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Guo X, Qi Z, Li J, Tong H, Ren N, You S. Overlooked volcanic effect during transmission of antibiotic resistance genes induced by copper and zinc. CHEMOSPHERE 2024; 362:142713. [PMID: 38944351 DOI: 10.1016/j.chemosphere.2024.142713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Adding heavy metals such as copper and zinc to animal feeds is common practice to promote growth, but meanwhile has side consequence of enhancing spread of antibiotic resistance genes (ARGs) in soil. This presents a global challenge to food security and human health. We in this study investigated the transmission of typical ARGs, i. e. β-lactamase genes (β-RGs), in dairy farm environments where dietary Cu and Zn were present in a wide range of concentration. The β-RGs were demonstrated to be highly prevalent across environmental media, with a relative abundance of 94.55%, dominated by mechanisms of antibiotic deactivation (93.75%) and cellular protection (6.25%). More importantly, we first found the transmission of ARGs to be highly dependent on the overlooked volcanic effect, i. e. low-concentration Cu (12-22 mg/kg) and Zn (45-80 mg/kg) acted as micronutrients necessary for microbial growth but facilitated ARGs transfer, whereas higher-concentration Cu (22-39 mg/kg) and Zn (80-153 mg/kg) became toxic to microbial communities and gene expression patterns. Notably, the specific microbial phyla Proteobacteria (2.28-82.94%), Bacteroidetes (0.02-56.48%) and Actinobacteria (1.62-12.92%) exhibited resistance at low concentration of Cu and Zn, which enhanced the transmission of β-RGs. However, this process was inhibited at higher concentration due to inactivation of microbes by Cu and Zn. The increase in resistance was first observed in class Gammaproteobacteria (2.02-88.51%) and Alphaproteobacteria (0.68-10.1%) with increased Cu and Zn concentration. This resulted in heightened transfer of ARGs by tnpA-07 (80.35%) due to protection of thicker cell membrane by chelation with Cu and Zn. This study not only offers mechanistic insights into the volcanic effect of dietary metals on dissemination of ARGs, but also has important implications for safe management of agricultural settings.
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Affiliation(s)
- Xiaorui Guo
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China; School of Food Engineering, Harbin University of Commerce, Harbin, 150028, PR China
| | - Zheng Qi
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China.
| | - Junsheng Li
- School of Food Engineering, Harbin University of Commerce, Harbin, 150028, PR China
| | - Hailong Tong
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Shijie You
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China.
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Ficagna CA, Galli GM, Zatti E, Zago I, do Amaral MAFD, de Vitt MG, Paiano D, da Silva AS. Addition of Butyric Acid and Lauric Acid Glycerides in Nursery Pig Feed to Replace Conventional Growth Promoters. Animals (Basel) 2024; 14:1174. [PMID: 38672322 PMCID: PMC11047760 DOI: 10.3390/ani14081174] [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: 10/27/2023] [Revised: 12/02/2023] [Accepted: 12/17/2023] [Indexed: 04/28/2024] Open
Abstract
(1) Background: This study determined whether adding butyric acid and lauric acid glycerides in nursing pigs' feed would improve growth performance, proteinogram, biochemical parameters, and antioxidant status. (2) Methods: Ninety male pigs were divided into five groups with six repetitions per group: NC, negative control (no additive); TRI-BUT, addition of tributyrin in the basal ration; MDT-BUT, addition of mono-, di-, and triglycerides of butyric acid in the basal feed; MDT-LAU, the addition of mono-, di-, and triglycerides of lauric acid in the basal feed; and PC, positive control (addition of gentamicin in the basal feed). (3) Results: PC, TRI-BUT, and MDT-LAU resulted in a high average daily WG from days 1 to 39 (p < 0.01). MDT-LAU, MDT-BUT, and PC resulted in a greater feed:gain from days 1 to 39 than the NC (p = 0.03). Great concentrations of the gamma globulin fraction in all groups were observed than in the NC (p = 0.01). Ceruloplasmin, haptoglobin, and C-reactive protein concentrations were lower in all groups than in the NC (p < 0.05). Higher serum glutathione S-transferase activity was observed in the TRI-BUT and MDT-BUT than in the PC (p = 0.04). (4) Conclusions: The addition of butyric acid and lauric acid glycerides in the diet of pigs in the nursery phase can replace growth promoters since the products improve the growth performance, reduce acute-phase proteins, and increase gamma globulin concentrations.
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Affiliation(s)
- Cássio Antônio Ficagna
- Graduate Program and Animal Science, University of Santa Catarina State (UDESC), Rua Beloni Trombeta Zanini, nº 680, Bairro Santo Antônio, Chapecó 89815-630, SC, Brazil; (C.A.F.); (E.Z.); (I.Z.); (M.A.F.D.d.A.); (M.G.d.V.); (D.P.)
| | - Gabriela Miotto Galli
- Graduate Program in Animal Science, Federal University of Rio Grande do Sul (UFRGS), Avenida Paulo Gama, nº 110, Farroupilha, Porto Alegre 90010-150, RS, Brazil;
| | - Emerson Zatti
- Graduate Program and Animal Science, University of Santa Catarina State (UDESC), Rua Beloni Trombeta Zanini, nº 680, Bairro Santo Antônio, Chapecó 89815-630, SC, Brazil; (C.A.F.); (E.Z.); (I.Z.); (M.A.F.D.d.A.); (M.G.d.V.); (D.P.)
| | - Isadora Zago
- Graduate Program and Animal Science, University of Santa Catarina State (UDESC), Rua Beloni Trombeta Zanini, nº 680, Bairro Santo Antônio, Chapecó 89815-630, SC, Brazil; (C.A.F.); (E.Z.); (I.Z.); (M.A.F.D.d.A.); (M.G.d.V.); (D.P.)
| | - Marco Aurélio Fritzen Dias do Amaral
- Graduate Program and Animal Science, University of Santa Catarina State (UDESC), Rua Beloni Trombeta Zanini, nº 680, Bairro Santo Antônio, Chapecó 89815-630, SC, Brazil; (C.A.F.); (E.Z.); (I.Z.); (M.A.F.D.d.A.); (M.G.d.V.); (D.P.)
| | - Maksuel Gatto de Vitt
- Graduate Program and Animal Science, University of Santa Catarina State (UDESC), Rua Beloni Trombeta Zanini, nº 680, Bairro Santo Antônio, Chapecó 89815-630, SC, Brazil; (C.A.F.); (E.Z.); (I.Z.); (M.A.F.D.d.A.); (M.G.d.V.); (D.P.)
| | - Diovani Paiano
- Graduate Program and Animal Science, University of Santa Catarina State (UDESC), Rua Beloni Trombeta Zanini, nº 680, Bairro Santo Antônio, Chapecó 89815-630, SC, Brazil; (C.A.F.); (E.Z.); (I.Z.); (M.A.F.D.d.A.); (M.G.d.V.); (D.P.)
| | - Aleksandro Schafer da Silva
- Graduate Program and Animal Science, University of Santa Catarina State (UDESC), Rua Beloni Trombeta Zanini, nº 680, Bairro Santo Antônio, Chapecó 89815-630, SC, Brazil; (C.A.F.); (E.Z.); (I.Z.); (M.A.F.D.d.A.); (M.G.d.V.); (D.P.)
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Li X, Tang X, Chen M, Wang S, Tong C, Xu J, Xie G, Ma B, Zou Y, Wang Y, Wen X, Wu Y. Intramuscular therapeutic doses of enrofloxacin affect microbial community structure but not the relative abundance of fluoroquinolones resistance genes in swine manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169794. [PMID: 38181963 DOI: 10.1016/j.scitotenv.2023.169794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
Livestock manure is a major source of veterinary antibiotics and antibiotic resistance genes (ARGs). Elucidation of the residual characteristics of ARGs in livestock manure following the administration of veterinary antibiotics is critical to assess their ecotoxicological effects and environmental contamination risks. Here, we investigated the effects of enrofloxacin (ENR), a fluoroquinolone antibiotic commonly used as a therapeutic drug in animal husbandry, on the characteristics of ARGs, mobile genetic elements, and microbial community structure in swine manure following its intramuscular administration for 3 days and a withdrawal period of 10 days. The results revealed the highest concentrations of ENR and ciprofloxacin (CIP) in swine manure at the end of the administration period, ENR concentrations in swine manure in groups L and H were 88.67 ± 45.46 and 219.75 ± 88.05 mg/kg DM, respectively. Approximately 15 fluoroquinolone resistance genes (FRGs) and 48 fluoroquinolone-related multidrug resistance genes (F-MRGs) were detected in swine manure; the relative abundance of the F-MRGs was considerably higher than that of the FRGs. On day 3, the relative abundance of qacA was significantly higher in group H than in group CK, and no significant differences in the relative abundance of other FRGs, F-MRGs, or MGEs were observed between the three groups on day 3 and day 13. The microbial community structure in swine manure was significantly altered on day 3, and the altered community structure was restored on day 13. The FRGs and F-MRGs with the highest relative abundance were qacA and adeF, respectively, and Clostridium and Lactobacillus were the dominant bacterial genera carrying these genes in swine manure. In summary, a single treatment of intramuscular ENR transiently increased antibiotic concentrations and altered the microbial community structure in swine manure; however, this treatment did not significantly affect the abundance of FRGs and F-MRGs.
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Affiliation(s)
- Xianghui Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyue Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Majan Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Shaoyu Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Chang Tong
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiaojiao Xu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Gaomiao Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Baohua Ma
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yongde Zou
- Foshan Customs Comprehensive Technology Center, Foshan 528200, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xin Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
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Yu J, Zuo B, Li Q, Zhao F, Wang J, Huang W, Sun Z, Chen Y. Dietary supplementation with Lactiplantibacillus plantarum P-8 improves the growth performance and gut microbiota of weaned piglets. Microbiol Spectr 2024; 12:e0234522. [PMID: 38169289 PMCID: PMC10845957 DOI: 10.1128/spectrum.02345-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 09/20/2023] [Indexed: 01/05/2024] Open
Abstract
Weaning is a stressful event in the pig life cycle. We hypothesized that probiotics could be potential alternatives to antibiotics for promoting growth and ameliorating stress in weaning piglets via gut microbiota modulation and, thus, investigated the beneficial effects of dietary probiotic supplementation in weaning pigs. Ninety weaning piglets (Landrace × large white, 45 males and 45 females, 25 days of age) were randomized into three dietary treatments (30 piglets/treatment, divided into five replicates/treatment, i.e., six piglets/replicate) in this 28-day trial: control (C group, basal diet); probiotic [lactic acid bacteria (LAB) group, basal diet plus Lactiplantibacillus plantarum P-8]; and antibiotic (A group; basal diet plus chlortetracycline). The piglets' growth performance [average daily gain, average daily feed intake (ADFI), and feed conversion ratio (FCR)], immune and antioxidant markers, ileal mucosal morphology, and ileal and colonic microbiomes were compared among treatment groups. Compared to the C and A groups, probiotic supplementation significantly decreased the ADFI, FCR, and ileal mucosal crypt depth while increasing the villus height-to-crypt depth ratio, hepatic glutathione peroxidase and catalase activities, and serum levels of interleukin-2. Both probiotic and antibiotic treatments modulated the piglets' gut microbiomes, with more L. plantarum in the LAB group and more Eubacterium rectale and Limosilactobacillus reuteri in the A group. Probiotic supplementation significantly increased the relative abundance of genes encoding the acetylene, galactose, and stachyose degradation pathways, potentially enhancing nutrient absorption, energy acquisition, and growth performance. Probiotics are effective alternatives to antibiotics for promoting the health of piglets, possibly via gut microbiome modulation.IMPORTANCEWeaning impacts piglet health, performance, and mortality. Antibiotic treatment during weaning can mitigate the negative effects on growth. However, antibiotic use in livestock production contributes to the emergence of antibiotic resistance, which is a threat to global public health. This comprehensive study describes the gut microbial composition and growth performance of weaned piglets after dietary supplementation with Lactiplantibacillus plantarum P-8 or antibiotics. L. plantarum P-8 ameliorated stress and improved antioxidant capacity and growth performance in weaned piglets, accompanied by gut microbiota improvement. L. plantarum P-8 is an effective substitute for antibiotics to promote the health of weaned piglets while avoiding the global concern of drug resistance.
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Affiliation(s)
- Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, China
| | - Bin Zuo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qi Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, China
| | - Feiyan Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, China
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Weiqiang Huang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, China
| | - Yongfu Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Huhhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot, China
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Musiyiwa K, Simbanegavi TT, Marumure J, Makuvara Z, Chaukura N, Gwenzi W. The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:12666-12682. [PMID: 38253827 DOI: 10.1007/s11356-023-31788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024]
Abstract
The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.
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Affiliation(s)
- Kumbirai Musiyiwa
- Department of Crop Science and Post-Harvest Technology, School of Agricultural Science and Technology, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
| | - Tinoziva T Simbanegavi
- Department of Soil Science and Environment, Faculty of Agriculture, Environment, and Food Systems, University of Zimbabwe, Mt. Pleasant, P.O. Box MP167, Harare, Zimbabwe
| | - Jerikias Marumure
- Department of Physics, Geography and Environmental Science, School of Natural Sciences, Great Zimbabwe University, P.O. Box 1235, Masvingo, Zimbabwe
- Department of Life and Consumer Sciences, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Zakio Makuvara
- Department of Physics, Geography and Environmental Science, School of Natural Sciences, Great Zimbabwe University, P.O. Box 1235, Masvingo, Zimbabwe
- Department of Life and Consumer Sciences, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Pretoria, South Africa
| | - Nhamo Chaukura
- Department of Physical and Earth Sciences, Sol Plaatje University, Kimberley, 8301, South Africa
| | - Willis Gwenzi
- Grassland Science and Renewable Plant Resources, Universitat Kassel, Steinstraβe 19, 37213, Witzenhausen, Germany.
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Marchiori MS, Paiano D, Zatti E, Tarasconi L, Ficagna C, Amaral MAFD, Milarch CF, Horn VW, Mendes RE, Galli GM, Vedovatto M, Da Silva AS. Butyric acid glycerides as substitutes for antibiotics as growth enhancers in the diet of nursery piglets. Res Vet Sci 2024; 167:105110. [PMID: 38150942 DOI: 10.1016/j.rvsc.2023.105110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023]
Abstract
This study aimed to determine whether the addition of butyric acid glycerides as substitutes to conventional growth promoters can provide adequate zootechnical performance and intestinal health in healthy piglets in the nursery phase. We used 90 male piglets (average weight of 6.5 kg) subdivided into five treatments with six replicates per treatment. The treatments had the same basal diet: NC-negative control (without growth promoter), PC-positive control (with gentamicin, oral), PSB-protected sodium butyrate, FSB-free sodium butyrate, and TRI-tributyrin. In these animals, zootechnical performance was evaluated on days 1, 10, 20 and 39, microbiological analysis on days 14 and 39, hematocrit, blood biochemistry and intestinal histology, intestinal oxidation and antioxidation on day 39. The average daily weight gain was higher in the TRI group on days 21 to 39 in the nursery (P = 0.03), with more significant weight gain from 1 to 39 days (P = 0.05). There were higher leukocyte counts in the PC group than in the TRI group and higher lymphocyte counts in the PC treatment than in the NC or TRI groups. Escherichia coli counts were lower in the PC, followed by the PSB and TRI groups on day 39 (P = 0.01). Lower crypt depths were found in the TRI and FSB groups, followed by PC, than in the NC group (P = 0.01). Higher values for crypt villosity ratio were found in the FSB and TRI groups than in the NC group (P = 0.05). Lower lipid peroxidation was found in analyzes of serum oxidative status (LPO: P = 0.01), associated with greater activities of superoxide dismutase - SOD (P = 0.08), glutathione S-transferase - GST (P = 0.09) in PSB and TRI groups than in the NC group. In conclusion, the use of butyric acid in the form of tributyrin can be used as growth enhancers in piglets in the nursery phase.
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Affiliation(s)
- Maiara S Marchiori
- Department of Animal Science, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil
| | - Diovani Paiano
- Department of Animal Science, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil
| | - Emerson Zatti
- Department of Animal Science, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil
| | - Lara Tarasconi
- Department of Animal Science, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil
| | - Cassio Ficagna
- Department of Animal Science, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil
| | - Marco A F D Amaral
- Department of Animal Science, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil
| | | | - Vitor W Horn
- Instituto Federal Catarinense, Concordia, SC, Brazil
| | | | | | | | - Aleksandro S Da Silva
- Department of Animal Science, Universidade do Estado de Santa Catarina, Chapecó, SC, Brazil.
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Chen D, Cheng K, Wan L, Cui C, Li G, Zhao D, Yu Y, Liao X, Liu Y, D'Souza AW, Lian X, Sun J. Daily occupational exposure in swine farm alters human skin microbiota and antibiotic resistome. IMETA 2024; 3:e158. [PMID: 38868515 PMCID: PMC10989081 DOI: 10.1002/imt2.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 06/14/2024]
Abstract
Antimicrobial resistance (AMR) is a major threat to global public health, and antibiotic resistance genes (ARGs) are widely distributed across humans, animals, and environment. Farming environments are emerging as a key research area for ARGs and antibiotic resistant bacteria (ARB). While the skin is an important reservoir of ARGs and ARB, transmission mechanisms between farming environments and human skin remain unclear. Previous studies confirmed that swine farm environmental exposures alter skin microbiome, but the timeline of these changes is ill defined. To improve understanding of these changes and to determine the specific time, we designed a cohort study of swine farm workers and students through collected skin and environmental samples to explore the impact of daily occupational exposure in swine farm on human skin microbiome. Results indicated that exposure to livestock-associated environments where microorganisms are richer than school environment can reshape the human skin microbiome and antibiotic resistome. Exposure of 5 h was sufficient to modify the microbiome and ARG structure in workers' skin by enriching microorganisms and ARGs. These changes were preserved once formed. Further analysis indicated that ARGs carried by host microorganisms may transfer between the environment with workers' skin and have the potential to expand to the general population using farm workers as an ARG vector. These results raised concerns about potential transmission of ARGs to the broader community. Therefore, it is necessary to take corresponding intervention measures in the production process to reduce the possibility of ARGs and ARB transmission.
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Affiliation(s)
- Dong‐Rui Chen
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Ke Cheng
- Veterinary CenterGuangxi State Farms Yongxin Animal Husbandry Group Co., Ltd.NanningChina
| | - Lei Wan
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Chao‐Yue Cui
- Laboratory Animal CentreWenzhou Medical UniversityWenzhouChina
| | - Gong Li
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Dong‐Hao Zhao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Yang Yu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Xiao‐Ping Liao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Ya‐Hong Liu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
| | - Alaric W. D'Souza
- Department of PediatricsBoston Children's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Xin‐Lei Lian
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary MedicineSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Jiangsu Co‐Innovation Center for the Prevention and Control of Important Animal Infectious Disease and ZoonosesYangzhou UniversityYangzhouChina
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8
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Kim K, Jinno C, Li X, Bravo D, Cox E, Ji P, Liu Y. Impact of an oligosaccharide-based polymer on the metabolic profiles and microbial ecology of weanling pigs experimentally infected with a pathogenic E. coli. J Anim Sci Biotechnol 2024; 15:1. [PMID: 38169416 PMCID: PMC10759389 DOI: 10.1186/s40104-023-00956-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/29/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Our previous study has reported that supplementation of oligosaccharide-based polymer enhances gut health and disease resistance of pigs infected with enterotoxigenic E. coli (ETEC) F18 in a manner similar to carbadox. The objective of this study was to investigate the impacts of oligosaccharide-based polymer or antibiotic on the host metabolic profiles and colon microbiota of weaned pigs experimentally infected with ETEC F18. RESULTS Multivariate analysis highlighted the differences in the metabolic profiles of serum and colon digesta which were predominantly found between pigs supplemented with oligosaccharide-based polymer and antibiotic. The relative abundance of metabolic markers of immune responses and nutrient metabolisms, such as amino acids and carbohydrates, were significantly differentiated between the oligosaccharide-based polymer and antibiotic groups (q < 0.2 and fold change > 2.0). In addition, pigs in antibiotic had a reduced (P < 0.05) relative abundance of Lachnospiraceae and Lactobacillaceae, whereas had greater (P < 0.05) Clostridiaceae and Streptococcaceae in the colon digesta on d 11 post-inoculation (PI) compared with d 5 PI. CONCLUSIONS The impact of oligosaccharide-based polymer on the metabolic and microbial profiles of pigs is not fully understood, and further exploration is needed. However, current research suggest that various mechanisms are involved in the enhanced disease resistance and performance in ETEC-challenged pigs by supplementing this polymer.
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Affiliation(s)
- Kwangwook Kim
- Department of Animal Science, University of California, Davis, CA, 95616, USA
- Present Affiliation: Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Cynthia Jinno
- Department of Animal Science, University of California, Davis, CA, 95616, USA
- Present Affiliation: Cedars-Sinai Medical Center, Los Angeles, CA, 90084, USA
| | - Xunde Li
- School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - David Bravo
- Pancosma|ADM, 1180, Rolle, Switzerland
- Present Affiliation: Nutreco Exploration, Nutreco, The Netherlands
| | - Eric Cox
- Department of Virology, Parasitology and Immunology, Ghent University, 9000, Ghent, Belgium
| | - Peng Ji
- Department of Nutrition, University of California, Davis, CA, 95616, USA
| | - Yanhong Liu
- Department of Animal Science, University of California, Davis, CA, 95616, USA.
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9
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Wang M, Zheng H, Wang S, Luo H, Li Z, Song X, Xu H, Li P, Sun S, Wang Y, Yuan Z. Comparative analysis of changes in diarrhea and gut microbiota in Beigang pigs. Microb Pathog 2023; 185:106441. [PMID: 37944676 DOI: 10.1016/j.micpath.2023.106441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Increasing evidence indicated that the gut microbiota is a large and complex organic combination, which is closely related to the host health. Diarrhea is a disease with devastating effects on livestock that has been demonstrated to be associated with gut microbiota. Currently, studies on gut microbiota and diarrhea have involved multiple species, but changes in gut microbiota of Beigang pigs during diarrhea have not been characterized. Here, we described gut microbial changes of Beigang pigs during diarrhea. Results indicated that a total of 4423 OTUs were recognized in diarrheic and healthy Beigang pigs, and Firmicutes and Bacteroidota were the most dominant phyla regardless of health status. However, the major components of the gut microbiota changed between diarrheic and healthy Beigang pigs. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla (Synergistota, Actinobacteriota and Spirochaetota) and 30 genera increased significantly during diarrhea, whereas the relative abundances of 3 phyla (Patescibacteria, Bacteroidota and Fibrobacterota) and 41 genera decreased significantly. In conclusion, this study found significant changes in the gut microbiota of Beigang pigs during diarrhea. Meanwhile, this also lays the foundation for the prevention and treatment of diarrhea in Beigang pigs and the further discovery of more anti-diarrhea probiotics.
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Affiliation(s)
- Meng Wang
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China; College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hao Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Shuaiwei Wang
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Houqiang Luo
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Ziwei Li
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Xianzhang Song
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Hongxi Xu
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Peide Li
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Siyu Sun
- College of Animal Science, Wenzhou Vocational College of Science and Technology, Wenzhou, 325006, China
| | - Yan Wang
- Tibet Livestock Research Institute, Tibet Academy of Agriculture and Animal Science, Lhasa, 850009, China.
| | - Zhenjie Yuan
- Tibet Livestock Research Institute, Tibet Academy of Agriculture and Animal Science, Lhasa, 850009, China.
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10
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Zhou Y, Li J, Wen X, Li Q. Antibiotic resistance gene profiles and evolutions in composting regulated by reactive oxygen species generated via nano ZVI loaded on biochar. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166487. [PMID: 37611721 DOI: 10.1016/j.scitotenv.2023.166487] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/14/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
In this study, nano zero-valent iron loaded on biochar (BC-nZVI) was analyzed for its effects on antibiotic resistance genes (ARGs) in composting. The results showed that BC-nZVI increased reactive oxygen species (ROS) production, and the peak values of H2O2 and OH were 22.95 % and 55.30 % higher than those of the control group, respectively. After 65 days, the relative abundances of representative ARGs decreased by 56.12 % in the nZVI group (with BC-nZVI added). An analysis of bacterial communities and networks revealed that Actinobacteria, Proteobacteria, and Firmicutes were the main hosts for ARGs, and BC-nZVI weakened the link between ARGs and host bacteria. Distance-based redundancy analysis showed that BC-nZVI altered the microbial community structure through environmental factors and that most ARGs were negatively correlated with ROS, suggesting that ROS significantly affected the relative abundance of ARGs. According to these results, BC-nZVI showed potential for decreasing the relative abundance of ARGs in composting.
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Affiliation(s)
- Yucheng Zhou
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Jixuan Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xiaoli Wen
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
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11
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Qin Y, Huang W, Yang J, Zhao Y, Zhao M, Xu H, Zhang M. The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang. Foods 2023; 12:3928. [PMID: 37959048 PMCID: PMC10647823 DOI: 10.3390/foods12213928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 108 total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.
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Affiliation(s)
- Yanan Qin
- Correspondence: ; Tel.: +86-13999236502
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12
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Liu JL, Yao J, Zhou DL, Liu B, Liu H, Li M, Zhao C, Sunahara G, Duran R. Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:104753-104766. [PMID: 37707732 DOI: 10.1007/s11356-023-29203-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/02/2023] [Indexed: 09/15/2023]
Abstract
Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.
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Affiliation(s)
- Jian-Li Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China.
| | - Jun Yao
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - De-Liang Zhou
- Beijing Zhongdianyida Technology Co., Ltd, Beijing, 100190, China
| | - Bang Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Houquan Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Miaomiao Li
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Chenchen Zhao
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Geoffrey Sunahara
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, H9X3V9, Canada
| | - Robert Duran
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing, 100083, China
- Université de Pau et des Pays de l'Adour/E2S UPPA, IPREM UMR CNRS 5254, BP 1155, 64013, Pau Cedex, France
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13
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Lin X, Ma J, Zhou Z, Qiao B, Li Y, Zheng W, Tian Y. Oil-contaminated sites act as high-risk pathogen reservoirs previously overlooked in coastal zones. WATER RESEARCH 2023; 242:120225. [PMID: 37329716 DOI: 10.1016/j.watres.2023.120225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/03/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
In addition to the organic pollutants and disturbance to the microbial, plant and animal systems, oil contamination can also enrich opportunistic pathogens. But little is known about whether and how the most common coastal oil-contaminated water bodies act as reservoirs for pathogens. Here, we delved into the characteristics of pathogenic bacteria in coastal zones by constructing seawater-based microcosms with diesel oil as a pollutant. 16S rRNA gene full-length sequencing and genomic exploration revealed that pathogenic bacteria with genes involved in alkane or aromatic degradation were significantly enriched under oil contamination, providing a genetic basis for them to thrive in oil-contaminated seawater. Moreover, high-throughput qPCR assays showed an increased abundance of the virulence gene and enrichment in antibiotics resistance genes (ARGs), especially those related to multidrug resistance efflux pumps, and their high relevance to Pseudomonas, enabling this genus to achieve high levels of pathogenicity and environmental adaptation. More importantly, infection experiments with a culturable P. aeruginosa strain isolated from an oil-contaminated microcosm provided clear evidence that the environmental strain was pathogenic to grass carp (Ctenopharyngodon idellus), and the highest lethality rate was found in the oil pollutant treatment, demonstrating the synergistic effect of toxic oil pollutants and pathogens on infected fish. A global genomic investigation then revealed that diverse environmental pathogenic bacteria with oil degradation potential are widely distributed in marine environments, especially in coastal zones, suggesting extensive pathogenic reservoir risks in oil-contaminated sites. Overall, the study uncovered a hidden microbial risk, showing that oil-contaminated seawater could be a high-risk pathogen reservoir, and provides new insights and potential targets for environmental risk assessment and control.
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Affiliation(s)
- Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiaxin Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | | | - Baoyi Qiao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yixin Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Wei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen 361102, China.
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14
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Raslan MA, Raslan SA, Shehata EM, Mahmoud AS, Lundstrom K, Barh D, Azevedo V, Sabri NA. Associations between Nutrigenomic Effects and Incidences of Microbial Resistance against Novel Antibiotics. Pharmaceuticals (Basel) 2023; 16:1093. [PMID: 37631008 PMCID: PMC10458141 DOI: 10.3390/ph16081093] [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: 05/07/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Nutrigenomics is the study of the impact of diets or nutrients on gene expression and phenotypes using high-throughput technologies such as transcriptomics, proteomics, metabolomics, etc. The bioactive components of diets and nutrients, as an environmental factor, transmit information through altered gene expression and hence the overall function and traits of the organism. Dietary components and nutrients not only serve as a source of energy but also, through their interactions with genes, regulate gut microbiome composition, the production of metabolites, various biological processes, and finally, health and disease. Antimicrobial resistance in pathogenic and probiotic microorganisms has emerged as a major public health concern due to the presence of antimicrobial resistance genes in various food products. Recent evidence suggests a correlation between the regulation of genes and two-component and other signaling systems that drive antibiotic resistance in response to diets and nutrients. Therefore, diets and nutrients may be alternatively used to overcome antibiotic resistance against novel antibiotics. However, little progress has been made in this direction. In this review, we discuss the possible implementations of nutrigenomics in antibiotic resistance against novel antibiotics.
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Affiliation(s)
- Mohamed A. Raslan
- Drug Research Centre, Cairo P.O. Box 11799, Egypt or (M.A.R.); or (S.A.R.); (E.M.S.)
| | - Sara A. Raslan
- Drug Research Centre, Cairo P.O. Box 11799, Egypt or (M.A.R.); or (S.A.R.); (E.M.S.)
| | - Eslam M. Shehata
- Drug Research Centre, Cairo P.O. Box 11799, Egypt or (M.A.R.); or (S.A.R.); (E.M.S.)
| | - Amr S. Mahmoud
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ain Shams University, Cairo P.O. Box 11566, Egypt;
| | | | - Debmalya Barh
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (D.B.); (V.A.)
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (D.B.); (V.A.)
| | - Nagwa A. Sabri
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo P.O. Box 11566, Egypt
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15
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Zhang Y, Cheng D, Xie J, Hu Q, Xie J, Shi X. Long-term field application of manure induces deep selection of antibiotic resistomes in leaf endophytes of Chinese cabbage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163334. [PMID: 37061064 DOI: 10.1016/j.scitotenv.2023.163334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/01/2023] [Accepted: 04/02/2023] [Indexed: 06/01/2023]
Abstract
Antibiotic resistomes in leaf endophytes of vegetables threaten human health through the food chain. However, little is known about the ability of long-term manure fertilization to impact the deep selection of antibiotic resistance genes (ARGs) in leaf endophytes of vegetables planted in different types of soils. Here, by high-throughput quantitative PCR, we characterized the ARGs of leaf endophytes of Chinese cabbage (Brassica pekinensis (Lour.) Rupr.) grown in long-term (14 year) manure-amended acidic, neutral and calcareous soils. In total, 87 ARGs and 4 mobile genetic elements (MGEs) were detected in all the samples. Manure fertilization significantly increased the ARG numbers and normalized abundance in leaf endophytes, especially in acidic soil. Moreover, in acidic soil, manure application also led to a higher increase in the normalized abundance of opportunist and specialist ARGs, and more opportunist and specialist ARGs posed a high risk according to their risk ranks. Random forest analysis revealed that Proteobacteria and MGEs were the major drivers affecting the normalized abundance of opportunist and specialist ARGs in both acidic and neutral soils, respectively. In calcareous soil, Cyanobacteria and Actinobacteria were the most important contributors. Collectively, this study expands our knowledge about the deep selection of plant resistomes under long-term manure application.
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Affiliation(s)
- Yu Zhang
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Jun Xie
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Qijuan Hu
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Jiawei Xie
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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16
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Adekolurejo OO, McDermott K, Greathead HMR, Miller HM, Mackie AR, Boesch C. Effect of Red-Beetroot-Supplemented Diet on Gut Microbiota Composition and Metabolite Profile of Weaned Pigs-A Pilot Study. Animals (Basel) 2023; 13:2196. [PMID: 37443994 DOI: 10.3390/ani13132196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Red beetroot is a well-recognized and established source of bioactive compounds (e.g., betalains and polyphenols) with anti-inflammatory and antimicrobial properties. It is proposed as a potential alternative to zinc oxide with a focus on gut microbiota modulation and metabolite production. In this study, weaned pigs aged 28 days were fed either a control diet, a diet supplemented with zinc oxide (3000 mg/kg), or 2% and 4% pulverized whole red beetroot (CON, ZNO, RB2, and RB4; respectively) for 14 days. After pigs were euthanized, blood and digesta samples were collected for microbial composition and metabolite analyses. The results showed that the diet supplemented with red beetroot at 2% improved the gut microbial richness relative to other diets but marginally influenced the cecal microbial diversity compared to a zinc-oxide-supplemented diet. A further increase in red beetroot levels (4%-RB4) led to loss in cecal diversity and decreased short chain fatty acids and secondary bile acid concentrations. Also, an increased Proteobacteria abundance, presumably due to increased lactate/lactic-acid-producing bacteria was observed. In summary, red beetroot contains several components conceived to improve the gut microbiota and metabolite output of weaned pigs. Future studies investigating individual components of red beetroot will better elucidate their contributions to gut microbiota modulation and pig health.
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Affiliation(s)
- Opeyemi O Adekolurejo
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Katie McDermott
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | - Helen M Miller
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alan R Mackie
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Christine Boesch
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
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17
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Xiao S, Mi J, Chen Y, Feng K, Mei L, Liao X, Wu Y, Wang Y. The abundance and diversity of antibiotic resistance genes in layer chicken ceca is associated with farm enviroment. Front Microbiol 2023; 14:1177404. [PMID: 37455745 PMCID: PMC10348872 DOI: 10.3389/fmicb.2023.1177404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/18/2023] [Indexed: 07/18/2023] Open
Abstract
Industrialized layer chicken feedlots harbor complex environmental microbial communities that affect the enrichment and exchange of gut bacteria and antibiotic resistance genes (ARGs). However, the contribution of different environmental sources to the gut ARGs of layer chickens is not clear. Here, layer chicken gut and environmental samples (air, water, feed, cage, feather, maternal hen feces, uropygial glands) were collected during the early 3 month period before the laying of eggs, and the source and characteristics of the gut microorganisms and ARGs were analyzed by performing 16S rRNA and metagenomic sequencing. The results showed that the abundances of Bacteroidetes and Actinobacteria in cecum of layer chickens gradually increased, while that of Proteobacteria decreased with age, and the number and relative abundance of ARGs decreased significantly with age. On day 5, 57% of the layer chicken cecal ARGs were from feather samples, and 30% were from cage samples. Subsequently, the contribution of cage ARGs became progressively more prominent over time. At days 30 and 57, the contribution of cage ARGs to the chick cecal ARGs reached 63.3 and 69.5%, respectively. The bacterial community composition (especially the abundances of Klebsiella pneumoniae and Escherichia coli) was the major factor impacting the ARG profile. K. pneumoniae and E. coli were mainly transmitted from feathers to the layer chicken cecum, and the contribution rates were 32 and 3.4%, respectively. In addition, we observed the transmission of ARG-carrying bacteria (Bacteroides fragilis) from the cage to the gut, with a contribution rate of 11.5%. It is noteworthy that B. fragilis is an opportunistic pathogen that may cause diarrhea in laying hens. These results can provide reference data for the healthy breeding of layer chickens and the prevention and control of ARG pollution.
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Affiliation(s)
- Shasha Xiao
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jiandui Mi
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yingxin Chen
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Kunxian Feng
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Liang Mei
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xindi Liao
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yinbao Wu
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yan Wang
- College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan, China
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18
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Wu J, Guo S, Li K, Li Z, Xu P, Jones DL, Wang J, Zou J. Effect of fertilizer type on antibiotic resistance genes by reshaping the bacterial community and soil properties. CHEMOSPHERE 2023; 336:139272. [PMID: 37343633 DOI: 10.1016/j.chemosphere.2023.139272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/05/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Conventional and bio-organic fertilizers play an important role in maintaining soil health and promoting crop growth. However, the effect of organic fertilizers on the prevalence of antibiotic resistance genes (ARGs) in the vegetable cropping system has been largely overlooked. In this study, we investigated the impacts of soil properties and biotic factors on ARG profiles by analyzing ARG and bacterial communities in vegetable copping soils with a long-term history of manure and bio-organic fertilizer application. The ARG abundance in the soil was significantly increased by 116% with manure application compared to synthetic NPK fertilizer application. This finding was corroborated by our meta-analysis that the longer the duration of manure application, the greater the response of increased soil ARG abundance. However, bio-organic fertilizers containing Trichoderma spp. Significantly reduced ARG contamination by 31% compared to manure application. About half of the ARG variation was explained by changes in bacterial abundance and structure, followed by soil properties. The mitigation of ARG by Trichoderma spp. Is achieved by altering the structure of the bacterial community and weakening the close association between bacteria and ARG prevalence. Taken together, these findings shed light on the contribution of bio-organic fertilizers in mitigating ARG contamination in agricultural soils, which can help manage the ecological risk posed by ARG inputs associated with manure application.
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Affiliation(s)
- Jie Wu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shumin Guo
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kejie Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhutao Li
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pinshang Xu
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK; SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA, 6105, Australia
| | - Jinyang Wang
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
| | - Jianwen Zou
- Key Laboratory of Green and Low-carbon Agriculture in Southeastern China, Ministry of Agriculture and Rural Affairs, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China.
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19
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Qi Z, Jin S, Guo X, Tong H, Ren N, You S. Distribution and transmission of β-lactamase resistance genes in meal-to-milk chain on dairy farm. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 331:121831. [PMID: 37209898 DOI: 10.1016/j.envpol.2023.121831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 05/22/2023]
Abstract
Antibiotics have been widely used in animal husbandry, which leads to high risk of food-borne transfer of antibiotic resistance genes (ARGs). The present study investigated the distribution of β-lactamase resistance genes (β-RGs) on dairy farm in the Songnen Plain of western Heilongjiang Province, China, to provide mechanistic insights into food-borne transmission of β-RGs through "meal-to-milk" chain under practically relevant circumstances. The results demonstrated that the abundance of β-RGs (91%) was much higher than that of other ARGs in the livestock farms. The blaTEM exhibited the content as high as 94.55% among all ARGs, and higher than 98% blaTEM was detected in meal, water and milk sample. The metagenomic taxonomy analysis indicated that the blaTEM should be carried by tnpA-04 (7.04%) and tnpA-03 (1.48%) hosted in Pseudomonas genus (15.36%) and Pantoea (29.02%) genus. Both tnpA-04 and tnpA-03 in the milk sample were identified to be the key mobile genetic elements (MGEs) responsible for transferring blaTEM along the "meal-manure-soil-surface water-milk" chain. The ARGs transfer across ecological boundaries underscored the need to evaluate potential dissemination of high-risk Proteobacteria and Bacteroidetes carried by humans and animals. They were capable of producing expanded-spectrum β-lactamases (ESBLs) and destroying commonly used antibiotics, leading to possible risk of food-borne horizontal transmission of ARGs. This study not only has important environmental implications for identifying the pathway for ARGs transfer, but also highlights the demand for appropriate policy toward safe regulation of dairy farm and husbandry products.
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Affiliation(s)
- Zheng Qi
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China
| | - Shuhan Jin
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China
| | - Xiaorui Guo
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, Harbin, 150076, PR China
| | - Hailong Tong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, PR China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Shijie You
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China.
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20
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Cui H, Zhu D, Ding L, Wang Y, Su J, Duan G, Zhu Y. Co-occurrence of genes for antibiotic resistance and arsenic biotransformation in paddy soils. J Environ Sci (China) 2023; 125:701-711. [PMID: 36375951 DOI: 10.1016/j.jes.2022.02.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 06/16/2023]
Abstract
Paddy soils are potential hotspots of combined contamination with arsenic (As) and antibiotics, which may induce co-selection of antibiotic resistance genes (ARGs) and As biotransformation genes (ABGs), resulting in dissemination of antimicrobial resistance and modification in As biogeochemical cycling. So far, little information is available for these co-selection processes and specific patterns between ABGs and ARGs in paddy soils. Here, the 16S rRNA amplicon sequencing and high-throughput quantitative PCR and network analysis were employed to investigate the dynamic response of ABGs and ARGs to As stress and manure application. The results showed that As stress increased the abundance of ARGs and mobile genetic elements (MGEs), resulting in dissemination risk of antimicrobial resistance. Manure amendment increased the abundance of ABGs, enhanced As mobilization and methylation in paddy soil, posing risk to food safety. The frequency of the co-occurrence between ABGs and ARGs, the host bacteria carrying both ARGs and ABGs were increased by As or manure treatment, and remarkably boosted in soils amended with both As and manure. Multidrug resistance genes were found to have the preference to be co-selected with ABGs, which was one of the dominant co-occurring ARGs in all treatments, and manure amendment increased the frequency of Macrolide-Lincosamide-Streptogramin B resistance (MLSB) to co-occur with ABGs. Bacillus and Clostridium of Firmicutes are the dominant host bacteria carrying both ABGs and ARGs in paddy soils. This study would extend our understanding on the co-selection between genes for antibiotics and metals, also unveil the hidden environmental effects of combined pollution.
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Affiliation(s)
- Huiling Cui
- 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
| | - Dong 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
| | - Longjun Ding
- 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
| | - Yifei Wang
- 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
| | - Jianqiang Su
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guilan Duan
- 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.
| | - Yongguan 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 Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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21
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Brinck JE, Lassen SB, Forouzandeh A, Pan T, Wang YZ, Monteiro A, Blavi L, Solà-Oriol D, Stein HH, Su JQ, Brandt KK. Impacts of dietary copper on the swine gut microbiome and antibiotic resistome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159609. [PMID: 36273560 DOI: 10.1016/j.scitotenv.2022.159609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Restrictions on antibiotic growth promoters have prompted livestock producers to use alternative growth promoters, and dietary copper (Cu) supplementation is currently being widely used in pig production. However, elevated doses of dietary Cu constitute a risk for co-selection of antibiotic resistance and the risk may depend on the type of Cu-based feed additives being used. We here report the first controlled experiment investigating the impact of two contrasting Cu-based feed additives on the overall swine gut microbiome and antibiotic resistome. DNA was extracted from fecal samples (n = 96) collected at four time points during 116 days from 120 pigs allotted to three dietary treatments: control, divalent copper sulfate (CuSO4; 250 μg Cu g-1 feed), and monovalent copper oxide (Cu2O; 250 μg Cu g-1 feed). Bacterial community composition, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) were assessed, and bioavailable Cu ([Cu]bio) was determined using whole-cell bacterial bioreporters. Cu supplementation to feed increased total Cu concentrations ([Cu]total) and [Cu]bio in feces 8-10 fold and at least 670-1000 fold, respectively, but with no significant differences between the two Cu sources. The swine gut microbiome harbored highly abundant and diverse ARGs and MGEs irrespective of the treatments throughout the experiment. Microbiomes differed significantly between pig growth stages and tended to converge over time, but only minor changes in the bacterial community composition and resistome could be linked to Cu supplementation. A significant correlation between bacterial community composition (i.e., bacterial taxa present) and ARG prevalence patterns were observed by Procrustes analysis. Overall, results of the experiment did not provide evidence for Cu-induced co-selection of ARGs or MGEs even at a Cu concentration level exceeding the maximal permitted level for pig diets in the EU (25 to 150 μg Cu g-1 feed depending on pig age).
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Affiliation(s)
- Julius Emil Brinck
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Simon Bo Lassen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Beijing, China
| | - Asal Forouzandeh
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Animal Nutrition and Welfare Service (SNiBA), Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Ting Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yan-Zi Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | | | - Laia Blavi
- Animal Nutrition and Welfare Service (SNiBA), Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - David Solà-Oriol
- Animal Nutrition and Welfare Service (SNiBA), Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Hans H Stein
- Department of Animal Sciences, University of Illinois, Urbana 61801, USA
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kristian K Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Sino-Danish Center for Education and Research (SDC), University of Chinese Academy of Sciences, 380 Huaibeizhuang, Beijing, China.
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22
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Ekhlas D, Argüello H, Leonard FC, Manzanilla EG, Burgess CM. Insights on the effects of antimicrobial and heavy metal usage on the antimicrobial resistance profiles of pigs based on culture-independent studies. Vet Res 2023; 54:14. [PMID: 36823539 PMCID: PMC9951463 DOI: 10.1186/s13567-023-01143-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
Antimicrobial resistance is a global threat to human, animal, and environmental health. In pig production, antimicrobials and heavy metals such as zinc oxide are commonly used for treatment and prevention of disease. Nevertheless, the effects of antimicrobials and heavy metals on the porcine resistome composition and the factors influencing this resistance profile are not fully understood. Advances in technologies to determine the presence of antimicrobial resistance genes in diverse sample types have enabled a more complete understanding of the resistome and the factors which influence its composition. The aim of this review is to provide a greater understanding of the influence of antimicrobial and heavy metal usage on the development and transmission of antimicrobial resistance on pig farms. Furthermore, this review aims to identify additional factors that can affect the porcine resistome. Relevant literature that used high-throughput sequencing or quantitative PCR methods to examine links between antimicrobial resistance and antimicrobial and heavy metal use was identified using a systematic approach with PubMed (NCBI), Scopus (Elsevier), and Web of Science (Clarivate Analytics) databases. In total, 247 unique records were found and 28 publications were identified as eligible for inclusion in this review. Based on these, there is clear evidence that antimicrobial and heavy metal use are positively linked with antimicrobial resistance in pigs. Moreover, associations of genes conferring antimicrobial resistance with mobile genetic elements, the microbiome, and the virome were reported, which were further influenced by the host, the environment, or the treatment itself.
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Affiliation(s)
- Daniel Ekhlas
- grid.6435.40000 0001 1512 9569Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin, Ireland ,grid.7886.10000 0001 0768 2743School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Héctor Argüello
- grid.4807.b0000 0001 2187 3167Animal Health Department, Veterinary Faculty, Universidad de León, León, Spain
| | - Finola C. Leonard
- grid.7886.10000 0001 0768 2743School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Edgar G. Manzanilla
- grid.7886.10000 0001 0768 2743School of Veterinary Medicine, University College Dublin, Dublin, Ireland ,grid.6435.40000 0001 1512 9569Pig Development Department, Teagasc Moorepark, Fermoy, Co. Cork Ireland
| | - Catherine M. Burgess
- grid.6435.40000 0001 1512 9569Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
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23
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Soundararajan M, Marincola G, Liong O, Marciniak T, Wencker FDR, Hofmann F, Schollenbruch H, Kobusch I, Linnemann S, Wolf SA, Helal M, Semmler T, Walther B, Schoen C, Nyasinga J, Revathi G, Boelhauve M, Ziebuhr W. Farming Practice Influences Antimicrobial Resistance Burden of Non-Aureus Staphylococci in Pig Husbandries. Microorganisms 2022; 11:microorganisms11010031. [PMID: 36677324 PMCID: PMC9865537 DOI: 10.3390/microorganisms11010031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Non-aureus staphylococci (NAS) are ubiquitous bacteria in livestock-associated environments where they may act as reservoirs of antimicrobial resistance (AMR) genes for pathogens such as Staphylococcus aureus. Here, we tested whether housing conditions in pig farms could influence the overall AMR-NAS burden. Two hundred and forty porcine commensal and environmental NAS isolates from three different farm types (conventional, alternative, and organic) were tested for phenotypic antimicrobial susceptibility and subjected to whole genome sequencing. Genomic data were analysed regarding species identity and AMR gene carriage. Seventeen different NAS species were identified across all farm types. In contrast to conventional farms, no AMR genes were detectable towards methicillin, aminoglycosides, and phenicols in organic farms. Additionally, AMR genes to macrolides and tetracycline were rare among NAS in organic farms, while such genes were common in conventional husbandries. No differences in AMR detection existed between farm types regarding fosfomycin, lincosamides, fusidic acid, and heavy metal resistance gene presence. The combined data show that husbandry conditions influence the occurrence of resistant and multidrug-resistant bacteria in livestock, suggesting that changing husbandry practices may be an appropriate means of limiting the spread of AMR bacteria on farms.
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Affiliation(s)
| | - Gabriella Marincola
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Olivia Liong
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Tessa Marciniak
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Freya D. R. Wencker
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Franka Hofmann
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Hannah Schollenbruch
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Iris Kobusch
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Sabrina Linnemann
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Silver A. Wolf
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Mustafa Helal
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, 13353 Berlin, Germany
| | - Christoph Schoen
- Institute of Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
| | - Justin Nyasinga
- Department of Pathology, Aga-Khan-University Hospital Nairobi, Nairobi, Kenya
- Department of Biomedical Sciences and Technology, The Technical University of Kenya, Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Aga-Khan-University Hospital Nairobi, Nairobi, Kenya
| | - Marc Boelhauve
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Correspondence: ; Tel.: +49-(0)931-31-2578
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24
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Zhang L, Ju Z, Su Z, Fu Y, Zhao B, Song Y, Wen D, Zhao Y, Cui J. The antibiotic resistance and risk heterogeneity between urban and rural rivers in a pharmaceutical industry dominated city in China: The importance of social-economic factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158530. [PMID: 36063953 DOI: 10.1016/j.scitotenv.2022.158530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Rivers are important environmental sources of human exposure to antibiotic resistance. Many factors can change antibiotic resistance in rivers, including bacterial communities, human activities, and environmental factors. However, the systematic comparison of the differences in antibiotics resistance and risks between urban rivers (URs) and rural rivers (RRs) in a pharmaceutical industry dominated city is still rare. In this study, Shijiazhuang City (China) was selected as an example to compare the differences in antibiotics resistance and risks between URs and RRs. The results showed higher concentrations of total quinolones (QNs) antibiotics in both water and sediment samples collected from URs than those from RRs. The subtypes and abundances of antibiotic resistance genes (ARGs) in URs were significantly higher than those in RRs, and most emerging ARGs (including OXA-type, GES-type, MCR-type, and tet(X)) were only detected in URs. The ARGs were mainly influenced by QNs in URs and social-economic factors (SEs) in RRs. The composition of the bacterial community was significantly different between URs and RRs. The abundance of antibiotic-resistant pathogenic bacteria (ARPBs) and virulence factors (VFs) were higher in URs than those in RRs. Therein, 371 and 326 pathogen types were detected in URs and RRs, respectively. Most emerging ARGs showed a significantly positive correlation with priority ARPBs. Variance partitioning analysis revealed that SEs were the main driving factors of ARGs (80 %) and microbial communities (92 %) both in URs and RRs. Structural equation models indicated that antibiotics (QNs) and microbial communities were the most direct influence of ARGs in URs and RRs, respectively. The cumulative resistance risk of QNs was high in URs, but relatively low in RRs. Enrofloxacin and flumequine posed the highest risk in water and sediment, respectively. This study could help us to better manage and control the risk of antibiotic resistance in different rivers.
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Affiliation(s)
- Lulu Zhang
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China; College of Environmental Science and Engineering, Peking University, 100871 Beijing, China.
| | - Zejia Ju
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
| | - Zhiguo Su
- College of Environmental Science and Engineering, Peking University, 100871 Beijing, China
| | - Yu Fu
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
| | - Bo Zhao
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
| | - Yuanmeng Song
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
| | - Donghui Wen
- College of Environmental Science and Engineering, Peking University, 100871 Beijing, China
| | - Yu Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
| | - Jiansheng Cui
- College of Environment Science and Engineering, Hebei University of Science and Technology, 050000 Shijiazhuang, Hebei Province, China
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Pillay S, Calderón-Franco D, Urhan A, Abeel T. Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings. Front Microbiol 2022; 13:1066995. [PMID: 36532424 PMCID: PMC9755710 DOI: 10.3389/fmicb.2022.1066995] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 08/12/2023] Open
Abstract
The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.
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Affiliation(s)
- Stephanie Pillay
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
| | | | - Aysun Urhan
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
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Lin D, Huang D, Zhang J, Yao Y, Zhang G, Ju F, Xu B, Wang M. Reduction of antibiotic resistance genes (ARGs) in swine manure-fertilized soil via fermentation broth from fruit and vegetable waste. ENVIRONMENTAL RESEARCH 2022; 214:113835. [PMID: 35810807 DOI: 10.1016/j.envres.2022.113835] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The issue of growing increase of antibiotic resistance genes (ARGs) in manure-fertilized soil needs urgently addressing. In this study, fermentation broth from fruit and vegetable waste was prepared to reduce ARG abundance in swine manure-fertilized soils. With a six-month field experiment, we found that swine manure-fertilized soil had significantly higher ARG abundance than soil applied with chemical fertilizer. As expected, the homemade fermentation broth significantly reduced ARG abundance in swine manure-fertilized soil, possibly through the decrease of abundance of Actinomyces, in which there was a 48.0%, 51.9%, and 66.7% decrease in the abundance of Nocardioides, Streptomyces, and Nonomuraea, respectively. With the bacteriostatic experiment, we observed that fermentation broth (5 mL/L) significantly inhibited the growth and metabolism in Actinomycetes spp. and Nocardioides sp., in terms of ATPase and PDH activity. These findings confirmed that the inhibition of Actinobacteria, some of the most dominant ARG hosts, was one of the main mechanisms responsible for the decrease in ARG abundance in fermentation broth-treated soil. This study provides field-scale evidence of a feasible strategy for controlling farmland ARG pollution, which is of utmost importance for soil health in the context of sustainable agriculture.
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Affiliation(s)
- Da Lin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Dan Huang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Jinghan Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Yanlai Yao
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Guoqing Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024, China
| | - Baile Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China.
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Zhang RM, Liao MN, Wu JE, Lu XQ, Tan HZ, Sun J, Liao XP, Liu YH. Metagenomic insights into the influence of mobile genetic elements on ARGs along typical wastewater treatment system on pig farms in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156313. [PMID: 35654190 DOI: 10.1016/j.scitotenv.2022.156313] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The wastewater treatment processes (WTP) on pig farms are heavily contaminated by antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) play an important role in shaping ARG profiles. Here we first employed metagenomic sequencing to follow the diversities and shifts of ARG associated mobile genetic elements (AAMGEs) including insertion sequences (ISs) and plasmids along the WTP for three pig farms in southeast China. The IS average relative abundance rose from the initial pig feces source to the wastewater storage lagoon (WSL) but decreased in the influent and rose in the effluent of the anaerobic digestor (AD). In contrast, plasmids were eliminated rapidly along this process. These results indicated that the AD reduced plasmid copies while IS abundance increased. We found a great diversity ISs, including IS91, ISNCY, IS630 and IS701, were large contributors to the transfer of multi-drug resistance. In addition, the tetracycline resistance genes co-occurred with a greater diversity of ISs than other ARG classes and this likely contributed to the high abundance of tetracycline resistance genes we found. The transfer of ARGs mediated by MGEs along the WTP of pig farms was a key contributor for the ARGs persistence in the environment of pig farms. Collectively, our findings demonstrated different fates for ISs and plasmids along the WTP for pig farms and suggested that AAMGE monitoring served as an important role in controlling ARGs in pig waste.
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Affiliation(s)
- Rong-Min Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Mei-Na Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Jia-En Wu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Qing Lu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Hui-Zhen Tan
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China.
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China; Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China.
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Wu R, Cao Z, Jiang Y, Chen W, Sun Y, Li Q, Mi J, Deng L, Liao X, Feng Y, Lan T, Ma J. Early life dynamics of ARG and MGE associated with intestinal virome in neonatal piglets. Vet Microbiol 2022; 274:109575. [PMID: 36191572 DOI: 10.1016/j.vetmic.2022.109575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 10/31/2022]
Abstract
The pre- and post-weaning stages for piglets are critical periods for the maturation of intestinal functions and contamination with antibiotic resistant bacterial pathogens will threaten their intestinal health. The presence of bacteriophage can also alter bacterial populations in the intestine but whether transmission of antibiotic resistance genes (ARG) is affected by phage during maturation of the neonatal piglet intestine is not known. We therefore identified the intestinal virome along with ARGs and mobile genetic elements (MGE) from piglet fecal samples collected from 3 to 28 days representing the different growth stages. We found wide fluctuations for the intestinal virome of weaning piglets and most virus - related antibiotic resistance was derived from temperate phage suggesting a reservoir of multidrug resistance was present in the neonatal porcine gut. Our results provide a comprehensive understanding of ARGs associated with the intestinal virome that therefore represents a potential risk for horizontal ARG transfer to pathogenic bacteria.
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Affiliation(s)
- Ruiting Wu
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Ze Cao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Yiming Jiang
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Virology, Technical University of Munich, Munich, Germany
| | - Wei Chen
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Yuan Sun
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Qianniu Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Jiandui Mi
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Virology, Technical University of Munich, Munich, Germany
| | - Xindi Liao
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, China
| | - Tian Lan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China
| | - Jingyun Ma
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China.
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Emergence and spread of antibiotic-resistant foodborne pathogens from farm to table. Food Sci Biotechnol 2022; 31:1481-1499. [PMID: 36065433 PMCID: PMC9435411 DOI: 10.1007/s10068-022-01157-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/26/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotics have been overused and misused for preventive and therapeutic purposes. Specifically, antibiotics are frequently used as growth promoters for improving productivity and performance of food-producing animals such as pigs, cattle, and poultry. The increasing use of antibiotics has been of great concern worldwide due to the emergence of antibiotic resistant bacteria. Food-producing animals are considered reservoirs for antibiotic resistance genes (ARGs) and residual antibiotics that transfer from the farm through the table. The accumulation of residual antibiotics can lead to additional antibiotic resistance in bacteria. Therefore, this review evaluates the risk of carriage and spread of antibiotic resistance through food chain and the potential impact of antibiotic use in food-producing animals on food safety. This review also includes in-depth discussion of promising antibiotic alternatives such as vaccines, immune modulators, phytochemicals, antimicrobial peptides, probiotics, and bacteriophages.
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A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms. Biomolecules 2022; 12:biom12081132. [PMID: 36009027 PMCID: PMC9406075 DOI: 10.3390/biom12081132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022] Open
Abstract
The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.
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Gaire TN, Odland C, Zhang B, Ray T, Doster E, Nerem J, Dee S, Davies P, Noyes N. The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs. MICROBIOME 2022; 10:118. [PMID: 35922873 PMCID: PMC9351240 DOI: 10.1186/s40168-022-01312-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups. RESULTS Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials. CONCLUSIONS The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.
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Affiliation(s)
- Tara N Gaire
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Carissa Odland
- Pipestone Veterinary Services, Pipestone, Minnesota, USA
| | - Bingzhou Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tui Ray
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Enrique Doster
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Joel Nerem
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Scott Dee
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Peter Davies
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Noelle Noyes
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.
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Qi Z, Le Z, Han F, Qi Y, Liu R. β-lactamase genes transmission influenced by tetracycline, sulfonamide and β-lactams antibiotics contamination in the on-site farm soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113753. [PMID: 35687999 DOI: 10.1016/j.ecoenv.2022.113753] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/04/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs), which have been identified as emerging environmental pollutants that pose a considerable risk to human health is widespread. The formation and transmission of ARGs are mainly associated with the antibiotic stress in an environment. And the abundance of ARGs also influenced by other categories antibiotics. The geographic information system was used to visualize the relative abundance of 28 types of ARGs and concentration of 18 types of antibiotics. The concentration of tetracycline antibiotics (TCs) and sulfonamide antibiotics (SAs) decreased gradually with increasing soil depth, while that of β-lactams (β-Ls) showed an increasing trend. The results revealed that TCs accounted for the largest proportion of all antibiotics. Furthermore, the abundance of β-lactam ARGs (β-RGs) increased with TCs and β-Ls increased. The abundance of tetracycline ARGs (TRGs) remained relatively stable with increasing concentrations of all antibiotics, while that of sulfonamide ARGs (SRGs) showed a decreasing trend. Although the abundance of β-RGs significantly increased with increasing levels of TCs and β-Ls. However, β-RGs were not significantly correlated with β-Ls, but with TCs. This study provided visual and comprehensive insights into the correlation between the distribution of typical antibiotics and ARGs and analyzed the synergy or antagonism between different antibiotics and ARGs. It is significant for soil remediation to reduce the likelihood of ARGs entering into and spreading in the human food chain via milk and beef consumption.
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Affiliation(s)
- Zheng Qi
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, 138 Tongda Street, Daoli District, Harbin 150076, China.
| | - Zhiwei Le
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, 138 Tongda Street, Daoli District, Harbin 150076, China
| | - Furui Han
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, 138 Tongda Street, Daoli District, Harbin 150076, China
| | - Yue Qi
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, 138 Tongda Street, Daoli District, Harbin 150076, China
| | - Rijia Liu
- Engineering Research Center for Medicine, Ministry of Education, Harbin University of Commerce, 138 Tongda Street, Daoli District, Harbin 150076, China.
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Antibiotic resistance genes and bacterial community distribution patterns in pig farms. Folia Microbiol (Praha) 2022; 67:913-921. [PMID: 35781864 DOI: 10.1007/s12223-022-00988-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/24/2022] [Indexed: 11/04/2022]
Abstract
Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, many studies have been carried out to investigate the role of gut microbiota as a pool of antibiotic resistance genes (ARGs) in human and animals. Both the structure and function of the gut bacterial community and related ARGs in pig remain unknown. In this study, we characterized the gut microbiomes and resistomes of fecal samples collected from sixteen pig farms located in sixteen cities of Shandong Province by metagenomic sequencing. Alpha diversity indicated that fecal samples from Dezhou (DZ) and Jinan (J) showed higher alpha diversity, and the lowest was from pig farms of Rizhao (RZ). Other pig farms showed similar alpha diversity. Besides, we found that the composition of gut bacterial among these pig farms varied greatly. Helcococcus massiliensis was the dominant bacterial species in pig farms of RZ and Zibo (ZB), while Prevotella sp. P5-92 occupied a superior proportion in Binzhou (BZ) and Yantai (YT). The proportion of Lactobacillus johnsonii was similar among farms of Qingdao (QD), Linyi (LY), Taian (TA), Weifang (WF), Weihai (WH), and YT. In total, 1112 ARGs were obtained and classified into 69 groups from 48 fecal samples. ARG abundance was higher in farms of Dongying (DY) and WH than others, while the lowest farms in BZ and ZB. Interestingly, it is found that BZ pig farm was exclusive, so the tetQ gene showed a higher abundance. In contrast, the load of APH(3') - IIIa in fecal samples from DY, J-1, LC, WF, and WH was high. Meanwhile, the most relevant ARGs and the corresponding microbes were screened out. Our metagenomic sequencing data provides new insights into the abundance, diversity, and structure of bacterial community in pig farms. Meanwhile, we screened ARG-carrying bacteria and explored the correlation between ARGs and bacterial community, which provide a comprehensive view of the pig fecial ARGs and microbes in different farms of Shandong.
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Li L, Xiao Y, Olsen RH, Wang C, Meng H, Shi L. Short- and long-read metagenomics insight into the genetic contexts and hosts of mobile antibiotic resistome in Chinese swine farms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154352. [PMID: 35259381 DOI: 10.1016/j.scitotenv.2022.154352] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Intensive swine farms are recognized as hotspots for antibiotic resistance genes (ARGs). However, antibiotic resistome and their genetic contexts, hosts, and transferability in Chinese swine farms remain largely unexplored. Here, we used Illumina and Oxford Nanopore metagenomics sequencing to investigate the antibiotic resistome context of 14 distantly located large-scale (10,000 animals per year) commercial swine farms in China. We identified high abundant and diverse ARGs (609,966.8 with 1433 types, belonging to 38 different antibiotic classes) in all samples, including those encoding resistance to clinically critical important antibiotics (such as mcr, tetX, optrA, poxtA, qnr and blaCTX-M). About 75% of the ARGs detected were carried by mobile genetic elements (mainly plasmids), suggesting their high transmission potential into receiving environments. Host-tracking analysis identified Clostridiales, Faecalibacterium prausnitzii and Escherichia coli as the predominant bacterial hosts of mobile ARGs. Notably, genome binning generated 246 high-completeness draft genomes. Genetic context analysis of the multiple resistant (MDR) genes in binned genomes showed the involvement of insertion sequences (ISs), integron and SGI2 genomic island, implying their importance role in promoting the development of MDR bacteria. Overall, these findings substantially expand our current knowledge of mobile antibiotic resistome in Chinese swine farms, and suggest reasonable management of animal wastes in swine farms to reduce the dissemination of antibiotic resistance to the environment.
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Affiliation(s)
- Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China; School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Yawen Xiao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Chong Wang
- Shandong New Hope Liuhe Group Ltd., Qingdao, China
| | - Hecheng Meng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China.
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China
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Apiwatsiri P, Pupa P, Sirichokchatchawan W, Sawaswong V, Nimsamer P, Payungporn S, Hampson DJ, Prapasarakul N. Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses. PLoS One 2022; 17:e0269959. [PMID: 35749527 PMCID: PMC9231746 DOI: 10.1371/journal.pone.0269959] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/01/2022] [Indexed: 01/12/2023] Open
Abstract
This study used metagenomic analysis to investigate the gut microbiota and resistome in piglets that were or were not challenged with enterotoxigenic Escherichia coli (ETEC) and had or had not received dietary supplementation with microencapsulated probiotics. The 72 piglets belonged to six groups that were either non-ETEC challenged (groups 1–3) or ETEC challenged (receiving 5ml of 109 CFU/ml pathogenic ETEC strain L3.2 one week following weaning at three weeks of age: groups 4–6). On five occasions at 2, 5, 8, 11, and 14 days of piglet age, groups 2 and 5 were supplemented with 109 CFU/ml of multi-strain probiotics (Lactiplantibacillus plantarum strains 22F and 25F, and Pediococcus acidilactici 72N) while group 4 received 109 CFU/ml of P. acidilactici 72N. Group 3 received 300mg/kg chlortetracycline in the weaner diet to mimic commercial conditions. Rectal faecal samples were obtained for metagenomic and resistome analysis at 2 days of age, and at 12 hours and 14 days after the timing of post-weaning challenge with ETEC. The piglets were all euthanized at 42 days of age. The piglets in groups 2 and 5 were enriched with several desirable microbial families, including Lactobacillaceae, Lachnospiraceae and Ruminococcaceae, while piglets in group 3 had increases in members of the Bacteroidaceae family and exhibited an increase in tetW and tetQ genes. Group 5 had less copper and multi-biocide resistance. Mobile genetic elements IncQ1 and IncX4 were the most prevalent replicons in antibiotic-fed piglets. Only groups 6 and 3 had the integrase gene (intl) class 2 and 3 detected, respectively. The insertion sequence (IS) 1380 was prevalent in group 3. IS3 and IS30, which are connected to dietary intake, were overrepresented in group 5. Furthermore, only group 5 showed genes associated with detoxification, with enrichment of genes associated with oxidative stress, glucose metabolism, and amino acid metabolism compared to the other groups. Overall, metagenomic analysis showed that employing a multi-strain probiotic could transform the gut microbiota, reduce the resistome, and boost genes associated with food metabolism.
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Affiliation(s)
- Prasert Apiwatsiri
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Pawiya Pupa
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pattaraporn Nimsamer
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - David J. Hampson
- School of Veterinary Medicine, Murdoch University, Perth, Western Australia, Australia
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Diagnosis and Monitoring of Animal Pathogens, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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Dey S, Rout AK, Behera BK, Ghosh K. Plastisphere community assemblage of aquatic environment: plastic-microbe interaction, role in degradation and characterization technologies. ENVIRONMENTAL MICROBIOME 2022; 17:32. [PMID: 35739580 PMCID: PMC9230103 DOI: 10.1186/s40793-022-00430-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/14/2022] [Indexed: 05/03/2023]
Abstract
It is undeniable that plastics are ubiquitous and a threat to global ecosystems. Plastic waste is transformed into microplastics (MPs) through physical and chemical disruption processes within the aquatic environment. MPs are detected in almost every environment due to their worldwide transportability through ocean currents or wind, which allows them to reach even the most remote regions of our planet. MPs colonized by biofilm-forming microbial communities are known as the ''plastisphere". The revelation that this unique substrate can aid microbial dispersal has piqued interest in the ground of microbial ecology. MPs have synergetic effects on the development, transportation, persistence, and ecology of microorganisms. This review summarizes the studies of plastisphere in recent years and the microbial community assemblage (viz. autotrophs, heterotrophs, predators, and pathogens). We also discussed plastic-microbe interactions and the potential sources of plastic degrading microorganisms. Finally, it also focuses on current technologies used to characterize those microbial inhabitants and recommendations for further research.
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Affiliation(s)
- Sujata Dey
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, West Bengal, 700120, India.
| | - Koushik Ghosh
- Aquaculture Laboratory, Department of Zoology, The University of Burdwan, Golapbag, Burdwan, West Bengal, 713104, India.
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Dias D, Fonseca C, Caetano T, Mendo S. Oh, deer! How worried should we be about the diversity and abundance of the faecal resistome of red deer? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153831. [PMID: 35151727 DOI: 10.1016/j.scitotenv.2022.153831] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The emergence of antimicrobial resistance (AMR) is a global threat to public health. Antimicrobials are used in animal production and human medicine, which contribute to the circulation of antibiotic resistance genes (ARGs) in the environment. Wildlife can be reservoirs of pathogens and resistant bacteria. Furthermore, anthropogenic pressure can influence their resistome. This work aimed to study the AMR of the faecal microbiome of red deer, one of the most important game species in Europe. To this end, a high-throughput qPCR approach was employed to screen a high number of ARGs and the antimicrobial susceptibility of indicator bacteria was determined. Several genes that confer resistance to different classes of antibiotics were identified, with the most abundant being tetracycline ARGs. Other genes were also present that are considered current and future threats to human health, and some of these were relatively abundant. Multidrug-resistant E. coli and Enterococcus spp. were isolated, although the overall level of antibiotic resistance was low. These results highlight the pressing need to know the origin and transmission of AMR in wildlife. Thus, and considering the One Health concept, studies such as this one shows the need for surveillance programs to prevent the spread of drug-resistant strains and ARGs.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Carlos Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
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Zhen Y, Ge L, Chen Q, Xu J, Duan Z, Loor JJ, Wang M. Latent Benefits and Toxicity Risks Transmission Chain of High Dietary Copper along the Livestock-Environment-Plant-Human Health Axis and Microbial Homeostasis: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6943-6962. [PMID: 35666880 DOI: 10.1021/acs.jafc.2c01367] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The extensive use of high-concentration copper (Cu) in feed additives, fertilizers, pesticides, and nanoparticles (NPs) inevitably causes significant pollution in the ecological environment. This type of chain pollution begins with animal husbandry: first, Cu accumulation in animals poisons them; second, high Cu enters the soil and water sources with the feces and urine to cause toxicity, which may further lead to crop and plant pollution; third, this process ultimately endangers human health through consumption of livestock products, aquatic foods, plants, and even drinking water. High Cu potentially alters the antibiotic resistance of soil and water sources and further aggravates human disease risks. Thus, it is necessary to formulate reasonable Cu emission regulations because the benefits of Cu for livestock and plants cannot be ignored. The present review evaluates the potential hazards and benefits of high Cu in livestock, the environment, the plant industry, and human health. We also discuss aspects related to bacterial and fungal resistance and homeostasis and perspectives on the application of Cu-NPs and microbial high-Cu removal technology to reduce the spread of toxicity risks to humans.
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Affiliation(s)
- Yongkang Zhen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang 832000, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qiaoqing Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jun Xu
- Institute for Quality and Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330000, China
| | - Zhenyu Duan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang 832000, China
| | - Juan J Loor
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang 832000, China
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Gaire TN, Noyes NR, Scott HM, Ericsson AC, Dunmire K, Tokach MD, Paulk CB, Vinasco J, Roenne B, Nagaraja TG, Volkova VV. A Longitudinal Investigation of the Effects of Age, Dietary Fiber Type and Level and Injectable Antimicrobials on the Fecal Microbiome and Antimicrobial Resistance of Finisher Pigs. J Anim Sci 2022; 100:6608493. [PMID: 35700748 DOI: 10.1093/jas/skac217] [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: 02/24/2022] [Accepted: 06/13/2022] [Indexed: 11/12/2022] Open
Abstract
Age and diet are among the factors that influence the community composition of the fecal microbiome. Additionally, antimicrobial use can alter the composition of bacterial communities. An 86-d study with finisher pigs aimed to evaluate age-related dynamics (d 98-177 of age), effects of types and levels of dietary fiber, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance (AMR) was conducted. A total of 287 pigs, housed in 36 pens, with 7 to 8 pigs per pen, fed a corn grain and soybean meal-based basal diet, formulated to contain 8.7% neutral detergent fiber (NDF), were randomly assigned to one of three treatments: 1. basal diet with no supplement, 2. basal diet supplemented with 20% distillers dried grains with solubles (DDGS) formulated to contain 13.6% NDF, or 3. basal diet supplemented with 14.5% sugar beet pulp (SBP) formulated to contain 13.6% NDF. Five finisher pigs from each treatment group were selected randomly, and fecal samples were collected on d 98, 110, 144, and 177 of age. In addition, fecal samples were collected from pigs that were injected intramuscularly ceftiofur hydrochloride or penicillin G on d 1 and 3 along with pen-mate untreated controls on d 1. Fecal samples were subjected to 16S rRNA amplicon-based microbiome analysis and culture methods to quantify the abundance of total and AMR coliforms and enterococci populations. The alpha diversity, such as species richness, increased with age, and the overall bacterial composition changed with age (P =0.001) and diet (P = 0.001). Diet-associated shifts in the specific bacterial taxa were observed. The richness, diversity, and evenness of bacterial taxa did not differ between pigs that were injected with ceftiofur versus their untreated pen mates or by dietary treatments, but differed in pigs that received penicillin G injection. Both antimicrobial treatments contributed to changes in the overall fecal bacterial composition at the genus level. Collectively, the data demonstrate that both age and the diet (control vs. DDGS-, control vs. SBP- or DDGS- vs. SBP-based diets) were associated with overall bacterial community composition and the impact of age on variations in fecal microbiome composition was greater than the diet. Antibiotic treatment had minimal effect on bacterial diversity and relative abundance of taxa. Further, diets and antimicrobial treatment had minimal impact on the overall counts of AMR coliforms and enterococci populations in feces.
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Affiliation(s)
- Tara N Gaire
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - H Morgan Scott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Aaron C Ericsson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, MO, USA
| | - Kara Dunmire
- Department of Grain Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, USA
| | - Michael D Tokach
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, USA
| | - Chad B Paulk
- Department of Grain Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, USA
| | - Javier Vinasco
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Boyd Roenne
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - T G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Victoriya V Volkova
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
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Recovery of the Structure and Function of the Pig Manure Bacterial Community after Enrofloxacin Exposure. Microbiol Spectr 2022; 10:e0200421. [PMID: 35604139 PMCID: PMC9241743 DOI: 10.1128/spectrum.02004-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A stable intestinal bacterial community balance is beneficial for animal health. Enrofloxacin is widely used in animal husbandry as a therapeutic drug, but it can cause intestinal environmental imbalance.
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Røken M, Forfang K, Wasteson Y, Haaland AH, Eiken HG, Hagen SB, Bjelland AM. Antimicrobial resistance- Do we share more than companionship with our dogs? J Appl Microbiol 2022; 133:1027-1039. [PMID: 35596927 PMCID: PMC9542740 DOI: 10.1111/jam.15629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/26/2022]
Abstract
Aims To investigate and compare antimicrobial resistance genes (ARGs) in faeces from cohabiting dogs and owners. Methods and Results DNA from faecal samples from 35 dogs and 35 owners was screened for the presence of 34 clinically relevant ARGs using high throughput qPCR. In total, 24 and 25 different ARGs were present in the dog and owner groups, respectively. The households had a mean of 9.9 ARGs present, with dogs and owners sharing on average 3.3 ARGs. ARGs were shared significantly more in households with dogs over 6 years old (3.5, interquartile range 2.75–5.0) than in households with younger dogs (2.5, interquartile range 2.0–3.0) (p = 0.02). Dogs possessed significantly more mecA and aminoglycoside resistance genes than owners. Conclusions Dogs and owners can act as reservoirs for a broad range of ARGs belonging to several antimicrobial resistance classes. A modest proportion of the same resistance genes were present in both dogs and owners simultaneously, indicating that ARG transmission between the dog and human gut is of minor concern in the absence of antimicrobial selection. Significance and Impact of the Study This study provides insight into the common dog and human gut resistomes, contributing to an improved knowledge base in risk assessments regarding ARG transmission between dogs and humans.
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Affiliation(s)
- Mari Røken
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine Department of Paraclinical Sciences, Ås, Norway
| | - Kristin Forfang
- Norwegian Institute of Bioeconomy Research, Division of Environment and Natural Resources, Ås, Norway
| | - Yngvild Wasteson
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine Department of Paraclinical Sciences, Ås, Norway
| | - Anita Haug Haaland
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine Department of Companion Animal Clinical Sciences, Ås, Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research, Division of Environment and Natural Resources, Ås, Norway
| | - Snorre B Hagen
- Norwegian Institute of Bioeconomy Research, Division of Environment and Natural Resources, Ås, Norway
| | - Ane Mohn Bjelland
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine Department of Paraclinical Sciences, Ås, Norway
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Guo Z, Lv L, Liu D, He X, Wang W, Feng Y, Islam MS, Wang Q, Chen W, Liu Z, Wu S, Abied A. A global meta-analysis of animal manure application and soil microbial ecology based on random control treatments. PLoS One 2022; 17:e0262139. [PMID: 35061792 PMCID: PMC8782357 DOI: 10.1371/journal.pone.0262139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: -1.15 and M-I: -1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.
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Affiliation(s)
- Zhenhua Guo
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- * E-mail: , (ZG); (DL)
| | - Lei Lv
- Wood Science Research Institute of Heilongjiang Academy of Forestry, Harbin, P. R. China
| | - Di Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- * E-mail: , (ZG); (DL)
| | - Xinmiao He
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Wentao Wang
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Yanzhong Feng
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Md. Saiful Islam
- Department of Animal Production & Management, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, Bangladesh
| | - Qiuju Wang
- Key laboratory of Heilongjiang Soil Environment and Plant Nutrient, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, P. R. China
| | - Wengui Chen
- Animal Science and Technology College, Northeast Agricultural University, Harbin, P. R. China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Saihui Wu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Adam Abied
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Khartoum, Sudan
- Projects and Programs Secretary of the Sudan Youth Organization on Climate Change, Khartoum, Sudan
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Zheng F, An XL, Zhou GW, Zhu D, Neilson R, Chen B, Yang XR. Mite gut microbiome and resistome exhibited species-specific and dose-dependent effect in response to oxytetracycline exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150802. [PMID: 34626628 DOI: 10.1016/j.scitotenv.2021.150802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The importance of the gut microbiome to host health is well recognized, but the effects of environmental pressures on the gut microbiome of soil fauna are poorly understood. Here, Illumina sequencing and high-throughput qPCR were applied to characterize the gut microbiomes and resistomes of two mites, Nenteria moseri and Chiropturopoda sp. AL5866, exposed to different concentrations of oxytetracycline (0, 0.01, 0.1 and 1 μg mg-1). Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant phyla in the gut microbiomes of both studied mite species, but the relative abundance of them was different between mites. After exposure to oxytetracycline, there was no variation in the gut microbiome and resistome of C. sp. AL5866, whereas the gut microbiome and resistome of N. moseri were altered significantly. The relative abundance of Proteobacteria significantly decreased, and those of Bacteroidetes and Firmicutes significantly increased at the high-concentration antibiotic treatments. Excepting the 0.01 μg mg-1 treatment, gut microbial diversity increased with ascending concentrations. A significant resistome enrichment of relative abundance in N. moseri gut microbiome at low-dose antibiotic treatment was noted. These results indicated that the gut microbiome in N. moseri was potentially more sensitive to antibiotics than C. sp. AL5866, which was supported by the greater relative abundance of key tetracycline-resistant genes in the gut microbiome of C. sp. AL5866 compared to N. moseri. Mite gut microbiomes were correlated with their associated resistomes, demonstrating the consistent changes between microbiome and resistome. Thus, this study showed that oxytetracycline amendment resulted in a dose-dependent and species-specific effect on the gut microbiomes and resistomes of two mite species. It will contribute to understanding the relationship between the soil mite gut microbiome and resistome under antibiotic exposure, and extend our knowledge regarding the emergence and transfer of resistomes in soil food webs.
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Affiliation(s)
- Fei Zheng
- School of Life Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guo-Wei Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Dong Zhu
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, DD2 5DA, Scotland, UK
| | - Bing Chen
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Dias D, Fonseca C, Mendo S, Caetano T. A closer look on the variety and abundance of the faecal resistome of wild boar. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118406. [PMID: 34710519 DOI: 10.1016/j.envpol.2021.118406] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/19/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance (AMR) is a serious problem for public and animal health, and also for the environment. Monitoring and reporting the occurrence of AMR determinants and bacteria with the potential to disseminate is a priority for health surveillance programs around the world and critical to the One Health concept. Wildlife is a reservoir of AMR, and human activities can strongly influence their resistome. The main goal of this work was to study the resistome of wild boar faecal microbiome, one of the most important game species in Europe using metagenomic and culturing approaches. The most abundant genes identified by the high-throughput qPCR array encode mobile genetic elements, including integrons, which can promote the dissemination of AMR determinants. A diverse set of genes (n = 62) conferring resistance to several classes of antibiotics (ARGs), some of them included in the WHO list of critically important antimicrobials were also detected. The most abundant ARGs confer resistance to tetracyclines and aminoglycosides. The phenotypic resistance of E. coli and Enterococcus spp. were also investigated, and together supported the metagenomic results. As the wild boar is an omnivorous animal, it can be a disseminator of AMR bacteria and ARGs to livestock, humans, and the environment. This study supports that wild boar can be a key sentinel species in ecosystems surveillance and should be included in National Action Plans to fight AMR, adopting a One Health approach.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Carlos Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801, Vila Real, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
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Wang H, Su X, Su J, Zhu Y, Ding K. Profiling the antibiotic resistome in soils between pristine and human-affected sites on the Tibetan Plateau. J Environ Sci (China) 2022; 111:442-451. [PMID: 34949372 DOI: 10.1016/j.jes.2021.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 06/14/2023]
Abstract
With increasing pressure from anthropogenic activity in pristine environments, the comprehensive profiling of antibiotic resistance genes (ARGs) is essential to evaluate the potential risks from human-induced antibiotic resistance in these under-studied places. Here, we characterized the microbial resistome in relatively pristine soil samples collected from four distinct habitats on the Tibetan Plateau, using a Smart chip based high-throughput qPCR approach. We compared these to soils from the same habitats that had been subjected to various anthropogenic activities, including residential sewage discharge, animal farming, atmospheric deposition, and tourism activity. Compared to pristine samples, an average of 23.7% more ARGs were detected in the human-affected soils, and the ARGs enriched in these soils mainly encoded resistances to aminoglycoside and beta-lactam. Of the four habitats studied, soils subjected to animal farming showed the highest risks of ARG enrichment and dissemination. As shown, the number of ARGs enriched (a total of 42), their fold changes (17.6 fold on average), and the co-occurrence complexity between ARGs and mobile genetic elements were all the highest in fecal-polluted soils. As well as antibiotics themselves, heavy metals also influenced ARG distributional patterns in Tibetan environments. However, compared to urban areas, the Tibetan Plateau had a low potential for ARG selection and exhibited low carriage of ARGs by mobile genetic elements, even in environments impacted by humans, suggesting that these ARGs have a limited capacity to disseminate. The present study examined the effects of multiple anthropogenic activities on the soil resistomes in relatively pristine environments.
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Affiliation(s)
- Hang Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Yunnan Key Laboratory of Plateau Wetland Conservation, Restoration and Ecological Services, Southwest Forestry University, Kunming 650224, China; National Plateau Wetlands Research Center, Southwest Forestry University, Kunming 650224, China
| | - Xiaoxuan Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yongguan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kai Ding
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Black Z, Balta I, Black L, Naughton PJ, Dooley JSG, Corcionivoschi N. The Fate of Foodborne Pathogens in Manure Treated Soil. Front Microbiol 2021; 12:781357. [PMID: 34956145 PMCID: PMC8702830 DOI: 10.3389/fmicb.2021.781357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022] Open
Abstract
The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice in agricultural systems based on high levels of manure production. It is important to consider soil health in relation to environment and land management practices in the context of the soil microflora and the introduction of pathogens on the health of the soil microbiome. Viable pathogens in manure spread on agricultural land may be distributed by leaching, surface run-off, water source contamination and contaminated crop removal. Thus it is important to understand how multiple pathogens can persist in manures and on soil at farm-scale and how crops produced under these conditions could be a potential transfer route for zoonotic pathogens. The management of pathogen load within livestock manure is a potential mechanism for the reduction and prevention of outbreaks infection with Escherichia coli, Listeria Salmonella, and Campylobacter. The ability of Campylobacter, E. coli, Listeria and Salmonella to combat environmental stress coupled with their survival on food crops and vegetables post-harvest emphasizes the need for further study of these pathogens along with the emerging pathogen Providencia given its link to disease in the immunocompromised and its’ high levels of antibiotic resistance. The management of pathogen load within livestock manure has been widely recognized as a potential mechanism for the reduction and prevention of outbreaks infection but any studies undertaken should be considered as region specific due to the variable nature of the factors influencing pathogen content and survival in manures and soil. Mediocre soils that require nutrients could be one template for research on manure inputs and their influence on soil health and on pathogen survival on grassland and in food crops.
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Affiliation(s)
- Zoe Black
- Grassland and Plant Sciences Branch, AFBI Crossnacreevy, Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - Igori Balta
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Faculty of Bioengineering of Animal Resources, Banat University of Animal Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
| | - Lisa Black
- Grassland and Plant Sciences Branch, AFBI Crossnacreevy, Sustainable Agri-Food Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Patrick J Naughton
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - James S G Dooley
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, United Kingdom
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom.,Faculty of Bioengineering of Animal Resources, Banat University of Animal Sciences and Veterinary Medicine, King Michael I of Romania, Timisoara, Romania
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Valiakos G, Kapna I. Colistin Resistant mcr Genes Prevalence in Livestock Animals (Swine, Bovine, Poultry) from a Multinational Perspective. A Systematic Review. Vet Sci 2021; 8:265. [PMID: 34822638 PMCID: PMC8619609 DOI: 10.3390/vetsci8110265] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 12/23/2022] Open
Abstract
The objective of this review is to collect and present the results of relevant studies on an international level, on the subject of colistin resistance due to mcr genes prevalence in livestock animals. After a literature search, and using PRISMA guidelines principles, a total of 40 swine, 16 bovine and 31 poultry studies were collected concerning mcr-1 gene; five swine, three bovine and three poultry studies referred to mcr-2 gene; eight swine, one bovine, two poultry studies were about mcr-3 gene; six swine, one bovine and one poultry manuscript studied mcr-4 gene; five swine manuscripts studied mcr-5 gene; one swine manuscript was about mcr-6, mcr-7, mcr-8, mcr-9 genes and one poultry study about mcr-10 gene was found. Information about colistin resistance in bacteria derived from animals and animal product foods is still considered limited and that should be continually enhanced; most of the information about clinical isolates are relative to enteropathogens Escherichia coli and Salmonella spp. This review demonstrates the widespread dispersion of mcr genes to livestock animals, indicating the need to further increase measures to control this important threat for public health issue.
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Affiliation(s)
- George Valiakos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece;
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Zhao Y, Hu HW, Su JQ, Hao X, Guo H, Liu YR, Zhu YG. Influence of Legacy Mercury on Antibiotic Resistomes: Evidence from Agricultural Soils with Different Cropping Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:13913-13922. [PMID: 34613706 DOI: 10.1021/acs.est.1c04030] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Agricultural soils are important reservoirs for antibiotic resistance genes (ARGs), which have close linkage to human health via crop production. Metal stress in environments may function as a selection pressure for antibiotic resistomes. However, there is still a lack of field studies focusing on the effect of historical mercury (Hg) contamination on antibiotic resistomes in agricultural soils. Here, we explored the ARG profile in soils with different cropping systems (paddy and upland) and linked them to legacy Hg exposure. We found that ARG profiles were significantly different between paddy and upland soils. However, both paddy and upland soils with long-term field Hg contamination harbored higher diversity and abundance of ARGs than non-polluted soils. The co-occurrence network reveals significant associations among Hg, Hg resistance genes, mobile genetic elements (MGEs), and ARGs. Together with path analysis showing legacy Hg possibly affecting soil resistomes through the shifts of soil microbiota, Hg resistance genes, and MGEs, we suggest that legacy Hg-induced potential co-selection might elevate the ARG level. Redundancy analysis further supports that legacy Hg pollution had a significant association with ARG variations in the paddy and upland soils (P < 0.01). Collectively, our results highlight the underappreciated role of legacy Hg as a potential persistent selecting agent in contributing to soil ARGs in agroecosystems.
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Affiliation(s)
- Yi Zhao
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Xiuli Hao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaming Guo
- School of Water Resources and Environment, China University of Geosciences, Beijing 100083, China
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
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Enrofloxacin Alters Fecal Microbiota and Resistome Irrespective of Its Dose in Calves. Microorganisms 2021; 9:microorganisms9102162. [PMID: 34683483 PMCID: PMC8537546 DOI: 10.3390/microorganisms9102162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 12/27/2022] Open
Abstract
Enrofloxacin is a fluoroquinolone drug used to prevent and control bovine respiratory disease (BRD) complex in multiple or single doses, ranging from 7.5 to 12.5 mg/kg body weight. Here, we examined the effects of high and low doses of a single subcutaneously injected enrofloxacin on gut microbiota and resistome in calves. Thirty-five calves sourced for this study were divided into five groups: control (n = 7), two low dose groups (n = 14, 7.5 mg/kg), and two high dose groups (n = 14, 12.5 mg/kg). One group in the low and high dose groups was challenged with Mannheimia haemolytica to induce BRD. Both alpha and beta diversities were significantly different between pre- and post-treatment microbial communities (q < 0.05). The high dose caused a shift in a larger number of genera than the low dose. Using metagenomic ProxiMeta Hi-C, 32 unique antimicrobial resistance genes (ARGs) conferring resistance to six antibiotic classes were detected with their reservoirs, and the high dose favored clonal expansion of ARG-carrying bacterial hosts. In conclusion, enrofloxacin treatment can alter fecal microbiota and resistome irrespective of its dose. Hi-C sequencing provides significant benefits for unlocking new insights into the ARG ecology of complex samples; however, limitations in sample size and sequencing depth suggest that further work is required to validate the findings.
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Zhu D, Lu L, Zhang Z, Qi D, Zhang M, O'Connor P, Wei F, Zhu YG. Insights into the roles of fungi and protist in the giant panda gut microbiome and antibiotic resistome. ENVIRONMENT INTERNATIONAL 2021; 155:106703. [PMID: 34139588 DOI: 10.1016/j.envint.2021.106703] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/15/2021] [Accepted: 06/06/2021] [Indexed: 06/12/2023]
Abstract
The mammal gut is a rich reservoir of antibiotic resistance genes (ARGs), and the relationship between bacterial communities and ARGs has been widely studied. Despite ecological significance of microeukaryotes (fungi and protists), our understanding of their roles in the mammal gut microbiome and antibiotic resistome is still limited. Here, we used amplicon sequencing, metagenomic sequencing and high-throughput quantitative PCR to examine microbiomes and antibiotic resistomes of 41 giant panda fecal samples from individuals with different genders, ages, sampling sites and diet. Our results show that diverse protists inhabit in the giant panda gut ecosystem, dominated by consumers. Higher abundance of protistan consumers was detected in the elder compared to sub-adult and adult giant pandas. Diet is the main driving factor of variation in ARGs in the giant panda gut microbiome. Weighted correlation network analysis identified two key microbial modules from multitrophic communities, which all contributed to the variation in ARGs in the giant panda gut. Protists occupied an important position in the two modules which were dominated by fungal taxa. Deterministic processes made a more important contribution to microbial community assembly of the two modules than to bacterial, fungal and protistan communities. This study sheds new light on how key microbial modules contribute to the variation in ARGs, which is crucial in understanding dynamics of antibiotic resistome in the mammal gut, particularly endangered species.
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Affiliation(s)
- Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lu Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China; College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Zejun Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Dunwu Qi
- Chengdu Research Base of Giant Panda Breeding, Chengdu 611081, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Patrick O'Connor
- Centre for Global Food and Resources, University of Adelaide, Adelaide 5005, Australia
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, 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; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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