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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.
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.
Rumen Beef cattle
(n = 10)
Yes Monensin and tylosin – predominant by tetracycline and MLS.
–No effect of antimicrobials on resistome.
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.
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.
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.
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.
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.
Feces Dairy cattle (n = 6) Yes –Predominant by tetracycline class.
–Ceftiofur enriched ARGs belonging to β-lactam class.
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.
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.
Feces Beef cattle (n = 16) Yes Tylosin –No effect of tylosin on the abundance of resistome.
–Predominant by tetracycline, MLS, and elfamycin.
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.
Feces Beef cattle (n = 12) Yes NS –Predominant by tetracycline and macrolide. [165]
  1. ARG antimicrobial resistant gene, MLS macrolide-lincosamide-streptogramin, MDR multidrug resistance, NM not mentioned, NS not specified.