Complexity of genomic epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Colombia urges the reinforcement of whole genome sequencing based surveillance programs

Saavedra, S. Y.; Bernal, J. F.; Escudero, E. M.; Arevalo, S. A.; Prada, D. A.; Valencia, M. F.; Moreno, J.; Hidalgo, A. M.; Abrudan, M.; Argimon, S.; Kekre, M.; Underwood, A.; Aanensen, D. M.; Duarte, C.; Donado-Godoy, P.

doi:10.1101/2021.06.21.449250

bioRxiv · 10.1101/2021.06.21.449250

Complexity of genomic epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Colombia urges the reinforcement of whole genome sequencing based surveillance programs

Saavedra, S. Y.·Bernal, J. F.·Escudero, E. M.·Arevalo, S. A.·Prada, D. A.·Valencia, M. F.·Moreno, J.·Hidalgo, A. M.·Abrudan, M.·Argimon, S.·Kekre, M.·Underwood, A.·Aanensen, D. M.·Duarte, C.·Donado-Godoy, P.

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Abstract

BackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)s 2013-2017 sample collection. MethodsA total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10(R)Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of AMR, and AGROSAVIA. ResultsOf the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases blaKPC-3, blaKPC-2, blaNDM-1, blaNDM-9, blaVIM-2, blaVIM-4, and blaVIM-24, and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin (clb3) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI> 99.9%). ConclusionsThe study outlines complex CRKP epidemiology in Colombia. CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of STs, MGE, and resistance and virulence genes. summaryIn Colombia, the dissemination of carbapenemases in carbapenem-resistant Klebsiella pneumoniae is attributed to horizontal gene transfer and successful circulation of CG258, and, to a lesser extent, other clones such as ST307, ST147, and ST152.

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Saavedra, S. Y., Bernal, J. F., Escudero, E. M., Arevalo, S. A., Prada, D. A., Valencia, M. F., Moreno, J., Hidalgo, A. M., Abrudan, M., Argimon, S., Kekre, M., Underwood, A., Aanensen, D. M., Duarte, C., Donado-Godoy, P.. 2021-06-22. Complexity of genomic epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Colombia urges the reinforcement of whole genome sequencing based surveillance programs. https://doi.org/10.1101/2021.06.21.449250

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