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Bai Y, Sun X, Guo Y, Qiu T, Xin H, Yu A, Wang X, Gao M. Particle-size stratification of airborne antibiotic resistant genes, mobile genetic elements, and bacterial pathogens within layer and broiler farms in Beijing, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:112799-112812. [PMID: 37843709 DOI: 10.1007/s11356-023-29975-8] [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: 06/06/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023]
Abstract
The particle-size distribution of antimicrobial resistant (AMR) elements is crucial in evaluating their environmental behavior and health risks, and exposure to the fecal microbiome via particle mass (PM) is an important route of transmission of AMR from livestock to humans. However, few studies have explored the association between air and fecal AMR in farm environments from the perspective of particle-size stratification. We collected feces and PMs of different sizes from layer and broiler farms, quantified antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and human pathogenic bacteria (HPB) using Droplet digital PCR (ddPCR), and analyzed the bacterial communities based on 16S rRNA sequencing. The particle-size distributions of 16S rRNA and AMR elements were similar and generally increased with larger particle sizes in chicken farms. In broiler farms, we observed a bimodal distribution with two peaks at 5.8-9.0 μm and 3.3-4.7 μm. The dominant airborne bacterial phyla were Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The dominant phyla in the feces were the same as those in the air, but the order of relative abundance varied. The particle-size distributions of specific bacterial genera differed between the animal-farm types. Overall, the degree of association between feces and different particulates increased with increasing particle size. The microbial communities in the coarse particles were similar to those in fecal samples. Escherichia coli, Staphylococcus spp., Campylobacter spp., and sul 2 (sulfonamide ARGs) tended to attach to small particles. We highlight the particle size-specific relationship between fecal and air microbes involving ARGs, MGEs, and HPB and provide valuable information for comprehensively assessing the transmission of fecal microorganisms through the airpath and its environmental and occupational health risks.
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Affiliation(s)
- Yuqiao Bai
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
- College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Xingbin Sun
- College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Yajie Guo
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Tianlei Qiu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Huibo Xin
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Aoyuan Yu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Xuming Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China
| | - Min Gao
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, No. 9 Shuguang Middle Road, Haidian District, Beijing, 100097, China.
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Ji B, Qin J, Ma Y, Liu X, Wang T, Liu G, Li B, Wang G, Gao P. Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:52087-52106. [PMID: 36826766 DOI: 10.1007/s11356-023-25962-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.
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Affiliation(s)
- Bingzhen Ji
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junjun Qin
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yijia Ma
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Xin Liu
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, 100097, China
| | - Tian Wang
- College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, 100097, China
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Guoliang Wang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
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Detection of Acquired Antibiotic Resistance Genes in Domestic Pig (Sus scrofa) and Common Carp (Cyprinus carpio) Intestinal Samples by Metagenomics Analyses in Hungary. Antibiotics (Basel) 2022; 11:antibiotics11101441. [PMID: 36290099 PMCID: PMC9598914 DOI: 10.3390/antibiotics11101441] [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: 09/30/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 11/26/2022] Open
Abstract
The aim of this study was metagenomics analyses of acquired antibiotic-resistance genes (ARGs) in the intestinal microbiome of two important food-animal species in Hungary from a One Health perspective. Intestinal content samples were collected from 12 domestic pigs (Sus scrofa) and from a common carp (Cyprinus carpio). Shotgun metagenomic sequencing of DNA purified from the intestinal samples was performed on the Illumina platform. The ResFinder database was applied for detecting acquired ARGs in the assembled metagenomic contigs. Altogether, 59 acquired ARG types were identified, 51 genes from domestic pig and 12 genes from the carp intestinal microbiome. ARG types belonged to the antibiotic classes aminoglycosides (27.1%), tetracyclines (25.4%), β-lactams (16.9%), and others. Of the identified ARGs, tet(E), a blaOXA-48-like β-lactamase gene, as well as cphA4, ampS, aadA2, qnrS2, and sul1, were identified only in carp but not in swine samples. Several of the detected acquired ARGs have not yet been described from food animals in Hungary. The tet(Q), tet(W), tet(O), and mef(A) genes detected in the intestinal microbiome of domestic pigs had also been identified from free-living wild boars in Hungary, suggesting a possible relationship between the occurrence of acquired ARGs in domestic and wild animal populations.
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Yang D, Heederik DJJ, Scherpenisse P, Van Gompel L, Luiken REC, Wadepohl K, Skarżyńska M, Van Heijnsbergen E, Wouters IM, Greve GD, Jongerius-Gortemaker BGM, Tersteeg-Zijderveld M, Portengen L, Juraschek K, Fischer J, Zając M, Wasyl D, Wagenaar JA, Mevius DJ, Smit LAM, Schmitt H. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1883-1893. [PMID: 35466367 PMCID: PMC9244224 DOI: 10.1093/jac/dkac133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background Real-time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains. Objectives We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed. Methods A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3′)-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman’s rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data. Results ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains (‘farm to fork’) was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman’s ρ > 0.7) between qPCR data and metagenomic data of pooled samples. Conclusions qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure.
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Affiliation(s)
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter Scherpenisse
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Roosmarijn E C Luiken
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Katharina Wadepohl
- Außenstelle für Epidemiologie, Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Eri Van Heijnsbergen
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Gerdit D Greve
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Monique Tersteeg-Zijderveld
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lützen Portengen
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Katharina Juraschek
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Dik J Mevius
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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