Table 3.
Antimicrobial resistance phenotype and characterisation by whole genome sequencing (WGS) of 29 E coli isolates from 84 cross-sectional study participants, ordered by MLST sequence type
| Isolate (participant†) | Phenotype | MDR | ESBL (3GCR) | ST | Serotype | Plasmid type | Antimicrobial Resistance Genes | Virulence Genes |
| 101 (F18) | AmpChlNalCipTmpTet | Y | –-(–) | 10 (CC-10) | O9:H9 | IncF RST F67:A6:B38 | aadA1, blaTEM-1A, dfrA1, floR, strA, strB, sul2, tet(A), tet(B) | astA, gad, mchB, mchC, mchF |
| 380 (S74) | AmpNalCipTmpTet | Y | – | 10 (CC-10) | H4 | Col(MP18)*; Col(BS512); Col156*; IncI1(ST-3); | blaTEM-1B, dfrA1, QnrB19, sul2, tet(A) | gad |
| 386 (S76) | AmpNalTmpTet | Y | – | 13 (CC-13) | H8 | Col(MP18)*; IncB/O/K/Z*; IncF RST C3*:A-:B1, IncQ1; | aadA1, blaTEM-1B, dfrA1, strA, strB, sul1, sul2, tet(A) | gad, iha, iss, lpfA |
| 59 (F11) | TmpTet | N | – (–) | 58 | O9:H25 | Col156; IncF RST F4:A-:B1; IncQ1 | aph(3')-Ia, blaTEM-1B, dfrA5, strA, strB, sul2, tet(A) | air, capU, gad, iha, ireA, iroN, iss, lpfA, mchF, mcmA, senB |
| 36 (F04) | AmpTmpTet | Y | – (–) |
59 (CC-59) | H7 | Col156*; IncF RST F4:A-:B10 | blaTEM-1C, dfrA17, tet(A) | air, capU, eilA, gad, iha, lpfA, sat, senB |
| 161 (F30) | AmpTmpTet | Y | – (–) | 69 (CC-69) | H1 | Col156*, IncF RST F87*:A4:B10, IncI1(ST-242)* | aadA5, blaTEM-1B, dfrA17, sul1 | air, gad, iss, lpfA, senB |
| 181 (E33) | AmpNalTmpTet | Y | – (–) | 69 (CC-69) | O15:H18 | Col156*; IncB/O/K/Z; IncF RST F52:A6*:B48, IncI1 Incomplete ST; IncQ1; | blaTEM-1B, dfrA7, strA, strB, sul1, sul2, tet(A) | air, celb, eilA, gad, iha, ireA, iroN, iss, lpfA |
| 121 (F22) | AmpChlTet | Y | – (–) | 88 (CC-23) | O9:H19 | IncF RST F2:A-:B-, IncI1 Unknown ST, IncI2* | aadA1, catA1, strA, strB, tet(B) | gad, iss, lpfA, mcmA |
| 299 (S59) | Amp | N | Y (Y) | 127 | O6:H31 | Col(BS512); Col(MG828)*; Col156*; IncB/O/K/Z; IncF RST F29:A-:B10, IncI1 Incomplete ST; IncX1*; | aadA5, aadA15, blaCTX-M-14, blaTEM-1A, cml, dfrA12, strB, sul1, tet(B) | celb, gad, ireA, iss, lpfA, senB, vat |
| 350 (S68) | AmpNalCip | N | Y (Y) | 131 | O25:H4 | Col(BS512); Col156*; IncF RST F1:A2:B20 | blaCTX-M-27 | gad, iha, iss, sat, senB |
| 151 (S27) | AmpTmpTet | Y | – (–) | 141 | H6 | IncI1(ST223*); IncX1*; p0111*; | aac(3)-IIa, aadA1, aph(3')-Ia, blaTEM-1B, dfrA1, strA, strB, sul2, tet(A) | astA, gad, iroN, iss, mchB, mchC, mchF, mcmA, vat |
| 229 (E42) | AmpChlTmpTet | Y | – (–) | 141 | O50/O2:H6 | IncF RST F40:A-:B-, IncQ1; | aac(3)-IId, aac(6')Ib-cr, aacA4, ARR-3, blaTEM-1B, catA1, catA2, dfrA12, mph(E), msr(E), strA, strB, sul1, sul2, tet(A) | cba, cma, gad, iroN, iss, mchB, mchC, mchF, mcmA, vat |
| 200 (E38) | AmpChlNalCipTmpTet | Y | Y (Y) | 405 (CC-405) | H6 | IncF RST F1:A1:B49, IncQ1; | aac(3)-IId, aac(6')Ib-cr, aadA5, blaCTX-M-15, blaOXA-1, blaTEM-1B, catB4, dfrA17, mph(A), strA, strB, sul1, sul2, tet(B) | air, gad |
| 288 (S57) | AmpAmcChlNalCipTmpTet | Y | Y (Y) | 405 (CC-405) | O102:H6 | Col(BS512); Col156*; IncF RST F87*:A4:B1, p0111*; |
aac(6')Ib-cr, aadA5, blaCTX-M-15, blaOXA-1, catB4, dfrA17, mph(A), strB, sul1, tet(B) | air, celb, eilA, gad, iha, ireA, iroN, iss, lpfA |
| 254 (E49) | AmpAmcChlNalCipTmp | Y | – (–) | 410 (CC-23) | H9 | IncI1(ST-26*) | aadA1, blaOXA-1, blaTEM-33, floR, sul1, sul2 | gad, lpfA |
| 258 (E49) | AmpAmcNalCip | N | – (–) | 410 (CC-23) | H9 | IncI1(ST-26*) | aadA1, blaOXA-1, blaTEM-33, strB, sul1 | gad, lpfA |
| 12 (F03) | AmpNalCip | N | Y (Y) | 648 | H6 | IncF RST F4:A-:B52, p0111* | aac(3)-IIa, aac(6')Ib-cr, blaCTX-M-15, blaOXA-1, blaTEM-1B, catB4 | air, gad, lpfA, nfaE, sat |
| 17 (F03) | AmpNalCipTet | Y | – (–) | 648 | H6 | IncF RST F4:A-:B52, p0111* | aac(3)-IIa, aac(6')Ib-cr, blaCTX-M-15, blaOXA-1, blaTEM-1B, catB4 | air, eilA, gad, lpfA, nfaE, sat |
| 91 (F16) | AmpChlNalCipTmpTet | Y | – (–) | 744 | O89:H10 | IncHI1(ST6*), IncQ1 | aadA5, aph(3')-Ia, blaTEM-1B, catA1, dfrA17, mph(A), strA, strB, sul1, sul2, tet(B) | gad, lpfA, pic, senB, vat |
| 175 (F32) | AmpAmcTmpTet | Y | – (–) | 778 | H18 | IncF RST F1:A1*:B1, IncQ1 | blaTEM-1B, dfrA14, dfrA8, mph(A), strA, strB, sul2, tet(A) | aap, astA, gad, iss, nfaE |
| 331 (S64) | AmpAmc | N | N (Y) | 963 | H18 | Col(BS512)*; Col156*; IncF RST F29:A-:B10 | blaCMY-2 | air, gad, senB |
| 05 (F01) | AmpAmcChlNalTmpTet | Y | – (–) | 1861 | O16:H5 | Col(BS512), IncF RST F31*:A-:B10*, IncI1 Incomplete ST | dfrA17 | gad, lpfA, pic, senB, vat |
| 199 (E37) | AmpNalTet | Y | – (–) | 2076 | O17/44:H18 | IncF RST F77:A-:B12* | blaTEM-1B | air, capU, celb, eilA, gad, lpfA |
| 266 (F51) | AmpAmcNalCip | N | N (Y) | 3944 | O8:H2 | IncI1(ST-12); IncY* | blaCMY-2 | gad |
| 267 (F51) | AmpAmcChlNalCipTmp | Y | N (Y) | 3944 | O8:H2 | IncI1(ST-12); IncX1*; IncY* | aadA1, aadA2, blaCMY-2, cmlA1, dfrA12, sul3 | gad |
| 73 (F13) | AmpAmcNalTmpTet | Y | – (–) | 6899 | H18 | IncF RST F40:A-:B-, IncN(ST3) | blaTEM-1B, QnrS1, strA, strB, sul2, tet(A) | air, eilA, gad, iss, lpfA |
| 123 (F22) | AmpAmcChlNalCipTmpTet | Y | – (–) | Unknown | O9 | IncF RST F-:A-:B38 | aadA1, dfrA1, strB, sul1, sul2, tet(B) | astA, gad, iss |
| 131 (E24) | AmpChlTet | Y | – (–) | Unknown | Unknown | IncHI1(ST11*) | blaSHV-40, fosA | None Detected |
| 411 (E79) | Amp | N | N (N) | Unknown | Unknown | IncF RST F-:A-:B50* | None Detected | gad, iss |
*Allelic match of <100%.
† Letter in front of participant’s ID number indicates workplace (E = equine hospital, S =small animal hospital, F =farm animal hospital).
–, not tested; 3GCR, resistance to at least one third-generation cephalosporin on double disc diffusion testing; Amc, amoxicillin clavulanate resistance; Amp, ampicillin resistance; CC, clonal complex; Chl, chloramphenicol resistance; Cip, ciprofloxacin resistance; ESBL, phenotypic ESBL-producer on double disc diffusion testing; MDR, multidrug resistance; n, no; Nal, nalidixic acid resistance; ST, sequence type; Tmp, trimethoprim resistance; Tet, tetracycline resistance; Y, yes.