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

• Published in: Genes & genomics Vol. 45; no. 5; pp. 569 - 579
• Main Authors: Barrios-Villa, Edwin, Pacheco-Flores, Brenda, Lozano-Zaraín, Patricia, Del Campo-Ortega, Rodolfo, de Jesús Ascencio-Montiel, Ivan, González-León, Margot, Camorlinga-Ponce, Margarita, Gaytán Cervantes, Francisco Javier, González Torres, Carolina, Aguilar, Emmanuel, González Ibarra, Joaquín, Torres López, Francisco Javier, Rosas-Vargas, Haydeé, González-Bonilla, César R., del Carmen Rocha-Gracia, Rosa
• Format: Journal Article
• Language: English
• Published: Singapore Springer Nature Singapore 01-05-2023; Springer; Springer Nature B.V; 한국유전학회
• Subjects: Agar; Agar - therapeutic use; Analysis; Animal Genetics and Genomics; Anti-Bacterial Agents; Antibacterial agents; Bacteria; Biochemical characteristics; Biomedical and Life Sciences; Blood; Blood culture; Colistin; Disease Outbreaks; Drug resistance in microorganisms; Enterobacteriaceae Infections - complications; Enterobacteriaceae Infections - epidemiology; Enterobacteriaceae Infections - genetics; Epidemiology; Escherichia coli; Fosfomycin; Gel electrophoresis; Genes; Genomes; Genomics; Health aspects; Hospitals; Hospitals, Public; Human Genetics; Humans; Leclercia adecarboxylata; Life Sciences; Medical examination; Methylene blue; Mexico - epidemiology; Microbial Genetics and Genomics; Nutrition; Outbreaks; Parenteral nutrition; Pathogenicity; Phylogeny; Plant Genetics and Genomics; Research Article; Sequence analysis; Strains (organisms); Virulence; Virulence (Microbiology); 생물학; Mexico; Emerging pathogen; Antibiotic resistance; Leclercia adecarboxylata
• ISSN: 1976-9571; 2092-9293
• DOI: 10.1007/s13258-022-01348-4

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
fosA
LA
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
fosA
LA
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.