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Whole-Genome Analysis of an Extensively Drug-Resistance Empedobacter falsenii Strain Reveals Distinct Features and the Presence of a Novel Metallo-ß-Lactamase (EBR-2)

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Abstract

The spread of antibiotic resistance is rapidly threatening the effectiveness of antibiotics in the clinical setting. Many infections are being caused by known and unknown pathogenic bacteria that are resistant to many or all antibiotics currently available. Empedobacter falsenii is a nosocomial pathogen that can cause human infections. E. falsenii Wf282 strain was found to be resistant to many antibiotics, including carbapenems and colistin. Whole-genome shotgun sequencing of the strain was performed, and distinct features were identified. A novel metallo-β-lactamase, named EBR-2, was found, suggesting a potential role of E. falsenii as a reservoir of β-lactamases and other resistance determinants also found in its genome. The EBR-2 protein showed the highest catalytic efficiency for penicillin G as compared to meropenem and ampicillin and was unable to hydrolyze cefepime. The results described in this work broaden the current understanding of the role of β-lactamases in the Flavobacteriaceae family and suggest that E. falsenii Wf282 may be a reservoir of these novel resistance determinants.

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Acknowledgements

Secretaría de Ciencia y Técnica de la Universidad de Buenos Aires” (UBACyT) to CV, Buenos Aires, Argentina. GMT, SM, and KC were supported by a Post-doctoral fellowship and doctoral fellowship from CONICET, and grant MHIRT 2T37MD001368 from the National Institute on Minority Health and Health Disparities, National Institute of Health, respectively. AI is a member of the “Sistema Nacional de Investigadores” and “PEDECIBA,” Uruguay.

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Authors and Affiliations

  1. Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA

    Chelsea Collins, Kevin Chiem, Marcelo Tolmasky & Maria Soledad Ramirez

  2. Laboratorio de Bacteriología Clínica, Departamento de Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Buenos Aires, Argentina

    Marisa Almuzara, German Traglia & Carlos Vay

  3. Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI- CONICET), 2000, Rosario, Argentina

    Mariana Saigo & Maria Alejandra Mussi

  4. Facultad de Medicina, Instituto de Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina

    Sabrina Montaña

  5. Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay

    Andres Iriarte

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  1. Chelsea Collins
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Correspondence to Maria Soledad Ramirez.

Electronic supplementary material

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284_2018_1498_MOESM1_ESM.pdf

Supplementary material 1 (PDF 77 KB) Maximum likelihood phylogenetic tree of the Flavobacteriaceae family based on 21 conserved ribosomal protein-coding genes. A blue arrow indicates the phylogenetic position of E. falsenii Wf282. Blue branches define the monophyletic group of the closely related genomes of E. falsenii Wf282, bootstrap support is indicated next to nodes. Assembly code of each genome is also indicated. The phylogeny is arbitrary rooted using the midpoint rooting method.

Supplementary material 2 (XLSX 44 KB)

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Supplementary material 4 (XLSX 149 KB)

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Collins, C., Almuzara, M., Saigo, M. et al. Whole-Genome Analysis of an Extensively Drug-Resistance Empedobacter falsenii Strain Reveals Distinct Features and the Presence of a Novel Metallo-ß-Lactamase (EBR-2). Curr Microbiol 75, 1084–1089 (2018). https://doi.org/10.1007/s00284-018-1498-9

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