TABLE 2.
Characterization and comparative analysis of the strains by two different methods, viz., PCR and whole-genome sequencing (WGS)a
| Strain characteristics |
PCR-based findings |
WGS-based findings |
|||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Strain ID | Year of isolation | ST/CCb | Aminoglycoside resistance genes | Beta-lactamases and carbapenemases (bla) | Quinolone resistance genes | Virulence determinants | PBRT and primer walking | Integron/integrase/GC array | Aminoglycoside resistance genes | Beta-lactamases (bla) | Carbapenemases (bla) | Quinolone resistance genes | Other resistance genes (family) | Virulence determinants; CPS cluster genes; capsular type; virulence sequence type; integrative conjugative element | Plasmid type | Integron/GC array | GenBank accession no. |
| Kp1 | 2013 | ST48/CC48 | Not found | CTX-M-15, TEM-1B, SHV-1, OXA-1, OXA-181 | oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH | IncFIIK, Col | intI1 | aac(3)-IIa, aph(6)-Id, aph(3″)-Ib, aadA2 | TEM-1B SHV-1, OXA-1, CTX-M-15 |
OXA-181 | oqxAB, aac(6′)-Ib-cr | fosA (fosfomycin); mph(A) (macrolide); catA1, catB3 (phenicol); sul1, sul2 (sulphonamide); dfrA12 (trimethoprim); arsABCDR (arsenic), pcoABCDERS (copper), silABCEFGPRS (silver) | mrkABCDFHIJ; fimABCDEFGHIK; iutA; entABCDEFS, fepABCDG, fes; iroEN; fyuA, irp1, irp2, ybtAEPQSTUX; rcsA, rcsB; T6SS-I/II/III; LPS rfb locus, wzi62, wzc62; K62, O1/O2v1; ybt14; ICEKp5 | IncFIIK, IncFIB (K), IncFIB (pQil), ColKP3 | In27 | VSLB00000000 |
| Kp2 | 2014 | ST48/CC48 | aac(6′)-Ib | CTX-M-15, TEM-1B, OXA-1, OXA-181 | qnrB, oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH | IncFII, IncFIIK, Col | In27, intI1 | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND |
| Kp3 | 2014 | ST14/CC15 | rmtB, aac(6′)-Ib | NDM-5, CTX-M-15, TEM-1B, SHV-28, OXA-1, OXA-232 | oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH, mrkD | IncFII, IncFIIK, IncR, Col | intI1 | rmtB, aac(6′)-Ib, aadA1, aadA2, aph(6)-Id, aph(3″)-Ib, aac(3)-IId | TEM-1B SHV-28 OXA-1,9, CTX-M-15 |
NDM-5, OXA-232 | oqxAB, aac(6′)-Ib-cr | fosA (fosfomycin); mph(A), ere(A), erm(B) (macrolide); catB3, cmlA1, catA1 (phenicol); sul1, sul2 (sulphonamide); dfrA1, dfrA12 (trimethoprim); arsABCDR (arsenic); pcoABCDER (copper); silACEFGPRS (silver); merACDEPRT (mercury) | mrkABCDFHIJ; fimABCDEFGHIK, pilW; iutA; entABCDEFS, fepABCDG, fes; iroEN; fyuA, irp1, irp2; ybtAEPQSTUX; rcsA, rcsB; T6SS-I/II/III; LPS rfb locus, wzi2, wzc2; K2, O1/O2v1; ybt14; ICEKp5 | IncR, IncFIIK, IncFII, IncFIB (K), IncFIA (HI1), ColKP3 | In27, In578 | VSLC00000000 |
| Kp4 | 2015 | ST15/CC15 | aac(6′)-Ib | CTX-M-15, SHV-28, OXA-1, OXA-181 | qnrB, oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH, mrkD | IncFIIK, Col | intI1 | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND |
| Kp5 | 2015 | ST15/CC15 | aac(6′)-Ib | CTX-M-15, TEM-1A, SHV-28, OXA-1, OXA-181 | qnrB, oqxAB, aac(6′)-Ib-cr | uge, fimH, mrkD | IncFII, IncFIIK | intI1 | aac(6′)-Ib, aadA1, aph(3″)-Ib, aph(6)-Id, aac(6′)-Ib3 | TEM-1A SHV-28 OXA-1,9, CTX-M-15 |
OXA-181 | qnrB1, oqxAB, aac(6′)-Ib-cr | fosA (fosfomycin); mph(A) (macrolide); catB3 (phenicol); sul2 (sulphonamide); tet(A) (tetracycline); dfrA14 (trimethoprim); arsABCR (arsenic); pcoABCDERS (copper); silABCEFGPRS (silver) | mrkCDH; fimCDHK; iutA; entCEFS, fepABCDG, fes; iroE; fyuA, irp1, irp2; ybtAEPQSUX; rcsA; T6SS-I/II/III; LPS rfb locus, wzi151; K48, O1v1; ybt1; ICEKp4 | IncFIIK, IncFII | In191 | WMCH00000000 |
| Kp6 | 2016 | ST23/CC23 | armA, aac(6′)-Ib | CTX-M-15, TEM-1B, SHV-190, OXA-232, CMY-4 | qnrB, oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH, mrkD, kfuBC, wcaJ, rmpA, magA | IncA/C, IncFIIK, IncX3, Col | intI1 |
armA, rmtF aac(6′)-Ib, aph(3″)-Ib, aph(6)-Id |
TEM-1B SHV-190, CTX-M-15, CMY-4 |
OXA-232 | qnrB1, oqxAB, aac(6′)-Ib-cr | fosA (fosfomycin); msr(E), mph(E) (macrolide); catA1 (phenicol); arr-2 (rifampin); sul1, sul2 (sulphonamide); dfrA14 (trimethoprim); pcoABCDER (copper); silCERS (silver); terABDEWZ (tellurite); pbrAR (lead) | mrkABCDFIJ; fimABCDEFGHIK; iutA, iucABCD; entABCDEFS, fepABCDG, fes; iroBCDEN; fyuA, irp1, irp2; ybtAEPQSTUX; allABCDRS; rmpA, rmpA2, magA; rcsA, rcsB; T6SS-I/II/III; LPS rfb locus, wzi1, wzc1; K1, O1v2; ybt9; ICEKp3 | Col4401I, Col4401II, ColKP3, IncA/C2, IncFIIK, IncX3, IncFIB (pQil) | aacA4, arr-2, dfrA14b | VINI00000000 |
| Kp7 | 2016 | ST23/CC23 | armA, aac(6′)-Ib | CTX-M-15, TEM-1B, SHV-11, OXA-232, CMY-4 | qnrB, oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH, mrkD, kfuBC, wcaJ | IncA/C, IncFIIK, IncX3, Col | intI1/aadA2, dfrA12, orfF | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND |
| Kp8 | 2016 | ST231/CC231 | aac(6′)-Ib | CTX-M-15, TEM-1B, SHV-28, OXA-232 | qnrS, oqxAB | wabG, uge, fimH, mrkD, kfuBC | IncFIIK, IncFIA, IncFIB-M, IncHIB-M, Col | In27/intI1 | rmtF, aac(6′)-Ib, aac(6′)-Ib-Hangzhou, aadA2 | TEM-1B SHV-28, CTX-M-15 |
OXA-232 |
qnrS1 oqxAB |
fosA (fosfomycin); mph(A) erm(B) (macrolide); catA1 (phenicol); arr-2 (rifampin); sul1 (sulphonamide); dfrA12 (trimethoprim);terABCDEXZ (tellurite) |
mrkABCDFHIJ; fimABCDEFGHIK, pilW; iucABCD, iutA; entABCDEFS, fepABCDG, fes; iroEN; fyuA, irp1, irp2, ybtAEPQSTUX; sitC, sitABCD; rcsA, rcsB; T6SS-I/II/III; LPS rfb locus; stbABCDE; wzi104; KL51, O1v2; ybt14; ICEKp5 | ColKP3, IncFIA, IncHI1B, IncFIB (Mar), IncFIB (pQil), IncFIIK, IncFII (pAMA1167-NDM-5) | In27, In406 | JAAGUA000000000 |
| Kp9 | 2016 | ST14/CC15 | rmtB, aac(6′)-Ib | NDM-5, CTX-M-15, TEM-1A, SHV-28, OXA-1, OXA-181 | oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH, mrkD, kfuBC | IncFII, IncFIIK, IncR, Col | intI1 | rmtB, aac(6′)-Ib, aadA1, aadA2, aph(6)-Id, aac(3)-IId, aph(3″)-Ib | TEM-1A SHV-28 OXA-1,9, CTX-M-15 |
NDM-5, OXA-181 | oqxAB, aac(6′)-Ib-cr | fosA (fosfomycin); mph(A), ere(A), erm(B) (macrolide); catB3, cmlA1, catA1 (phenicol); sul1, sul2 (sulphonamide); dfrA1, dfrA12 (trimethoprim); arsABCDR (arsenic); pcoABCDER (copper); silACEFGPRS (silver); merACDEPRT (mercury) | mrkABCDFHIJ; fimABCDEFGHIK, pilW; iutA; entABCDEFS; fepABCDG, fes, iroEN, fyuA, irp2, ybtAEQSTUX; rcsA, rcsB; T6SS-I/II/III; LPS rfb locus, wzi2, wzc2; K2, O1v1; ybt 14; ICEKp5 | ColKP3, IncFIA (HI1), IncFIB (K), IncFIB (pKPHS1), IncR, IncFIIK, IncFII | In27, In1329 | VSJI00000000 |
| Kp10 | 2016 | ST14/CC15 | rmtB, aac(6′)-Ib | NDM-5, CTX-M-15, TEM-1A, SHV-28, OXA-1, OXA-181 | oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH, mrkD, kfuBC | IncFII, IncFIIK, IncR, Col | intI1 | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND |
| Kp11 | 2016 | ST14/CC15 | rmtB, aac(6′)-Ib | NDM-5, CTX-M-15, TEM-1A, SHV-28, OXA-1, OXA-181 | oqxAB, aac(6′)-Ib-cr | wabG, uge, fimH, mrkD, kfuBC | IncFII, IncFIIK, IncR, Col | intI1 | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND | WGS ND |
a
Terms used: Inc, incompatibility group; intI1, integrase 1; GC, gene cassette; mrk, type-3 fimbriae operon; fim, type-1 fimbriae operon; pil, type IV pili; iuc and iut, aerobactin; ent, fep, and fes, enterobactin; iro, salmochelin; all, allantoin utilization/nutritional factor; sitC, ferrous iron transporter; sit, iron/manganese transporter; rcs, RcsAB operon; T6SS, type-6-secretion system; LPS rfb locus, for serum resistance; fyuA, irp, and ybt, yersiniabactin; stb, fimbrae adherence determinants; YbST, yersiniabactin sequence type; ICE, integrative conjugative element; WGS ND, whole-genome sequencing not done.
b
ST, sequence type; CC, clonal complex.