Table 3 Resistome in the digestive tract of ruminants based on metagenome sequencing
From: A review of the resistome within the digestive tract of livestock
Site | Animal | Use of antimicrobials | Name of antimicrobial | Major findings | Reference |
|---|---|---|---|---|---|
Rumen | Dairy cattle (n = 49) | No | – | –Predominant by tetracycline class. –Abundance of resistome could be linked to milk protein yield. | [25] |
Rumen | Beef cattle (n = 50) | No | – | –Higher diversity and abundance in high concentrate diet. –Chloramphenicol, microcin are predominant in high forage diet. –Aminoglycoside, streptomycin are predominant in high concentrate diet. –No breed effect on resistome. | [152] |
Rumen | Beef cattle (n = 10) | Yes | Monensin and tylosin | – predominant by tetracycline and MLS. –No effect of antimicrobials on resistome. | [151] |
Rumen | Sheep (n = 10) | NM | – | –Daptomycin and colistin are present in all samples. | [153] |
Feces | Dairy calf (n = 12) | No | – | –329 ARGs conferring resistance to 17 classes of ARG. –The abundance of ARGs declines during nursing. | [85] |
Feces | Beef cattle (n = 8) | Yes | NS | –Predominant by tetracyclines, macrolides, aminoglycoside. –The number of reads being assigned to ARGs, but not the relative proportions of ARGs, increased with sequencing depth. | [114] |
Feces | Beef cattle (n = 14) | Yes | NS | –Trimethoprim and aminoglycoside classes were only identified in calf feces, while tetracycline major facilitator superfamily (MFS) alignments only in adult cattle feces. –More abundant macrolide efflux pumps and lincosamide nucleotidyltransferases in adult cattle feces. | [154] |
Feces | Beef cattle (n = 16) | Yes | NS | –Predominant by tetracycline and MLS classes. –Diversity of resistome decreased over time. –AMR were not identified in beef products. | [155] |
Feces | Beef cattle and dairy cattle (n = 8) | Yes | NS | –Feces had the greatest number of ARGs in conventional system. –More tetracycline, macrolide, and aminoglycoside in conventional system. –Tetracycline and MLS classes are more abundant in feedlot cattle than in dairy cow. –β-lactam class is more abundant in dairy cow feces. | [156] |
Feces | Dairy cattle (n = 6) | Yes | – | –Predominant by tetracycline class. –Ceftiofur enriched ARGs belonging to β-lactam class. | [157] |
Feces | Beef cattle (n = 16) | Yes | Ceftiofur and Chlortetracyclin | –Ceftiofur was not associated with changes to β-lactam resistance genes. –Chlortetracycline increased relative abundance of tetracycline resistance genes. | [158] |
Feces | Beef cattle (n = 6) | Yes | NS | –Predominant by tetracycline, MLS, β-lactam, and aminoglycoside. –No difference in the profiles of resistome between two systems. | [159] |
Feces | Beef cattle (n = 16) | Yes | Tylosin | –No effect of tylosin on the abundance of resistome. –Predominant by tetracycline, MLS, and elfamycin. | [160] |
Feces | Beef cattle (n = 30) | Yes | Tulathromycin | –No effect of antimicrobials on resistome. | [161] |
Feces | Veal calf (n = 42) | Yes | Oxytetracycline | –Sub-therapeutic administration of oxytetracycline do not result in increased tetM resistance levels as observed in the therapeutic group. | [162] |
Feces | Veal calf (n = 24) | NM | – | –Predominant by tetracyclines, aminoglycosides and MLS. | [163] |
Feces | Beef cattle (n = 28) | No | – | –Tetracycline (62.3%) and macrolide (25.6%) classes are predominant. –S. cerevisiae fermentation product did not impact resistome. | [164] |
Feces | Beef cattle (n = 12) | Yes | NS | –Predominant by tetracycline and macrolide. | [165] |