Comparative metagenomic analysis of the resistome and virulome and their potential dissemination risk in the rumen and hindgut of dairy cows with differing long-term productivity

Resistance and virulence factor genes pose a major global public health concern. Strategies aimed at promoting sustainable livestock production through expanding populations of dairy cows with persistent productivity may potentially influence the composition and distribution of antibiotic resistance genes (ARGs), biocide and metal resistance genes (BMRGs), and virulence factor genes (VFGs) within the gastrointestinal tract of dairy herds. In this study, metagenomic sequencing was employed to characterize the rumen and rectum resistome and virulome profiles of dairy cows exhibiting different levels of persistent productivity. The results showed that, in the rumen, long-lived high-yielding (LH) cows exhibited higher relative abundances and a greater number of enriched ARGs (31 vs. 9), BMRGs (32 vs. 11), VFGs (43 vs. 16), and mobile genetic elements (MGEs; 16 vs. 9) compared with long-lived low-yielding (LL) cows. In contrast, no significant differences in overall abundance were observed in the rectum, where these elements were more frequently enriched in LL cows (ARGs: 7 vs. 5; BMRGs: 6 vs. 3; VFGs: 5 vs. 2; MGEs: 2 vs. 1). The proportion of plasmid-associated antibiotic resistance contigs (ARCs) was lower in the rumen of LH cows. However, neither the proportion nor the relative abundance of MGE-associated ARGs, BMRGs, or VFGs differed significantly between the two groups in either gastrointestinal compartment. Co-occurrence network analysis revealed distinct MGE-associated horizontal gene transfer (HGT) patterns between LH and LL cows, with integrase-related associations predominating in the hindgut of LH cows and transposase-related associations being more prominent in the hindgut of LL cows. In summary, LH cows exhibited greater enrichment of resistance- and virulence-related genes in the rumen than LL cows. However, no significant differences were observed between groups in the abundance of MGE-associated ARGs, BMRGs, or VFGs in the rectum, suggesting that the enrichment observed in the rumen was not accompanied by a corresponding increase in dissemination-related genetic features in the hindgut.