Table 2. Genetic features of 2020-ST147 Klebsiella pneumoniae strains described in this study compared with six strains representative of the 2018–2019-ST147 outbreak, Pisa, Italy (n = 8 strains).
| Strain SRA |
Year | Acquired beta-lactamases | Other acquired resistance genes | Replicon content | TygR, ColR, and FosR chromosomal loci |
|---|---|---|---|---|---|
| Kp-P1 SRR12785639 |
2020 | NDM-9, CTX-M-15, OXA-1, OXA-9, TEM-1A | armA, aadA1, aac(6')-Ib, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIIk-FIB(pKpQIL); FIB(pKpN3); R; FIB(pKPHS1); Col(pHAD28); ColRNAI |
ramR (C364→T)-ΔRamR mgrB (A7→T)-ΔMgrB glpT (C401→T)-ΔGlpT |
| Kp-P2 SRR12785638 |
2020 | NDM-9, CTX-M-15, OXA-1, OXA-9, TEM-1A | armA, aadA1, aac(6')-Ib3, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIIk-FIB(pKpQIL); FIB(pKpN3); R; N; FIB(pKPHS1); Col(pHAD28); ColRNAI |
ramR (C364→T)-ΔRamR mgrB (A7→T)-ΔMgrB glpT (C401→T)-ΔGlpT |
| Kp-8Pi SRR12518027 |
2018 | NDM-1, CTX-M-15, OXA-1, OXA-9, TEM-1A | armA, aadA1, aac(6')-Ib, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIB(pKpQIL); R; FIB(pKPHS1) | RamR wt MgrB wt GlpT wt |
| Kp-9Pi SRR12518023 |
2018 | NDM-1, CTX-M-15, OXA-1, OXA-9, TEM-1A | armA, aadA1, aac(6')-Ib, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIB(pKpQIL); R; FIB(pKPHS1) | RamR wt MgrB wt GlpT wt |
| Kp-11Pi SRR12518041 |
2018 | NDM-1, CTX-M-15, OXA-1, OXA-9, TEM-1A | armA, aadA1, aac(6')-Ib, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIB(pKpQIL); FIIk-FIB(pKpN3); R; FIB(pKPHS1) |
ramR (C364→T)-ΔRamR MgrB wt GlpT wt |
| Kp-12Pi SRR12518021 |
2019 | NDM-1, CTX-M-15, OXA-1, OXA-9, TEM-1A | armA, aadA1, aac(6')-Ib, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIB(pKpQIL); FIIk-FIB(pKpN3); R; FIB(pKPHS1); ColRNAI |
ramR (C364→T)-ΔRamR PmrA mut MgrB wt GlpT wt |
| Kp-14Pi SRR12518062 |
2019 | NDM-1, CTX-M-15, OXA-1, OXA-9, TEM-1A | armA, aadA1, aac(6')-Ib, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIB(pKpQIL); R; FIB(pKPHS1); ColRNAI | RamR wt MgrB wt GlpT wt |
| Kp-16Pi SRR12518060 |
2019 | NDM-1, CTX-M-15, OXA-1, OXA-9, TEM-1A | armA, aadA1, aac(6')-Ib, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIB(pKpQIL); FIIk-FIB(pKpN3); R; FIB(pKPHS1); ColRNAI |
ramR (C364→T)-ΔRamR mgrB (A7→T)-ΔMgrB glpT (G1088→C)-GlpT mut |
| Kp-17Pi SRR12518059 |
2019 | NDM-1, CTX-M-15, OXA-1, OXA-9, TEM-1B | armA, aadA1, aac(6')-Ib, aph(3')-VI, aph(3')-1A, catB3, dfrA5, mph(E), msr(E), qnrS1, sul1, sul2 | HI1B-FIB(pNDM-Mar); FIB(pKpQIL); R; FIB(pKPHS1); X4 | RamR wt MgrB wt GlpT wt |
GlpT: glycerol-3-phosphate transporter; mut: mutation; NDM: New Delhi metallo-beta-lactamase; OXA: oxacillinase; PmrA: multi-drug resistance efflux pump PmrA; RamR: resistance antibiotic multiple (Ram)A regulator; SRA: Sequence Read Archive accession number at the National Center for Biotechnology Information database (NCBI; https://www.ncbi.nlm.nih.gov/); ST: sequence type; wt: wild type.
Kp-P1 and Kp-P2 are the K. pneumoniae strains derived from patient 1 and patient 2, in 2020 in Pisa, who are described in this study. The rest of the strains in the table are representative of the 2018–2019 outbreak in Pisa.
Kp Δ is used when mutations caused premature termination of translation of the deduced protein sequence. Mut indicates that the deduced protein sequence is mutated with respect to the wt amino-acid sequence.