Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period

Abstract

This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. − 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. − 3–D.3, Alistipes (6.9–12.7%) and Bacteroides (5.2–8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. − 3 (1.2%) and D. − 3–D.3 (0.2–0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide–lincosamide–streptogramin (mefA), β-lactam (cfxA6 and aci1) and phenicol (rlmN). In contrast, at D. − 3–D.3, a high abundance of determinants with aminoglycoside (AMG) (sat, aac(6')-aph(2''), aadA and acrF), β-lactam (fus-1, cepA and mrdA), multidrug resistance (MDR) (gadW, mdtE, emrA, evgS, tolC and mdtB), phenicol (catB4 and cmlA4), and sulfonamide patterns (sul3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac(6')-aph(2''), emrA, mdtB, catB4 and cmlA4 at D. − 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mefA, cfxA6 and aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs

“…The dramatic impact of weaning on the swine microbiome has been previously reported, and our results confirm that microbiome richness and diversity increase significantly post-weaning [57][58][59][60][61]. As with previous reports, we found that Bacteroides were predominant in the samples taken just prior to weaning [61,62]. Using DMM enterotyping, we observed that pre-weaning samples were also characterized by a relative dominance of Alistipes, Cloacibacillus, Escherichia, and Intestinimonas.…”

“…Indeed, these four genera did not reach the top 10 most prevalent genera in any of the post-weaning samples, suggesting that their relative abundance within the pre-weaning samples is a defining characteristic of the suckling piglet fecal microbiome. Previous studies of the peri-weaning microbiome also found a predominance of Alistipes [ 62 ].…”

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

“…Previous studies have shown that tetracyclines and MLSs are the most common antibiotic resistance classes in weaned pigs receiving or not receiving in-feed antibiotics, and the findings of the current study are consistent with this [8,47]. High levels of beta-lactam resistance also were found in both the negative control and the antibiotic groups.…”

“…These genera are regarded as being beneficial microbes due to a variety of characteristics, including the ability to produce antibacterial substances (e.g., bacteriocins, organic acids) that inhibit growth of pathogens, the ability to increase carbohydrate metabolism by utilizing dietary starch and fiber, and the ability to produce short-chain fatty acids (SCFAs) that reduce gut inflammation [2,7,13,40,[43][44][45][46]. The group receiving chlortetracycline showed an increase in Proteobacteria and Bacteroidetes, which is consistent with prior research demonstrating that antibiotic administration could boost these phyla [6][7][8]47]. However, several studies have suggested that enhanced numbers of Bacteroidetes may promote host health by enhancing nutrient digestion and absorption [2,7].…”

“…However, since the existence of some antibiotic genes may not indicate phenotypic resistance, a weakness in the current study was the lack of comparison between AMR genotypic and phenotypic features. Phenotypic determinations should be performed on fresh faecal samples, and this was not possible with the frozen samples [6,47].…”