Table 1.
Characteristics of K. pneumoniae strains used for whole-genome sequence analysis.
| Feature/strain | B185/19 | B16K/19 | B2523/18 | B2580/14 | B1261/19 |
|---|---|---|---|---|---|
| SCPM-O | SCPM-O-B-9222 | SCPM-O-B-9221 | SCPM-O-B-9220 | SCPM-O-B-7852 | SCPM-O-B-9223 |
| Isolation date | 30-Jan-2019 | 09-Jan-2019 | 30-Aug-2018 | 21-Jul-2014 | 27-May-2019 |
| Source | wound | urine | blood | urine | urine |
| GenBank | JAGVVR000000000.1 | JAGVVS000000000.1 | JAGRZF000000000.1 | PUXF00000000.1 | JAGVVQ000000000.1 |
| Genome size, bp | 5,812,311 | 5,532,115 | 5,430,135 | 5,773,846 | 5,570,452 |
| Number of contigs | 267 | 180 | 125 | 360 | 160 |
| Genetic line | ST395K47 | ST147K64 | ST86K2 | ST23K1 | ST23K57 |
| String-test | Negative | Negative | Positive | Positive | Positive |
| Antimicrobial resistance phenotype | AMP, SAM, CXM, FOX, CRO, CAZ, CSL, FEP, ETP, IPM, TET, CIP, CHL, GEN, TOB, AMK, SXT, NIT | AMP, SAM, CXM, FOX, CRO, CAZ, CSL, FEP, ETP, IPM, CIP, GEN, TOB, AMK, SXT, NIT | AMP | AMP, SAM, CXM, CRO, TET, CIP, CHL, TOB, SXT, NIT | AMP, SAM, CXM, FOX, CRO, CAZ, CSL, FEP, ETP, IPM, TET, TGC, CIP, CHL, GEN, TOB, SXT, NIT |
| Beta-lactamases | blaSHV-12, blaTEM-1B, blaCTX-M-15, blaOXA-1, blaOXA-48, blaNDM-1 | blaSHV-67, blaTEM-1B, blaCTX-M-15, blaOXA-1, blaOXA-48, blaNDM-1 | bla SHV-28 | blaSHV-190, blaTEM-1B, blaCTX-M-15, blaOXA-1, blaOXA-48 | blaSHV-33, blaCTX-M-55, blaOXA-1, blaOXA-48, blaNDM-1 |
| AG-resistance | aadA2, aph(3′)-Ia, armA | aph(3′)-VI, aadA1, aadA2, aadA5, armA | - | aph(6)-Id, aac(6′)-Ib-cr, aph(3″)-Ib | aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, aac(3)-IIa, aac(3)-IId, aadA16 |
| FOS-resistance | fosA | fosA | fosA | fosA | fosA |
| STR-resistance | msr(E) | msr(E) | - | - | |
| PHE-resistance | catB3 | catB3 | - | catB3 | catB3, floR |
| QNL-resistance | aac(6′)-Ib-cr, oqxA, oqxB | aac(6′)-Ib-cr, oqxA, oqxB | oqxA, oqxB | qnrB1, oqxA, oqxB | aac(6′)-Ib-cr, oqxA, oqxB |
| SUL-resistance | sul1 | sul1 | - | sul2 | sul1, sul2 |
| TET-resistance | tet(A) | - | - | tet(A) | tet(A) |
| TRI-resistance | dfrA1, dfrA12 | dfrA12, dfrA17. | - | dfrA14 | dfrA27 |
| MCR-resistance | mph(A), mph(E) | mph(E) | - | - | mph(A) |
| RIF-resistance | - | - | - | - | ARR-3 |
| HM-resistance | ars, pco, sil | sil | pbr, pco, sil, ter | pbr, pco, sil, ter | pbr, pco, sil, ter |
| Efflux pums | acr, oqx, kpn, kde, kex | acr, oqx, kpn, kde, kex | acr, oqx, kpn, kde, kex | acr, oqx, kpn, kde | acr, oqx, kpn, kde, kex |
| Virulence genes | uge, wabG, fimH, irp, iut, mrk, ybt, fyu, treC, cellB, ureA | uge, wabG, fimH, mrk, treC, cellB, ureA | peg-344, rmpA, iro, ent uge, wabG, fimH, irp, iuc, iut, mrk, ybt, fyu, treC, cellB, ureA | peg-344, rmpA, rmpA2, iro, ent, uge, wabG, kfu, fimH, allR, irp, iuc, iut, mrk, ybt, fyu, treC, cellB, ureA | peg-344, rmpA, ent, wabG, fimH, irp, iuc, iut, mrk, ybt, fyu, treC, cellB, ureA |
| Plasmid | ColRNAI, IncFIB(K), IncFII(K), IncR, IncX3 | IncFIA(HI1), IncFIB(K), IncFIB, IncFII(K), IncHI1B, IncM2 | IncHI1B, repB | IncFII(K), IncHI1B, IncL, repB | ColRNAI, IncC, IncFIA(HI1), IncFII, IncFII(K), IncL, repB |
Note: SCPM-O, State Collection of Pathogenic Microbes, AMP, ampicillin; SAM, ampicillin-sulbactam; CXM, cefuroxime; FOX, cefoxitin; CRO, ceftriaxone; CAZ, ceftazidime; CSL, cefoperazone-sulbactam; FEP, cefepime; ETP, ertapenem; IPM, imipenem; TET, tetracycline; TGC, tigecycline; CIP, ciprofloxacin; CHL, chloramphenicol; GEN, gentamicin; TOB, tobramycin; AMK, amikacin; SXT, trimethoprim-sulfamethoxazole; NIT, nitrofurantoin; AG, aminoglycosides; FOS, fosfomycin; STR, streptogramin; PHE, phenicol; QNL, quinolone; SUL, sulfonamide; TRI, trimethoprim; RIF, rifamycin; HM, heavy metal.