Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region
Abstract
:1. Introduction
2. Materials and Methods
2.1. Setting
2.2. Strains Selection
2.3. DNA Extraction and Whole-Genome Sequencing (WGS)
2.4. Bioinformatic Analysis
3. Results
3.1. WGS of K. pneumoniae
3.2. K. pneumoniae MLST
3.3. Plasmids Replicons and pMLST
3.4. β-Lactam Resistance Genes
3.5. Fluoroquinolone Resistance Genes
3.6. Other Antimicrobial Resistance Genes
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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LTCFs | No. Isolates | ST | Resistance Profile |
---|---|---|---|
CDS_RO | 15 | 307, 2623 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP |
POCS_VR | 2 | 16 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP, SXT |
2 | 35 | AMX, TZP, CTX, CAZ, CIP, MEM, SXT | |
3 | 512 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP | |
POVSG_VR | 2 | 512 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP |
IPABMC_VI | 2 | 253, 1519 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP, SXT |
CAR_VI | 2 | 512, 1519 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP, SXT |
IPABRS_VI | 11 | 37 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP, SXT |
IPABRT_VI | 5 | 512 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP, SXT |
IPABSC_VI | 3 | 416 | AMX, TZP, CTX, CAZ, MEM, CIP, SXT |
SSA_BL | 5 | 321 | AMX, TZP, CTX, CAZ, MEM, CIP, SXT |
ISRAA_TV | 7 | 307 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP, SXT |
CRMC_VE | 5 | 11, 273 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP, SXT |
SAF_VE | 4 | 307 | AMX, TZP, CTX, CAZ, ERT, MEM, CIP, SXT |
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 |
β-lactamases | Classes | Isolates No. (%) | ST |
---|---|---|---|
TEM-1 | A | 44 (65) | 16, 35, 37, 273, 307, 512, 1519, 2623, 3227 |
KPC-2 | A | 17 (25) | 37, 307 |
KPC-3 | A | 30 (44) | 16, 35, 307, 512, 1519, 2623, 3227 |
KPC-9 | A | 2 (3) | 512, 3227 |
SHV-1 | A | 5 (7) | 16, 2623 |
SHV-11 | A | 21 (31) | 11, 37, 273, 307, 512, 1519 |
SHV-14 | A | 1 (1.5) | 416 |
SHV-28 | A | 17 (25) | 307 |
SHV-33 | A | 2 (3) | 35 |
SHV-36 | A | 1 (1.5) | 253 |
SHV-99 | A | 5 (7) | 321 |
CTX-M-15 | A | 35 (51) | 11, 16, 37, 273, 307, 512, 2623, 3227 |
LEN-7 | A | 2 (3) | 512, 3227 |
LEN-12 | A | 9 (13) | 512, 3227 |
OKP-B3 | A | 2 (3) | 416 |
VIM-1 | B | 9 (13) | 253, 321, 416 |
NDM-1 | B | 3 (4.5) | 11 |
OXA-1 | D | 40 (59) | 16, 37, 273, 307, 512, 2623, 3227 |
OXA-9 | D | 33 (48) | 35, 307, 512, 1519, 2623, 3227 |
OXA-23 | D | 2 (3) | 512 |
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Piccirilli, A.; Cherubini, S.; Azzini, A.M.; Tacconelli, E.; Lo Cascio, G.; Maccacaro, L.; Bazaj, A.; Naso, L.; Amicosante, G.; LTCF-Veneto Working Group; et al. Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region. Microorganisms 2021, 9, 1985. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091985
Piccirilli A, Cherubini S, Azzini AM, Tacconelli E, Lo Cascio G, Maccacaro L, Bazaj A, Naso L, Amicosante G, LTCF-Veneto Working Group, et al. Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region. Microorganisms. 2021; 9(9):1985. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091985
Chicago/Turabian StylePiccirilli, Alessandra, Sabrina Cherubini, Anna Maria Azzini, Evelina Tacconelli, Giuliana Lo Cascio, Laura Maccacaro, Alda Bazaj, Laura Naso, Gianfranco Amicosante, LTCF-Veneto Working Group, and et al. 2021. "Whole-Genome Sequencing (WGS) of Carbapenem-Resistant K. pneumoniae Isolated in Long-Term Care Facilities in the Northern Italian Region" Microorganisms 9, no. 9: 1985. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091985