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†)PhenotypeMDRESBL (3GCR)STSerotypePlasmid typeAntimicrobial Resistance GenesVirulence Genes
101 (F18)AmpChlNalCipTmpTetY–-(–)10 (CC-10)O9:H9IncF RST F67:A6:B38 aadA1, bla TEM-1A , dfrA1, floR, strA, strB, sul2, tet(A), tet(B) astA, gad, mchB, mchC, mchF
380 (S74)AmpNalCipTmpTetY10 (CC-10)H4Col(MP18)*; Col(BS512); Col156*; IncI1(ST-3); bla TEM-1B , dfrA1, QnrB19, sul2, tet(A) gad
386 (S76)AmpNalTmpTetY13 (CC-13)H8Col(MP18)*; IncB/O/K/Z*; IncF RST C3*:A-:B1, IncQ1; aadA1, bla TEM-1B , dfrA1, strA, strB, sul1, sul2, tet(A) gad, iha, iss, lpfA
59 (F11)TmpTetN– (–)58O9:H25Col156; IncF RST F4:A-:B1; IncQ1 aph(3')-Ia, bla TEM-1B , dfrA5, strA, strB, sul2, tet(A) air, capU, gad, iha, ireA, iroN, iss, lpfA, mchF, mcmA, senB
36 (F04)AmpTmpTetY
(–)
59 (CC-59)H7Col156*; IncF RST F4:A-:B10 bla TEM-1C , dfrA17, tet(A) air, capU, eilA, gad, iha, lpfA, sat, senB
161 (F30)AmpTmpTetY– (–)69 (CC-69)H1Col156*, IncF RST F87*:A4:B10, IncI1(ST-242)* aadA5, bla TEM-1B , dfrA17, sul1 air, gad, iss, lpfA, senB
181 (E33)AmpNalTmpTetY– (–)69 (CC-69)O15:H18Col156*; IncB/O/K/Z; IncF RST F52:A6*:B48, IncI1 Incomplete ST; IncQ1; bla TEM-1B , dfrA7, strA, strB, sul1, sul2, tet(A) air, celb, eilA, gad, iha, ireA, iroN, iss, lpfA
121 (F22)AmpChlTetY– (–)88 (CC-23)O9:H19IncF RST F2:A-:B-, IncI1 Unknown ST, IncI2* aadA1, catA1, strA, strB, tet(B) gad, iss, lpfA, mcmA
299 (S59)AmpNY (Y)127O6:H31Col(BS512); Col(MG828)*; Col156*; IncB/O/K/Z; IncF RST F29:A-:B10, IncI1 Incomplete ST; IncX1*; aadA5, aadA15, bla CTX-M-14 , bla TEM-1A , cml, dfrA12, strB, sul1, tet(B) celb, gad, ireA, iss, lpfA, senB, vat
350 (S68)AmpNalCipNY (Y)131O25:H4Col(BS512); Col156*; IncF RST F1:A2:B20 bla CTX-M-27 gad, iha, iss, sat, senB
151 (S27)AmpTmpTetY– (–)141H6IncI1(ST223*); IncX1*; p0111*; aac(3)-IIa, aadA1, aph(3')-Ia, bla TEM-1B , dfrA1, strA, strB, sul2, tet(A) astA, gad, iroN, iss, mchB, mchC, mchF, mcmA, vat
229 (E42)AmpChlTmpTetY– (–)141O50/O2:H6IncF RST F40:A-:B-, IncQ1; aac(3)-IId, aac(6')Ib-cr, aacA4, ARR-3, bla TEM-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)AmpChlNalCipTmpTetYY (Y)405 (CC-405)H6IncF RST F1:A1:B49, IncQ1; aac(3)-IId, aac(6')Ib-cr, aadA5, bla CTX-M-15 , bla OXA-1 , bla TEM-1B , catB4, dfrA17, mph(A), strA, strB, sul1, sul2, tet(B) air, gad
288 (S57)AmpAmcChlNalCipTmpTetYY (Y)405 (CC-405)O102:H6Col(BS512); Col156*;
IncF RST F87*:A4:B1, p0111*;
aac(6')Ib-cr, aadA5, bla CTX-M-15 , bla OXA-1 , catB4, dfrA17, mph(A), strB, sul1, tet(B) air, celb, eilA, gad, iha, ireA, iroN, iss, lpfA
254 (E49)AmpAmcChlNalCipTmpY– (–)410 (CC-23)H9IncI1(ST-26*) aadA1, bla OXA-1 , bla TEM-33 , floR, sul1, sul2 gad, lpfA
258 (E49)AmpAmcNalCipN– (–)410 (CC-23)H9IncI1(ST-26*) aadA1, bla OXA-1 , bla TEM-33 , strB, sul1 gad, lpfA
12 (F03)AmpNalCipNY (Y)648H6IncF RST F4:A-:B52, p0111* aac(3)-IIa, aac(6')Ib-cr, bla CTX-M-15 , bla OXA-1 , bla TEM-1B , catB4 air, gad, lpfA, nfaE, sat
17 (F03)AmpNalCipTetY– (–)648H6IncF RST F4:A-:B52, p0111* aac(3)-IIa, aac(6')Ib-cr, bla CTX-M-15 , bla OXA-1 , bla TEM-1B , catB4 air, eilA, gad, lpfA, nfaE, sat
91 (F16)AmpChlNalCipTmpTetY– (–)744O89:H10IncHI1(ST6*), IncQ1 aadA5, aph(3')-Ia, bla TEM-1B , catA1, dfrA17, mph(A), strA, strB, sul1, sul2, tet(B) gad, lpfA, pic, senB, vat
175 (F32)AmpAmcTmpTetY– (–)778H18IncF RST F1:A1*:B1, IncQ1 bla TEM-1B , dfrA14, dfrA8, mph(A), strA, strB, sul2, tet(A) aap, astA, gad, iss, nfaE
331 (S64)AmpAmcNN (Y)963H18Col(BS512)*; Col156*; IncF RST F29:A-:B10 bla CMY-2 air, gad, senB
05 (F01)AmpAmcChlNalTmpTetY– (–)1861O16:H5Col(BS512), IncF RST F31*:A-:B10*, IncI1 Incomplete ST dfrA17 gad, lpfA, pic, senB, vat
199 (E37)AmpNalTetY– (–)2076O17/44:H18IncF RST F77:A-:B12* bla TEM-1B air, capU, celb, eilA, gad, lpfA
266 (F51)AmpAmcNalCipNN (Y)3944O8:H2IncI1(ST-12); IncY* bla CMY-2 gad
267 (F51)AmpAmcChlNalCipTmpYN (Y)3944O8:H2IncI1(ST-12); IncX1*; IncY* aadA1, aadA2, bla CMY-2 , cmlA1, dfrA12, sul3 gad
73 (F13)AmpAmcNalTmpTetY– (–)6899H18IncF RST F40:A-:B-, IncN(ST3) bla TEM-1B , QnrS1, strA, strB, sul2, tet(A) air, eilA, gad, iss, lpfA
123 (F22)AmpAmcChlNalCipTmpTetY– (–)UnknownO9IncF RST F-:A-:B38 aadA1, dfrA1, strB, sul1, sul2, tet(B) astA, gad, iss
131 (E24)AmpChlTetY– (–)UnknownUnknownIncHI1(ST11*) bla SHV-40 , fosA None Detected
411 (E79)AmpNN (N)UnknownUnknownIncF 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.