Table 1.
Antimicrobial resistance genes identified using metagenomic functional selections of chicken gut microbiomes.
| Antibiotic (conc.) (number of clones) |
Conventional Diet |
Organic Diet |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| Top hit | DNA % ID | Nucleotide Position (Gene length) | Gene | Top hit | DNA % ID | Nucleotide Position (Gene length) | Gene | ||
| Bacteria [GB ID] (number of clones) | Bacteria [GB ID] (number of clones) | ||||||||
| β lactam | |||||||||
| Amoxicillin (4 µg/mL) (n=10) | Escherichia coli [CP004009.1] (n=6) | 99 | 367564–368697 (1133) | ampC (β lactamase) | Escherichia coli [AP010960.1](n=10) | 98 | 5154506–5155639 (1133) | ampC (d-alanine carboxypeptidase) | |
| Escherichia coli [AP010960.1] (n=4) | 98 | 5154506–5155639 (1133) | ampC (d-alanine carboxypeptidase) | ||||||
| Amoxicillin (8 µg/mL) (n=10) | Escherichia coli [AP010960.1] (n=8) | 98 | 5154506–5155639 (1133) | ampC (d-alanine carboxypeptidase) | Escherichia coli [AP010960.1] (n=10) | 98 | 5154506–5155639 (1133) | ampC (d-alanine carboxypeptidase) | |
| Enterobacter asburiae [EU427302.2](n=2) | 98 | 1476–2618 (1142) | β lactamase ACT 3’ | ||||||
| Amoxycillin (16 µg/mL) (n=10) | Escherichia coli [CP002967.1](n=10) | 99 | 4631143–4633212 (2089) | sugE (membrane transporter) ampC (β lactamase) | Escherichia coli [AP010960.1] (n=10) | 98 | 5154506–5155639 (1133) | ampC (d-alanine carboxypeptidase) | |
| Penicillin (32 µg/mL) (n=10) | Escherichia coli [AP010958.1] (n=5) | 99 | 5135487–5137556 (2069) | sugE (membrane transporter) ampC (β lactamase) | Escherichia coli [AP010960.1] (n=10) | 98 | 5154506–5155639 (1133) | ampC (d-alanine carboxypeptidase) | |
| Escherichia coli [CP004009.1] (n=5) | 98 | 367564–368697 (1133) | ampC (β lactamase) | ||||||
| Amphenols | |||||||||
| Chloramphenicol (4 µg/mL) (n=10) | Escherichia coli [CP003301.1] (n=10) | 99 | 3550043–3551275 (1232) | mdfA (multidrug efflux system translocase) | Escherichia coli [CP002291.1] (n=10) | 96 | 1663943–1664581 (638) | marA-marB (multiple antibiotic resistance operon) | |
| Chloramphenicol (8 µg/mL) (n=10) | Escherichia coli [AP010958.1] (n=4) | 99 | 968295–969527 (1232) | cmr (multidrug efflux system) | None | ||||
| Escherichia coli [CU928160.2] (n=6) | 98 | 935786–937018 (1232) | cmr (multidrug efflux system) | ||||||
| Chloramphenicol (16 µg/mL) (n=10) | Escherichia coli [AP010958.1] (n=5) | 99 | 968295–969527 (1232) | cmr (multidrug efflux system) | None | ||||
| Escherichia coli [CU928160.2] (n=6) | 98 | 935786–937018 (1232) | cmr (multidrug efflux system) | ||||||
| Florfenicol (4 µg/mL) (n=10) | Escherichia coli [CP003301.1] (n=10) | 99 | 4494426–4493557 (869) | creB-araC(response regulator -transcription activator) | Escherichia coli [AP010958.1] (n=10) | 96 | 5442103–5443656 (1553) | rob-creA (transcription activator) | |
| Florfenicol (8 µg/mL) (n=10) | Escherichia coli [CP002967.1] (n=10) | 99 | 2240178–2241239 (1061) | UDP-Glucose-4-epimerase Glycosyl transferase | Escherichia coli [AP009240.1] (n=10) | 96 | 2212192–2211261 (931) | ABC transporter | |
| Florfenicol (16 µg/mL) (n=10) | None | None | |||||||
| Aminoglycoside | |||||||||
| Gentamicin (4 µg /mL) (n=10) (8 µg/mL) (n=10) | Campylobacter jejuni [AY701528.1] (n=12) | 98 | 9696–10589 (893) | aacA/aphD (bifunctional amino- glycoside N-acetyl/phospho transferase ) | Staphylococcus aureus [CP005288.1] (n=13) | 96 | 2265687–2267126 (1439) | aacA/aphD (bifunctional amino- glycoside N-acetyl/phospho transferase ) | |
| Staphylococcus aureus [HF569094.1] (n=8) | 99 | 36923–38362 (1439) | aacA/aphD (bifunctional amino- glycoside N-acetyl/phospho transferase ) | Enterococcus faecium [AB206333.1] (n=7) | 96 | 62171–63610 (1439) | aacA/aphD (bifunctional amino- glycoside N-acetyl/phospho transferase ) | ||
| Gentamicin (16 µg/mL) (n=10) | Staphylococcus epidermidis [JX910899.1] (n=8) | 98 | 1303–2742 (1439) | aacA/aphD (bifunctional amino- glycoside N-acetyl/phospho transferase ) | None | ||||
| Streptococcus faecalis [M13771.1] (n=2) | 98 | 304–1743 (1439) | aacA/aphD (bifunctional amino- glycoside N-acetyl/phospho transferase ) | ||||||
| Spectinomycin (64 µg/mL) (n=10) | Bacteroides uniformis [AY345595.1] (n=3) | 95 | 38057–38677 (620) | acetyltransferase gram positive like | None | ||||
| Salmonella enterica [AB576781.1] (n=4) | 99 | 17352–18362 (1010) | spectinomycin/streptomycin adenyltransferase | ||||||
| Clostridium cellulolyticum [CP001348.1] (n=3) | 98 | 3366196–3367416 (1220) | N-acetyltransferase | ||||||
| Tetracycline | |||||||||
| Oxytetracycline (4 µg /mL) (n=10) (8 µg/mL) (n=10) | Corynebacterium glutamicum [AF121000.1] (n=12) | 99 | 13133–13732 (599) | tetR (tetracycline repressor) | Mennheimia haemolytica [CP005383.1] (n=20) | 99 | 2178268–2178891 (623) | tetR (tetracycline repressor) | |
| Corynebacterium glutamicum [AF121000.1] (n=8) | 99 | 11880–13034 (1154) | tetA(tetracycline resistance) | ||||||
| Oxytetracycline 16 µg/mL) (n=10) | Uncultured bacterium [FJ012881.1] (n=10) | 99 | 40470–41630 (1160) | tetX(tetracycline resistance) | Uncultured bacterium [KC734562.1] (n=10) | 99 | 3601–5520 (1919) | tetR-tetH(tetracycline resistance) | |
| Tetracycline (4 µg /mL) (n=10) (8 µg/mL) (n=10) | Corynebacterium glutamicum [AF121000.1] (n=11) | 99 | 13133–13732 (599) | tetR (tetracycline repressor) | Enterococcus faecium [HM636636.1] (n=11) | 97 | 18678–20597 (1919) | tetR-tetH(tetracycline resistance) | |
| Corynebacterium glutamicum [AF121000.1] (n=9) | 11880–13034 (1154) | tetA(tetracycline resistance) | Streptococcus agalactiae [HF952106.1] (n=9) | 95 | 639169–641088 (1919) | tetM (tetracycline resistance) | |||
| Tetracycline 16 µg/mL) (n=10) | Acinetobacter sp [AY743590.1] (n=10) | 99 | 42–1936 (1894) | tetR- tetA(tetracycliner resistance) | Uncultured bacterium [FJ012881.1] (n=10) | 97 | 40470–41630 (1160) | tetX(tetracycline resistance) | |