Table 5.
E coli isolates with blaCTX-M, blaTEM, blaSHV, blaOXA or blaAmpC genes as determined by PCR assay25–30 and/or characterised by whole-genome sequencing (WGS) from 16 (n=27) longitudinal study participants over a six-week study period
| Participant* (occupation) | Week | Isolate | Resistance profile | MDR | Phenotypic ESBL (3GCR) | Resistance genes by PCR assay | ST (CC) | Serotype | Plasmid type | Antimicrobial resistance genes | Virulence genes |
| F01 (Vet) | 1 | 416 | AmpNalCipChlTmpTet | Y | N (–) | blaAmpC (CIT) | – | – | – | – | – |
| F03 (Vet) | 1 | 1279 | AmpTmp | N | Y (Y) | blaCTX-M Grp 1 | 278 (CC-278) | O131:H4 | ColpVC*, IncB/O/K/Z*, IncF RST F17:A-:B5, IncI1 Incomplete ST | aadA5, blaCTX-M-15, dfrA17, mph(A), sul1 | aap, aaiC, aatA, aggR, capU, gad, iha, iss, lpfA, mchB, mchC, mchF, ORF4, pic, sat, sepA |
| 1281 | AmpTmpTet | Y | – (–) | – | 69 (CC-69) | O15:H18 | IncF RST F35:A6:B48, IncQ1 | blaTEM-1B, dfrA7, strA, strB, sul1, sul2, tet(A) | air, eilA, gad, iha, iroN, iss, lpfA | ||
| 1286 | AmpNalCipTmpTet | Y | – (–) | – | 131 | O16:H5 | Col156*, IncF RST F1:A1:B66 | blaCTX-M-15, dfrA14, mph(A), tet(B) | gad, iha, sat, senB | ||
| 2 | 735 | AmpTmp | N | Y (Y) | blaCTX-M Grp 1 | – | – | – | – | – | |
| 736 | Amp | N | Y (Y) | blaCTX-M Grp 1, blaTEM | 93 (CC-168) | O88:H38 | Col(BS512), IncB/O/K/Z, IncF RST F58:A-:B- | aadA1, blaCTX-M-15, blaTEM-1B, QnrS1 | aap, astA, gad, iss | ||
| 3 | 769 | AmpTmp | N | Y (Y) | blaCTX-M Grp 1 | – | – | – | – | – | |
| 768 | Amp | N | Y (Y) | blaCTX-M Grp 1, blaTEM | – | – | – | – | – | ||
| 770 | AmpNalTmp | Y | – (–) | – | 34 (CC-10) | O62:H30 | Col(BS512), Col156*, IncB/O/K/Z, IncF RST F36*:A-:B-, IncI1 Incomplete ST | blaTEM-1B, dfrA12, dfrA14, strA, strB, sul2, sul3, tet(A) | aap, capU, cba, gad, iha, iss, mchB, mchC, mchF | ||
| 4 | 1010 | AmpTmp | N | Y (Y) | blaCTX-M Grp 1 | – | – | – | – | – | |
| 1011 | AmpChlTmp | Y | Y (Y) | blaCTX-M Grp 1, blaTEM | 130 (CC-31) | O15:H12 | IncF RST F1:A6*:B33, IncQ1 | aac(3)-IId, aadA2, blaCTX-M-15, blaTEM-1B, catA1, dfrA12, mph(A), strA, strB, sul1, sul2, tet(A) | aap, aaiC, aar, agg3A, agg3B, agg3D, aggR, capU, eilA, gad, iha, iroN, iss, lpfA, nfaE, ORF4, pic | ||
| 1012 | AmpTmpTet | Y | – (–) | – | 10 (CC-10) | O2:H48 | Col(BS512), Col(MG828)*, Col156*, IncF RST F98:A-:B65 | blaTEM-1B, strA, strB, sul2, tet(A) | gad, iha, senB, sigA | ||
| 1017 | AmpAmcChlNalCipTmpTet | Y | – (–) | – | 88 (CC-23) | O25:H17 | Col156*, IncF RST F67:A6:B38 | aadA1, aph(3')-Ic, dfrA1, floR, strB, sul1, sul2, tet(B) | astA, gad, iha, iss, lpfA, mcmA, senB | ||
| 5 | 1149 | AmpChlTmp | Y | Y (Y) | blaCTX-M Grp 1, blaTEM | – | – | – | – | – | |
| 1151 | AmpNalTmp | Y | – (–) | – | 34 (CC-10) | H30 | Col(BS512), IncB/O/K/Z, IncF RST F2:A-:B- | blaTEM-1C, dfrA14, strA, strB, sul2 | aap, capU, cba, gad, iha, mchB, mchC, mchF, sat | ||
| 6 | 1214 | AmpChlTmp | Y | Y (Y) | blaCTX-M Grp 1, blaTEM | 130 (CC-31) | O17/O44:H1 | IncF RST F1:A-:B33 | aac(3)-IId, aadA2, blaCTX-M-15, blaTEM-1B, catA1, dfrA12, mph(A), sul1 | aap, aaiC, aar, agg3B, agg3C, agg3D, air, capU, eilA, gad, iha, lpfA, nfaE, ORF3, ORF4, pic | |
| F06 (Vet) | 3 | 662 | AmcTet | N | N (Y) | blaAmpC (ACC) | – | – | – | – | – |
| E10 (Vet) | 1 | 442 | AmpAmc | N | N (Y) | blaAmpC (CIT) | – | – | – | – | – |
| F13 (Vet) | 2 | 615 | AmpAmcTet | N | N (Y) | blaTEM, blaOXA | – | – | – | – | – |
| E15 (Vet) | 2 | 479 | None | N | N (N) | blaOXA | – | – | – | – | – |
| 4 | 701 | Amp | N | N (-) | blaAmpC (ACC) | – | – | – | – | – | |
| U16 (UVS) | 5 | 871 | Chl | N | Y (Y) | blaCTX-M Grp 9 | – | – | – | – | – |
| E21 (Vet) | 5 | 1018 | AmpChlTet | Y | Y (Y) | blaCTX-M Grp 1 | – | – | – | – | – |
| E24 (Vet) | 1 | 508 | Chl | N | N (N) | blaTEM, blaOXA | – | – | – | – | – |
| S25 (Vet) | 1 | 682 | AmpNalCip | N | Y (Y) | blaCTX-M Grp 9 | 131 | O25:H4 | Col156*, IncF RST F1:A-:B20 | blaCTX-M-27 | gad, iha, iss, senB |
| 684 | AmpTmpTet | Y | – (–) | – | 58 (CC-155) | O8:H8 | Col156*, IncF RST F29:A-:B10, IncX1*, IncY* | blaCTX-M-14, blaTEM-1B, dfrA14, fosA7, QnrS1, tet(A) | capU, gad, iroN, iss, lpfA, mchC, senB | ||
| 2 | 817 | AmpNalCip | N | Y (Y) | blaCTX-M Grp 9 | – | – | – | – | – | |
| 819 | AmpTmpTet | Y | – (–) | – | 69 (CC-69) | H18 | Col(BS512)*, IncQ1 | blaTEM-207, dfrA7, strA, strB, sul1, sul2, tet(A) | air, gad, iss, lpfA | ||
| 3 | 1026 | AmpNalCip | N | Y (Y) | blaCTX-M Grp 9 | 131 | O16:H4 | Col156*, IncF RST F1:A6:B20 | blaCTX-M-27, dfrA14 | espA, espF, gad, iha, iss, nfaE, sat, senB | |
| 1027 | AmpNal | N | Y (Y) | blaCTX-M Grp 9 | 131 | O25:H4 | Col156*, IncF RST F1:A2:B20 | blaCTX-M-27 | gad, iha, iss, sat, senB | ||
| 4 | 1233 | AmpNalCip | N | Y (Y) | blaCTX-M Grp 9, blaAmpC (ACC) | 131 | O25:H12 | Col156*, IncF RST F1:A2:B20 | aadA2, blaCTX-M-27, blaTEM-1B, dfrA12 | aaiC, agg3B, gad, iha, iss, nfaE, sat, senB | |
| 1234 | AmpNalCip | N | Y (Y) | blaCTX-M Grp 9 | – | – | – | – | – | ||
| 5 | 1242 | AmpNalCip | N | Y (Y) | blaCTX-M Grp 9 | – | – | – | – | – | |
| 1241 | AmpNal | N | Y (Y) | blaCTX-M Grp 9 | 38 (CC-38) | O86:H18 | Col(MG828)*, IncB/O/K/Z, IncF RST F51:A-:B10, IncI1 Incomplete ST | blaCTX-M-14, dfrA7 | air, capU, eilA, gad, iha, iss, nfaE, sat, senB | ||
| 6 | 1322 | AmpNalCip | N | Y (Y) | blaCTX-M Grp 9 | – | – | – | – | – | |
| 1316 | AmpNal | N | Y (Y) | blaCTX-M Grp 9 | – | – | – | – | – | ||
| S29 (Vet) | 5 | 1034 | AmpTmp | N | Y (Y) | blaCTX-M Grp 1 | – | – | – | – | – |
| E31 (Vet) | 1 | 540 | None | N | N (N) | blaTEM, blaOXA | – | – | – | – | – |
| 6 | 1272 | AmpAmc | N | N (Y) | blaAmpC (CIT) | – | – | – | – | – | |
| E41 (Vet) | 1 | 509 | AmpAmc | N | N (Y) | blaTEM, blaOXA | – | – | – | – | – |
| 2 | 610 | AmpAmc | N | N (-) | blaAmpC (CIT) | – | – | – | – | – | |
| E46 (VN) | 4 | 1082 | AmpTmpTet | Y | Y (Y) | blaCTX-M Grp 1 | – | – | – | – | – |
| S55 (AS) | 1 | 516 | AmpChlTet | Y | N (N) | blaSHV | – | – | – | – | – |
| 6 | 1133 | AmpAmcChlNalTmpTet | Y | – (–) | – | 75 | H8 | Col156; IncF RST F29:A-:B10, IncX1; | fosA7 | gad, ireA, iroN, iss, lpfA, mchB, mchC, mchF, mcmA, pic, senB | |
| S59 (Vet) | 1 | 1002 | Amp | N | Y (Y) | blaCTX-M Grp 9, blaTEM | 127 | H31 | Col(BS512), Col156*, IncB/O/K/Z, IncF RST F29:A-:B10, IncI1 Incomplete ST | blaCTX-M-14, blaTEM-1A | gad, ireA, iss, senB, vat |
| 1005 | AmpNalTet | Y | – (–) | – | 69 (CC-69) | O25:H4 | Col(BS512)*, Col156*, IncF RST F95:A-:B1 | blaTEM-1B, tet(B) | air, gad, iss, lpfA, senB | ||
| 1008 | AmpNalCip | N | – (–) | – | 38 (CC-38) | O1:H15 | Col(BS512), Col156*, IncF RST F29:A-:B10 | blaTEM-1B | air, eilA, gad, iss, senB | ||
| 2 | 1105 | Amp | N | Y (Y) | blaCTX-M Grp 9, blaTEM | 127 | O6:H31 | Col156*, IncB/O/K/Z, IncF RST F29:A-:B10, IncI1 Incomplete ST | blaCTX-M-14, blaTEM-1A, QnrS1 | gad, ireA, iss, senB, vat | |
| 3 | 1192 | AmpTet | N | Y (Y) | blaCTX-M Grp 9, blaTEM | 127 | H31 | Col(BS512), Col156*, IncB/O/K/Z, IncF RST F29:A-:B10, IncI1 Unknown ST | aadA2, blaCTX-M-14, blaTEM-1A, strB, sul2, tet(A) | aaiC, agg3B, cba, gad, iss, senB, vat | |
| 5 | 1338 | AmpTmpTet | Y | Y (Y) | blaCTX-M Grp 9, blaTEM | Unknown | O16:H19 | IncB/O/K/Z, IncF RST F1:A2:B15, IncI1 Incomplete ST | blaCTX-M-27, blaTEM-1B, dfrA8, dfrA14, strA, strB, sul2, tet(B) | astA, eae, espA, espI, etpD, iha, iss, nfaE, nleA, nleB, senB, tir | |
| 6 | 1345 | Amp | N | Y (Y) | blaCTX-M Grp 9, blaTEM | – | – | – | – | – |
*Letter in front of participant’s ID number indicates workplace (E=equine hospital, S=small animal hospital, F=farm animal hospital, U=undergraduate veterinary student).
–, not tested; 3GCR, resistance to at least one third-generation cephalosporin on double disc diffusion testing; Amc, amoxicillin clavulanate resistance; Amp, ampicillin resistance; AS, auxiliary staff; CC, clonal complex; Chl, chloramphenicol resistance; Cip, ciprofloxacin resistance; Grp, group; MDR, multidrug resistance; n, no; Nal, nalidixic acid resistance; ST, sequence type; Tet, tetracycline resistance; UVS, undergraduate veterinary student; Vet, veterinary surgeon; VN, veterinary nurse; Y, yes.