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Rethinking Manure Application: Increase in Multidrug-Resistant Enterococcus spp. in Agricultural Soil Following Chicken Litter Application. Microorganisms 2021; 9:microorganisms9050885. [PMID: 33919134 PMCID: PMC8170873 DOI: 10.3390/microorganisms9050885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
The current study investigated the impact of chicken litter application on the abundance of multidrug-resistant Enterococcus spp. in agricultural soil. Soil samples were collected from five different strategic places on a sugarcane farm before and after manure application for four months. Chicken litter samples were also collected. Enterococci were enumerated using the Enterolert®/Quanti-Tray 2000® system and confirm and differentiated into species using real-time PCR. The antibiotic susceptibility profile of the isolates was determined using the disk diffusion method following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The overall mean bacterial count was significantly higher (p < 0.05) in manure-amended soil (3.87 × 107 MPN/g) than unamended soil (2.89 × 107 MPN/g). Eight hundred and thirty-five enterococci (680 from soil and 155 from litter) were isolated, with E. casseliflavus being the most prevalent species (469; 56.2%) and E. gallinarum being the least (16; 1.2%). Approximately 56% of all the isolates were resistant to at least one antibiotic tested, with the highest resistance observed against tetracycline (33%) and the lowest against chloramphenicol (0.1%); 17% of E. faecium were resistant to quinupristin-dalfopristin. Additionally, 27.9% (130/466) of the isolates were multidrug-resistant, with litter-amended soil harbouring more multidrug-resistant (MDR) isolates (67.7%; 88/130) than unamended soil (10.0%; 13/130). All isolates were susceptible to tigecycline, linezolid and gentamicin. About 7% of the isolates had a multiple antimicrobial resistance index > 0.2, indicative of high antibiotic exposure. Although organic fertilizers are regarded as eco-friendly compared to chemical fertilizers for improving soil fertility, the application of untreated animal manure could promote the accumulation of antibiotics and their residues and antibiotic-resistant bacteria in the soil, creating an environmental reservoir of antimicrobial resistance, with potential human and environmental health risks.
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Bangsgaard EO, Græsbøll K, Andersen VD, Clasen J, Jasinskytė D, Hansen JE, Folkesson A, Christiansen LE. Mixed effect modeling of tetracycline resistance levels in Danish slaughter pigs. Prev Vet Med 2021; 191:105362. [PMID: 33895502 DOI: 10.1016/j.prevetmed.2021.105362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/10/2021] [Accepted: 04/12/2021] [Indexed: 11/24/2022]
Abstract
Mathematical and statistical modeling can be a very useful tool in understanding and fighting antimicrobial resistance (AMR). Here we present investigations of mixed effect models of varying complexity in order to identify and address possible management factors affecting the tetracycline AMR levels in Danish pig farms. Besides antimicrobial exposure during pigs life cycle, the type of production seems to also have an influence. The results concludes that not only fully integrated farms (CHR integrated) but also farms in a production network with a single ownership (CVR integrated) might have a preventive effect on levels of tetracycline AMR compared to more complex trading patterns.
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Affiliation(s)
| | - Kaare Græsbøll
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | | | - Julie Clasen
- Department of Bioengineering and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Džiuginta Jasinskytė
- Department of Bioengineering and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Julie Elvekjær Hansen
- Department of Bioengineering and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Anders Folkesson
- Department of Bioengineering and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lasse Engbo Christiansen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
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53
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Zhou G, Qiu X, Wu X, Lu S. Horizontal gene transfer is a key determinant of antibiotic resistance genes profiles during chicken manure composting with the addition of biochar and zeolite. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124883. [PMID: 33370695 DOI: 10.1016/j.jhazmat.2020.124883] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Livestock manure is an important reservoir of antibiotic resistance genes (ARGs). Biochar and zeolite are commonly used to improve the quality of compost, however, little is known about the impacts of these additives on the fate of ARGs during composting and the underlying mechanisms involved. In this study, zeolite (ZL), biochar (BC), or zeolite and biochar (ZB) simultaneously were added to chicken manure compost to evaluate their effects on the ARGs patterns. After composting, the abundance of ARGs reduced by 92.6% in control, while the reductions were 95.9%, 98.7% and 98.2% for ZL, BC, ZB, respectively. Co-occurrence network analysis indicated that the potential hosts for most ARGs were predominantly affiliated to Firmicutes such as Lactobacillus and Fastidiosipila. Furthermore, shifts in ARGs were significantly correlated with class 1 integrase gene (intI1), and structural equation models further revealed that intI1 gene contributed most (standardized total effect 0.92) to the ARGs-removal, which was trigged by horizontal gene transfer. Together these results suggest that the addition of zeolite and biochar mitigate the accumulation and spread of ARGs during composting, and the crucial role of horizontal gene transfer (HGT) on the behaviors of ARGs should pay more attention to in the future.
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Affiliation(s)
- Guixiang Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Jiangxi Province Key Laboratory of Industrial Ecological Simulation and Environmental Health in Yangtze River Basin, Jiujiang University, Jiujiang 332005, China
| | - Xiuwen Qiu
- Jiangxi Province Key Laboratory of Industrial Ecological Simulation and Environmental Health in Yangtze River Basin, Jiujiang University, Jiujiang 332005, China; College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shunbao Lu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
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54
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Raza S, Jo H, Kim J, Shin H, Hur HG, Unno T. Metagenomic exploration of antibiotic resistome in treated wastewater effluents and their receiving water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 765:142755. [PMID: 33071135 DOI: 10.1016/j.scitotenv.2020.142755] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/14/2020] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
Environmental dissemination of antimicrobial resistance is a global health problem. Antimicrobial-resistant bacteria and antibiotic-resistant genes (ARGs) are constantly released into the environment through effluents (EFs) from wastewater treatment plants (WWTPs). Thus, requiring a better understanding of the selection and fate of ARGs in wastewater treatment processes. Therefore, we investigated the impacts of urban WWTP EFs on receiving water in the context of their resistomes and mobilomes. We used a HiSeq-based short read metagenomic approach to address the dynamics and diversity of ARGs in WWTP EF as well as the upstream (UP) and downstream (DN) river waters, followed by an investigation of plasmid-mediated ARGs. The abundance of ARGs at each site varied from 7.2 × 10-2 to 7.4 × 10-1 ARG copies per 16S rRNA gene copy, and EF samples showed the highest abundance, followed by DN and UP water samples. ARG diversity ranged from 121 to 686 types per site, and EF had the most diverse ARGs. Commonly identified ARGs in the EF and DN samples were clinically important and were absent in UP samples. The abundance of ARGs, mobile genetic elements (MGEs), and plasmid contigs found only in EF and DN were positively correlated with each other, indicating the importance of mobilomes in the dissemination of ARGs in the environment. Moreover, the proportions of plasmid-mediated ARGs was highest in the EF samples, followed by the DN and UP samples. These findings suggest that WWTP EF may act as a driving factor shaping the resistomes and mobilomes of receiving waters. In particular, a higher abundance of plasmid-mediated ARGs in WWTP EF suggests higher transmissibility in the DN environment.
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Affiliation(s)
- Shahbaz Raza
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 63243, Republic of Korea
| | - Hyejun Jo
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 63243, Republic of Korea
| | - Jungman Kim
- Research Institute for Basic Sciences (RIBS), Jeju National University, Jeju 63243, Republic of Korea
| | - Hanseob Shin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hor-Gil Hur
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Tatsuya Unno
- Faculty of Biotechnology, College of Applied Life Sciences, SARI, Jeju National University, Jeju 63243, Republic of Korea.
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55
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Characterization of Environmental and Cultivable Antibiotic-Resistant Microbial Communities Associated with Wastewater Treatment. Antibiotics (Basel) 2021; 10:antibiotics10040352. [PMID: 33810449 PMCID: PMC8066808 DOI: 10.3390/antibiotics10040352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify phenotypically resistant cultivable portions of these bacterial communities and characterized the composition of the culturable subset of these populations. Resistant taxa were more abundant in raw sewage and wastewater before the biological aeration treatment stage. While some antibiotic-resistant bacteria (ARB) were detectable downstream of treated wastewater release, these organisms are not enriched relative to effluent-free upstream water, indicating efficient removal during treatment. Combined culture-dependent and -independent analyses revealed a stark difference in community composition between culturable fractions and the environmental source material, irrespective of culturing conditions. Higher proportions of the environmental populations were recovered than predicted by the widely accepted 1% culturability paradigm. These results represent baseline abundance and compositional data for ARB communities for reference in future studies addressing the dissemination of antibiotic resistance associated with urban wastewater treatment ecosystems.
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56
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Dong L, Meng L, Liu H, Wu H, Hu H, Zheng N, Wang J, Schroyen M. Effect of therapeutic administration of β-lactam antibiotics on the bacterial community and antibiotic resistance patterns in milk. J Dairy Sci 2021; 104:7018-7025. [PMID: 33741154 DOI: 10.3168/jds.2020-20025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/04/2021] [Indexed: 01/21/2023]
Abstract
Dairy cows with mastitis are frequently treated with antibiotics. The potential effect of antibiotics on the milk microbiome is still not clear. Therefore, the objective of this research was to investigate the effect of 2 commonly used cephalosporins on the milk microbiota of dairy cows and the antibiotic resistance genes in the milk. The milk samples were collected from 7 dairy cows at the period before medication (d 0), medication (d 1, 2, 3), withdrawal period (d 4, 6, 8), and the period after withdrawal (d 9, 11, 13, 15). We applied 16S rRNA sequencing to explore the microbiota changes, and antibiotic resistance patterns were investigated by quantitative PCR. The microbiota richness and diversity in each sample were calculated using the Chao 1 (richness), Shannon (diversity), and Simpson (diversity) indices. The cephalosporins treatment lowered the Simpson diversity value at the period of withdrawal. Members of the Enterobacter genera were the most affected bacteria associated with mastitis. Meanwhile, antibiotic resistance genes in the milk were also influenced by antibiotic treatment. The cephalosporins treatment raised the proportion of blaTEM in milk samples at the period of withdrawal. Therefore, the treatment of cephalosporins led to change in the milk microbiota and increase of β-lactam resistance gene in the milk at the time of withdrawal period.
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Affiliation(s)
- Lei Dong
- Key Laboratory of Quality and Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, Gembloux 5030, Belgium
| | - Lu Meng
- Key Laboratory of Quality and Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Huimin Liu
- Key Laboratory of Quality and Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Haoming Wu
- Key Laboratory of Quality and Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Haiyan Hu
- Key Laboratory of Quality and Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Nan Zheng
- Key Laboratory of Quality and Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Jiaqi Wang
- Key Laboratory of Quality and Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China.
| | - Martine Schroyen
- Precision Livestock and Nutrition Laboratory, Teaching and Research Centre (TERRA), Gembloux Agro-Bio Tech, University of Liège, Gembloux 5030, Belgium
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57
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Lu H, Wang J, Huang L, Wang X, Zhou J, Wang J. Effect of immobilized anthraquinone-2-sulfonate on antibiotic resistance genes and microbial community in biofilms of anaerobic reactors. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 282:111967. [PMID: 33454531 DOI: 10.1016/j.jenvman.2021.111967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Quinone compounds could significantly accelerate anaerobic biotransformation of refractory pollutants. However, the effect of quinone compounds application on the propagation of antibiotic resistance genes (ARGs) in the bio-treatment of these pollutants-containing wastewater is not available. In this study, the catalytic performance of anthraquinone-2-sulfonate immobilized on polyurethane foam (AQS-PUF), changes of ARGs, mobile gene elements (MGEs) and microbial community structure attached on AQS-PUF and PUF in the up-flow anaerobic bioreactors were investigated. The results showed that AQS-PUF could significantly accelerate the decolorization of azo dye RR X-3B. Meanwhile, metagenomics analysis showed that the total absolute abundance of ARGs increased in the presence of the immobilized AQS. Among ARGs, the number of the efflux pump-encoding ARGs in the biofilm of AQS-PUF accounted for 35.7% of the total ARGs, which was slightly higher than that of PUF (32.1%) due to the presence of the immobilized AQS. The relative abundances of ARGs conferring resistance to MLS (macrolide, lincosamide and streptogramin), tetracycline and sulfonamide, which were deeply concerned, reduced 10%, 21.7% and 7.3% in the presence of the immobilized AQS, respectively. Moreover, the immobilized AQS resulted in the decreased relative abundance of plasmids, transposons and class I integrons. Among the detected 31 ARG subtypes located in MGEs, the relative abundances of only lnuF, msrE and mphD in the biofilm of AQS-PUF were over 2-fold higher compared with those in the biofilm of PUF. However, the three ARGs and their host Gammaproteobacteria was not dominant in microbial community. The relative abundances of more ARGs including MLS (lnuB and EreA), tetracycline (tetH) resistance genes located in MGEs decreased, which was attributed to the decreased relative abundance of their hosts. These studies showed that the addition of the immobilized AQS (around 0.25 mM) had a beneficial effect on reducing the spread of ARGs during dyeing wastewater bio-treatment.
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Affiliation(s)
- Hong Lu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Jiaojiao Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Liping Huang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xiaolei Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jiti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jing Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
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58
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Muurinen J, Richert J, Wickware CL, Richert B, Johnson TA. Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential. Sci Rep 2021; 11:5485. [PMID: 33750827 PMCID: PMC7970892 DOI: 10.1038/s41598-021-84759-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Even though the use of antibiotics for food-producing animals may contribute to the emergence of antimicrobial resistance, antibiotics are still used as growth promoters. Due to consumer and regulatory pressures, the use of alternatives to antibiotics as growth promoters is increasing, thus more information is needed on their capability to disseminate antimicrobial resistance compared to antibiotics. We investigated the impacts of carbadox (antibiotic), copper sulfate and zinc oxide (metals) and mushroom powder (natural product) on the pig fecal resistome and microbiome. Antibiotic resistance gene (ARG) and mobile genetic element (MGE) abundances were measured using a high-throughput qPCR array with 382 primer pairs. Bacterial community composition was determined by 16S rRNA gene sequencing. More ARGs co-occurred with MGEs in the growth promoter group samples than in the control group samples. Community composition could not be linked to resistome in the growth promoter group samples, indicating a potential decoupling of ARGs and phylogeny. Additionally, machine-learning methods aided in defining the community and resistome differences in response to treatments. Since increased ARG mobility potential was the primary response to the dietary additives used in this study, we suggest that ARG mobility should be considered when designing antimicrobial use policies and antimicrobial resistance surveillances.
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Affiliation(s)
- Johanna Muurinen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
| | - Jacob Richert
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Carmen L Wickware
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Brian Richert
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Timothy A Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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59
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Stoica C, Cox G. Old problems and new solutions: antibiotic alternatives in food animal production. Can J Microbiol 2021; 67:427-444. [PMID: 33606564 DOI: 10.1139/cjm-2020-0601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The antimicrobial resistance crisis is a Global Health challenge that impacts humans, animals, and the environment alike. In response to increased demands for animal protein and by-products, there has been a substantial increase in the use of antimicrobial agents in the animal industry. Indeed, they are extensively used to prevent, control, and (or) treat disease in animals. In addition to infection control, in-feed supplementation with antimicrobials became common practice for growth promotion of livestock. Unfortunately, the global overuse of antimicrobials has contributed to the emergence and spread of resistance. As such, many countries have implemented policies and approaches to eliminate the use of antimicrobials as growth promoters in food animals, which necessitates the need for alternate and One Health strategies to maintain animal health and welfare. This review summarizes the antimicrobial resistance crisis from Global Health and One Health perspectives. In addition, we outline examples of potential alternate strategies to circumvent antimicrobial use in animal husbandry practices, including antivirulence agents, bacteriophages, and nutritional measures to control bacterial pathogens. Overall, these alternate strategies require further research and development efforts, including assessment of efficacy and the associated development, manufacturing, and labor costs.
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Affiliation(s)
- Celine Stoica
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada.,Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Georgina Cox
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada.,Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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60
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Wang W, Wei X, Wu L, Shang X, Cheng F, Li B, Zhou X, Zhang J. The occurrence of antibiotic resistance genes in the microbiota of yak, beef and dairy cattle characterized by a metagenomic approach. J Antibiot (Tokyo) 2021; 74:508-518. [PMID: 34103703 PMCID: PMC8313426 DOI: 10.1038/s41429-021-00425-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/13/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023]
Abstract
Drug resistance has been partly driven by the overuse of antimicrobials in agricultural animal feed. Better understanding of antibiotic resistance in bovine gut is needed to assess its potential effects based on metagenomic approach and analysis. In this study, we collected 40 fecal samples to explore drug resistance derived from antibiotic use in the bacterial community by an analysis of the diversities and differences of antibiotic-resistant genes (ARGs) in the gut microbiota from yak, beef, and dairy cattle. Overall, 1688 genes were annotated, including 734 ARG subtypes. The ARGs were related to tetracyclines, quinolones, β-lactam, and aminoglycosides, in accordance with the antibiotics widely used in the clinic for humans or animals. The emergence, prevalence, and differences in resistance genes in the intestines of yaks, beef, and dairy cattle may be caused by the selective pressure of different feeding patterns, where yaks were raised without antibiotics for growth promotion. In addition, the abundance of ARGs in yak was lower than in beef and dairy cattle, whereas the abundance of integron, a kind of mobile genetic elements (MGEs) was higher in yaks than those in beef and dairy cattle. Furthermore, the results of this study could provide the basis for a comprehensive profile of various ARGs among yak, beef, and dairy cattle in future.
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Affiliation(s)
- Weiwei Wang
- grid.32566.340000 0000 8571 0482Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050 PR China ,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050 PR China ,grid.410727.70000 0001 0526 1937Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050 PR China
| | - Xiaojuan Wei
- grid.32566.340000 0000 8571 0482Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050 PR China ,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050 PR China ,grid.410727.70000 0001 0526 1937Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050 PR China
| | - Lingyu Wu
- grid.32566.340000 0000 8571 0482Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050 PR China ,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050 PR China ,grid.410727.70000 0001 0526 1937Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050 PR China
| | - Xiaofei Shang
- grid.32566.340000 0000 8571 0482Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050 PR China ,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050 PR China ,grid.410727.70000 0001 0526 1937Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050 PR China
| | - Fusheng Cheng
- grid.32566.340000 0000 8571 0482Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050 PR China ,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050 PR China ,grid.410727.70000 0001 0526 1937Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050 PR China
| | - Bing Li
- grid.32566.340000 0000 8571 0482Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050 PR China ,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050 PR China ,grid.410727.70000 0001 0526 1937Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050 PR China
| | - Xuzheng Zhou
- grid.32566.340000 0000 8571 0482Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050 PR China ,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050 PR China ,grid.410727.70000 0001 0526 1937Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050 PR China
| | - Jiyu Zhang
- grid.32566.340000 0000 8571 0482Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050 PR China ,Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050 PR China ,grid.410727.70000 0001 0526 1937Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050 PR China
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Dulay H, Tabares M, Kashefi K, Reguera G. Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens. Front Microbiol 2020; 11:600463. [PMID: 33324382 PMCID: PMC7726332 DOI: 10.3389/fmicb.2020.600463] [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: 08/30/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria in the genus Geobacter thrive in iron- and manganese-rich environments where the divalent cobalt cation (CoII) accumulates to potentially toxic concentrations. Consistent with selective pressure from environmental exposure, the model laboratory representative Geobacter sulfurreducens grew with CoCl2 concentrations (1 mM) typically used to enrich for metal-resistant bacteria from contaminated sites. We reconstructed from genomic data canonical pathways for CoII import and assimilation into cofactors (cobamides) that support the growth of numerous syntrophic partners. We also identified several metal efflux pumps, including one that was specifically upregulated by CoII. Cells acclimated to metal stress by downregulating non-essential proteins with metals and thiol groups that CoII preferentially targets. They also activated sensory and regulatory proteins involved in detoxification as well as pathways for protein and DNA repair. In addition, G. sulfurreducens upregulated respiratory chains that could have contributed to the reductive mineralization of the metal on the cell surface. Transcriptomic evidence also revealed pathways for cell envelope modification that increased metal resistance and promoted cell-cell aggregation and biofilm formation in stationary phase. These complex adaptive responses confer on Geobacter a competitive advantage for growth in metal-rich environments that are essential to the sustainability of cobamide-dependent microbiomes and the sequestration of the metal in hitherto unknown biomineralization reactions.
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Affiliation(s)
- Hunter Dulay
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Marcela Tabares
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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62
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Poudel A, Kang Y, Mandal RK, Kalalah A, Butaye P, Hathcock T, Kelly P, Walz P, Macklin K, Cattley R, Price S, Adekanmbi F, Zhang L, Kitchens S, Kaltenboeck B, Wang C. Comparison of microbiota, antimicrobial resistance genes and mobile genetic elements in flies and the feces of sympatric animals. FEMS Microbiol Ecol 2020; 96:5762668. [PMID: 32105329 DOI: 10.1093/femsec/fiaa027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/25/2020] [Indexed: 11/14/2022] Open
Abstract
Flies are well-known vectors of bacterial pathogens, but there are little data on their role in spreading microbial community and antimicrobial resistance. In this study, we compared the bacterial community, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in flies with those in the feces of sympatric animals. A 16S rRNA-based microbial analysis identified 23 bacterial phyla in fecal samples and 25 phyla in flies; all the phyla identified in the fecal samples were also found in the flies. Bray-Curtis dissimilarity analysis showed that the microbiota of the flies were more similar to the microbiota of the feces of their sympatric animals than those of the feces from the three other animal species studied. The qPCR array amplified 276 ARGs/MGEs in fecal samples, and 216 ARGs/MGEs in the flies, while 198 of these genes were identified in both flies and feces. Long-term studies with larger sample numbers from more geospatially distinct populations and infection trials are indicated to further evaluate the possibility of flies as sentinels for antimicrobial resistance.
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Affiliation(s)
- Anil Poudel
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Yuan Kang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Rabindra K Mandal
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anwar Kalalah
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Patrick Butaye
- Department of Biosciences, Ross University School of Veterinary Medicine; 00265, Basseterre, St Kitts, West Indies.,Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University; B-9000 Ghent, Ghent, Belgium
| | - Terri Hathcock
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Patrick Kelly
- Department of Biosciences, Ross University School of Veterinary Medicine; 00265, Basseterre, St Kitts, West Indies
| | - Paul Walz
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Kenneth Macklin
- Department of Poultry Science, College of Agriculture, Auburn University; AL, 36830, Auburn, AL, USA
| | - Russell Cattley
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Stuart Price
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Folasade Adekanmbi
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Lixin Zhang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA
| | - Steven Kitchens
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Bernhard Kaltenboeck
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, AL36849, Auburn, AL, USA
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63
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Liang Z, Zhang Y, He T, Yu Y, Liao W, Li G, An T. The formation mechanism of antibiotic-resistance genes associated with bacterial communities during biological decomposition of household garbage. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122973. [PMID: 32492618 DOI: 10.1016/j.jhazmat.2020.122973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/17/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
Food wastes are significant reservoir of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) available for exchange with clinical pathogens. However, food wastes-related changes of antibiotic resistance in long-period decomposition have been overlooked. Here, we evaluated the comprehensive ARG profile and its association with microbial communities, explained how this might vary with household garbage decomposition. Average of 128, 150 and 91 ARGs were detected in meat, vegetable and fruit wastes, respectively, with multidrug and tetracycline as the predominant ARG types. ARG abundance significantly increased at initial stage of waste fermentation and then decreased. High abundance of Eubacterium-coprostanoligenes, Sporanaerobacter, Peptoniphilus, Peptostreptococcus might be explained for the high relative abundance of ARGs in meat, while high abundance of Advenella, Prevotella, Solobacterium was attributed to the high diversity of ARGs in vegetables. Significant correlations were observed among volatile organic compounds, mobile genetic elements and ARGs, implying that they might contribute to transfer and transport of ARGs. Network analysis revealed that aph(2')-Id-01, acrA-05, tetO-1 were potential ARG indicators, while Hathewaya, Paraclostridium and Prevotellaceae were possible hosts of ARGs. Our work might unveil underlining mechanism of the effects of food wastes decomposition on development and spread of ARGs in environment and also clues to ARG mitigation.
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Affiliation(s)
- Zhishu Liang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yuna Zhang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Tao He
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yun Yu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Wen Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
| | - Guiying Li
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China
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64
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Gao FZ, He LY, He LX, Zou HY, Zhang M, Wu DL, Liu YS, Shi YJ, Bai H, Ying GG. Untreated swine wastes changed antibiotic resistance and microbial community in the soils and impacted abundances of antibiotic resistance genes in the vegetables. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 741:140482. [PMID: 32615438 DOI: 10.1016/j.scitotenv.2020.140482] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 05/05/2023]
Abstract
Animal waste fertilization is a traditional agricultural practice, which may have adverse effects to soil ecosystem. However, the side-effects of animal waste fertilization on vegetables are less studied. Here we selected a swine farming village for investigation with a nearby village without swine farming as comparison. In the swine farming village, the farmers use untreated swine manure and wastewater as fertilizers for vegetable cultivation. In the reference village, the farmers mainly use commercial organic fertilizers. The objective of this study is to assess the impacts of untreated swine waste fertilization on both soils and vegetables in terms of antibiotics, antibiotic resistance genes (ARGs) and bacterial microbial communities. The results indicate that untreated swine waste fertilization caused both antibiotic and ARG contaminations and changed the microbial community compositions in the soils. Varieties of tetracyclines and related resistance genes were detected especially in swine wastewater treated soils. The soil quality was impacted with the relations to bacterial abundances and microbial geochemical functions. Proteobacteria and Bacteroidetes were prevalent and positively correlated to ARGs in soils, indicating they were potential antibiotic resistant bacteria. Antibiotics and ARGs were detected in vegetables of both villages. The abundances of ARGs were relatively higher in some vegetable samples of the swine farming village than the reference village. In addition, intracellular parasites Rickettsiales with positive correlation to ARGs were prevalent in some vegetables of swine farming village, indicating potential health risks through eating contaminated vegetables. The results of this study suggest that untreated swine wastes may cause adverse effects to not only agricultural soils but also associated vegetables.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Hai-Yan Zou
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Dai-Ling Wu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Yi-Jing Shi
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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65
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Shapiro JT, Leboucher G, Myard-Dury AF, Girardo P, Luzzati A, Mary M, Sauzon JF, Lafay B, Dauwalder O, Laurent F, Lina G, Chidiac C, Couray-Targe S, Vandenesch F, Flandrois JP, Rasigade JP. Metapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards. eLife 2020; 9:54795. [PMID: 33106223 PMCID: PMC7690951 DOI: 10.7554/elife.54795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between-ward patient transfers (or connectivity) impact population-level AMR in hospital networks can help optimize antibiotic stewardship and infection control strategies. Here, we used a metapopulation framework to explain variations in the incidence of infections caused by seven major bacterial species and their drug-resistant variants in a network of 357 hospital wards. We found that ward-level antibiotic consumption volume had a stronger influence on the incidence of the more resistant pathogens, while connectivity had the most influence on hospital-endemic species and carbapenem-resistant pathogens. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data provide evidence that both antibiotic use and connectivity measurably influence hospital AMR. Finally, we provide a ranking of key antibiotics by their estimated population-level impact on AMR that might help inform antimicrobial stewardship strategies.
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Affiliation(s)
- Julie Teresa Shapiro
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | | | - Anne-Florence Myard-Dury
- Pôle de Santé Publique, Département d'Information Médicale, Hospices Civils de Lyon, Lyon, France
| | - Pascale Girardo
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Anatole Luzzati
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Mélissa Mary
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | | | - Bénédicte Lafay
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, University of Lyon, Lyon, France
| | - Olivier Dauwalder
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Laurent
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Gerard Lina
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Christian Chidiac
- Service des Maladies Infectieuses et Tropicales, Hospices Civils de Lyon, Lyon, France
| | - Sandrine Couray-Targe
- Pôle de Santé Publique, Département d'Information Médicale, Hospices Civils de Lyon, Lyon, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Jean-Pierre Flandrois
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, University of Lyon, Lyon, France
| | - Jean-Philippe Rasigade
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
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66
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Lin Y, Dong X, Sun R, Wu J, Tian L, Rao D, Zhang L, Yang K. Migratory birds-one major source of environmental antibiotic resistance around Qinghai Lake, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:139758. [PMID: 32540654 PMCID: PMC7260505 DOI: 10.1016/j.scitotenv.2020.139758] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 05/26/2023]
Abstract
Migratory birds are potential transmitters of bacterial antibiotic resistance. However, their role in the environmental dissemination of bacterial antibiotic resistance and the extent of their impact on the environment are not yet clear. Qinghai Lake is one of the most important breeding and stopover ground for the migratory birds along the Central Asian Flyway. Here, we investigated the bacterial antibiotic resistance in the environment and among the migratory birds around the lake. The results of culture-based analysis of bacterial antibiotic resistance, quantitative PCR and metagenomic sequencing indicate that migratory birds are one major source of bacterial antibiotic resistance in the environment around Qinghai Lake. Network analysis reveals the co-occurrence patterns of antibiotic resistance genes (ARGs) and bacterial genera. Genetic co-localization analysis suggests high co-selection potential (with incidence of 35.8%) among different ARGs, but limited linkage (with incidence of only 3.7%) between ARGs and biocide/metal resistance genes (BMRGs). The high genetic linkage between ARGs and mobile genetic elements (MGEs) is still largely confined to the bacterial community in migratory birds (accounting for 96.0% of sequencing reads of MGE-linked ARGs), which indicates limited horizontal transfer of ARGs to the environment. Nevertheless, the antibiotic resistance determinants carried by migratory birds and their specific genetic properties (high co-selection and mobility potential of the ARGs) remind us that the role of migratory birds in the environmental dissemination of bacterial antibiotic resistance deserves more attention.
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Affiliation(s)
- Yufei Lin
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Xiaohong Dong
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Rui Sun
- Tianjin Academy of Eco-Environment Sciences, Tianjin 300191, China
| | - Jiao Wu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Lejin Tian
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Dawei Rao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Lihua Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China.
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67
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Achard CS, Dupouy V, Cauquil L, Arpaillange N, Bousquet-Melou A, Floc’h NL, Zemb O. Early Inoculation of Microbial Suspension in Suckling Piglets Affects the Transmission of Maternal Microbiota and the Associated Antibiotic Resistance Genes. Microorganisms 2020; 8:microorganisms8101576. [PMID: 33066283 PMCID: PMC7602062 DOI: 10.3390/microorganisms8101576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/29/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic resistance of microbes thriving in the animal gut is a growing concern for public health as it may serve as a hidden reservoir for antibiotic resistance genes (ARGs). We compared 16 control piglets to 24 piglets fed for 3 weeks with S1 or S2 fecal suspensions from two sows that were not exposed to antibiotics for at least 6 months: the first suspension decreased the erythromycin resistance gene ermB and the aminoglycoside phosphotransferase gene conferring resistance to kanamycine (aphA3), while the second decreased the tetracycline resistance gene tetL, with an unexpected increase in ARGs. Using 16S RNA sequencing, we identified microbial species that are likely to carry ARGs, such as the lincosamide nucleotidyltransferase lnuB, the cephalosporinase cepA, and the tetracycline resistance genes tetG and tetM, as well as microbes that never co-exist with the tetracycline resistance gene tetQ, the erythromycin resistance gene ermG and aphA3. Since 73% of the microbes detected in the sows were not detected in the piglets at weaning, a neutral model was applied to estimate whether a microbial species is more important than chance would predict. This model confirmed that force-feeding modifies the dynamics of gut colonization. In conclusion, early inoculation of gut microbes is an interesting possibility to stimulate gut microbiota towards a desirable state in pig production, but more work is needed to be able to predict which communities should be used.
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Affiliation(s)
- Caroline S. Achard
- Génétique Physiologie et Systèmes d’Elevage (GenPhySE), Université de Toulouse, Institut National De Recherche Pour L’agriculture, L’alimentation Et L’environnement (INRAE), Institut National Polytechnique de Toulouse (INPT), École nationale vétérinaire de Toulouse (ENVT), F-31320 Castanet Tolosan, France; (C.S.A.); (L.C.)
- Lallemand SAS, 19 rue des Briquetiers, BP 59, 31702 Blagnac CEDEX, France
| | - Veronique Dupouy
- Innovations thérapeutiques et résistances (INTHERES), Université de Toulouse, INRAE, ENVT, F-31300 Toulouse, France; (V.D.); (N.A.); (A.B.-M.)
| | - Laurent Cauquil
- Génétique Physiologie et Systèmes d’Elevage (GenPhySE), Université de Toulouse, Institut National De Recherche Pour L’agriculture, L’alimentation Et L’environnement (INRAE), Institut National Polytechnique de Toulouse (INPT), École nationale vétérinaire de Toulouse (ENVT), F-31320 Castanet Tolosan, France; (C.S.A.); (L.C.)
| | - Nathalie Arpaillange
- Innovations thérapeutiques et résistances (INTHERES), Université de Toulouse, INRAE, ENVT, F-31300 Toulouse, France; (V.D.); (N.A.); (A.B.-M.)
| | - Alain Bousquet-Melou
- Innovations thérapeutiques et résistances (INTHERES), Université de Toulouse, INRAE, ENVT, F-31300 Toulouse, France; (V.D.); (N.A.); (A.B.-M.)
| | - Nathalie Le Floc’h
- Physiologie, Environnement et Génétique pour l’Animal et les Systèmes d’Élevage (PEGASE), Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, 35590 Saint-Gilles, France;
| | - Olivier Zemb
- Génétique Physiologie et Systèmes d’Elevage (GenPhySE), Université de Toulouse, Institut National De Recherche Pour L’agriculture, L’alimentation Et L’environnement (INRAE), Institut National Polytechnique de Toulouse (INPT), École nationale vétérinaire de Toulouse (ENVT), F-31320 Castanet Tolosan, France; (C.S.A.); (L.C.)
- Correspondence:
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68
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Yang F, Han B, Gu Y, Zhang K. Swine liquid manure: a hotspot of mobile genetic elements and antibiotic resistance genes. Sci Rep 2020; 10:15037. [PMID: 32929149 PMCID: PMC7490410 DOI: 10.1038/s41598-020-72149-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/25/2020] [Indexed: 11/25/2022] Open
Abstract
The overuse or abuse of antibiotics as veterinary medicine and growth promoters accelerates antibiotic resistance, creating a serious threat to public health in the world. Swine liquid manure as an important reservoir of antibiotic resistance genes (ARGs) has received much attention, but little information is known regarding the occurrence, persistence and fate of ARGs-associated mobile genetic elements (MGEs) in swine farms, especially their change patterns and removal in full-scale piggery wastewater treatment systems (PWWTSs). In this study, we searched the presence and distribution of MGEs and associated ARGs in swine farms, and addressed their fate and seasonal variation in full-scale PWWTSs by real-time quantitative PCR (qPCR). Our results revealed class 1 integrons, class 2 integrons and conjugative plasmids were prevalent in pig feces and piggery wastewater. A clear pattern of these MGE levels in swine liquid manure was also observed, i.e., intI1 > intI2 > traA (p < 0.01), and their absolute abundances in winter were all higher than that in summer with 0.07-2.23 logs. Notably, MGEs and ARGs prevailed through various treatment units of PWWTSs, and considerable levels of them were present in the treated effluent discharged from swine farms (up to 101-107 copies/mL for MGEs and 103-108 copies/mL for ARGs). There were significant correlations between most ARG abundance and MGE levels (p < 0.05), such as tetQ and traA (r = 0.775), sul1 and intI1 (r = 0.847), qnrS and inI2 (r = 0.859), suggesting the potential of ARGs-horizontal transfer. Thus the high prevalence and enrichment of MGEs and ARGs occurred in pig feces and piggery wastewater, also implicating that swine liquid manure could be a hotspot for horizontal transfer of ARGs.
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Affiliation(s)
- Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yanru Gu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150036, China
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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69
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Ricker N, Spoja BS, May N, Chalmers G. Incorporating the plasmidome into antibiotic resistance surveillance in animal agriculture. Plasmid 2020; 113:102529. [PMID: 32771502 DOI: 10.1016/j.plasmid.2020.102529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/06/2020] [Accepted: 07/11/2020] [Indexed: 12/25/2022]
Abstract
Mobile genetic elements (MGE) carrying resistance genes represent a unique challenge to risk assessment and surveillance of antimicrobial resistance (AMR). Yet determining the mobility of resistance genes within animal microbiomes is essential to evaluating the potential dissemination from livestock to potential human pathogens, as well as evaluating co-selection mechanisms that may impact persistence of resistance genes with changing antibiotic use patterns. Current surveillance efforts utilize phenotypic testing and sequencing of individual isolates for tracking of AMR in livestock. In this work, we investigated the utility of using long-read sequencing of the plasmids from mixed Enterobacterales enrichments of swine fecal samples as a surveillance strategy for AMR plasmids. Enrichments were performed in either MacConkey broth without selection or with selection by addition of tetracycline or ceftriaxone, and plasmids were extracted and sequenced in order to evaluate the diversity of plasmids enriched by each method. Intact resistance plasmids were successfully assembled, as well as complex resistance transposons carrying multiple repeated elements that would interfere with assembly by short read sequencing technologies. Comparison of the assembled plasmids with representatives from public databases confirmed the quality of the assemblies and also revealed the occurrence of IncI2 plasmids carrying blaCMY-2 in Ontario swine samples, which have not been found in previous studies.
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Affiliation(s)
- N Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.
| | - B S Spoja
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - N May
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - G Chalmers
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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70
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Zhou R, Zeng S, Hou D, Liu J, Weng S, He J, Huang Z. Temporal variation of antibiotic resistance genes carried by culturable bacteria in the shrimp hepatopancreas and shrimp culture pond water. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 199:110738. [PMID: 32447139 DOI: 10.1016/j.ecoenv.2020.110738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
The increasing prevalence of antibiotic resistance genes (ARGs) is a challenge to the health of humans, animals and the environments. Human activities and aquatic environments can increase ARGs. Few studies have focused on the temporal variation of aquatic bacteria with multiple ARGs in aquatic environments affected by human production activity. We studied culturable bacteria (CB) carrying ARGs, including sul1, sul2, floR, strA and gyrA in the shrimp hepatopancreas (HP) and in pond water during shrimp culture. The relative abundance of ARGs carried by CB in HP was higher than that in water (P < 0.05). However, CB carrying ARGs generally varied in random pattern. The correlation of sul2 abundance was significantly positive in HP, while that of strA abundance was significantly negative in water (P < 0.05) during shrimp culture. Among all of the CB, 33.59% carried multiple ARGs. Temporal distance-decay analysis indicated that CB carrying ARGs in water were more resistant to the effects of human activity. CB carrying ARGs varied temporally in HP and pond water during shrimp culture. These results demonstrate that multiple ARGs are carried by CB, and these varied with the phase of aquatic culture.
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Affiliation(s)
- Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jian Liu
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
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71
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Peng H, Gu J, Wang X, Wang Q, Sun W, Hu T, Guo H, Ma J, Bao J. Insight into the fate of antibiotic resistance genes and bacterial community in co-composting green tea residues with swine manure. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 266:110581. [PMID: 32310121 DOI: 10.1016/j.jenvman.2020.110581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 02/03/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Green tea residues (GTRs) are byproducts of tea production and processing, and this type of agricultural waste retains nutritious components. This study investigated the co-composting of GTRs with swine manure, as well as the effects of GTRs on antibiotic resistance genes (ARGs) and the bacterial community during co-composting. The temperature and C/N ratio indicate compost was mature after processing. The addition of GTRs effectively promoted the reduction in the abundances of most targeted ARGs (tet and sul genes), mobile genetic element (MGE; intI1), and metal resistance genes (MRGs; pcoA and tcrB). Redundancy analysis (RDA) showed that GTRs can reduce the abundance of MRGs and ARGs by reducing the bioavailability of heavy metals. Network analysis shows that Firmicutes and Actinobacteria were the main hosts of ARGs and ARGs, MGEs, and MRGs shared the same potential host bacteria. Adding GTRs during composting may reduce ARGs transmission through horizontal gene transfer (HGT). GTRs affected the bacterial community, thereby influencing the variations in the ARG profiles and reducing the potential risk associated with the compost product.
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Affiliation(s)
- Huiling Peng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qianzhi Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wei Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ting Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Honghong Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiyue Ma
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jianfeng Bao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
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72
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Sosa-Moreno A, Comstock SS, Sugino KY, Ma TF, Paneth N, Davis Y, Olivero R, Schein R, Maurer J, Zhang L. Perinatal risk factors for fecal antibiotic resistance gene patterns in pregnant women and their infants. PLoS One 2020; 15:e0234751. [PMID: 32555719 PMCID: PMC7302573 DOI: 10.1371/journal.pone.0234751] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/01/2020] [Indexed: 12/14/2022] Open
Abstract
Perinatal factors can shape fecal microbiome patterns among pregnant women and their infants. However, there is scarce information about the effect of maternal demographics and perinatal exposures on antibiotic resistance genes (ARG) and mobile genetic element (MGE) patterns in pregnant women and infants. We examined fecal samples from pregnant women during their third trimester of pregnancy (n = 51) and 6-month-old infants (n = 40). Of the 91 participants, 72 represented 36 maternal-infant dyads, 15 were additional pregnant women, and 4 were additional infants. We assessed the effects of demographics, pre-pregnancy BMI, smoking and parity in the pregnancy resistome and the effects of demographics, delivery mode, feeding habits and prenatal antibiotic treatment on the infancy resistome. ARG and MGE richness and abundance were assessed using a SmartChip qPCR-array. Alpha diversity (Shannon and Inverse Simpson index) and beta diversity (Sorensen and Bray-Curtis index) were calculated. The Wilcoxon and the Kruskal non-parametric test were used for comparisons. There is a high variability in shared resistome patterns between pregnant women and their infants. An average of 29% of ARG and 24% of MGE were shared within dyads. Infants had significantly greater abundance and higher diversity of ARG and MGE compared to pregnant women. Pregnancy and infancy samples differed in ARG and MGE gene composition and structure. Composition of the fecal resistome was significantly associated with race in pregnant women, with non-white women having different patterns than white women, and, in infants, with extent of solid food consumption. Our data showed that the pregnancy and infancy resistome had different structure and composition patterns, with maternal race and infant solid food consumption as possible contributors to ARG. By characterizing resistome patterns, our results can inform the mechanism of antibiotic resistome development in pregnant women and their infants.
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Affiliation(s)
- Andrea Sosa-Moreno
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States of America
| | - Sarah S. Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States of America
| | - Kameron Y. Sugino
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, United States of America
| | - Teng F. Ma
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States of America
| | - Nigel Paneth
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States of America
| | - Yelena Davis
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, East Lansing, MI, United States of America
- Helen DeVos Children’s Hospital of Spectrum Health, Grand Rapids, MI, United States of America
| | - Rosemary Olivero
- Helen DeVos Children’s Hospital of Spectrum Health, Grand Rapids, MI, United States of America
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing, MI, United States of America
| | - Rebecca Schein
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing, MI, United States of America
| | - Joel Maurer
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, East Lansing, MI, United States of America
| | - Lixin Zhang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States of America
- * E-mail:
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Hoque MN, Istiaq A, Clement RA, Gibson KM, Saha O, Islam OK, Abir RA, Sultana M, Siddiki AMAMZ, Crandall KA, Hossain MA. Insights Into the Resistome of Bovine Clinical Mastitis Microbiome, a Key Factor in Disease Complication. Front Microbiol 2020; 11:860. [PMID: 32582039 PMCID: PMC7283587 DOI: 10.3389/fmicb.2020.00860] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 04/09/2020] [Indexed: 12/23/2022] Open
Abstract
Bovine clinical mastitis (CM) is one of the most prevalent diseases caused by a wide range of resident microbes. The emergence of antimicrobial resistance in CM bacteria is well-known, however, the genomic resistance composition (the resistome) at the microbiome-level is not well characterized. In this study, we applied whole metagenome sequencing (WMS) to characterize the resistome of the CM microbiome, focusing on antibiotics and metals resistance, biofilm formation (BF), and quorum sensing (QS) along with in vitro resistance assays of six selected pathogens isolated from the same CM samples. The WMS generated an average of 21.13 million reads (post-processing) from 25 CM samples that mapped to 519 bacterial strains, of which 30.06% were previously unreported. We found a significant (P = 0.001) association between the resistomes and microbiome composition with no association with cattle breed, despite significant differences in microbiome diversity among breeds. The in vitro investigation determined that 76.2% of six selected pathogens considered "biofilm formers" actually formed biofilms and were also highly resistant to tetracycline, doxycycline, nalidixic acid, ampicillin, and chloramphenicol and remained sensitive to metals (Cr, Co, Ni, Cu, Zn) at varying concentrations. We also found bacterial flagellar movement and chemotaxis, regulation and cell signaling, and oxidative stress to be significantly associated with the pathophysiology of CM. Thus, identifying CM microbiomes, and analyzing their resistomes and genomic potentials will help improve the optimization of therapeutic schemes involving antibiotics and/or metals usage in the prevention and control of bovine CM.
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Affiliation(s)
- M. Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Department of Gynecology, Obstetrics and Reproductive Health, Faculty of Veterinary Medicine and Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Arif Istiaq
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Department of Developmental Neurobiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Rebecca A. Clement
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Keylie M. Gibson
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Ovinu Kibria Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - AMAM Zonaed Siddiki
- Department of Pathology and Parasitology, Chittagong Veterinary and Animal Sciences University, Chittagong, Bangladesh
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - M. Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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74
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Riaz L, Wang Q, Yang Q, Li X, Yuan W. Potential of industrial composting and anaerobic digestion for the removal of antibiotics, antibiotic resistance genes and heavy metals from chicken manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137414. [PMID: 32105920 DOI: 10.1016/j.scitotenv.2020.137414] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
Composting and anaerobic digestion techniques are widely used for manure recycling, but these methods have shown conflicting results in the removal of antibiotics, antibiotic resistance genes (ARGs), and heavy metals. In the present study, anaerobically digested chicken manure and various types of composted chicken manure were investigated on an industrial scale. Antibiotics, ARGs, and heavy metals had shown inconsistent results for anaerobic digestion and composting. The different composting processes either declined or completely removed the blaCTX-M, intl1 and oqxB genes. In addition, composting processes decreased the absolute abundance of aac6'-Ib and aadA genes, while increased the absolute abundance of qnrD, sul1, and tet(A) genes. On the other hand, anaerobic digestion of chicken manure increased the absolute abundance of ere(A) and tet(A). High throughput sequencing showed that Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria dominated the total bacterial composition of composted and anaerobically digested samples. Network analysis revealed the co-occurrence of ARGs and intl1. The redundancy analysis showed a significant correlation between some heavy metals and ARGs. Similarly, the bacterial composition showed a positive correlation with the prevalence of ARGs in treated manure. These findings suggest that bacterial community, heavy metals, and mobile genetic elements can play a significant role in the abundance and variation of ARGs during composting and anaerobic digestion. In conclusion, anaerobic digestion and composting methods at industrial scale need to be improved for the effective removal of antibiotics, ARGs and heavy metals from chicken manure.
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Affiliation(s)
- Luqman Riaz
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
| | - Qianqian Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China.
| | - Xunan Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
| | - Wei Yuan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology (Henan Provincial Department of Science and Technology), Henan Normal University, Xinxiang 453007, China
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75
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Ricker N, Trachsel J, Colgan P, Jones J, Choi J, Lee J, Coetzee JF, Howe A, Brockmeier SL, Loving CL, Allen HK. Toward Antibiotic Stewardship: Route of Antibiotic Administration Impacts the Microbiota and Resistance Gene Diversity in Swine Feces. Front Vet Sci 2020; 7:255. [PMID: 32509805 PMCID: PMC7249142 DOI: 10.3389/fvets.2020.00255] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Oral antibiotics are a critical tool for fighting bacterial infections, yet their use can have negative consequences, such as the disturbance of healthy gut bacterial communities and the dissemination of antibiotic residues in feces. Altering antibiotic administration route may limit negative impacts on intestinal microbiota and reduce selective pressure for antimicrobial resistance genes (ARG) persistence and mobility. Thus, a study was performed in pigs to evaluate route of therapeutic oxytetracycline (oxytet) administration, an antibiotic commonly used in the U.S. swine industry, on intestinal microbial diversity and ARG abundance. Given that oral antibiotics would be in direct contact with intestinal bacteria, we hypothesized that oral administration would cause a major shift in intestinal bacterial community structure when compared to injected antibiotic. We further postulated that the impact would extend to the diversity and abundance of ARG in swine feces. At approximately 3 weeks-of-age, piglets were separated into three groups (n = 21–22 per group) with two groups receiving oxytet (one via injection and the second via feed) and a third non-medicated group. Oxytet levels in the plasma indicated injected antibiotic resulted in a spike 1 day after administration, which decreased over time, though oxytet was still detected in plasma 14 days after injection. Conversely, in-feed oxytet delivery resulted in lower but less variable oxytet levels in circulation and high concentrations in feces. Similar trends were observed in microbial community changes regardless of route of oxytet administration; however, the impact on the microbial community was more pronounced at all time points and in all samples with in-feed administration. Fecal ARG abundance was increased with in-feed administration over injected, with genes for tetracycline and aminoglycoside resistance enriched specifically in the feces of the in-feed group. Sequencing of plasmid-enriched samples revealed multiple genetic contexts for the resistance genes detected and highlighted the potential role of small plasmids in the movement of antibiotic resistance genes. The findings are informative for disease management in food animals, but also manure management and antibiotic therapy in human medicine for improved antibiotic stewardship.
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Affiliation(s)
- Nicole Ricker
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States.,Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Julian Trachsel
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
| | - Phillip Colgan
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Jennifer Jones
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
| | - Jinlyung Choi
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Jaejin Lee
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Johann F Coetzee
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Adina Howe
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Susan L Brockmeier
- Virus and Prion Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
| | - Crystal L Loving
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA, United States
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76
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Leng Y, Xiao H, Li Z, Wang J. Tetracyclines, sulfonamides and quinolones and their corresponding resistance genes in coastal areas of Beibu Gulf, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136899. [PMID: 32019000 DOI: 10.1016/j.scitotenv.2020.136899] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
As the rapid development of aquaculture in the Beibu Gulf, large number of antibiotics was released into marine aquatic environment. But little integrated studies concerned on the occurrence and correlation of antibiotics with their corresponding ARGs in this region. We investigated the abundance of three prevalent categories of antibiotics and corresponding antibiotic resistance genes (ARGs), analyzed the potential correlation among antibiotics, ARGs and sediment properties in eight terminal rivers, nine semi-closed sites and eight nearshore areas from Beibu Gulf. Residual concentrations of total antibiotics ranged from 51.04 to 137.64 μg/kg, TETs had higher concentrations than FQs and SAs. Conventional PCR of ARGs revealed intI1, sul2, tetB, tetC and tetG had 100% detection frequency in all samples. Quantitative analysis showed sul genes were dominant compared to tet genes. The abundance of antibiotics and ARGs were decreased from river to open sea. Significant correlations (p < .05) between intI1 and ARGs (sul2 and tetG) were revealed by Pearson analysis, indicating that intI1 gene played a significant role in the occurrence and diffusion of ARGs. Significant correlations among the ARGs, the corresponding or irrelevant residual antibiotics and sediment characteristics were observed by redundancy analysis and network. Due to the potential health risks of antibiotics with corresponding ARGs, the control and treatment measures should deserve wide attention.
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Affiliation(s)
- Yifei Leng
- School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, PR China
| | - Henglin Xiao
- School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, PR China
| | - Zhu Li
- School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, PR China
| | - Jun Wang
- School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, PR China.
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77
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Du S, Shen JP, Hu HW, Wang JT, Han LL, Sheng R, Wei WX, Fang YT, Zhu YG, Zhang LM, He JZ. Large-scale patterns of soil antibiotic resistome in Chinese croplands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136418. [PMID: 31927444 DOI: 10.1016/j.scitotenv.2019.136418] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/27/2019] [Accepted: 12/28/2019] [Indexed: 05/11/2023]
Abstract
Soil is a vital reservoir of antibiotic resistance genes (ARGs), but we still know little about their distribution in cropland soils and the main driving forces. Here we performed an investigation for ARGs patterns in 105 cropland soils (planted with maize, peanut or soybean) along a 2, 200 km transect in China using high-throughput quantitative PCR approaches. Totally, 204 ARGs were detected, with a higher diversity found in central China than that in northeast and south China. The most abundant (top 50%) and highly shared (present in >50% samples) ARGs regarded as core resistome were dominated by multidrug resistance genes such as oprJ, acrA-05 and acrA-04. Regressive analyses revealed that the relative abundance of total ARGs and core resistome both had significant relationships with mobile genetic elements (MGEs). Anthropogenic factors including the consumption of plastic films and soil properties including heavy metals showed good correlations with the diversity of ARGs. Structural equation modelling analysis further explained that anthropogenic factors were the main forces shaping the ARGs patterns. These findings highlight the importance of human activities in shaping soil antibiotic resistome in the croplands, providing potential management strategies to mitigate the dissemination of ARGs to humans via food chain.
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Affiliation(s)
- Shuai Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hang-Wei Hu
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Rong Sheng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wen-Xue Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Yun-Ting Fang
- State Key Laboratory of Forest Ecology and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Zheng He
- University of Chinese Academy of Sciences, Beijing 100049, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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Liu Y, Dyall-Smith M, Marenda M, Hu HW, Browning G, Billman-Jacobe H. Antibiotic Resistance Genes in Antibiotic-Free Chicken Farms. Antibiotics (Basel) 2020; 9:antibiotics9030120. [PMID: 32183177 PMCID: PMC7148458 DOI: 10.3390/antibiotics9030120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
Rising concern about the use of antibiotics in food production has resulted in many studies on the occurrence of antibiotic resistance genes (ARGs) in animal-associated bacterial communities. There are few baseline data on the abundance of ARGs on farms where chickens are intensively raised with little or no use of antibiotics. This study used a high-throughput quantitative PCR array to survey two antibiotic-free chicken farms for the occurrence of ARGs and mobile genetic elements known to enhance the spread of ARGs. No antibiotics had been used on the study farms for five years prior to this study. The results provide a baseline for the occurrence of resistance genes in the chicken production system without direct selective pressure.
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Affiliation(s)
- Yuhong Liu
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
| | - Michael Dyall-Smith
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
| | - Marc Marenda
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Glenn Browning
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
| | - Helen Billman-Jacobe
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia; (Y.L.); (M.D.-S.); (M.M.); (G.B.)
- National Centre for Antimicrobial Stewardship, The Peter Doherty Institute, Elizabeth St Melbourne, VIC 3000, Australia
- Correspondence:
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79
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Wang F, Han W, Chen S, Dong W, Qiao M, Hu C, Liu B. Fifteen-Year Application of Manure and Chemical Fertilizers Differently Impacts Soil ARGs and Microbial Community Structure. Front Microbiol 2020; 11:62. [PMID: 32117108 PMCID: PMC7015874 DOI: 10.3389/fmicb.2020.00062] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022] Open
Abstract
Manure, which contains large amounts of antibiotics and antibiotic resistance genes (ARGs), is widely used in agricultural soils and may lead to the evolution and dispersal of ARGs in the soil environment. In the present study, soils that received manure or chemical fertilizers for 15 years were sampled on the North China Plain (NCP), which is one of the primary areas of intensive agriculture in China. High-throughput quantitative PCR and sequencing technologies were employed to assess the effects of long-term manure or chemical fertilizer application on the distribution of ARGs and microbial communities. A total of 114 unique ARGs were successfully amplified from all soil samples. Manure application markedly increased the relative abundance and detectable numbers of ARGs, with up to 0.23 copies/16S rRNA gene and 81 unique ARGs. The increased abundance of ARGs in manure-fertilized soil was mainly due to the manure increasing the abundance of indigenous soil ARGs. In contrast, chemical fertilizers only moderately affected the diversity of ARGs and had no significant effect on the relative abundance of the total ARGs. In addition, manure application increased the abundance of mobile genetic elements (MGEs), which were significantly and positively correlated with most types of ARGs, indicating that horizontal gene transfer via MGEs may play an important role in the spread of ARGs. Furthermore, the application of manure and chemical fertilizers significantly affected microbial community structure, and variation partitioning analysis showed that microbial community shifts represented the major driver shaping the antibiotic resistome. Taken together, our results provide insight into the long-term effects of manure and chemical fertilization on the dissemination of ARGs in intensive agricultural ecosystems.
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Affiliation(s)
- Fenghua Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wanxue Han
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuaimin Chen
- Institute of Agricultural Resource and Environment, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Min Qiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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80
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Gao Q, Dong Q, Wu L, Yang Y, Hale L, Qin Z, Xie C, Zhang Q, Van Nostrand JD, Zhou J. Environmental antibiotics drives the genetic functions of resistome dynamics. ENVIRONMENT INTERNATIONAL 2020; 135:105398. [PMID: 31862641 DOI: 10.1016/j.envint.2019.105398] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
The increasing prevalence of antibiotic-resistant microorganisms imposes a global threat to public health. The over reliant use of antibiotics in the food industry has contributed considerably to the dissemination of antibiotics into various environments, yet the mechanisms by which antibiotic dissemination influences the assembly of the microbial community continues to remain obscure. Here, we examine bacterial and fungal community assemblies in swine manure, compost, compost amended, and unamended agricultural soil in five suburban areas of Beijing, China. Total antibiotic concentration decreased by factors of 10-1000 from manure and compost to soils. The bacterial α-diversity was found to be low in manure and compost samples, while the fungal α-diversity was similar across all samples. We detected significantly (p < 0.05) higher relative abundances of well recognized pathogenic microbial taxa, virulence associated genes, and antibiotic resistance genes (ARGs) in manure and compost than those in agricultural soils, revealing the higher microbial capacity of pathogenicity, virulence and antibiotic resistance. Unexpectedly, the relative abundances of both bacterial and fungal taxa did not predict the antibiotic concentration. A possible explanation was that bacterial and fungal communities were mainly shaped by random assemblies. Rather, antibiotic concentration could be well predicted by relative abundances of antibiotic resistance, stress and virulence associated genes. Despite the weak interconnection between ARGs and the microbiome, we demonstrate that microbial genes should be the focal point in tracking the ecological effects of antibiotic dissemination by revealing microbial community patterns along the dissemination chain of antibiotics.
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Affiliation(s)
- Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qiang Dong
- Institute of Chemical Defense, Beijing 102205, China
| | - Linwei Wu
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Lauren Hale
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA; Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, USDA, Parlier, CA 93648-9757, USA
| | - Ziyan Qin
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Changyi Xie
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qiuting Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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81
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Græsbøll K, Larsen I, Clasen J, Birkegård AC, Nielsen JP, Christiansen LE, Olsen JE, Angen Ø, Folkesson A. Effect of tetracycline treatment regimens on antibiotic resistance gene selection over time in nursery pigs. BMC Microbiol 2019; 19:269. [PMID: 31791243 PMCID: PMC6889206 DOI: 10.1186/s12866-019-1619-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/22/2019] [Indexed: 12/29/2022] Open
Abstract
Background The majority of antimicrobials given during the production of pigs are given to nursery pigs. The influence of antimicrobial use on the levels of antimicrobial resistant (AMR) genes is important to quantify to be able to assess the impact of resistance on the food chain and risk to human and animal health. Results This study investigated the response on the levels of nine AMR genes to five different treatment strategies with oxytetracycline, and the dynamics of gene abundance over time by following 1167 pigs from five different farms in Denmark. The results showed no significant difference between treatments and an increase in abundance for the efflux pump encoding tet(A) gene and the genes encoding the ribosomal protection proteins tet(O) and tet(W) tetracycline resistant genes following treatment, while tet(M) showed no response to treatment. However, it was also observed that the levels of tet(O), tet(W), and ermB in some farms would drift more over time compared to a single treatment-course with antibiotic. Conclusion This study underlines the large variation in AMR levels under natural conditions and the need for increased investigation of the complex interactions of antimicrobial treatment and other environmental and managerial practices in swine production on AMR gene abundance.
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Affiliation(s)
- Kaare Græsbøll
- DTU Compute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inge Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julie Clasen
- DTU Vet. Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Jens Peter Nielsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Øystein Angen
- DTU Vet. Technical University of Denmark, Kongens Lyngby, Denmark.,Present address: SSI, Copenhagen, Denmark
| | - Anders Folkesson
- DTU BioEngineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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82
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Xu M, Stedtfeld RD, Wang F, Hashsham SA, Song Y, Chuang Y, Fan J, Li H, Jiang X, Tiedje JM. Composting increased persistence of manure-borne antibiotic resistance genes in soils with different fertilization history. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 689:1172-1180. [PMID: 31466157 DOI: 10.1016/j.scitotenv.2019.06.376] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/21/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
Different long-term fertilization regimes may change indigenous microorganism diversity in the arable soil and thus might influence the persistence and transmission of manure-born antibiotic resistance genes (ARGs). Different manure origins and composting techniques might affect the fate of introduced ARGs in farmland. A four-month microcosm experiment was performed using two soils, which originated from the same field and applied with the same chemical fertilizer or swine manure for 26 years, to investigate the dynamics of ARGs in soil amended with manure or compost from the farm and an agro-technology company. High throughput qPCR and sequencing were applied to quantify ARGs using 144 primer sets and microorganism in soil. Fertilization history had little effect on dynamics of manure-borne ARGs in soil regardless of manure origin or composting. Very different half-lives of ARGs and mobile genetic elements from farm manure and commercial manure were observed in both soils. Composting decreased abundance of most ARGs in manure, but increased the persistence of manure-introduced ARGs in soil irrespective of fertilization history, especially for those from farm manure. These findings help understanding the fate of ARGs in manured soil and may inform techniques to mitigate ARGs transmission.
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Affiliation(s)
- Min Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
| | - Yang Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahui Chuang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| | - Jianbo Fan
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Center for Microbial Ecology, Michigan State University, MI 48824, USA
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83
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Duan M, Zhang Y, Zhou B, Wang Q, Gu J, Liu G, Qin Z, Li Z. Changes in antibiotic resistance genes and mobile genetic elements during cattle manure composting after inoculation with Bacillus subtilis. BIORESOURCE TECHNOLOGY 2019; 292:122011. [PMID: 31442833 DOI: 10.1016/j.biortech.2019.122011] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
This study explored the effects of Bacillus subtilis at four levels (0, 0.5%, 1%, and 2% w/w compost) on the variations in ARGs, mobile genetic elements (MGEs), and the bacterial community during composting. The composting process had a greater impact on ARGs than Bacillus subtilis. The main ARG detected was sul1. The addition of Bacillus subtilis at 0.5% reduced the relative abundances of ARGs, MGEs, and human pathogenic bacteria (by 2-3 logs) in the mature products. Network and redundancy analyses suggested that intI1, Firmicutes, and pH were mainly responsible for the changes in ARGs, thus controlling these factors might help to inhibit the spread of ARGs.
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Affiliation(s)
- Manli Duan
- State Key Laboratory of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China
| | - Yuhua Zhang
- State Key Laboratory of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China
| | - Beibei Zhou
- State Key Laboratory of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China.
| | - Quanjiu Wang
- State Key Laboratory of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Guohuan Liu
- State Key Laboratory of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China
| | - Zhenlun Qin
- State Key Laboratory of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China
| | - Zhijian Li
- State Key Laboratory of Eco-hydraulic Engineering in Arid Area, Xi'an University of Technology, Xi'an 710048, China
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84
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Smith SD, Colgan P, Yang F, Rieke EL, Soupir ML, Moorman TB, Allen HK, Howe A. Investigating the dispersal of antibiotic resistance associated genes from manure application to soil and drainage waters in simulated agricultural farmland systems. PLoS One 2019; 14:e0222470. [PMID: 31527917 PMCID: PMC6748443 DOI: 10.1371/journal.pone.0222470] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/29/2019] [Indexed: 02/03/2023] Open
Abstract
Manure from animals that have been treated with antibiotics is often used to fertilize agricultural soils and its application has previously been shown to enrich for genes associated with antibiotic resistance in agroecosystems. To investigate the magnitude of this effect, we designed a column experiment simulating manure-treated agricultural soil that utilizes artificial subsurface drainage to determine the duration and extent which this type of manure fertilization impacts the set of genes associated with antibiotic resistance in drainage water. We classified ARGs in manure-treated drainage effluent water by its source of origin. Overall, we found that 61% and 7% of the total abundance of ARGs found in drainage water samples could be attributed to manure enrichment and manure addition, respectively. Among these ARGs, we identified 75 genes unique to manure that persisted in both soil and drainage water throughout a drainage season typical of the Upper Midwestern United States. While most of these genes gradually decreased in abundance over time, the IS6100-associated tet(33) gene accrued. These results demonstrate the influence of manure applications on the composition of the resistome observed in agricultural drainage water and highlight the importance of anthropogenic ARGs in the environment.
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Affiliation(s)
- Schuyler D. Smith
- Bioinformatics and Computational Biology Department, Iowa State University, Ames, Iowa, United States of America
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Phillip Colgan
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Fan Yang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Elizabeth L. Rieke
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Thomas B. Moorman
- United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Heather K. Allen
- United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Adina Howe
- Bioinformatics and Computational Biology Department, Iowa State University, Ames, Iowa, United States of America
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
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85
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Sun Y, Qiu T, Gao M, Shi M, Zhang H, Wang X. Inorganic and organic fertilizers application enhanced antibiotic resistome in greenhouse soils growing vegetables. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 179:24-30. [PMID: 31022652 DOI: 10.1016/j.ecoenv.2019.04.039] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/02/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in fertilizers pose risks to human health and their variation in soil after fertilization has been reported. However, some important questions, such as the origin of ARG and ARB observed in soil following fertilization, which are present in soil regardless of fertilizer type (i.e., core (shared) ARGs and ARB), and the contribution of various ARG subtypes to the soil antibiotic resistome, need to be addressed. In this study, the effects of a long-term (9-year) application of organic (manure) and inorganic (chemistry) fertilizers on ARGs in greenhouse soils growing vegetables were investigated using metagenomic sequencing. The results showed that both organic and inorganic fertilizers application increased the diversity and abundance of soil ARGs. The dominant ARG types in organic fertilizer (OF) were different from that in organic fertilizer treated soil (SO), inorganic fertilizer treated soil (SI) and no fertilizer control plots (SC). The difference of core ARGs abundance reflected the variation of ARG profiles among SC, SI and SO. The OF is likely a source of the elevated ARG subtypes in soil and almost all the soil core ARG subtypes can be detected in organic fertilizer. Fifteen ARG types were enriched in the soil with OF, and some ARG subtypes such as sul1, sul2, tetX and tetL might derived from OF while others including as vanR, tcmA, rosB, and mexF might be from indigenous microbes in soil. The nutrition factors were found to influence the ARG profiles in fertilized soil. In summary, this study revealed the possible reason for the soil total ARG numbers and their relative abundance increase after fertilization, which will facilitate the control of ARGs and ARB dissemination.
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Affiliation(s)
- Yanmei Sun
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Tianlei Qiu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Min Gao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Mingming Shi
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; College of Chemical Engineering, Northeast Dianli University, Jilin 132012, China
| | - Haifeng Zhang
- College of Chemical Engineering, Northeast Dianli University, Jilin 132012, China
| | - Xuming Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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86
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Zhou S, Zhu Y, Yan Y, Wang W, Wang Y. Deciphering extracellular antibiotic resistance genes (eARGs) in activated sludge by metagenome. WATER RESEARCH 2019; 161:610-620. [PMID: 31254887 DOI: 10.1016/j.watres.2019.06.048] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance genes (ARGs) including extracellular ARGs (eARGs) and intracellular ARGs (iARGs), are recognized as emerging environmental contaminants. Despite extensive efforts to profile ARGs in their "hotspots" wastewater treatment plants (WWTPs), the contribution of eARGs to antibiotic resistance spread remains unclear. Here, we applied metagenomic sequencing to investigate the distribution, mobility and microbial hosts of eARGs in activated sludge from five WWTPs. The total relative abundance eARGs ranged from 9.5 × 10-6 to 1.3 × 10-4, mainly encompassing elfamycin, dual drug, and aminoglycoside resistance genes. Multiple eARGs (e.g., EF-Tu, ropB, and rpsL mutants) were shared among the five WWTPs, and some clustered in the same genetic element (e.g., EF-Tu-rpsJ). eARGs were found to frequently co-localize with the eMGEs (e.g., sul1-3'CS-TnAs3, sul2-intI1-ISVsa3, and tetX-p63039), which may facilitate the mobilization of eARGs. Most eARGs likely originated from the genera Mycobacterium (6.7%), Nitrosomonas (5.3%), Steroidobacter (5.3%), Nitrospira (5.2%) and Pseudomonas (5.1%). No significant difference in the diversity, abundance, and mobility was observed between eARGs and iARGs. The host composition of eARGs and iARGs from municipal WWTPs are consistently dominated by Nitrosomonas, Steroidobacter, Nitrospira and Pseudomonas, while some differentially enriched genera (especially Nitrospira) in the hosts of iARGs compared with those of eARGs from the swine WWTP were identified. Our findings corroborate the mobile eARGs reservoir in WWTPs, thereby laying foundation for mitigating widespread antibiotic resistance.
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Affiliation(s)
- Shuai Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Yijing Zhu
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Yuan Yan
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Weigang Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai, 200092, PR China.
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87
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Rovira P, McAllister T, Lakin SM, Cook SR, Doster E, Noyes NR, Weinroth MD, Yang X, Parker JK, Boucher C, Booker CW, Woerner DR, Belk KE, Morley PS. Characterization of the Microbial Resistome in Conventional and "Raised Without Antibiotics" Beef and Dairy Production Systems. Front Microbiol 2019; 10:1980. [PMID: 31555225 PMCID: PMC6736999 DOI: 10.3389/fmicb.2019.01980] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/12/2019] [Indexed: 01/14/2023] Open
Abstract
Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide–lincosamide–streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause–effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms’ records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the “resistance potential” of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.
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Affiliation(s)
- Pablo Rovira
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Tim McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Steven M Lakin
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Shaun R Cook
- Alberta Agriculture and Forestry, Lethbridge, AB, Canada
| | - Enrique Doster
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Noelle R Noyes
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, United States
| | - Maggie D Weinroth
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Xiang Yang
- Department of Animal Sciences, University of California, Davis, Davis, CA, United States
| | - Jennifer K Parker
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, United States
| | - Calvin W Booker
- Feedlot Health Management Services, Ltd., Okotoks, AB, Canada
| | - Dale R Woerner
- Department of Animal and Food Sciences, College of Agricultural Sciences & Natural Resources, Texas Tech University, Lubbock, TX, United States
| | - Keith E Belk
- Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States
| | - Paul S Morley
- VERO - Veterinary Education, Research, and Outreach Program, Texas A&M University and West Texas A&M University, Canyon, TX, United States
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88
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Achard CS, Dupouy V, Siviglia S, Arpaillange N, Cauquil L, Bousquet-Mélou A, Zemb O. Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits. Front Microbiol 2019; 10:1503. [PMID: 31333614 PMCID: PMC6615258 DOI: 10.3389/fmicb.2019.01503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/14/2019] [Indexed: 01/16/2023] Open
Abstract
Reducing antibiotic use is a necessary step toward less antibiotic resistance in livestock, but many antibiotic resistance genes can persist for years, even in an antibiotic-free environment. In this study, we investigated the potential of three fecal complex microbial communities from antibiotic-naive does to drive the microbiota of kits from antibiotic-exposed dams and outcompete bacteria-carrying antibiotic-resistant genes. The fecal complex microbial communities were either orally delivered or simply added as fresh fecal pellets in four to five nests that were kept clean from maternal feces. Additionally, four nests were cleaned for the maternal feces and five nests were handled according to the common farm practice (i.e., cleaning once a week) as controls. At weaning, we measured the relative abundance of 26 antibiotic resistance genes, the proportion of Enterobacteriaceae resistant to tetracycline and sulfonamide antibiotics, and the taxonomic composition of the microbiota by sequencing the 16S rRNA genes of one kit per nest. Changing the surrounding microbes of the kits can hinder the transmission of antibiotic resistance genes from one generation to the next, but the three communities widely differed in their ability to orient gut microbes and in their impact on antibiotic resistance genes. The most efficient delivery of the microbial community reduced the proportion of resistant Enterobacteria from 93 to 9%, decreased the relative abundance of eight antibiotic resistance genes, and changed the gut microbes of the kits at weaning. The least efficient did not reduce any ARG or modify the bacterial community. In addition, adding fecal pellets was more efficient than the oral inoculation of the anaerobic suspension derived from these fecal pellets. However, we were unable to predict the outcome of the exclusion from the data of the donor does (species composition and abundance of antibiotic resistance genes). In conclusion, we revealed major differences between microbial communities regarding their ability to exclude antibiotic resistance genes, but more work is needed to understand the components leading to the successful exclusion of antibiotic resistance genes from the gut. As a consequence, studies about the impact of competitive exclusion should use several microbial communities in order to draw general conclusions.
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Affiliation(s)
| | | | - Suzanne Siviglia
- GenPhySE, INRA, ENVT, Université de Toulouse, Toulouse, France.,InTheRes, INRA, ENVT, Université de Toulouse, Toulouse, France
| | | | - Laurent Cauquil
- GenPhySE, INRA, ENVT, Université de Toulouse, Toulouse, France
| | | | - Olivier Zemb
- GenPhySE, INRA, ENVT, Université de Toulouse, Toulouse, France
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89
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Zhang YJ, Hu HW, Yan H, Wang JT, Lam SK, Chen QL, Chen D, He JZ. Salinity as a predominant factor modulating the distribution patterns of antibiotic resistance genes in ocean and river beach soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 668:193-203. [PMID: 30851680 DOI: 10.1016/j.scitotenv.2019.02.454] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/18/2019] [Accepted: 02/28/2019] [Indexed: 06/09/2023]
Abstract
Growing evidence points to the pivotal role of the environmental factors in influencing the transmission of antibiotic resistance genes (ARGs) and the propagation of resistant human pathogens. However, our understanding of the ecological and evolutionary environmental factors that contribute to development and dissemination of antibiotic resistance is lacking. Here, we profiled a wide variety of ARGs using the high-throughput quantitative PCR analysis in 61 soil samples collected from ocean and river beaches, which are hotspots for human activities and platforms for potential transmission of environmental ARGs to human pathogens. We identified the dominant abiotic and biotic factors influencing the diversity, abundance and composition of ARGs in these ecosystems. A total of 110 ARGs conferring resistance to eight major categories of antibiotics were detected. The core resistome was mainly affiliated into β-lactam and multidrug resistance, accounting for 66.9% of the total abundance of ARGs. The oprJ gene conferring resistance to multidrug was the most widespread ARG subtype detected in all the samples. The relative abundances of total ARGs and core resistome were significantly correlated with salinity-related properties including electrical conductivity and concentrations of sodium and chloride. Random forest analysis and structural equation modelling revealed that salinity was the most important factor modulating the distribution patterns of beach soil ARGs after accounting for multiple drivers. These findings suggest that beach soil is a rich reservoir of ARGs and that salinity is a predominant factor shaping the distribution patterns of soil resistome.
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Affiliation(s)
- Yu-Jing Zhang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Hui Yan
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shu Kee Lam
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Qing-Lin Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Deli Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ji-Zheng He
- Faculty of Veterinary and Agricultural Sciences, 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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90
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Holman DB, Yang W, Alexander TW. Antibiotic treatment in feedlot cattle: a longitudinal study of the effect of oxytetracycline and tulathromycin on the fecal and nasopharyngeal microbiota. MICROBIOME 2019; 7:86. [PMID: 31167657 PMCID: PMC6549328 DOI: 10.1186/s40168-019-0696-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/19/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Beef cattle in North America frequently receive an antibiotic injection after feedlot placement to control and manage bovine respiratory disease. The potential collateral effect of these antibiotics on the bovine microbiome is largely unknown. Therefore, we determined the longitudinal impact of two commonly administered veterinary antibiotics, oxytetracycline and tulathromycin, on the fecal and nasopharyngeal (NP) microbiota of beef cattle that were transported to a feedlot. We also report the effect these antibiotics have on several antibiotic resistance determinants in both the fecal and NP microbiome. RESULTS Oxytetracycline and tulathromycin perturbation of the bovine fecal and NP microbiota was greatest at days 2 and 5. Although the NP microbiota of the tulathromycin-treated cattle had recovered by day 12, the NP microbiota of the oxytetracycline-treated group remained altered through day 34. Overall, the NP microbiota appeared to be more sensitive to antibiotic treatment than the fecal microbiota. Members of the bacterial Microbacteriaceae family were most notably affected by antibiotic administration in the NP microbiota. Both antibiotics protected against Pasteurella spp. in the nasopharynx at days 2 and 5. Despite very similar diets at both locations, the largest shift in the fecal and NP microbiota occurred after transport to the feedlot (P < 0.05). Antibiotic resistance determinants in the NP microbiome were also affected more strongly by antibiotic treatment than those in the fecal microbiome. Oxytetracycline increased the proportion of erm(X), sul2, tet(H), tet(M), and tet(W) in NP samples and tet(M) and tet(W) in fecal samples, at day 12 (P < 0.05). The effect of tulathromycin on the relative abundance of resistance genes in the NP microbiome was greatest at day 34 as erm(X), sul2, and tet(M) were enriched (P < 0.05). CONCLUSIONS Administration of a single injection of oxytetracycline and tulathromycin resulted in significant changes in the NP and fecal microbiota during the first 5 days after treatment. Antibiotic treatment also increased the relative abundance of several antibiotic resistance determinants in the fecal and NP microbiome at either day 12 or 34.
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Affiliation(s)
- Devin B Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Wenzhu Yang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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91
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Awasthi MK, Liu T, Chen H, Verma S, Duan Y, Awasthi SK, Wang Q, Ren X, Zhao J, Zhang Z. The behavior of antibiotic resistance genes and their associations with bacterial community during poultry manure composting. BIORESOURCE TECHNOLOGY 2019; 280:70-78. [PMID: 30754007 DOI: 10.1016/j.biortech.2019.02.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
In this paper, the influence of clay amendment on antibiotic resistance genes (ARGs) fate and their relation with bacterial diversity in poultry manure (PM) composting was evaluated. The results confirmed that 4% clay amendment was significantly reduce the relative abundances (RAs) 94% of ARGs, while higher dosage of clay blended treatments (T5 and T6) composts were observed relatively very high percentage of ARGs as compared to other clay blended treatments. Clay addition play potential role on the occurrence and distribution of ARGs during the composting by altering the overall RAs of Firmicutes and Proteobacteria, and there host bacterial species. The heat map correlation figure also indicated that reduction of ARGs was significantly associated with the alteration of microbial dynamics and physicochemical parameters during the composting. Therefore, the addition of 4% clay in to PM composting system could efficiently mitigate the greater concentration of ARGs in PM compost and also environmental risk associated with its application.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Hongyu Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Shivpal Verma
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Yumin Duan
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Sanjeev Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xiuna Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Junchao Zhao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China.
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92
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Blau K, Jacquiod S, Sørensen SJ, Su JQ, Zhu YG, Smalla K, Jechalke S. Manure and Doxycycline Affect the Bacterial Community and Its Resistome in Lettuce Rhizosphere and Bulk Soil. Front Microbiol 2019; 10:725. [PMID: 31057496 PMCID: PMC6477490 DOI: 10.3389/fmicb.2019.00725] [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] [Received: 02/07/2019] [Accepted: 03/22/2019] [Indexed: 12/23/2022] Open
Abstract
Manure application to agricultural soil introduces antibiotic residues and increases the abundance of antibiotic-resistant bacteria (ARB) carrying antibiotic resistance genes (ARGs), often located on mobile genetic elements (MGEs). The rhizosphere is regarded as a hotspot of microbial activity and gene transfer, which can alter and prolong the effects of organic fertilizers containing antibiotics. However, not much is known about the influence of plants on the effects of doxycycline applied to soil via manure. In this study, the effects of manure spiked with or without doxycycline on the prokaryotic community composition as well as on the relative abundance of ARGs and MGEs in lettuce rhizosphere and bulk soil were investigated by means of a polyphasic cultivation-independent approach. Samples were taken 42 days after manure application, and total community DNA was extracted. Besides a pronounced manure effect, doxycycline spiking caused an additional enrichment of ARGs and MGEs. High-throughput quantitative PCR revealed an increase in tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes associated with the application of manure spiked with doxycycline. This effect was unexpectedly lower in the rhizosphere than in bulk soil, suggesting a faster dissipation of the antibiotic and a more resilient prokaryotic community in the rhizosphere. Interestingly, the tetracycline resistance gene tetA(P) was highly enriched in manure-treated bulk soil and rhizosphere, with highest values observed in doxycycline-treated bulk soil, concurring with an enrichment of Clostridia. Thus, the gene tetA(P) might be a suitable marker of soil contamination by ARB, ARGs, and antibiotics of manure origin. These findings illustrate that the effects of manure and doxycycline on ARGs and MGEs differ between rhizosphere and bulk soil, which needs to be considered when assessing risks for human health connected to the spread of ARGs in the environment.
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Affiliation(s)
- Khald Blau
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kornelia Smalla
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Sven Jechalke
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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93
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Maeschli A, Schmidt A, Ammann W, Schurtenberger P, Maurer E, Walkenhorst M. [Einfluss eines komplementärmedizinischen telefonischen Beratungssystems auf den Antibiotikaeinsatz bei Nutztieren in der Schweiz]. Complement Med Res 2019; 26:174-181. [PMID: 30965320 DOI: 10.1159/000496031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 12/04/2018] [Indexed: 11/19/2022]
Abstract
Hintergrund: Der Antibiotikaeinsatz bei Nutztieren fördert die Entwicklung antibiotikaresistenter Bakterien. Die Komplementärmedizin könnte einen Beitrag zur Reduktion von Antibiotika leisten, wird bisher jedoch nicht flächendeckend angeboten. Das Beratungsprogramm "Kometian" unter-stützt teilnehmende Landwirte darin, ihre Tiere komplementärmedizinisch zu behandeln. Methoden und Resultate: 128 von 223 teilnehmenden Betrieben nutzten in den ersten 3 Projektjahren die telefonische Beratung von Kometian. Die Mehrheit der Landwirte hielt Milchkühe. Frühestens 1 Woche nach der Kometianberatung wurde eine telefonische Nachfrage beim Tierbesitzer hinsichtlich des Gesundheitszustandes des Tieres durchgeführt. Es konnten so 661 Beratungsfälle recherchiert werden. In 486 Fällen erfolgte keine weitere schulmedizinische Behandlung, in 373 Fällen gab der Landwirt einen Behandlungserfolg an. Von 188 angefragten und seit mindestens einem Jahr an Kometian teilnehmenden Betrieben stellten 46 ihre Behandlungsjournale zur Verfügung. Die betriebliche antibiotische Behandlungsinzidenz sank signifikant (p < 0,001) von 27 vor Beitritt auf 18 Behandlungen pro 100 Tiere im ersten Jahr. Schlussfolgerung: Es scheint, dass Kometian einen Beitrag dazu leisten konnte, den Antibiotikaeinsatz auf Betriebsebene zu reduzieren. BACKGROUND A regular use of antibiotics in farm animals is assumed to induce antibiotic-resistant bacteria. Complementary and alternative medicine (CAM) may contribute to a reduction of antibiotic use but it is not extensively offered by Swiss veterinarians. The advisory program “Kometian” supports farmers in treating their animals with CAM. METHODS AND RESULTS 128 out of 223 participating farmers used the telephone consultations of Kometian in the first 3 years of the project. The majority of the farmers kept dairy cattle. No sooner than 1 week after such a consultation, the famer was questioned by phone about the health progress of the animal. Thus, the development of health could be verified in 661 cases (of 714). 486 cases were not treated further by conventional medicine; in 373 cases the farmer reported a positive treatment effect. Of 188 examined farms, which had participated in the advisory program for at least 1 year, 46 made their treatment records available. The incidence of antibiotic treatment decreased significantly (p < 0.001) from 27 before entering the program to 18 treatments per 100 animals in the first year. CONCLUSION It seems that the advisory program Kometian could contribute to reduce the use of antibiotics on the farm level.
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Affiliation(s)
- Ariane Maeschli
- Forschungsinstitut für biologischen Landbau (FiBL), Frick, Schweiz,
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Birkegård AC, Græsbøll K, Clasen J, Halasa T, Toft N, Folkesson A. Continuing occurrence of vancomycin resistance determinants in Danish pig farms 20 years after removing exposure to avoparcin. Vet Microbiol 2019; 232:84-88. [PMID: 31030850 DOI: 10.1016/j.vetmic.2019.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 03/31/2019] [Accepted: 04/05/2019] [Indexed: 11/17/2022]
Abstract
Vancomycin-resistant Enterococcus spp. is a major health problem worldwide and livestock have been implicated in constituting a reservoir for the transmission of vancomycin resistance to zoonotic pathogens. Vancomycin resistance determinants can be situated on mobile genetic elements and transferred between bacterial species The livestock reservoir must therefore be included in a risk assessment of the vancomycin resistance burden. Avoparcin, a vancomycin analogue, has not been used in Danish pig production for over 20 years and vancomycin has never been used. The objective of this study was to screen faecal samples from Danish pig farms for nine selected vancomycin resistance determinants. We found at least four different vancomycin resistance determinants in all screened Danish pig farms (665 finisher farms and 78 sow farms). The vancomycin resistance determinants present in vanB or vanG clusters were found at significantly different levels in sow and finisher farms. However, vanA was not detected in any of the farms. In conclusion, vancomycin resistance determinants are still present in Danish pig production 25 years after the ban on avoparcin use.
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Affiliation(s)
- Anna Camilla Birkegård
- Technical University of Denmark, Department of Applied Mathematics and Computer Science, Asmussens Allé Building 303B, 2800, Kgs. Lyngby, Denmark
| | - Kaare Græsbøll
- Technical University of Denmark, Department of Applied Mathematics and Computer Science, Asmussens Allé Building 303B, 2800, Kgs. Lyngby, Denmark
| | - Julie Clasen
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Kemitorvet Building 204, 2800, Kgs. Lyngby, Denmark
| | - Tariq Halasa
- Technical University of Denmark, National Veterinary Institute, Kemitorvet Building 204, 2800, Kgs. Lyngby, Denmark
| | - Nils Toft
- Technical University of Denmark, National Veterinary Institute, Kemitorvet Building 204, 2800, Kgs. Lyngby, Denmark
| | - Anders Folkesson
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Kemitorvet Building 204, 2800, Kgs. Lyngby, Denmark.
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Higher Temperatures Do Not Always Achieve Better Antibiotic Resistance Gene Removal in Anaerobic Digestion of Swine Manure. Appl Environ Microbiol 2019; 85:AEM.02878-18. [PMID: 30683745 DOI: 10.1128/aem.02878-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/15/2019] [Indexed: 11/20/2022] Open
Abstract
This study employed high-throughput quantitative PCR and 16S rRNA sequencing to evaluate the effect of temperature and residual antibiotics on the dynamics of antibiotic resistance genes (ARGs) and microbial communities during anaerobic digestion of swine manure. The abundances of total ARGs and 16S rRNA genes significantly decreased in all of four treatments (25°C, 37°C, and 37°C with 50 mg of wet weight antibiotics of body weight, and 55°C). The abundances of most ARG types were significantly correlated with those of the 16S rRNA gene and transposase gene (P < 0.01). However, the abundances of total ARGs at 55°C were much higher than those of other treatments. Meanwhile, the microbial communities at 55°C, where the Streptococcus pathogen remained at a relatively high abundance and cellulose degraders and hydrogen producers, such as Ethanoligenens and Coprococcus bacteria, increased, were markedly different from those of other treatments. Redundancy analysis indicates that temperature, pH, and the genus Streptococcus had the highest explanation for ARG variation among experimental factors, chemical properties, and representative genera, respectively. Network analysis further showed that the genus Streptococcus contributed greatly to the higher ARG abundance at 55°C. The moderate antibiotic residue only caused a slight and transitory inhibition for microbially diverse populations and promotion for ARG abundance, probably due to the degradation of antibiotics and microbial adaptability. Our results clarify the cooperativity of gene transfer-related items on ARG variation and intensively prove that higher temperature cannot always achieve better ARG removal in anaerobic digestion unless pathogens and gene transfer elements are more efficiently inhibited.IMPORTANCE Antibiotic resistance genes (ARGs) are frequently detected with high abundance in manure-applied soils. Anaerobic digestion is one of widely used processes for animal waste treatment. Thus, it is critical to understand the potential of anaerobic digestion to attenuate ARGs. Although some previous studies recommended thermophilic digestion for ARG removal, they did not get sufficient evidence to support this view. The antibiotics applied to animals are mostly excreted through feces and urine because of incomplete metabolism. It is indispensable to know whether residual antibiotics in manure will hinder ARG attenuation in anaerobic digesters. The significance of our research is in comprehensively understanding the evolution and mechanism of ARGs in anaerobic digestion of swine manure affected by temperature and residual antibiotics, which will allow the development of an ARG elimination strategy before their release into the environment.
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96
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Che Y, Xia Y, Liu L, Li AD, Yang Y, Zhang T. Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing. MICROBIOME 2019; 7:44. [PMID: 30898140 PMCID: PMC6429696 DOI: 10.1186/s40168-019-0663-0] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/11/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown. RESULTS In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge, and effluent of three WWTPs and simultaneously track the hosts of the ARGs. The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Nanopore and Illumina sequencing platforms demonstrated the feasibility of Nanopore sequencing for resistome quantification. CONCLUSION Overall, these findings substantially expand our current knowledge of resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.
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Affiliation(s)
- You Che
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yu Xia
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lei Liu
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - An-Dong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yu Yang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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97
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Zhao R, Feng J, Liu J, Fu W, Li X, Li B. Deciphering of microbial community and antibiotic resistance genes in activated sludge reactors under high selective pressure of different antibiotics. WATER RESEARCH 2019; 151:388-402. [PMID: 30616051 DOI: 10.1016/j.watres.2018.12.034] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Currently, the effects of high antibiotic concentrations on the performance of microbiota and antibiotic resistance genes (ARGs) in activated sludge (AS) process are not well characterized. Lab-scale batch reactors were performed to evaluate the dynamics of microbial community and ARGs in response to six antibiotics at different concentrations using high-throughput sequencing-based 16S rRNA gene and metagenomic analyses. The presence of antibiotics remarkably decreased the microbial diversity, caused a great change of the microbiota structure, and exerted a selective pressure on the enrichment of potential antibiotic resistant bacteria (ARB), such as Arthrobacter, Thauera, Geothrix, Rudaea, Aridibacter, Conexibacter, Terrimonas, etc. High antibiotic selective pressures increased ARG abundance but simultaneously reduced ARG number. In total, 491 ARG subtypes belonging to 20 ARG types were detected and kanamycin treatment showed the highest ARG abundances. A core set of 54 ARG subtypes that accounted for 66.7%-99.6% of the total ARG abundances were shared by all samples. The increase of the abundances of both corresponding and non-corresponding ARGs under a specific antibiotic treatment revealed the collateral effects of antibiotic selective pressure. Microbial community may play an important role in the composition of ARGs. Network analysis indicated that both internal-type and external-type of ARGs exhibited higher non-random co-occurrence incidences and 18 genera were speculated as the possible hosts for multiple ARGs. This study deciphered the profiles and relationships between microbial community and ARGs in AS process treating wastewater with high antibiotic concentrations and could provide helpful guidance for controlling the development and dissemination of ARB and ARGs.
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Affiliation(s)
- Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jie Feng
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Jie Liu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Wenjie Fu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China; School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China.
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98
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Sun W, Gu J, Wang X, Qian X, Peng H. Solid-state anaerobic digestion facilitates the removal of antibiotic resistance genes and mobile genetic elements from cattle manure. BIORESOURCE TECHNOLOGY 2019; 274:287-295. [PMID: 30529334 DOI: 10.1016/j.biortech.2018.09.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/29/2018] [Accepted: 09/01/2018] [Indexed: 06/09/2023]
Abstract
Livestock manure is a hotspot for antibiotic resistance genes (ARGs). Solid-state anaerobic digestion (SAD) is a high efficiency livestock manure treatment, but the changes in ARGs and microbial communities during SAD are unknown. Therefore, thermophilic SAD (55 °C), mesophilic SAD (35 °C), and liquid anaerobic digestion (35 °C) were conducted to investigate the impacts of SAD on ARGs, mobile genetic elements, and microbial communities. Compared with liquid anaerobic digestion, SAD significantly reduced at least 7/10 ARGs and all of the mobile genetic elements considered, where the total abundance of ARG was 23.7% higher in the thermophilic SAD product than the mesophilic SAD product. Firmicutes and Proteobacteria were the main potential hosts for ARGs, and their decreased abundances were mainly responsible for the reductions in ARGs during SAD. This study demonstrated that SAD is a promising method for decreasing the ARGs risk in livestock manure.
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Affiliation(s)
- Wei Sun
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiling Peng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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99
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Yang Y, Liu G, Song W, Ye C, Lin H, Li Z, Liu W. Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes. ENVIRONMENT INTERNATIONAL 2019; 123:79-86. [PMID: 30502597 DOI: 10.1016/j.envint.2018.11.061] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 05/25/2023]
Abstract
Plastics have been accumulated offshore and in the deep oceans at an unprecedented scale. Microbial communities have colonized the plastisphere, which has become a reservoir for both antibiotic and metal resistance genes (ARGs and MRGs). This is the first analysis of the diversity, abundance, and co-occurrence of ARGs and MRGs, and their relationships within the microbial community, using metagenomic data of plastic particles observed in the North Pacific Gyre obtained from the National Centre for Biotechnology Information Sequence Read Archive database. The abundance of ARGs and MRGs in microbial communities on the plastics were in the ranges 7.07 × 10-4-1.21 × 10-2 and 5.51 × 10-3-4.82 × 10-2 copies per 16S rRNA, respectively. Both the Shannon-Wiener indices and richness of ARGs and MRGs in plastics microbiota were significantly greater than those of ARGs and MRGs in seawater microbiota in the North Pacific Gyre via one-way analysis of variance. Multidrug resistance genes and multi-metal resistance genes were the main classes of genes detected in plastic microbiota. There were no significant differences in the abundance or diversity of ARGs and MRGs between macroplastics biota and microplastics biota, indicating that particle size had no effect on resistance genes. Procrustes analysis suggested that microbial community composition was the determining factor of the ARG profile but not for MRG. Some ARGs and MRGs had a higher incidence of non-random co-occurrence, suggesting that the co-effects of selection for antibiotic or metal resistance are important factors influencing the resistome of the microbiota on the plastic particles.
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Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Guihua Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Wenjuan Song
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Chen Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Hui Lin
- Institute of Environmental Resources and Soil Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zan Li
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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100
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Guo H, Gu J, Wang X, Tuo X, Yu J, Zhang R. Key role of cyromazine in the distribution of antibiotic resistance genes and bacterial community variation in aerobic composting. BIORESOURCE TECHNOLOGY 2019; 274:418-424. [PMID: 30553081 DOI: 10.1016/j.biortech.2018.12.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/25/2018] [Accepted: 12/01/2018] [Indexed: 06/09/2023]
Abstract
The risks that have not been noted so far have come from the use of non-antibiotics. In this study, non-antibiotic drug (cyromazine) was used in composting to investigate its possible effects on the distribution of ARGs and changes of bacterial community. Results showed that cyromazine increased the abundances of highly-risky ARGs (blaCTX-M and blaVIM), and heavy metal resistance genes (MRGs). Low and high concentrations of cyromazine increased the abundance of Tn916/1545 by 18.27% and 64.26%, respectively, compared with the control treatment. Mobile genetic elements (MGEs) and MRGs were not the major cause of the dynamic changes in ARGs, but instead the bacterial community succession changed according to the moisture content, pH, and bio-Cu. Network analysis showed that Proteobacteria and Actinobacteria were the major hosts for ARGs, and there was a significant correlation between tcrB, sul1 and Tn916/1545.
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Affiliation(s)
- Honghong Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaxia Tuo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ranran Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
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