Genomic insights of Leclercia adecarboxylata strains linked to an outbreak in public hospitals in Mexico

Edwin Barrios-Villa, Brenda Pacheco-Flores, Patricia Lozano-Zaraín, Rodolfo Del Campo-Ortega, Ivan de Jesús Ascencio-Montiel, Margot González-León, Margarita Camorlinga-Ponce, Francisco Javier Gaytán Cervantes, Carolina González Torres, Emmanuel Aguilar, Joaquín González Ibarra, Francisco Javier Torres López, Haydeé Rosas-Vargas, César R. González-Bonilla, Rosa del Carmen Rocha-Gracia*

*Autor correspondiente de este trabajo

Producción científica: Contribución a una revistaArtículorevisión exhaustiva

1 Cita (Scopus)

Resumen

Background: Leclercia adecarboxylata is a bacteria closely related to Escherichia coli according to its biochemical characteristics and is commonly considered non-pathogenic although a growing number of publications classify it as an emerging pathogen. Fosfomycin resistance is a common trait for L. adecarboxylata encoded by fosALA gene. Objective: To analyze genomic traits of sixteen L. adecarboxylata strains isolated from blood culture and a bottle of total parenteral nutrition. Methods: Twenty-eight L. adecarboxylata strains isolated from blood culture and a bottle of total parenteral nutrition were identified biochemically with a Vitek ® automated system. The strains were phenotyped by their growth on Eosin Methylene Blue agar or MacConkey agar plates. Additionally, Pulsed field gel electrophoresis (PFGE) was performed to establish the clonal relationship. The genomic DNA of sixteen strains was obtained using a Qubit ® dsDNA HS Assay Kit and sequenced on an Illumina ® MiSeq instrument. Draft genomes were assembled using PROKKA and Rast. Assemblies were submitted to Resfinder and PathogenFinder from the Center for Genomic Epidemiology in order to find resistance genes and pathogenic potential. IslandViewer4 was also used to find Pathogenicity and Phage Islands. For identification of the fosA gene, manual curation and Clustal analysis was performed. A novel FosA variant was identified. Finally, phylogenetic analysis was performed using VAMPhyRE software and Mega X. Results: In this paper, we report the genomes of sixteen strains of Leclercia adecarboxylata causing an outbreak associated with parenteral nutrition in public hospitals in Mexico. The genomes were analyzed for genetic determinants of virulence and resistance. A high pathogenic potential (pathogenicity index 0.82) as well as multiple resistance genes including carbapenemics, colistin and efflux pumps were determined. Based on sequence analysis, a new variant of the fosALA gene was described. Finally, the outbreak was confirmed by establishing the clonal relationship among the sixteen genomes obtained. Conclusions: Commensal strains of L. adecarboxylata may acquire genetic determinants that provide mechanisms of host damage and go unnoticed in clinical diagnosis. L. adecarboxylata can evolve in a variety of ways including the acquisition of resistance and virulence genes representing a therapeutic challenge in patient care.

Idioma originalInglés
Páginas (desde-hasta)569-579
Número de páginas11
PublicaciónGenes and Genomics
Volumen45
N.º5
DOI
EstadoPublicada - may. 2023

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© 2023, The Author(s) under exclusive licence to The Genetics Society of Korea.

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