Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene

Catarina Ferreira; Santosh Kumar Bikkarolla; Karolin Frykholm; Saga Pohjanen; Margarida Brit; Catarina Lameiras; Olga C. Nunes; Fredrik Westerlund; Célia M. Manaia

doi:10.1371/journal.pone.0247058

Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene

Catarina Ferreira, Santosh Kumar Bikkarolla, Karolin Frykholm, Saga Pohjanen, Margarida Brit, Catarina Lameiras, Olga C. Nunes, Fredrik Westerlund, Célia M. Manaia

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Abstract

Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.

Original language	English
Article number	e0247058
Pages (from-to)	1 to 18
Number of pages	18
Journal	PLoS ONE
Volume	16
Issue number	2
DOIs	https://doi.org/10.1371/journal.pone.0247058
Publication status	Published (in print/issue) - 26 Feb 2021

Bibliographical note

Funding Information:
This work was supported by National Funding Agencies supporting the EuroNanoMed Joint Transnational Call project "Nanofluidics for ultrafast diagnosis of bacterial infections" (NanoDiaBac, ENMed/0001/2014): The Swedish Research Council, Sweden; Fundacão para a Ciência e a Tecnologia (FCT), Portugal and by FEDER through project "Assessing the risks associated with environmental antibiotic resistant bacteria: propagation and transmission to humans" (PTDC/CTA-AMB/28196/2017) - Programa Operacional Competitividade e Internacionalizacão, and by National Funds from FCT - Fundacão para a Ciéncia e a Tecnologia. The authors acknowledge the FCT support provided by the host research centers, UID/Multi/50016/2019, UID/EQU/00511/ 2019 and "LEPABE-2-ECO-INNOVATION" - NORTE-01-0145- FEDER-000005 (Laboratory for Process Engineering, Environment, Biotechnology and Energy) funded by the European Regional Development Fund (ERDF), through COMPETE2020 - Programa Operacional Competitividade e Internacionalizacão (POCI) and by national funds, through FCT - Funda??o para a Ci?ncia e a Tecnologia, and by Norte Portugal Regional Operational Programme (NORTE 2020), under PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). SKB has a personal grant from the Wenner-Gren foundation. CF has a Research Contract from the project PTDC/CTA-AMB/28196/.

Publisher Copyright:
© 2021 Ferreira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.

Funding

Funding Information: This work was supported by National Funding Agencies supporting the EuroNanoMed Joint Transnational Call project "Nanofluidics for ultrafast diagnosis of bacterial infections" (NanoDiaBac, ENMed/0001/2014): The Swedish Research Council, Sweden; Fundacão para a Ciência e a Tecnologia (FCT), Portugal and by FEDER through project "Assessing the risks associated with environmental antibiotic resistant bacteria: propagation and transmission to humans" (PTDC/CTA-AMB/28196/2017) - Programa Operacional Competitividade e Internacionalizacão, and by National Funds from FCT - Fundacão para a Ciéncia e a Tecnologia. The authors acknowledge the FCT support provided by the host research centers, UID/Multi/50016/2019, UID/EQU/00511/ 2019 and "LEPABE-2-ECO-INNOVATION" - NORTE-01-0145- FEDER-000005 (Laboratory for Process Engineering, Environment, Biotechnology and Energy) funded by the European Regional Development Fund (ERDF), through COMPETE2020 - Programa Operacional Competitividade e Internacionalizacão (POCI) and by national funds, through FCT - Funda??o para a Ci?ncia e a Tecnologia, and by Norte Portugal Regional Operational Programme (NORTE 2020), under PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). SKB has a personal grant from the Wenner-Gren foundation. CF has a Research Contract from the project PTDC/CTA-AMB/28196/. Publisher Copyright: © 2021 Ferreira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

Keywords

Anti-Bacterial Agents/toxicity
Bacterial Proteins/genetics
Carbapenems/toxicity
Conjugation, Genetic
Evolution, Molecular
Humans
Klebsiella Infections/microbiology
Klebsiella pneumoniae/drug effects
beta-Lactam Resistance/genetics
beta-Lactamases/genetics

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10.1371/journal.pone.0247058Licence: CC BY

Polyphasic characterization of carbapenemresistantFinal published version, 1.8 MBLicence: CC BY

Cite this

Ferreira, C., Bikkarolla, S. K., Frykholm, K., Pohjanen, S., Brit, M., Lameiras, C., Nunes, O. C., Westerlund, F., & Manaia, C. M. (2021). Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene. PLoS ONE, 16(2), 1 to 18. Article e0247058. https://doi.org/10.1371/journal.pone.0247058

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title = "Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene",

abstract = "Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.",

keywords = "Anti-Bacterial Agents/toxicity, Bacterial Proteins/genetics, Carbapenems/toxicity, Conjugation, Genetic, Evolution, Molecular, Humans, Klebsiella Infections/microbiology, Klebsiella pneumoniae/drug effects, beta-Lactam Resistance/genetics, beta-Lactamases/genetics",

author = "Catarina Ferreira and Bikkarolla, \{Santosh Kumar\} and Karolin Frykholm and Saga Pohjanen and Margarida Brit and Catarina Lameiras and Nunes, \{Olga C.\} and Fredrik Westerlund and Manaia, \{C{\'e}lia M.\}",

note = "Funding Information: This work was supported by National Funding Agencies supporting the EuroNanoMed Joint Transnational Call project {"}Nanofluidics for ultrafast diagnosis of bacterial infections{"} (NanoDiaBac, ENMed/0001/2014): The Swedish Research Council, Sweden; Fundac{\~a}o para a Ci{\^e}ncia e a Tecnologia (FCT), Portugal and by FEDER through project {"}Assessing the risks associated with environmental antibiotic resistant bacteria: propagation and transmission to humans{"} (PTDC/CTA-AMB/28196/2017) - Programa Operacional Competitividade e Internacionalizac{\~a}o, and by National Funds from FCT - Fundac{\~a}o para a Ci{\'e}ncia e a Tecnologia. The authors acknowledge the FCT support provided by the host research centers, UID/Multi/50016/2019, UID/EQU/00511/ 2019 and {"}LEPABE-2-ECO-INNOVATION{"} - NORTE-01-0145- FEDER-000005 (Laboratory for Process Engineering, Environment, Biotechnology and Energy) funded by the European Regional Development Fund (ERDF), through COMPETE2020 - Programa Operacional Competitividade e Internacionalizac{\~a}o (POCI) and by national funds, through FCT - Funda??o para a Ci?ncia e a Tecnologia, and by Norte Portugal Regional Operational Programme (NORTE 2020), under PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). SKB has a personal grant from the Wenner-Gren foundation. CF has a Research Contract from the project PTDC/CTA-AMB/28196/. Publisher Copyright: {\textcopyright} 2021 Ferreira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

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AU - Bikkarolla, Santosh Kumar

AU - Frykholm, Karolin

AU - Pohjanen, Saga

AU - Brit, Margarida

AU - Lameiras, Catarina

AU - Nunes, Olga C.

AU - Westerlund, Fredrik

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PY - 2021/2/26

Y1 - 2021/2/26

N2 - Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.

AB - Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.

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KW - Bacterial Proteins/genetics

KW - Carbapenems/toxicity

KW - Conjugation, Genetic

KW - Evolution, Molecular

KW - Humans

KW - Klebsiella Infections/microbiology

KW - Klebsiella pneumoniae/drug effects

KW - beta-Lactam Resistance/genetics

KW - beta-Lactamases/genetics

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Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene

Abstract

Bibliographical note

Funding

Keywords

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