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Microorganisms
Volume 12
Issue 7
10.3390/microorganisms12071408
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Article

Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil

by
Amanda Yaeko Yamada
1,2,
Andreia Rodrigues de Souza
1,
Amanda Maria de Jesus Bertani
1,
Karoline Rodrigues Campos
1,
Claudio Tavares Sacchi
1,
Denise Brandão de Assis
3,
Enéas de Carvalho
4,
Elizabeth Harummyy Takagi
1,
Marcos Paulo Vieira Cunha
2,
Monique Ribeiro Tiba-Casas
1 and
Carlos Henrique Camargo
1,2,*
1
Instituto Adolfo Lutz, São Paulo 01246-000, Brazil
2
Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-000, Brazil
3
Divisão de Infecção Hospitalar, Centro de Vigilância Epidemiológica, São Paulo 01246-000, Brazil
4
Instituto Butantan, São Paulo 05503-900, Brazil
*
Author to whom correspondence should be addressed.
Microorganisms 2024, 12(7), 1408; https://doi.org/10.3390/microorganisms12071408
Submission received: 20 June 2024 / Revised: 1 July 2024 / Accepted: 4 July 2024 / Published: 12 July 2024
(This article belongs to the Special Issue Advancements in Pathogenic Bacteria: Detection, Genomic Analysis, and Antibiotic Resistance)
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Abstract

Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca. However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The blaNDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes.
Keywords: carbapenem-resistance; conjugation; genetic characterization; IncFIB plasmid; whole genome sequencing carbapenem-resistance; conjugation; genetic characterization; IncFIB plasmid; whole genome sequencing

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MDPI and ACS Style

Yamada, A.Y.; Souza, A.R.d.; Bertani, A.M.d.J.; Campos, K.R.; Sacchi, C.T.; Assis, D.B.d.; Carvalho, E.d.; Takagi, E.H.; Cunha, M.P.V.; Tiba-Casas, M.R.; et al. Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil. Microorganisms 2024, 12, 1408. https://doi.org/10.3390/microorganisms12071408

AMA Style

Yamada AY, Souza ARd, Bertani AMdJ, Campos KR, Sacchi CT, Assis DBd, Carvalho Ed, Takagi EH, Cunha MPV, Tiba-Casas MR, et al. Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil. Microorganisms. 2024; 12(7):1408. https://doi.org/10.3390/microorganisms12071408

Chicago/Turabian Style

Yamada, Amanda Yaeko, Andreia Rodrigues de Souza, Amanda Maria de Jesus Bertani, Karoline Rodrigues Campos, Claudio Tavares Sacchi, Denise Brandão de Assis, Enéas de Carvalho, Elizabeth Harummyy Takagi, Marcos Paulo Vieira Cunha, Monique Ribeiro Tiba-Casas, and et al. 2024. "Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil" Microorganisms 12, no. 7: 1408. https://doi.org/10.3390/microorganisms12071408

APA Style

Yamada, A. Y., Souza, A. R. d., Bertani, A. M. d. J., Campos, K. R., Sacchi, C. T., Assis, D. B. d., Carvalho, E. d., Takagi, E. H., Cunha, M. P. V., Tiba-Casas, M. R., & Camargo, C. H. (2024). Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil. Microorganisms, 12(7), 1408. https://doi.org/10.3390/microorganisms12071408

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