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China.
| | - Yatao Xiao
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Zhenjie Du
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Feng Gao
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Xiangyang Fan
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Chao Hu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
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Djenadi K, Zhang L, Murray AK, Gaze WH. Carbapenem resistance in bacteria isolated from soil and water environments in Algeria. J Glob Antimicrob Resist 2018; 15:262-267. [DOI: 10.1016/j.jgar.2018.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/25/2022] Open
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Cai Q, Hu J. Effect of UVA/LED/TiO 2 photocatalysis treated sulfamethoxazole and trimethoprim containing wastewater on antibiotic resistance development in sequencing batch reactors. WATER RESEARCH 2018; 140:251-260. [PMID: 29723814 DOI: 10.1016/j.watres.2018.04.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/30/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Controlling of antibiotics is the crucial step for preventing antibiotic resistance genes (ARGs) dissemination; UV photocatalysis has been identified as a promising pre-treatment technology for antibiotics removal. However, information about the effects of intermediates present in the treated antibiotics wastewater on the downstream biological treatment processes or ARGs development is very limited. In the present study, continuous UVA/LED/TiO2 photocatalysis removed more than 90% of 100 ppb sulfamethoxazole (SMX)/trimethoprim (TMP), the treated wastewater was fed into SBR systems for over one year monitoring. Residual SMX/TMP (2-3 ppb) and intermediates present in the treated wastewater did not adversely affect SBR performance in terms of TOC and TN removal. SMX and TMP resistance genes (sulI, sulII, sulIII, dfrII, dfrV and dfr13) were also quantified in SBRs microbial consortia. Results suggested that continuous feeding of treated SMX/TMP containing wastewaters did not trigger any ARGs promotion during the one year operation. By stopping the input of 100 ppb SMX/TMP, abundance of sulII and dfrV genes were reduced by 83% and 100%, respectively. sulI gene was identified as the most persistence ARG, and controlling of 100 ppb SMX input did not achieve significant removal of sulI gene. A significant correlation between sulI gene and class 1 integrons was found at the level of p = 1.4E-10 (r = 0.94), and sulII gene positively correlated with the plasmid transfer efficiency (r = 2.442E-10, r = 0.87). Continuous input of 100 ppb SMX enhanced plasmid transfer efficiency in the SBR system, resulting in sulII gene abundance increasing more than 40 times.
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Affiliation(s)
- Qinqing Cai
- Department of Civil and Environmental Engineering, National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore
| | - Jiangyong Hu
- Department of Civil and Environmental Engineering, National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore.
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Pinilla-Redondo R, Cyriaque V, Jacquiod S, Sørensen SJ, Riber L. Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives. Plasmid 2018; 99:56-67. [PMID: 30086339 DOI: 10.1016/j.plasmid.2018.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 10/28/2022]
Abstract
The emergence of antimicrobial resistant bacteria constitutes an increasing global health concern. Although it is well recognized that the cornerstone underlying this phenomenon is the dissemination of antimicrobial resistance via plasmids and other mobile genetic elements, the antimicrobial resistance transfer routes remain largely uncharted. In this review, we describe different methods for assessing the transfer frequency and host ranges of plasmids within complex microbiomes. The discussion is centered around the critical evaluation of recent advances for monitoring the fate of fluorescently tagged plasmids in bacterial communities through the coupling of fluorescence activated cell sorting and next generation sequencing techniques. We argue that this approach constitutes an exceptional tool for obtaining quantitative data regarding the extent of plasmid transfer, key disseminating taxa, and possible propagation routes. The integration of this information will provide valuable insights on how to develop alternative avenues for fighting the rise of antimicrobial resistant pathogens, as well as the means for constructing more comprehensive risk assessment models.
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Affiliation(s)
| | - Valentine Cyriaque
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, Mons, Belgium
| | | | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Leise Riber
- Section for Functional Genomics, University of Copenhagen, Copenhagen, Denmark.
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Petroleum contamination and bioaugmentation in bacterial rhizosphere communities from Avicennia schaueriana. Braz J Microbiol 2018; 49:757-769. [PMID: 29866608 PMCID: PMC6175736 DOI: 10.1016/j.bjm.2018.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 02/01/2018] [Accepted: 02/14/2018] [Indexed: 11/23/2022] Open
Abstract
Anthropogenic activity, such as accidental oil spills, are typical sources of urban mangrove pollution that may affect mangrove bacterial communities as well as their mobile genetic elements. To evaluate remediation strategies, we followed over the time the effects of a petroleum hydrocarbon degrading consortium inoculated on mangrove tree Avicennia schaueriana against artificial petroleum contamination in a phytoremediation greenhouse experiment. Interestingly, despite plant protection due to the inoculation, denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene fragments amplified from the total community DNA indicated that the different treatments did not significantly affect the bacterial community composition. However, while the bacterial community was rather stable, pronounced shifts were observed in the abundance of bacteria carrying plasmids. A PCR-Southern blot hybridization analysis indicated an increase in the abundance of IncP-9 catabolic plasmids. Denaturing gradient gel electrophoresis of naphthalene dioxygenase (ndo) genes amplified from cDNA (RNA) indicated the dominance of a specific ndo gene in the inoculated petroleum amendment treatment. The petroleum hydrocarbon degrading consortium characterization indicated the prevalence of bacteria assigned to Pseudomonas spp., Comamonas spp. and Ochrobactrum spp. IncP-9 plasmids were detected for the first time in Comamonas sp. and Ochrobactrum spp., which is a novelty of this study.
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Mastrorilli E, Pietrucci D, Barco L, Ammendola S, Petrin S, Longo A, Mantovani C, Battistoni A, Ricci A, Desideri A, Losasso C. A Comparative Genomic Analysis Provides Novel Insights Into the Ecological Success of the Monophasic Salmonella Serovar 4,[5],12:i:. Front Microbiol 2018; 9:715. [PMID: 29719530 PMCID: PMC5913373 DOI: 10.3389/fmicb.2018.00715] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 03/27/2018] [Indexed: 12/27/2022] Open
Abstract
Over the past decades, Salmonella 4,[5],12:i:- has rapidly emerged and it is isolated with high frequency in the swine food chain. Although many studies have documented the epidemiological success of this serovar, few investigations have tried to explain this phenomenon from a genetic perspective. Here a comparative whole-genome analysis of 50 epidemiologically unrelated S. 4,[5],12:i:-, isolated in Italy from 2010 to 2016 was performed, characterizing them in terms of genetic elements potentially conferring resistance, tolerance and persistence characteristics. Phylogenetic analyses indicated interesting distinctions among the investigated isolates. The most striking genetic trait characterizing the analyzed isolates is the widespread presence of heavy metals tolerance gene cassettes: most of the strains possess genes expected to confer resistance to copper and silver, whereas about half of the isolates also contain the mercury tolerance gene merA. A functional assay showed that these genes might be useful for preventing the toxic effects of metals, thus supporting the hypothesis that they can contribute to the success of S. 4,[5],12:i:- in farming environments. In addition, the analysis of the distribution of type II toxin-antitoxin families indicated that these elements are abundant in this serovar, suggesting that this is another factor that might favor its successful spread.
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Affiliation(s)
- Eleonora Mastrorilli
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Lisa Barco
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Serena Ammendola
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Sara Petrin
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Alessandra Longo
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Claudio Mantovani
- Science Communication Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Antonia Ricci
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Carmen Losasso
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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Zhang J, Mao F, Loh KC, Gin KYH, Dai Y, Tong YW. Evaluating the effects of activated carbon on methane generation and the fate of antibiotic resistant genes and class I integrons during anaerobic digestion of solid organic wastes. BIORESOURCE TECHNOLOGY 2018; 249:729-736. [PMID: 29096147 DOI: 10.1016/j.biortech.2017.10.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023]
Abstract
The effects of activated carbon (AC) on methane production and the fate of antibiotic resistance genes (ARGs) were evaluated through comparing the anaerobic digestion performance and transformation of ARGs among anaerobic mono-digestion of food waste, co-digestion of food waste and chicken manure, and co-digestion of food waste and waste activated sludge. Results showed that adding AC in anaerobic digesters improved methane yield by at least double through the enrichment of bacteria and archaea. Conventional digestion process showed ability in removing certain types of ARGs, such as tetA, tetX, sul1, sul2, cmlA, floR, and intl1. Supplementing AC in anaerobic digester enhanced the removal of most of the ARGs in mono-digestion of food waste. The effects tended to be minimal in co-digestion of co-substrates such as chicken manure and waste activated sludge, both of which contain a certain amount of antibiotics.
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Affiliation(s)
- Jingxin Zhang
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore
| | - Feijian Mao
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Kai-Chee Loh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore; Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Yanjun Dai
- Institute of Refrigeration and Cryogenics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yen Wah Tong
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore.
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49
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Zhang YJ, Hu HW, Gou M, Wang JT, Chen D, He JZ. Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1621-1632. [PMID: 28964602 DOI: 10.1016/j.envpol.2017.09.074] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/20/2017] [Accepted: 09/20/2017] [Indexed: 05/11/2023]
Abstract
Land application of animal manure is a common agricultural practice potentially leading to dispersal and propagation of antibiotic resistance genes (ARGs) in environmental settings. However, the fate of resistome in agro-ecosystems over time following application of different manure sources has never been compared systematically. Here, soil microcosm incubation was conducted to compare effects of poultry, cattle and swine manures spiked with or without the antibiotic tylosin on the temporal changes of soil ARGs. The high-throughput quantitative PCR detected a total of 185 unique ARGs, with Macrolide-Lincosamide-Streptogramin B resistance as the most frequently encountered ARG type. The diversity and abundance of ARGs significantly increased following application of manure and manure spiked with tylosin, with more pronounced effects observed in the swine and poultry manure treatments than in the cattle manure treatment. The level of antibiotic resistance gradually decreased over time in all manured soils but was still significantly higher in the soils treated with swine and poultry manures than in the untreated soils after 130 days' incubation. Tylosin-amended soils consistently showed higher abundances of ARGs than soils treated with manure only, suggesting a strong selection pressure of antibiotic-spiked manure on soil ARGs. The relative abundance of ARGs had significantly positive correlations with integrase and transposase genes, indicative of horizontal transfer potential of ARGs in manure and tylosin treated soils. Our findings provide evidence that application of swine and poultry manures might enrich more soil ARGs than cattle manure, which necessitates the appropriate treatment of raw animal manures prior to land application to minimise the spread of environmental ARGs.
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Affiliation(s)
- Yu-Jing Zhang
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Min Gou
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Deli Chen
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia; State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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50
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Liu P, Jia S, He X, Zhang X, Ye L. Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils. CHEMOSPHERE 2017; 188:455-464. [PMID: 28898777 DOI: 10.1016/j.chemosphere.2017.08.162] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 07/03/2017] [Accepted: 08/25/2017] [Indexed: 06/07/2023]
Abstract
Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
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