Table 2.
Genome analysis of K. pneumoniae isolated from residents of twelve LTCFs (Northern Italy).
| LTCFs | No. Isolates | Genome Size (bp) | MLST | Plasmid Replicons/pMLST | β-lactams Resistance Genes | Other Antibiotics Resistance Genes |
|---|---|---|---|---|---|---|
| SSA_BL | 5 | 5,736,085 | ST321 | IncFII(K), IncFIB(K), IncFIA(HI1), IncN/fii_k1 fia_19 |
blaVIM-1, blaSHV-99 |
aadA1, aph(3′)-XV, aacA4, fosA, mph(A), aac(6′)Ib-cr,oqxA, oqxB, qnrS1, sul1 dfrA14, catB2 |
| ISRAA_TV | 2 | 5,497,503 | ST307 | IncFIB(K), IncFII(K)/fii_k7 |
blaSHV-28, blaKPC-2, blaOXA-9, blaTEM-1A, blaCTX-M-15 |
fosA, dfrA14, qnrB66 |
| 2 | 5,164,710 | ST307 | IncFIB(K), IncFII(K)/fii_k7 | blaKPC-2, blaTEM-1A, blaOXA-9, blaCTX-M-15, blaSHV-28, blaOXA-1 | aac(6′)-Ib-cr, fosA, dfrA14, qnrB66, catB4 | |
| 2 | 5,578,258 | ST307 | IncFIB(K), IncFII(K)/fii_k7 | blaKPC-2, blaTEM-1A, blaOXA-9, blaCTX-M-15, blaSHV-28, blaOXA-1 | aac(6′)-Ib-cr, fosA, dfrA14, qnrB66, catB4, oqxA, oqxB | |
| 1 | 5,505,674 | ST307 | IncFIB(K), IncFII(K)/fii_k7 | blaKPC-2, blaTEM-1A, blaOXA-9, blaCTX-M-15, blaSHV-28, blaOXA-1 | aac(6′)-Ib-cr, fosA, dfrA14, catB4, oqxA, oqxB | |
| SAF_VE | 1 | 5,545,376 | ST307 | IncFIB(K), IncFII(K)/fii_k7 | blaKPC-2, blaTEM-1A, blaOXA-9, blaCTX-M-15, blaSHV-28, blaOXA-1 | aac(6′)-Ib-cr, fosA, dfrA14, qnrB66, catB4, oqxA, oqxB |
| 1 | 5,330,546 | ST3227 | IncFIB(pQil), IncFIB(K)/fii_k7 | blaKPC-9, blaTEM-1B, blaOXA-9, blaLEN-12, blaCTX-M-15, blaOXA-1 | aph(3′)-IIa, aac(6′)-Ib-cr, fosA, strA, strB, sul2, dfrA14, qnrB66, catB4 | |
| 1 | 5,545,568 | ST3227 | IncFIB(pQil), IncFII(K), IncFIB(K)/fii_k9 | blaOXA-9, blaTEM-1A, blaKPC-3, blaLEN-12, blaLEN-7, blaOXA-1 | aac(6′)-Ib-cr, aph(3′)-IIa, fosA, dfrA14, oqxB, qnrB66, catB4 | |
| 1 | 5,540,988 | ST307 | IncFII(K), IncFIB(K), IncR, IncL/M (pOXA-48)/fii_k5 | blaTEM-1A, blaSHV-11 | aph(3′)-Ia, fosA, qnrB19, oqxB | |
| CRMC_VE | 3 | 5,531,831 | ST11 | IncFII(pKPX1), ColpVC, Col(MG828)/fii_k7 | blaSHV-11, blaCTX-M-15, blaNDM-1 | aac(6′)-Ib-cr, fosA, oqxB, oqxA |
| 2 | 5,387,384 | ST273 | IncFII(K), IncFIB(K), Col(MG828)/fii_k7 | blaSHV-11, blaTEM-1B, blaOXA-1, blaCTX-M-15 | aac(3′)-IIa, aac(6′)-Ib-cr, strA, strB, fosA, sul2, dfrA14, oqxA, oqxB, catB4 | |
| CDS_RO | 3 | 5,424,562 | ST2623 | IncFII(K), IncFIB(K), IncFIA(HI1), ColRNAI/fii_k1 fia_10 |
blaCTX-M-15, blaSHV-1, blaTEM-1B, blaOXA-1 |
aac(6′)-Ib-cr, strA, strB, sul2 oqxA, oqxB, qnrB66, tet(D), catB4 |
| 3 | 5,666,417 | ST 2623 | IncFIB(pQil), IncFII(K), IncFIB(K), IncFIA(HI1), ColRNAI/fii_k1 fia_10 |
blaCTX-M-15, blaOXA-9, blaTEM-1B, blaOXA-1, blaKPC-3 | aac(6′)-Ib-cr, fosA, strA, strB, sul2, oqxA, oqxB, qnrB66, tet(D), catB4 | |
| 2 | 5,607,404 | ST307 | IncFIB(pQil), IncFII(K), IncFIA(HI1)/fii_k2 fia_19 |
blaTEM-1A, blaOXA-9, blaSHV-28, blaCTX-M-15, blaOXA-1, blaKPC-3 | aac(6′)-Ib-cr, strA, strB, fosA, sul2, oqxA, oqxB, qnrB66, catB4 | |
| 37 | 5,496,232 | ST307 | IncFIB(pQil), IncFII(K)/fii_k2 | blaCTX-M-15, blaTEM-1A, blaOXA-9, blaSHV-28, blaOXA-1, blaKPC-3 | aac(6′)-Ib-cr, fosA, sul2, oqxA, oqxB, qnrB66, catB4 | |
| 2 | 5,566,824 | ST307 | IncFIB(pQil), IncFII(K), IncFIA(HI1)/fii_k2 fia_19 |
blaCTX-M-15, blaTEM-1A, blaOXA-9, blaSHV-28, blaOXA-1, blaKPC-3 |
aac(6′)-Ib-cr, strA, strB, fosA, sul2, oqxA, oqxB qnrB66, catB4 |
|
| 2 | 5,634,072 | ST307 | IncFIB(pQil), IncFII(K), IncFIB(K)/fii_k2 | blaCTX-M-15, blaTEM-1A, blaOXA-9, blaSHV-28, blaOXA-1, blaKPC-3 | aac(6′)-Ib-cr, aac(3)-IIa, strA, strB, fosA, sul2, dfrA14, oqxA, oqxB, qnrB66, catB4 | |
| CAR_VI | 1 | 5,649,046 | ST512 | IncX3, IncFIB(K), IncFIB(pQil) IncFII(K)/fii_k2 | blaKPC-3, blaTEM-1A, blaOXA-9, blaSHV-11 | aadA2, aph(3′)-Ia, fosA, mph(A), sul1, dfrA12, oqxA, oqxB, catA1 |
| 1 | 5,487,176 | ST1519 | ColRNAI, IncFIB(pQil), IncFII(K)/fii_k2 |
blaKPC-3, blaOXA-9, blaSHV-11, blaTEM-1A | aadA2, aac(6′)-Ib-cr, fosA, sul1, oqxA, oqxB | |
| IPABMC_VI | 1 | 5,311,196 | ST1519 | ColRNAI, IncFIB(pQil), IncFII(K), IncFIB(K)/fii_k2 | blaSHV-11, blaKPC-3 | aac(6′)-Ib-cr, aadA2, fosA, mph(A), sul1, dfrA12, oqxB, catA1 |
| 1 | 5,651,358 | ST253 | ColRNAI, IncFIB(pQil), IncFII(K), IncFIB(K), IncN/ fii_k5/ST7 |
blaVIM-1, blaSHV-36 | aac(6′)-Ib-cr, aadA1, aacA4, fosA, sul1, dfrA14, qnrS1, catB2 | |
| IPABRS_VI | 2 | 5,167,604 | ST37 | ColRNAI, IncFII(K), IncFIB(K)/fii_k7 | blaCTX-M-15, blaSHV-11, blaOXA-1, blaTEM-1B | aac(6′)-Ib-cr, strA, strB, fosA, sul2, dfrA14, oqxA, oqxB, catB4 |
| 4 | 5,451,323 | ST37 | ColRNAI, IncFIB(pQil), IncFII(K), IncFIB(K), IncN/ fii_k7 |
blaSHV-11, blaOXA-1, blaKPC-2 | aac(6′)-Ib-cr, fosA, dfrA14, dfrA30, oqxB, oqxA, catB4 | |
| 3 | 5,424,901 | ST37 | ColRNAI, IncFIB(pQil), IncFII(K), IncFIB(K), IncN/ IncF: fii_k7 IncN: unknown |
blaSHV-11, blaOXA-1, blaKPC-2 |
aac(6′)-Ib-cr, fosA, dfrA30, dfrA14, oqxA, oqxB, catB4 | |
| 2 | 5,444,858 | ST37 | ColRNAI, IncFIB(pQil), IncFII(K), IncFIB(K), IncN/ IncF: fii_k7 |
blaSHV-11, blaOXA-1, blaKPC-2 |
aac(6′)-Ib-cr, fosA, dfrA30, dfrA14, oqxA, oqxB, catB4 | |
| IPABRT_VI | 5 | 5,406,932 | ST512 | ColRNAI, IncFIB(pQil), IncFII(K), IncFIB(K)/fii_k2 |
blaLEN-12, blaTEM-1A, blaKPC-3, blaOXA-9 |
aac(6′)-Ib-cr, aadA1, fosA, sul1, dfrA1, oqxB, tet(D) |
| IPABSC_VI | 1 | 5,634,812 | ST416 | IncFII(K), IncFIA(HI1), ColRNAI, IncN, IncFIB(K)/ IncF: fii_k4, fia_18 IncN: ST7 |
blaVIM-1, blaSHV-14 | aadA1, aph(3′)-XV, aacA4, fosA, sul1, dfrA14, oqxA, oqxB, qnrS1, catB2 |
| 2 | 5,477,368 | ST416 | IncFII(K), IncFIB(Mar), ColRNAI, IncN, IncFIB(K)/ IncF: fii_k5 IncN: ST7 |
blaVIM-1, blaOKP-B-3 | aadA1, aph(3′)-XV, aacA4, aac(6′)-Ib-cr, fosA, sul1, qnrS1, catB2, oqxB, oqxA | |
| POVSG_VR | 1 | 5,346,528 | ST512 | ColRNAI, IncFIB(K)/fii_k2 | blaLEN-7, blaOXA-9, blaTEM-1A | aph(3′)-IIa, aadA2, aac(6′)-Ib-cr, fosA, sul1 |
| 1 | 5,101,877 | ST512 | ColRNAI, IncFIB(pQil), IncFII(K), IncFIB(K)/fii_k2 |
blaKPC-9, blaOXA-9, blaTEM-1A |
aph(3′)-IIa, aadA2, aac(6′)-Ib-cr, fosA, sul1 | |
| POCS_VR | 1 | 5,548,552 | ST512 | IncFIB(pQil), IncFII(K), IncFIB(K), ColRNAI, IncX3/ fii_k2 |
blaOXA-9, blaSHV-11, blaTEM-1A, blaKPC-3 |
aadA2, aac(6′)-Ib-cr, mph(A), sul1, dfrA12, oqxB, oqxA, catA1 |
| 2 | 5,589,508 | ST512 | IncFII(K), IncFIA(HI1), ColRNAI, IncFIB(K), Col(MG828), FIA(pBK30683)/fii_k12 fia_10 |
blaOXA-23, blaLEN-12, blaCTX-M-15, blaOXA-1 |
aac(3)-IIa, aac(6′)-Ib-cr, aadA1, fosA, sul1, dfrA1, oqxB, qnrB6, tet(D), tet(B), catB4, catA1 | |
| 2 | 5,604,773 | ST16 | IncFIB(pQil), IncFII(K), IncFIB(K), IncX4/fii_k2 |
blaKPC-3, blaCTX-M-15, blaTEM-1B, blaSHV-1, blaOXA-1 |
strA, aac(6′)-Ib-cr, strB, fosA, sul2, dfrA14, oqxB, oqxA, qnrB66, tet(A), catB4 | |
| 2 | 5,589,102 | ST35 | IncFIB(pQil), IncFII(K), IncFIB(K)/fii_k2 |
blaTEM-1A, blaOXA-9, blaKPC-3, blaSHV-33 |
fosA, oqxB, oqxA |
For legal aspects, we only used the acronym of the twelve LTCFs.