Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolates
2.2. Whole-Genome Sequencing
2.3. Phylogenetic Analysis
2.4. In Silico MLST, Plasmid Replicons, Drug Resistance Associated Genes and Capsular Types
3. Results
3.1. Whole Genome Sequencing Enables Identification of K. variicola Misidentified as K. pneumoniae
3.2. Genomic Population Structure and High-Resolution Phylogenomic Analysis Unveils Multiple Healthcare-Associated Transmission Clusters
3.3. KPC-3 as the Main Driver of Carbapenem Resistance in Northern Portugal and First Description of KPC-3 Producing K. variicola
3.4. Virulome of K. pneumoniae Highlights the Occurrence of Multiple Virulence Factors and ST-Specific Patterns
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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ID | Isolates | Patient | Sample | Hospital Ward | Date | ST |
---|---|---|---|---|---|---|
5141 | K. pneumoniae | P1 | Rectal swab | Medicine | 2 May 2018 | ST147 |
5142 | K. pneumoniae | P2 | Rectal swab | ICU | 3 May 2018 | ST147 |
5144 | K. pneumoniae | P3 | Rectal swab | Emergency | 4 May 2018 | ST147 |
5147 | K. pneumoniae | P4 | Urine | Emergency | 6 May 2018 | ST147 |
5151 | K. pneumoniae | P5 | Dialysis liquid | Dialysis Clinic | 15 May 2018 | ST147 |
5152 | K. pneumoniae | Purulent exudate | Dialysis Clinic | 15 May 2018 | ST147 | |
5143 | K. pneumoniae | P6 | Rectal swab | Surgery | 16 May 2018 | ST147 |
5160 | K. pneumoniae | P7 | Rectal swab | Neurology | 25 May 2018 | ST147 |
5161 | K. pneumoniae | P8 | Rectal swab | Emergency | 26 May 2018 | ST147 |
5155 | K. pneumoniae | P9 | Urine | Oncology Clinic | 29 May 2018 | ST147 |
5158 | K. pneumoniae | P10 | Urine | Surgery | 4 June 2018 | ST147 |
5164 | K. pneumoniae | P11 | Urine | Medicine | 4 June 2018 | ST147 |
5167 | K. pneumoniae | P12 | Rectal swab | Medicine | 4 June 2018 | ST147 |
5168 | K. pneumoniae | P13 | Urine | Outpatient Clinic | 11 June 2018 | ST147 |
5173 | K. pneumoniae | P14 | Urine | Emergency | 17 June 2018 | ST147 |
5174 | K. pneumoniae | P15 | Blood | Emergency | 19 June 2018 | ST147 |
5175 | K. pneumoniae | P16 | Rectal swab | Surgery | 19 June 2018 | ST147 |
5146 | K. pneumoniae | P17 | Urine | Emergency | 3 May 2018 | ST15 |
5149 | K. pneumoniae | P18 | Hepatic liquid | Surgery | 9 May 2018 | ST15 |
5154 | K. pneumoniae | P19 | Blood | Hematology | 28 May 2018 | ST15 |
5159 | K. pneumoniae | P20 | Rectal swab | Emergency | 25 May 2018 | ST15 |
5156 | K. pneumoniae | Sputum | Emergency | 30 May 2018 | ST15 | |
5157 | K. pneumoniae | P21 | Biopsy | Plastic Surgery | 4 June 2018 | ST15 |
5166 | K. pneumoniae | P22 | Urina | Nephrology clinic | 6 June 2018 | ST15 |
5148 | K. pneumoniae | P23 | Urine | ICU | 7 May 2018 | ST34 |
5150 | K. pneumoniae | P24 | Urine | Orthopaedic | 13 May 2018 | ST1079 |
5153 | K. pneumoniae | P25 | RTS/DLC a | Nephrology | 21 May 2018 | ST29 |
5162 | K. pneumoniae | P26 | Rectal swab | ICU | 29 May 2018 | ST461 |
5165 | K. pneumoniae | P27 | Rectal swab | Emergency | 5 June 2018 | ST307 |
5163 | K. variicola | P28 | Rectal swab | Medicine | 29 May 2018 | ST4197 |
5172 | K. pneumoniae | Rectal swab | Medicine | 18 June 2018 | ST280 |
Isolates ID | Sequence Type | Genomic Cluster | bla_Carb | bla_ESBL | bla_narrow Spectrum | Aminoglycoside | aac(6′)-Ib-cr5 | qnr | Phe | Rif | Fos | oqxAB | tmp | qacEdelta1 | sul | tet | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Kp5141 | ST147 | GC1 | KPC-3 | CTX-M-15 | SHV-11 | TEM-1 | OXA-1 | aph(6)-Id; aph(3″)-Ib | aac(3)-IIa | aac(6′)-Ib-cr5 | catB3 | fosA | oqxAB | dfrA14 | sul2 | ||||
Kp5142 | ST147 | GC1 | KPC-3 | SHV-11 | aadA1 | fosA | oqxAB | dfrA1 | qacEdelta1 | sul1 | |||||||||
Kp5144 | ST147 | GC1 | KPC-3 | SHV-11 | aadA16 | aac(6′)-Ib-cr5 | qnrB6 | - | arr-3 | fosA | oqxAB | dfrA27 | sul1 | ||||||
Kp5147 | ST147 | GC1 | KPC-3 | - | SHV-11 | aadA16 | aac(6′)-Ib-cr5 | - | arr-3 | fosA | oqxAB | dfrA27 | qacEdelta1 | sul1 | |||||
Kp 5151 | ST147 | GC1 | KPC-3 | - | SHV-11 | aadA16 | aac(6′)-Ib-cr5 | qnrB6 | - | arr-3 | fosA | oqxAB | dfrA27 | qacEdelta1 | sul1 | ||||
Kp5152 | ST147 | GC1 | KPC-3 | - | SHV-11 | aadA16 | aac(6′)-Ib-cr5 | qnrB6 | - | arr-3 | fosA | oqxAB | dfrA27 | qacEdelta1 | sul1 | ||||
Kp5143 | ST147 | GC4 | KPC-3 | SHV-12 | TEM-1 | aph(6)-Id; aph(3″)-Ib | qnrB1 | fosA | oqxAB | dfrA14 | qacEdelta1 | sul2 | tet(A) | ||||||
Kp5160 | ST147 | GC1 | KPC-3 | - | SHV-11 | aadA1 | - | - | fosA | oqxAB | dfrA1 | qacEdelta1 | sul1 | ||||||
Kp5161 | ST147 | GC1 | KPC-3 | - | SHV-11 | aadA1 | - | - | fosA | oqxAB | dfrA1 | qacEdelta1 | sul1 | ||||||
Kp5155 | ST147 | GC1 | KPC-3 | SHV-11 | TEM-33 | - | - | - | fosA | oqxAB | - | ||||||||
Kp5158 | ST147 | GC1 | KPC-3 | - | SHV-1 | aadA16 | aac(6′)-Ib-cr5 | qnrB6 | - | arr-3 | fosA | oqxAB | dfrA27 | qacEdelta1 | sul1 | ||||
Kp5164 | ST147 | GC1 | KPC-3 | - | SHV-11 | aadA16 | aac(6′)-Ib-cr5 | qnrB6 | - | arr-3 | fosA | oqxAB | dfrA27 | qacEdelta1 | sul1 | ||||
Kp5167 | ST147 | GC1 | KPC-3 | - | SHV-11 | aadA1 | - | - | fosA | oqxAB | dfrA1 | qacEdelta1 | sul1 | ||||||
Kp5168 | ST147 | GC1 | KPC-3 | SHV-12 | TEM-1 | OXA-9 | aph(6)-Id; aph(3″)-Ib | aac(6′)-Ib; aadA1 | qnrB1 | - | - | fosA | oqxAB | dfrA14 | sul2 | tet(A) | |||
Kp5173 | ST147 | GC1 | KPC-3 | - | SHV-11 | aadA16 | aac(6′)-Ib-cr5 | qnrB6 | - | arr-3 | fosA | oqxAB | dfrA27 | qacEdelta1 | sul1 | ||||
Kp5174 | ST147 | GC3 | KPC-3 | - | SHV-1 | aadA16 | aac(6′)-Ib-cr5 | qnrB6 | - | arr-3 | fosA | oqxAB | dfrA27 | qacEdelta1 | sul1 | ||||
Kp5175 | ST147 | GC3 | KPC-3 | - | SHV-11 | aadA16 | aac(6′)-Ib-cr5 | qnrB6 | - | arr-3 | fosA | oqxAB | dfrA27 | qacEdelta1 | sul1 | ||||
Kp5146 | ST15 | GC2 | OXA-48 | CTX-M-15 | SHV-28 | TEM-1 | OXA-1 | aph(6)-Id; aph(3″)-Ib | aac(3)-IIa | aac(6′)-Ib-cr5 | qnrB1 | catA1; catB3 | - | fosA | oqxAB | dfrA14 | sul2 | ||
Kp5149 | ST15 | GC2 | KPC-3 | - | SHV-28 | TEM-1 | OXA-9 | aph(6)-Id; aph(3″)-Ib | aac(6′)-Ib; aadA1 | - | - | fosA | oqxAB | dfrA14 | sul2 | ||||
Kp5154 | ST15 | GC2 | CTX-M-15 | SHV-28 | TEM-1 | aph(6)-Id; aph(3″)-Ib | aac(3)-IIa | qnrB1 | catA1; catB3 | - | fosA | oqxAB | dfrA14 | sul2 | |||||
Kp5159 | ST15 | GC2 | KPC-3 | - | SHV-28 | TEM-1 | OXA-9 | aph(6)-Id; aph(3″)-Ib | aadA1 | qnrB1 | catA1 | - | fosA | oqxAB | dfrA14 | sul2 | tet(A) | ||
Kp5156 | ST15 | KPC-3 | CTX-M-15 | TEM-1 | OXA-9 | aph(6)-Id; aph(3″)-Ib | aac(6′)-Ib; aadA1 | qnrB1 | - | - | fosA | oqxAB | dfrA14 | sul2 | |||||
Kp5157 | ST15 | GC2 | KPC-3 | - | SHV-28 | TEM-1 | OXA-9 | aph(6)-Id; aph(3″)-Ib | aac(6′)-Ib; aadA1 | - | - | fosA | oqxAB | dfrA14 | sul2 | ||||
Kp5166 | ST15 | GC2 | KPC-3 | - | SHV-28 | TEM-1 | OXA-9 | aph(6)-Id; aph(3″)-Ib | aadA1 | qnrB1 | catA1 | - | fosA | oqxAB | dfrA14 | sul2 | tet(A) | ||
Kp5148 | ST34 | KPC-3 | - | SHV-26 | - | - | - | fosA | oqxA10; oqxB19 | - | |||||||||
Kp5150 | ST1079 | KPC-3 | - | SHV-1 | TEM-1 | OXA-9 | aph(6)-Id; aph(3″)-Ib | aac(6′)-Ib; aadA1 | - | - | fosA | oqxA; oqxB19 | dfrA14 | sul2 | |||||
Kp5153 | ST29 | KPC-3 | - | SHV-187 | TEM-1 | OXA-9 | aph(6)-Id; aph(3″)-Ib | aac(6′)-Ib; aadA1 | qnrS1 | - | - | fosA | oqxA; oqxB25 | dfrA14 | sul2 | ||||
Kp5162 | ST451 | KPC-3 | - | SHV-1 | - | - | - | fosA | oqxA10; oqxB25 | - | |||||||||
Kp5165 | ST307 | CTX-M-15 | SHV-28 | TEM-1 | aph(6)-Id; aph(3″)-Ib | aac(3)-IIa; aadA16 | aac(6′)-Ib-cr5 | qnrB6 | catA2 | arr-3 | fosA | oqxA; oqxB19 | dfrA27 | qacEdelta1 | sul1;sul2 | tet(D) | |||
Kv5163 | ST4197 | KPC-3 | - | LEN-2 | - | - | - | fosA | oqxA; oqxB15 | - | |||||||||
Kp5172 | ST280 | KPC-3 | CTX-M-15 | SHV-27 | TEM-1 | OXA-1; OXA-9 | aph(6)-Id; aph(3″)-Ib | aac(3)-IIa; aac(6′)-Ib; aadA1 | aac(6′)-Ib-cr5 | qnrB1 | catB3 | - | fosA | oqxA; oqxB19 | dfrA14 | sul2 | tet(A) |
K. pneumoniae | K. variicola | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Replicon | ST147 ** | ST15 | ST461 | ST1079 | ST29 | ST307 | ST280 | ST34 | ST4197 | Identity/% | N° Isolates/% |
IncFIA (HI1) | 6 | 7 | 1 | 1 | 1 | 1 | 1 | 94.59–100 | 18/58.1 | ||
IncFIB (pQil)_1_pQil | 1 * | 1 * | 100 | 02/06.4 | |||||||
IncFIB (K)_1_Kpn3 | 12 (9 *) | 7 * | 1 | 1 | 1 * | 1 | 1 * | 98.93–100 | 24/77.4 | ||
IncFIB (pKPHS1) | 14 | 97.32–100 | 14/45.5 | ||||||||
IncFIB (Mar)_1_pNDM | 1 | 1 | 1 * | 99.77–100 | 03/09.7 | ||||||
IncFII_1_pKP91 | 10 | 5 | 1 | 1 | 1 | 85.47–88.55 | 18/58.1 | ||||
IncFII (Yp) | 6 | 5 | 1 | 1 | 1 | 85.71 | 14/45.5 | ||||
IncFII (pMET)_1_pMET1 | 1 | 98.09 | 01/03,2 | ||||||||
IncR_1 | 4 (2 *) | 2 * | 1 | 99.2–100 | 07/22.5 | ||||||
IncN_1 | 16 | 1 | 99.42 | 17/54.8 | |||||||
IncL/M (pOXA-48) | 1 * | 100 | 01/03.2 | ||||||||
IncX4_1 | 1 | 99.73 | 01/03.2 | ||||||||
repA-pKPC-2 | 1 | 99.71 | 01/03.2 | ||||||||
Col (MG828)1 | 1 | 93.51 | 01/03.2 | ||||||||
ColRNAI_1 | 4 (2 *) | 6 | 1 | 1 | 1 | 1 | 85.5–100 | 14/45.5 | |||
ColpVC_1 | 1 | 98.45 | 01/03.2 |
Isolates ID | Sequence Type | wzi | K_locus | O_locus | Enterobactin * | Ferric Iron ** | Ybt *** | Type I Fimbriae | Type 3 Fimbriae | Type VI SSE |
---|---|---|---|---|---|---|---|---|---|---|
Kp5141 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5142 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5144 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5147 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5151 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5152 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5143 | ST147 | wzi64 | KL64 | O2v1 | entB | |||||
Kp5160 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5161 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5155 | ST147 | wzi64 | KL64 | O2v1 | entB | |||||
Kp5158 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5164 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5167 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5168 | ST147 | wzi64 | KL64 | O2v1 | entB | fimH | mrkD_12 | tle1; tli1 | ||
Kp5173 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5174 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5175 | ST147 | wzi64 | KL64 | O2v1 | entB | ybtQ | fimH | mrkD_12 | tle1; tli1 | |
Kp5146 | ST15 | wzi19 | KL19 | O1v2 | entB | kfuA_3 | ybtQ | fimH | ||
Kp5149 | ST15 | wzi19 | KL19 | O1v2 | entB | kfuA_3 | ybtQ | fimH | ||
Kp5154 | ST15 | wzi19 | KL19 | O1v2 | entB | kfuA_3 | ybtQ | fimH | ||
Kp5159 | ST15 | wzi19 | KL19 | O1v2 | entB | kfuA_3 | ybtQ | fimH | ||
Kp5156 | ST15 | wzi19 | KL19 | O1v2 | entB | kfuA_3 | fimH | |||
Kp5157 | ST15 | wzi19 | KL19 | O1v2 | entB | kfuA_3 | fimH | |||
Kp5166 | ST15 | wzi19 | KL19 | O1v2 | entB | kfuA_3 | ybtQ | fimH | ||
Kp5148 | ST34 | wzi50 | KL15 | O4 | entB | fimH | tle1; tli1 | |||
Kp5150 | ST1079 | wzi236 | KL10 | O1v2 | entB | fimH | ||||
Kp5153 | ST29 | wzi115 | KL54 | O1v2 | entB | fimH | ||||
Kp5162 | ST451 | wzi38 | KL38 | O1v2 | entB | kfuA_26 | fimH | |||
Kp5165 | ST307 | wzi173 | KL102 | O2v2 | entB | fimH | tle1; tli1 | |||
Kv5163 | ST4197 | - | KL64 | O5 | entB | kfuA_8 | fimH | tle1; tli1 | ||
Kp5172 | ST280 | wzi82 | KL23 | O2v2 | entB | fimH | tle1; tli1 |
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Perdigão, J.; Caneiras, C.; Elias, R.; Modesto, A.; Spadar, A.; Phelan, J.; Campino, S.; Clark, T.G.; Costa, E.; Saavedra, M.J.; et al. Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain. Microorganisms 2020, 8, 1986. https://doi.org/10.3390/microorganisms8121986
Perdigão J, Caneiras C, Elias R, Modesto A, Spadar A, Phelan J, Campino S, Clark TG, Costa E, Saavedra MJ, et al. Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain. Microorganisms. 2020; 8(12):1986. https://doi.org/10.3390/microorganisms8121986
Chicago/Turabian StylePerdigão, João, Cátia Caneiras, Rita Elias, Ana Modesto, Anton Spadar, Jody Phelan, Susana Campino, Taane G. Clark, Eliana Costa, Maria José Saavedra, and et al. 2020. "Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain" Microorganisms 8, no. 12: 1986. https://doi.org/10.3390/microorganisms8121986
APA StylePerdigão, J., Caneiras, C., Elias, R., Modesto, A., Spadar, A., Phelan, J., Campino, S., Clark, T. G., Costa, E., Saavedra, M. J., & Duarte, A. (2020). Genomic Epidemiology of Carbapenemase Producing Klebsiella pneumoniae Strains at a Northern Portuguese Hospital Enables the Detection of a Misidentified Klebsiella variicola KPC-3 Producing Strain. Microorganisms, 8(12), 1986. https://doi.org/10.3390/microorganisms8121986