Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms

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...

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Published inEnvironmental science and pollution research international Vol. 30; no. 18; pp. 52087 - 52106
Main Authors Ji, Bingzhen, Qin, Junjun, Ma, Yijia, Liu, Xin, Wang, Tian, Liu, Guiming, Li, Bugao, wang, Guoliang, Gao, Pengfei
Format Journal Article
LanguageEnglish
Published Berlin/Heidelberg Springer Berlin Heidelberg 01.04.2023
Springer Nature B.V
Subjects
Aminoglycoside antibiotics
Aminoglycosides
Animals
Anti-Bacterial Agents - pharmacology
Antibiotic resistance
Antibiotics
Aquatic Pollution
Atmospheric Protection/Air Quality Control/Air Pollution
Bacteria
Bacteria - genetics
Bacteroides
Butyrivibrio
China
Drug Resistance, Bacterial - genetics
Earth and Environmental Science
Ecotoxicology
Environment
Environmental Chemistry
Environmental Health
Environmental science
family
Farms
Genes
Genes, Bacterial
Genetic analysis
human health
Humans
Macrolides
Manure
Manures
Metagenomics
Microbial activity
Microorganisms
phenol
Phenols
Pig manure
Pollution control
Prevotella
Research Article
Swine
tetracycline
Waste Water Technology
Water Management
Water Pollution Control
China
Pig manure
Bacterial host
Mobility
Antibiotic resistance genes
Metagenomic
Online AccessGet full text

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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.
AbstractList 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.
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.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.
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.
Author Ji, Bingzhen
Qin, Junjun
Li, Bugao
Liu, Guiming
Gao, Pengfei
Ma, Yijia
Liu, Xin
wang, Guoliang
Wang, Tian
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  organization: College of Animal Science, Shanxi Agricultural University
BackLink https://www.ncbi.nlm.nih.gov/pubmed/36826766$$D View this record in MEDLINE/PubMed
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Thu Apr 24 22:53:23 EDT 2025
Tue Jul 01 02:31:57 EDT 2025
Fri Feb 21 02:43:34 EST 2025
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Issue 18
Keywords Pig manure
Bacterial host
Mobility
Antibiotic resistance genes
Metagenomic
Language English
License 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
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Snippet In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the...
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SubjectTerms Aminoglycoside antibiotics
Aminoglycosides
Animals
Anti-Bacterial Agents - pharmacology
Antibiotic resistance
Antibiotics
Aquatic Pollution
Atmospheric Protection/Air Quality Control/Air Pollution
Bacteria
Bacteria - genetics
Bacteroides
Butyrivibrio
China
Drug Resistance, Bacterial - genetics
Earth and Environmental Science
Ecotoxicology
Environment
Environmental Chemistry
Environmental Health
Environmental science
family
Farms
Genes
Genes, Bacterial
Genetic analysis
human health
Humans
Macrolides
Manure
Manures
Metagenomics
Microbial activity
Microorganisms
phenol
Phenols
Pig manure
Pollution control
Prevotella
Research Article
Swine
tetracycline
Waste Water Technology
Water Management
Water Pollution Control
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Title Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms
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