| Species (no. of isolates)/ atmospherea . | CuT genes (no. of isolates) . | Sources (no. of isolates)b . | CuSO4 MICs (mM)c,d . | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 . | 2 . | 4 . | 8 . | 12 . | 16 . | 20 . | 24 . | 28 . | 32 . | 36 . | >36 . | |||
| E. faecium (139) | ||||||||||||||
| aerobiosis | tcrB + cueO (50) | PG (27), PC (2), AQ (2), T (2), HV (11), C (4), HS (2) | 2 | 6 | 15 | 10 | 14 | 3 | ||||||
| tcrB (8) | PG (6), HV (1), HS (1) | 1 | 3 | 1 | 1 | 2 | ||||||||
| cueO (13) | PG (9), PC (1), T (1), HV (1), C (1) | 2 | 3 | 6 | 1 | 1 | ||||||||
| none (68) | PG (44), PC (1), AQ (6), T (1) HV (7), C (4), HS (4), R (1) | 11 | 10 | 25 | 22 | |||||||||
| anaerobiosis | tcrB + cueO (50) | PG (27), PC (2), AQ (2), T (2), HV (11), C (4), HS (2) | 3e | 3 | 30 | 8 | 5 | 1 | ||||||
| tcrB (8) | PG (6), HV (1), HS (1) | 1e | 1 | 3 | 1 | 1 | 1 | |||||||
| cueO (13) | PG (9), PC (1), T (1), HV (1), C (1) | 3 | 4 | 6 | ||||||||||
| none (68) | PG (44), PC (1), AQ (6), T (1) HV (7), C (4), HS (4), R (1) | 2 | 8 | 20 | 33 | 5 | ||||||||
| E. faecalis (47) | ||||||||||||||
| aerobiosis | tcrB + cueO (7) | PG (4), AQ (1), HV (2) | 1 | 6 | ||||||||||
| tcrB (2) | PC (2) | 2 | ||||||||||||
| cueO (3) | PG (2), HV (1) | 1 | 1 | 1 | ||||||||||
| none (35) | PG (14), PC (2), AQ (10), T (1), HV (4), C (2), HS (2) | 1 | 2 | 2 | 2 | 8 | 20 | |||||||
| anaerobiosis | tcrB + cueO (7) | PG (4), AQ (1), HV (2) | 1e | 1 | 3 | 2 | ||||||||
| tcrB (2) | PC (2) | 1 | 1 | |||||||||||
| cueO (3) | PG (2), HV (1) | 2 | 1 | |||||||||||
| none (35) | PG (14), PC (2), AQ (10), T (1), HV (4), C (2), HS (2) | 2 | 7 | 18 | 8 | |||||||||
| E. casseliflavus (5) | ||||||||||||||
| aerobiosis | tcrB + cueO (2) | PG (1), AQ (1) | 1 | 1 | ||||||||||
| tcrB (2) | PG (1), RTS (1) | 2 | ||||||||||||
| none (1) | AQ (1) | 1 | ||||||||||||
| anaerobiosis | tcrB + cueO (2) | PG (1), AQ (1) | 1 | 1 | ||||||||||
| tcrB (2) | PG (1), RTS (1) | 1 | 1 | |||||||||||
| none (1) | AQ (1) | 1 | ||||||||||||
| E. gallinarum (10) | ||||||||||||||
| aerobiosis | tcrB (1) | PG (1) | 1 | |||||||||||
| none (9) | PG (2), PC (6), HV (1) | 3 | 2 | 3 | 1 | |||||||||
| anaerobiosis | tcrB (1) | PG (1) | 1 | |||||||||||
| none (9) | PG (2), PC (6), HV (1) | 2 | 4 | 2 | 1 | |||||||||
| E. hirae (20) | ||||||||||||||
| aerobiosis | tcrB + cueO (6) | PG (2), AQ (4) | 1 | 3 | 2 | |||||||||
| tcrB (1) | PG (1) | 1 | ||||||||||||
| none (13) | PG (9), AQ (2), T (2) | 8 | 4 | 1 | ||||||||||
| anaerobiosis | tcrB + cueO (6) | PG (2), AQ (4) | 1 | 5 | ||||||||||
| tcrB (1) | PG (1) | 1 | ||||||||||||
| none (13) | PG (9), AQ (2), T (2) | 1 | 2 | 5 | 5 | |||||||||
| E. durans (4) | ||||||||||||||
| aerobiosis | none (4) | T (4) | 3 | 1 | ||||||||||
| anaerobiosis | none (4) | T (4) | 4 | |||||||||||
| Species (no. of isolates)/ atmospherea . | CuT genes (no. of isolates) . | Sources (no. of isolates)b . | CuSO4 MICs (mM)c,d . | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 . | 2 . | 4 . | 8 . | 12 . | 16 . | 20 . | 24 . | 28 . | 32 . | 36 . | >36 . | |||
| E. faecium (139) | ||||||||||||||
| aerobiosis | tcrB + cueO (50) | PG (27), PC (2), AQ (2), T (2), HV (11), C (4), HS (2) | 2 | 6 | 15 | 10 | 14 | 3 | ||||||
| tcrB (8) | PG (6), HV (1), HS (1) | 1 | 3 | 1 | 1 | 2 | ||||||||
| cueO (13) | PG (9), PC (1), T (1), HV (1), C (1) | 2 | 3 | 6 | 1 | 1 | ||||||||
| none (68) | PG (44), PC (1), AQ (6), T (1) HV (7), C (4), HS (4), R (1) | 11 | 10 | 25 | 22 | |||||||||
| anaerobiosis | tcrB + cueO (50) | PG (27), PC (2), AQ (2), T (2), HV (11), C (4), HS (2) | 3e | 3 | 30 | 8 | 5 | 1 | ||||||
| tcrB (8) | PG (6), HV (1), HS (1) | 1e | 1 | 3 | 1 | 1 | 1 | |||||||
| cueO (13) | PG (9), PC (1), T (1), HV (1), C (1) | 3 | 4 | 6 | ||||||||||
| none (68) | PG (44), PC (1), AQ (6), T (1) HV (7), C (4), HS (4), R (1) | 2 | 8 | 20 | 33 | 5 | ||||||||
| E. faecalis (47) | ||||||||||||||
| aerobiosis | tcrB + cueO (7) | PG (4), AQ (1), HV (2) | 1 | 6 | ||||||||||
| tcrB (2) | PC (2) | 2 | ||||||||||||
| cueO (3) | PG (2), HV (1) | 1 | 1 | 1 | ||||||||||
| none (35) | PG (14), PC (2), AQ (10), T (1), HV (4), C (2), HS (2) | 1 | 2 | 2 | 2 | 8 | 20 | |||||||
| anaerobiosis | tcrB + cueO (7) | PG (4), AQ (1), HV (2) | 1e | 1 | 3 | 2 | ||||||||
| tcrB (2) | PC (2) | 1 | 1 | |||||||||||
| cueO (3) | PG (2), HV (1) | 2 | 1 | |||||||||||
| none (35) | PG (14), PC (2), AQ (10), T (1), HV (4), C (2), HS (2) | 2 | 7 | 18 | 8 | |||||||||
| E. casseliflavus (5) | ||||||||||||||
| aerobiosis | tcrB + cueO (2) | PG (1), AQ (1) | 1 | 1 | ||||||||||
| tcrB (2) | PG (1), RTS (1) | 2 | ||||||||||||
| none (1) | AQ (1) | 1 | ||||||||||||
| anaerobiosis | tcrB + cueO (2) | PG (1), AQ (1) | 1 | 1 | ||||||||||
| tcrB (2) | PG (1), RTS (1) | 1 | 1 | |||||||||||
| none (1) | AQ (1) | 1 | ||||||||||||
| E. gallinarum (10) | ||||||||||||||
| aerobiosis | tcrB (1) | PG (1) | 1 | |||||||||||
| none (9) | PG (2), PC (6), HV (1) | 3 | 2 | 3 | 1 | |||||||||
| anaerobiosis | tcrB (1) | PG (1) | 1 | |||||||||||
| none (9) | PG (2), PC (6), HV (1) | 2 | 4 | 2 | 1 | |||||||||
| E. hirae (20) | ||||||||||||||
| aerobiosis | tcrB + cueO (6) | PG (2), AQ (4) | 1 | 3 | 2 | |||||||||
| tcrB (1) | PG (1) | 1 | ||||||||||||
| none (13) | PG (9), AQ (2), T (2) | 8 | 4 | 1 | ||||||||||
| anaerobiosis | tcrB + cueO (6) | PG (2), AQ (4) | 1 | 5 | ||||||||||
| tcrB (1) | PG (1) | 1 | ||||||||||||
| none (13) | PG (9), AQ (2), T (2) | 1 | 2 | 5 | 5 | |||||||||
| E. durans (4) | ||||||||||||||
| aerobiosis | none (4) | T (4) | 3 | 1 | ||||||||||
| anaerobiosis | none (4) | T (4) | 4 | |||||||||||
aClonality obtained by MLST and antibiotic resistance profiles are described in Silveira et al.3E. faecium STs included 5, 17, 18, 19, 30, 94, 101, 108, 123, 132, 133, 150, 184, 185, 393, 421, 428, 430, 432, 434, 670, 798, 845, 846, 847, 848, 859, 891 and 892, and E. faecalis STs included 9, 49, 53, 159, 224 and 330. MDR (resistant to at least three antibiotics of different families) isolates represent 64% of the isolates included (n = 143/225).3
bPG, pig + piggeries environment; AQ, aquaculture trout and environment; PC, poultry carcass; T, trout from supermarket; RTS, ready to eat salad; C, clinical isolates; HV, healthy human faeces; HS, hospital sewage water; R, river water.
cControl isolates: positive control, E. coli ED8739 (plasmid pRJ1004 with pco gene; MICCuSO4 = 28–36 mM in aerobiosis; MICCuSO4 = 16–20 mM in anaerobiosis);10 and negative control, E. faecium BM4105RF (negative for tcrB/cueO genes; MICCuSO4 = 8–12 mM in aerobiosis;3 MICCuSO4 = 2–4 mM in anaerobiosis).
dA black vertical line is positioned at the proposed tolerance cut-off of ≥16 mM under anaerobiosis.
eIsolates with no tcrYAZB amplicon by long PCR (Supplementary Data).
| Species (no. of isolates)/ atmospherea . | CuT genes (no. of isolates) . | Sources (no. of isolates)b . | CuSO4 MICs (mM)c,d . | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 . | 2 . | 4 . | 8 . | 12 . | 16 . | 20 . | 24 . | 28 . | 32 . | 36 . | >36 . | |||
| E. faecium (139) | ||||||||||||||
| aerobiosis | tcrB + cueO (50) | PG (27), PC (2), AQ (2), T (2), HV (11), C (4), HS (2) | 2 | 6 | 15 | 10 | 14 | 3 | ||||||
| tcrB (8) | PG (6), HV (1), HS (1) | 1 | 3 | 1 | 1 | 2 | ||||||||
| cueO (13) | PG (9), PC (1), T (1), HV (1), C (1) | 2 | 3 | 6 | 1 | 1 | ||||||||
| none (68) | PG (44), PC (1), AQ (6), T (1) HV (7), C (4), HS (4), R (1) | 11 | 10 | 25 | 22 | |||||||||
| anaerobiosis | tcrB + cueO (50) | PG (27), PC (2), AQ (2), T (2), HV (11), C (4), HS (2) | 3e | 3 | 30 | 8 | 5 | 1 | ||||||
| tcrB (8) | PG (6), HV (1), HS (1) | 1e | 1 | 3 | 1 | 1 | 1 | |||||||
| cueO (13) | PG (9), PC (1), T (1), HV (1), C (1) | 3 | 4 | 6 | ||||||||||
| none (68) | PG (44), PC (1), AQ (6), T (1) HV (7), C (4), HS (4), R (1) | 2 | 8 | 20 | 33 | 5 | ||||||||
| E. faecalis (47) | ||||||||||||||
| aerobiosis | tcrB + cueO (7) | PG (4), AQ (1), HV (2) | 1 | 6 | ||||||||||
| tcrB (2) | PC (2) | 2 | ||||||||||||
| cueO (3) | PG (2), HV (1) | 1 | 1 | 1 | ||||||||||
| none (35) | PG (14), PC (2), AQ (10), T (1), HV (4), C (2), HS (2) | 1 | 2 | 2 | 2 | 8 | 20 | |||||||
| anaerobiosis | tcrB + cueO (7) | PG (4), AQ (1), HV (2) | 1e | 1 | 3 | 2 | ||||||||
| tcrB (2) | PC (2) | 1 | 1 | |||||||||||
| cueO (3) | PG (2), HV (1) | 2 | 1 | |||||||||||
| none (35) | PG (14), PC (2), AQ (10), T (1), HV (4), C (2), HS (2) | 2 | 7 | 18 | 8 | |||||||||
| E. casseliflavus (5) | ||||||||||||||
| aerobiosis | tcrB + cueO (2) | PG (1), AQ (1) | 1 | 1 | ||||||||||
| tcrB (2) | PG (1), RTS (1) | 2 | ||||||||||||
| none (1) | AQ (1) | 1 | ||||||||||||
| anaerobiosis | tcrB + cueO (2) | PG (1), AQ (1) | 1 | 1 | ||||||||||
| tcrB (2) | PG (1), RTS (1) | 1 | 1 | |||||||||||
| none (1) | AQ (1) | 1 | ||||||||||||
| E. gallinarum (10) | ||||||||||||||
| aerobiosis | tcrB (1) | PG (1) | 1 | |||||||||||
| none (9) | PG (2), PC (6), HV (1) | 3 | 2 | 3 | 1 | |||||||||
| anaerobiosis | tcrB (1) | PG (1) | 1 | |||||||||||
| none (9) | PG (2), PC (6), HV (1) | 2 | 4 | 2 | 1 | |||||||||
| E. hirae (20) | ||||||||||||||
| aerobiosis | tcrB + cueO (6) | PG (2), AQ (4) | 1 | 3 | 2 | |||||||||
| tcrB (1) | PG (1) | 1 | ||||||||||||
| none (13) | PG (9), AQ (2), T (2) | 8 | 4 | 1 | ||||||||||
| anaerobiosis | tcrB + cueO (6) | PG (2), AQ (4) | 1 | 5 | ||||||||||
| tcrB (1) | PG (1) | 1 | ||||||||||||
| none (13) | PG (9), AQ (2), T (2) | 1 | 2 | 5 | 5 | |||||||||
| E. durans (4) | ||||||||||||||
| aerobiosis | none (4) | T (4) | 3 | 1 | ||||||||||
| anaerobiosis | none (4) | T (4) | 4 | |||||||||||
| Species (no. of isolates)/ atmospherea . | CuT genes (no. of isolates) . | Sources (no. of isolates)b . | CuSO4 MICs (mM)c,d . | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 . | 2 . | 4 . | 8 . | 12 . | 16 . | 20 . | 24 . | 28 . | 32 . | 36 . | >36 . | |||
| E. faecium (139) | ||||||||||||||
| aerobiosis | tcrB + cueO (50) | PG (27), PC (2), AQ (2), T (2), HV (11), C (4), HS (2) | 2 | 6 | 15 | 10 | 14 | 3 | ||||||
| tcrB (8) | PG (6), HV (1), HS (1) | 1 | 3 | 1 | 1 | 2 | ||||||||
| cueO (13) | PG (9), PC (1), T (1), HV (1), C (1) | 2 | 3 | 6 | 1 | 1 | ||||||||
| none (68) | PG (44), PC (1), AQ (6), T (1) HV (7), C (4), HS (4), R (1) | 11 | 10 | 25 | 22 | |||||||||
| anaerobiosis | tcrB + cueO (50) | PG (27), PC (2), AQ (2), T (2), HV (11), C (4), HS (2) | 3e | 3 | 30 | 8 | 5 | 1 | ||||||
| tcrB (8) | PG (6), HV (1), HS (1) | 1e | 1 | 3 | 1 | 1 | 1 | |||||||
| cueO (13) | PG (9), PC (1), T (1), HV (1), C (1) | 3 | 4 | 6 | ||||||||||
| none (68) | PG (44), PC (1), AQ (6), T (1) HV (7), C (4), HS (4), R (1) | 2 | 8 | 20 | 33 | 5 | ||||||||
| E. faecalis (47) | ||||||||||||||
| aerobiosis | tcrB + cueO (7) | PG (4), AQ (1), HV (2) | 1 | 6 | ||||||||||
| tcrB (2) | PC (2) | 2 | ||||||||||||
| cueO (3) | PG (2), HV (1) | 1 | 1 | 1 | ||||||||||
| none (35) | PG (14), PC (2), AQ (10), T (1), HV (4), C (2), HS (2) | 1 | 2 | 2 | 2 | 8 | 20 | |||||||
| anaerobiosis | tcrB + cueO (7) | PG (4), AQ (1), HV (2) | 1e | 1 | 3 | 2 | ||||||||
| tcrB (2) | PC (2) | 1 | 1 | |||||||||||
| cueO (3) | PG (2), HV (1) | 2 | 1 | |||||||||||
| none (35) | PG (14), PC (2), AQ (10), T (1), HV (4), C (2), HS (2) | 2 | 7 | 18 | 8 | |||||||||
| E. casseliflavus (5) | ||||||||||||||
| aerobiosis | tcrB + cueO (2) | PG (1), AQ (1) | 1 | 1 | ||||||||||
| tcrB (2) | PG (1), RTS (1) | 2 | ||||||||||||
| none (1) | AQ (1) | 1 | ||||||||||||
| anaerobiosis | tcrB + cueO (2) | PG (1), AQ (1) | 1 | 1 | ||||||||||
| tcrB (2) | PG (1), RTS (1) | 1 | 1 | |||||||||||
| none (1) | AQ (1) | 1 | ||||||||||||
| E. gallinarum (10) | ||||||||||||||
| aerobiosis | tcrB (1) | PG (1) | 1 | |||||||||||
| none (9) | PG (2), PC (6), HV (1) | 3 | 2 | 3 | 1 | |||||||||
| anaerobiosis | tcrB (1) | PG (1) | 1 | |||||||||||
| none (9) | PG (2), PC (6), HV (1) | 2 | 4 | 2 | 1 | |||||||||
| E. hirae (20) | ||||||||||||||
| aerobiosis | tcrB + cueO (6) | PG (2), AQ (4) | 1 | 3 | 2 | |||||||||
| tcrB (1) | PG (1) | 1 | ||||||||||||
| none (13) | PG (9), AQ (2), T (2) | 8 | 4 | 1 | ||||||||||
| anaerobiosis | tcrB + cueO (6) | PG (2), AQ (4) | 1 | 5 | ||||||||||
| tcrB (1) | PG (1) | 1 | ||||||||||||
| none (13) | PG (9), AQ (2), T (2) | 1 | 2 | 5 | 5 | |||||||||
| E. durans (4) | ||||||||||||||
| aerobiosis | none (4) | T (4) | 3 | 1 | ||||||||||
| anaerobiosis | none (4) | T (4) | 4 | |||||||||||
aClonality obtained by MLST and antibiotic resistance profiles are described in Silveira et al.3E. faecium STs included 5, 17, 18, 19, 30, 94, 101, 108, 123, 132, 133, 150, 184, 185, 393, 421, 428, 430, 432, 434, 670, 798, 845, 846, 847, 848, 859, 891 and 892, and E. faecalis STs included 9, 49, 53, 159, 224 and 330. MDR (resistant to at least three antibiotics of different families) isolates represent 64% of the isolates included (n = 143/225).3
bPG, pig + piggeries environment; AQ, aquaculture trout and environment; PC, poultry carcass; T, trout from supermarket; RTS, ready to eat salad; C, clinical isolates; HV, healthy human faeces; HS, hospital sewage water; R, river water.
cControl isolates: positive control, E. coli ED8739 (plasmid pRJ1004 with pco gene; MICCuSO4 = 28–36 mM in aerobiosis; MICCuSO4 = 16–20 mM in anaerobiosis);10 and negative control, E. faecium BM4105RF (negative for tcrB/cueO genes; MICCuSO4 = 8–12 mM in aerobiosis;3 MICCuSO4 = 2–4 mM in anaerobiosis).
dA black vertical line is positioned at the proposed tolerance cut-off of ≥16 mM under anaerobiosis.
eIsolates with no tcrYAZB amplicon by long PCR (Supplementary Data).
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