Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics

• Published in: Applied and environmental microbiology Vol. 87; no. 8; pp. 1 - 21
• Main Authors: Tunsagool, Paiboon, Mhuantong, Wuttichai, Tangphatsornruang, Sithichoke, Am-In, Nutthee, Chuanchuen, Rungtip, Luangtongkum, Taradon, Suriyaphol, Gunnaporn
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 01.04.2021
• Subjects: Abundance; Additives; Antibiotics; Antimicrobial agents; Antimicrobial resistance; Bacteroides; Cecum; Chlortetracycline; Clusters; Copper; E coli; Feed additives; Food additives; Fusobacterium; Gene sequencing; Genes; Genomes; Heavy metals; Metagenomics; Microbiomes; Microbiota; Parturition; Prevotella; Public and Environmental Health Microbiology; Zinc; raised without antibiotics; pigs; antimicrobial resistance genes; microbiome; whole-genome shotgun sequencing; pig
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.02684-20

This study aimed to detect 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 the enrichment of (33%) and (13%), whereas (40%), and (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 highest abundance (Q) (35.7%) and (A) (12.7%) were markedly observed in the ABF group whereas (Q) (26.2%) and (W) (10.4%) were shown in the C group. (Q) was positively correlated to in ABF and C1 samples. In the C2 group, the prominent (W) was positively correlated to and Pigs have never received tetracycline but pregnant sows used chlortetracycline once 7 d before parturition. Chromosomal Cu and Zn resistance genes were also shown in both groups regardless the received Cu and Zn feed additives. A higher abundance of multi-metal resistance genes was observed in the C group (44%) compared with the ABF group (41%). In conclusion, the microbiome clusters in some C pigs were similar to that in ABF pigs. High abundant tetracycline resistance genes interrelated to major bacteria were observed in both ABF and C pigs. MRGs were also observed. Owing to the increased problem of AMR in farm animals, raising farm animals without antibiotics is one method that could solve this problem. Our study showed that only some tetracycline and macrolide resistance genes, (Q), (W) and (A), were markedly abundant in ABF and C groups. The (Q) and (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, not depending on the use of Cu and Zn additives in both farms. The association of MRGs and AMR genotypes and phenotypes together with the method to re-sensitize bacteria to antibiotics should be studied further to unveil the cause of high resistance genes and solve the problems.