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Identification of beta-Lactamases and beta-Lactam-Related Proteins in Human Pathogenic Bacteria using a Computational Search Approach

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Abstract

A systematic analysis of beta-lactamases based on comparative proteomics has not been performed thus far. In this report, we searched for the presence of beta-lactam-related proteins in 591 bacterial proteomes belonging to 52 species that are pathogenic to humans. The amino acid sequences for 19 different types of beta-lactamases (ACT, CARB, CifA, CMY, CTX, FOX, GES, GOB, IMP, IND, KPC, LEN, OKP, OXA, OXY, SHV, TEM, NDM, and VIM) were obtained from the ARG-ANNOT database and were used to construct 19 HMM profiles, which were used to identify potential beta-lactamases in the completely sequenced bacterial proteomes. A total of 2877 matches that included the word “beta-lactamase” and/or “penicillin” in the functional annotation and/or in any of its regions were obtained. These enzymes were mainly described as “penicillin-binding proteins,” “beta-lactamases,” and “metallo-beta-lactamases” and were observed in 47 of the 52 species studied. In addition, proteins classified as “beta-lactamases” were observed in 39 of the species included. A positive correlation between the number of beta-lactam-related proteins per species and the proteome size was observed (R 0.78, P < 0.00001). This correlation partially explains the high presence of beta-lactam-related proteins in large proteomes, such as Nocardia brasiliensis, Bacillus anthracis, and Mycobacterium tuberculosis, along with their absence in small proteomes, such as Chlamydia spp. and Mycoplasma spp. We detected only five types of beta-lactamases (TEM, SHV, CTX, IMP, and OXA) and other related proteins in particular species that corresponded with those reported in the literature. We additionally detected other potential species-specific beta-lactamases that have not yet been reported. In the future, better results will be achieved due to more accurate sequence annotations and a greater number of sequenced genomes.

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Acknowledgements

We wish to thank to CONACyT for the scholarship granted to AJLBT to perform the present study. The publication of this article was partially funded by DGAPA-UNAM (IN-201117) to E. P-R.

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Authors and Affiliations

  1. Departamento de Psicología Básica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Sierra Mojada #950, colonia Independencia, C.P. 44340, Guadalajara, Jalisco, Mexico

    Aniel Jessica Leticia Brambila-Tapia

  2. Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas (IIMAS), Unidad Académica de Ciencias y Tecnología Universidad Nacional Autónoma de México (UNAM), Mérida, Yucatán, Mexico

    Ernesto Perez-Rueda

  3. Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología (IBT), (UNAM), Cuernavaca, Morelos, Mexico

    Ernesto Perez-Rueda

  4. Departamento de Diagnóstico Epidemiológico, Instituto Nacional de Salud Pública, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca, Morelos, Mexico

    Humberto Barrios

  5. Instituto de Genética Humana, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico

    Nory Omayra Dávalos-Rodríguez & Ingrid Patricia Dávalos-Rodríguez

  6. División de Genética, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico

    Ingrid Patricia Dávalos-Rodríguez

  7. Departamento de Fisiología, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Sierra Mojada #950, colonia Independencia, C.P. 44340, Guadalajara, Jalisco, Mexico

    Ernesto Germán Cardona-Muñoz & Mario Salazar-Páramo

  8. División de Investigación en Salud, UMAE, Centro Médico Nacional de Occidente (CMNO), Guadalajara, Jalisco, Mexico

    Mario Salazar-Páramo

Authors
  1. Aniel Jessica Leticia Brambila-Tapia
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  2. Ernesto Perez-Rueda
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  3. Humberto Barrios
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  4. Nory Omayra Dávalos-Rodríguez
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  5. Ingrid Patricia Dávalos-Rodríguez
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  6. Ernesto Germán Cardona-Muñoz
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  7. Mario Salazar-Páramo
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Corresponding authors

Correspondence to Aniel Jessica Leticia Brambila-Tapia or Mario Salazar-Páramo.

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Brambila-Tapia, A.J.L., Perez-Rueda, E., Barrios, H. et al. Identification of beta-Lactamases and beta-Lactam-Related Proteins in Human Pathogenic Bacteria using a Computational Search Approach. Curr Microbiol 74, 915–920 (2017). https://doi.org/10.1007/s00284-017-1265-3

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  • DOI: https://doi.org/10.1007/s00284-017-1265-3

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