Table 1.
Prevalence and origin of Salmonella isolates used in this study, distribution of ESBL/pAmpC genes and selection of isolates for WGS.
| Number of samples | Salmonella-positive (%) | ESBL/pAmpC-producing Salmonella (%) a | blaCMY-2-like | blaCTX-M-2 group | blaSHV family | blaCMY-2-like-blaCTX-M-2 group | blaCMY-2-like-blaSHV family | |
|---|---|---|---|---|---|---|---|---|
| Farms | 74 | 28 (38) | 17 (61) | 16/2b | – | – | – | 1/1b |
| 2008 | 65 | 23 | 17 | 16 | – | – | – | 1 |
| 2009 | 9 | 5 | – | – | – | – | – | – |
| Slaughter | 644 | 140 (22) | 82 (59) | 54/4b | 25/2b | – | 2/2b | 1/1b |
| 2008 | 40 | 5 | 3 | 3 | – | – | – | – |
| 2012 | 251 | 76 | 39 | 31 | 8 | – | – | – |
| 2013 | 353 | 59 | 40 | 20 | 17 | – | 2 | 1 |
| Retail | 1554 | 410 (26) | 136 (33) | 98/7b | 27/6b | 7/7b | 1/1b | 3/3b |
| 2009 | 179 | 38 | 11 | 11 | – | – | – | – |
| 2010 | 387 | 156 | 35 | 29 | 1 | 4 | – | 1 |
| 2011 | 823 | 170 | 76 | 49 | 22 | 2 | 1 | 2 |
| 2012 | 165 | 46 | 14 | 9 | 4 | 1 | – | – |
| Total | 2272 | 578 (25) | 235 (41) | 168/13 b | 52/8b | 7/7b | 3/3b | 5/5b |
a
Based on PCR screening of ESBL/pAmpC genes.
b
ESBL/pAmpC-positive samples/Selected for whole genome sequencing.