Table 5

E coli isolates with bla CTX-M, bla TEM, bla SHV, bla OXA or bla AmpC 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)WeekIsolateResistance profileMDRPhenotypic ESBL (3GCR)Resistance genes by PCR assayST (CC)SerotypePlasmid typeAntimicrobial resistance genesVirulence genes
F01 (Vet)1416AmpNalCipChlTmpTetYN (–) bla AmpC (CIT)
F03 (Vet)11279AmpTmpNY (Y) bla CTX-M Grp 1278 (CC-278)O131:H4ColpVC*, IncB/O/K/Z*, IncF RST F17:A-:B5, IncI1 Incomplete ST aadA5, bla CTX-M-15 , dfrA17, mph(A), sul1 aap, aaiC, aatA, aggR, capU, gad, iha, iss, lpfA, mchB, mchC, mchF, ORF4, pic, sat, sepA
1281AmpTmpTetY– (–) 69 (CC-69)O15:H18IncF RST F35:A6:B48, IncQ1 bla TEM-1B , dfrA7, strA, strB, sul1, sul2, tet(A) air, eilA, gad, iha, iroN, iss, lpfA
1286AmpNalCipTmpTetY– (–)131O16:H5Col156*, IncF RST F1:A1:B66 bla CTX-M-15 , dfrA14, mph(A), tet(B) gad, iha, sat, senB
 2735AmpTmpNY (Y) bla CTX-M Grp 1
736AmpNY (Y) bla CTX-M Grp 1, bla TEM 93 (CC-168)O88:H38Col(BS512), IncB/O/K/Z, IncF RST F58:A-:B- aadA1, bla CTX-M-15 , bla TEM-1B , QnrS1 aap, astA, gad, iss
 3769AmpTmpNY (Y) bla CTX-M Grp 1
768AmpNY (Y) bla CTX-M Grp 1, bla TEM
770AmpNalTmpY– (–) 34 (CC-10)O62:H30Col(BS512), Col156*, IncB/O/K/Z, IncF RST F36*:A-:B-, IncI1 Incomplete ST bla TEM-1B , dfrA12, dfrA14, strA, strB, sul2, sul3, tet(A) aap, capU, cba, gad, iha, iss, mchB, mchC, mchF
 41010AmpTmpNY (Y) bla CTX-M Grp 1
1011AmpChlTmpYY (Y) bla CTX-M Grp 1, bla TEM 130 (CC-31)O15:H12IncF RST F1:A6*:B33, IncQ1 aac(3)-IId, aadA2, bla CTX-M-15 , bla TEM-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
1012AmpTmpTetY– (–) 10 (CC-10)O2:H48Col(BS512), Col(MG828)*, Col156*, IncF RST F98:A-:B65 bla TEM-1B , strA, strB, sul2, tet(A) gad, iha, senB, sigA
1017AmpAmcChlNalCipTmpTetY– (–) 88 (CC-23)O25:H17Col156*, IncF RST F67:A6:B38 aadA1, aph(3')-Ic, dfrA1, floR, strB, sul1, sul2, tet(B) astA, gad, iha, iss, lpfA, mcmA, senB
 51149AmpChlTmpYY (Y) bla CTX-M Grp 1, bla TEM
1151AmpNalTmpY– (–) 34 (CC-10)H30Col(BS512), IncB/O/K/Z, IncF RST F2:A-:B- bla TEM-1C , dfrA14, strA, strB, sul2 aap, capU, cba, gad, iha, mchB, mchC, mchF, sat
 61214AmpChlTmpYY (Y) bla CTX-M Grp 1, bla TEM 130 (CC-31)O17/O44:H1IncF RST F1:A-:B33 aac(3)-IId, aadA2, bla CTX-M-15 , bla TEM-1B , catA1, dfrA12, mph(A), sul1 aap, aaiC, aar, agg3B, agg3C, agg3D, air, capU, eilA, gad, iha, lpfA, nfaE, ORF3, ORF4, pic
F06 (Vet)3662AmcTetNN (Y) bla AmpC (ACC)
E10 (Vet)1442AmpAmcNN (Y) bla AmpC (CIT)
F13 (Vet)2615AmpAmcTetNN (Y) bla TEM, bla OXA
E15 (Vet)2479NoneNN (N) bla OXA
 4701AmpNN (-) bla AmpC (ACC)
U16 (UVS)5871ChlNY (Y) bla CTX-M Grp 9
E21 (Vet)51018AmpChlTetYY (Y) bla CTX-M Grp 1
E24 (Vet)1508ChlNN (N) bla TEM, bla OXA
S25 (Vet)1682AmpNalCipNY (Y) bla CTX-M Grp 9131O25:H4Col156*, IncF RST F1:A-:B20 bla CTX-M-27 gad, iha, iss, senB
684AmpTmpTetY– (–) 58 (CC-155)O8:H8Col156*, IncF RST F29:A-:B10, IncX1*, IncY* bla CTX-M-14 , bla TEM-1B , dfrA14, fosA7, QnrS1, tet(A) capU, gad, iroN, iss, lpfA, mchC, senB
 2817AmpNalCipNY (Y) bla CTX-M Grp 9
819AmpTmpTetY– (–) 69 (CC-69)H18Col(BS512)*, IncQ1 bla TEM-207 , dfrA7, strA, strB, sul1, sul2, tet(A) air, gad, iss, lpfA
 31026AmpNalCipNY (Y) bla CTX-M Grp 9131O16:H4Col156*, IncF RST F1:A6:B20 bla CTX-M-27 , dfrA14 espA, espF, gad, iha, iss, nfaE, sat, senB
1027AmpNalNY (Y) bla CTX-M Grp 9131O25:H4Col156*, IncF RST F1:A2:B20 bla CTX-M-27 gad, iha, iss, sat, senB
 41233AmpNalCipNY (Y) bla CTX-M Grp 9, bla AmpC (ACC)131O25:H12Col156*, IncF RST F1:A2:B20 aadA2, bla CTX-M-27 , bla TEM-1B , dfrA12 aaiC, agg3B, gad, iha, iss, nfaE, sat, senB
1234AmpNalCipNY (Y) bla CTX-M Grp 9
 51242AmpNalCipNY (Y) bla CTX-M Grp 9
1241AmpNalNY (Y) bla CTX-M Grp 938 (CC-38)O86:H18Col(MG828)*, IncB/O/K/Z, IncF RST F51:A-:B10, IncI1 Incomplete ST bla CTX-M-14 , dfrA7 air, capU, eilA, gad, iha, iss, nfaE, sat, senB
 61322AmpNalCipNY (Y) bla CTX-M Grp 9
1316AmpNalNY (Y) bla CTX-M Grp 9
S29 (Vet)51034AmpTmpNY (Y) bla CTX-M Grp 1
E31 (Vet)1540NoneNN (N) bla TEM, bla OXA
 61272AmpAmcNN (Y) bla AmpC (CIT)
E41 (Vet)1509AmpAmcNN (Y) bla TEM, bla OXA
 2610AmpAmcNN (-) bla AmpC (CIT)
E46 (VN)41082AmpTmpTetYY (Y) bla CTX-M Grp 1
S55 (AS)1516AmpChlTetYN (N) bla SHV
 61133AmpAmcChlNalTmpTetY– (–) 75H8Col156; IncF RST F29:A-:B10, IncX1; fosA7 gad, ireA, iroN, iss, lpfA, mchB, mchC, mchF, mcmA, pic, senB
S59 (Vet)11002AmpNY (Y) bla CTX-M Grp 9, bla TEM 127H31Col(BS512), Col156*, IncB/O/K/Z, IncF RST F29:A-:B10, IncI1 Incomplete ST bla CTX-M-14 , bla TEM-1A gad, ireA, iss, senB, vat
1005AmpNalTetY– (–) 69 (CC-69)O25:H4Col(BS512)*, Col156*, IncF RST F95:A-:B1 bla TEM-1B , tet(B) air, gad, iss, lpfA, senB
1008AmpNalCipN– (–) 38 (CC-38)O1:H15Col(BS512), Col156*, IncF RST F29:A-:B10 bla TEM-1B air, eilA, gad, iss, senB
 21105AmpNY (Y) bla CTX-M Grp 9, bla TEM 127O6:H31Col156*, IncB/O/K/Z, IncF RST F29:A-:B10, IncI1 Incomplete ST bla CTX-M-14 , bla TEM-1A , QnrS1 gad, ireA, iss, senB, vat
 31192AmpTetNY (Y) bla CTX-M Grp 9, bla TEM 127H31Col(BS512), Col156*, IncB/O/K/Z, IncF RST F29:A-:B10, IncI1 Unknown ST aadA2, bla CTX-M-14 , bla TEM-1A , strB, sul2, tet(A) aaiC, agg3B, cba, gad, iss, senB, vat
 51338AmpTmpTetYY (Y) bla CTX-M Grp 9, bla TEM UnknownO16:H19IncB/O/K/Z, IncF RST F1:A2:B15, IncI1 Incomplete ST bla CTX-M-27 , bla TEM-1B , dfrA8, dfrA14, strA, strB, sul2, tet(B) astA, eae, espA, espI, etpD, iha, iss, nfaE, nleA, nleB, senB, tir
 61345AmpNY (Y) bla CTX-M Grp 9, bla TEM
  • *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.