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Metagenomics of Antimicrobial and Heavy Metal Resistance in the Cecal Microbiome of Fattening Pigs Raised without Antibiotics
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Document Title
Metagenomics of Antimicrobial and Heavy Metal Resistance in the Cecal Microbiome of Fattening Pigs Raised without Antibiotics
Author
Tunsagool P., Mhuantong W., Tangphatsornruang S., Am-In N., Chuanchuen R., Luangtongkum T., Suriyaphol G.
Name from Authors Collection
Affiliations
Biochemistry Unit, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand; Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand; National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand; Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand; Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
Type
Article
Source Title
Applied and Environmental Microbiology
ISSN
00992240
Year
2021
Volume
87
Issue
8
Page
44197
Open Access
All Open Access, Green
Publisher
American Society for Microbiology
DOI
10.1128/AEM.02684-20
Format
Abstract
This study aimed to assess the cecal microbiome, antimicrobial resistance (AMR), and heavy-metal resistance genes (MRGs) in fattening pigs raised under antibiotic-free (ABF) conditions compared with ordinary industrial pigs (control, C) using whole-genome shotgun sequencing. ABF pigs showed enrichment of Prevotella (33%) and Lactobacillus (13%), whereas Escherichia coli (40%), Fusobacterium, and Bacteroides (each at 4%) were notably observed in the C group. Distinct clusters of cecal microbiota of ABF and C pigs were revealed; however, microbiota of some C pigs (C1) appeared in the same cluster as ABF and were totally separated from the remaining C pigs (C2). For AMR genes, the most abundant genes, tet(Q) (35.7%) and mef(A) (12.7%), were markedly observed in the ABF group, whereas tet(Q) (26.2%) and tet(W) (10.4%) were prominently shown in the C group. tet(Q) was positively correlated with Prevotella in ABF and C1 samples. In the C2 group, the prominent tet(W) was positively correlated with Fusobacterium and Bacteroides. The pigs studied here have never received tetracycline, but pregnant sows received chlortetracycline once every 7 days before parturition. Chromosomal Cu and Zn resistance genes were also shown in both groups regardless of the received Cu and Zn feed additives. A higher abundance of multimetal resistance genes was observed in the C group (44%) than with the ABF group (41%). In conclusion, the microbiome clusters in some C pigs were similar to that in ABF pigs. Highabundance tetracycline resistance genes interrelated to major bacteria were observed in both ABF and C pigs. MRGs were also observed. IMPORTANCE AMR is an increasing problem in farm animals, and raising farm animals without antibiotics is one method that could solve this problem. Our study showed that only some tetracycline and macrolide resistance genes, tet(Q), tet(W), and mef (A), were markedly abundant in ABF and C groups. The tet(Q) and tet(W) genes interrelated to different predominant bacteria in each group, showing the potential role of major bacteria as reservoirs of AMR genes. In addition, chromosomal Cu and Zn resistance genes were also observed in both pig groups, independent of the use of Cu and Zn additives on both farms. The association of MRGs and AMR genotypes and phenotypes, together with the method to resensitize bacteria to antibiotics, should be studied further to unveil the cause of genes conferring high-level resistance and solve these problems. © 2021 American Society for Microbiology. All Rights Reserved.
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
Chulalongkorn University
License
N/A
Rights
N/A
Publication Source
Scopus