Genomic characterization of carbapenemase-producing Klebsiella pneumoniae ST307 revealed multiple introductions in Buenos Aires, Argentina

Francisco González-Espinosa; Vincenzo Di Pilato; Francisco Magariños; Jose Di Conza; Gian Maria Rossolini; Gabriel Gutkind; Marcela Radice; Daniela Cejas

doi:10.1016/j.jgar.2024.03.017

Genomic characterization of carbapenemase-producing Klebsiella pneumoniae ST307 revealed multiple introductions in Buenos Aires, Argentina

J Glob Antimicrob Resist. 2024 Apr 5:37:176-178. doi: 10.1016/j.jgar.2024.03.017. Online ahead of print.

Authors

Francisco González-Espinosa¹, Vincenzo Di Pilato², Francisco Magariños³, Jose Di Conza¹, Gian Maria Rossolini⁴, Gabriel Gutkind¹, Marcela Radice¹, Daniela Cejas⁵

Affiliations

¹ Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Ciudad Autónoma de Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Argentina.
² University of Genoa, Department of Surgical Sciences and Integrated Diagnostics (DISC), Genoa, Italy.
³ Hospital Donación Francisco Santojanni, Ciudad Autónoma de Buenos Aires, Argentina.
⁴ University of Florence, Department of Experimental and Clinical Medicine, Florence, Italy.
⁵ Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Ciudad Autónoma de Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Ciudad Autónoma de Buenos Aires, Argentina. Electronic address: danielacejas@ffyb.uba.ar.

PMID: 38583573
DOI: 10.1016/j.jgar.2024.03.017

Abstract

Objectives: To describe at genomic level nine carbapenemase-producing Klebsiella pneumoniae ST307 (Kp-ST307) clinical isolates recovered in Buenos Aires during 2017 to 2021, investigating their resistome, virulome, and phylogeny.

Methods: Antimicrobial susceptibility was determined according to Clinical and Laboratory Standards Intitute (CLSI). Genomic DNA was sequenced by Illumina MiSeq and analysed using SPAdes, PROKKA, and Kleborate. Phylogeny of 355 randomly selected Kp-ST307 genomes and those from nine local isolates was inferred by a maximum-likelihood approach. The tree was visualized using Microreact.

Results: Besides resistance to ß-lactams and fluoroquinolones, six out of nine Kp-ST307 were also resistant to ceftazidime/avibactam (CZA). This difficult-to-treat resvistance phenotype was mediated by bla_SHV-28 and GyrA-83I/ParC-80I mutations in addition to carbapenemase coding genes. Among CZA susceptible isolates, two of them harboured bla_KPC-3 while the other harboured bla_KPC-2+bla_CTX-M-15. Regarding CZA-resistant isolates, three harboured bla_KPC-3+bla_NDM-1+bla_CMY-6, two carried bla_KPC-2+bla_NDM-5+bla_CTX-M-15, and bla_NDM-5+bla_CTX-M-15 were detected in the remaining isolate. Furthermore, five colistin-resistant isolates presented a nonsense mutation in mgrB. Global Kp-ST307 isolates were distributed in two deep-branching lineages while local isolates were set in the main clade of the phylogenetic tree. The five isolates from the same hospital, harbouring bla_KPC-3 or bla_KPC-3+bla_NDM-1+bla_CMY-6, clustered in a monophyletic subclade with Italian isolates. Also, an isolate harbouring bla_KPC-2+bla_NDM-5+bla_CTX-M-15 recovered in another hospital was closed to this group. The remaining local Kp-ST307 were grouped in other subclades containing isolates of diverse geographical origin.

Conclusion: The inferred resistome was consistent with the resistant phenotype. Phylogeny suggested multiple introduction events in our region and a single major introduction in one hospital followed by local spread.

Keywords: Argentina; KPC; Klebsiella pneumoniae; NDM; ST307.