Santiago Castillo Ramírez

Evolutionary Genomics Researcher
Unidad de Análisis Bioinformáticos Researcher

Associate Professor

Academic history

Santiago received his PhD in Biological Sciences from the Center for Genomic Sciences (CCG) at the National Autonomous University of Mexico, conducting phylogenomic studies of Alphaproteobacteria. He then pursued postdoctoral research in microevolution and phylogeography of methicillin-resistant Staphylococcus aureus at the University of Bath, under the supervision of Professor Edward J. Feil. Santiago is Associate Professor in the Evolutionary Genomics Research Program at the Center for Genomic Sciences. His research focuses on diverse aspects of the evolution of bacterial pathogens, including phylogeography and evolutionary genomics. Although his initial work concentrated on the molecular evolution and the phylogeography of Staphylococcus aureus and Borrelia burgdoferi, his most recent work employs comparative genomics to study the processes underpinning the genomic variation and the dispersal of Acinetobacter baumannii -an important human pathogen, source of many nosocomial infections. To date Santiago has published over 30 articles and 4 book chapters.

He is Associate Editor of the journal Bioscience Horizons, member of the editorial board of Applied Environmental Microbiology and Review Editor for Frontiers in Microbiology. He has served as reviewer for several journals in bacterial genomics (Applied Environmental Microbiology, Genome Biology and Evolution), molecular evolution (Molecular Biology and Evolution, Molecular Ecology, Infection, Genetics and Evolution) and infectious diseases (Lancet Infectious Diseases). Additionally, he has acted as a reviewer for grant agencies in Mexico (National Council for Science and Technology) and Canada (NSERC Discovery grants).


Google Scholar
Thomson Reuters ResearcherID

Selected publications

1.- Castillo-Ramírez S, Graña-Miraglia L. Inaccurate Multilocus Sequence Typing of Acinetobacter baumannii. Emerg Infect Dis. 2019 Jan;25(1):186-187.
2.- Graña-Miraglia L, ArreguíN-Pérez C, López-Leal G, Muñoz A, Pérez-Oseguera A, Miranda-Miranda E, Cossío-Bayúgar R, Castillo-Ramírez S. Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus. PeerJ. 2018 Oct 24;6:e5839.
3.- Graña-Miraglia L, Lozano LF, Velázquez C, Volkow-Fernández P, Pérez-Oseguera Á, Cevallos MA, Castillo-Ramírez S. Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen. Front Microbiol. 2017 Sep 20;8:1817.
4.- Castillo-Ramírez S, Fingerle V, Jungnick S, Straubinger RK, Krebs S, Blum H,Meinel DM, Hofmann H, Guertler P, Sing A, Margos G. Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto. Sci Rep. 2016 Mar 9;6:22794.
5.- Castillo-Ramírez S, Corander J, Marttinen P, Aldeljawi M, Hanage WP, Westh H, Boye K, Gulay Z, Bentley SD, Parkhill J, Holden MT, Feil EJ. Phylogeographic variation in recombination rates within a global clone of Methicillin-Resistant Staphylococcus aureus. Genome Biology. 2012 Dec 27;13(12):R126.
6.- Castillo-Ramírez S, Harris SR, Holden MTG, He M, Parkhill J, Feil EJ. The Impact of Recombination on dN/dS within Recently Emerged Bacterial Clones. Plos Pathogens. 2011, 7(7): e1002129.

Telephone: (777) 3133881


2018Frisch MB, Castillo-Ramirez S, Petit RA 3rd, Farley MM, Ray SM, Albrecht VS, Limbago BM, Hernandez J, See I, Satola SW, Read TD. (2018). "Invasive methicillin-resistant Staphylococcus aureus USA500 strains from the U.S. Emerging Infections Program constitute three geographically distinct lineages". mSphere. 3(3):e00571-17-. [doi:10.1128/mSphere.00571-17]29720528
2017Pérez-Oseguera Á, Castro-Jaimes S, Salgado-Camargo AD, Silva-Sanchez J, Garza-González E, Castillo-Ramírez S, Cevallos MÁ. (2017). "Complete genome sequence of a blaOXA-58-producing Acinetobacter baumannii strain isolated from a Mexican hospital". Genome Announcements. 5(36):e00949-17-. [doi:10.1128/genomeA.00949-17]28883144
2017Angel Vences-Guzman, M, Goetting-Minesky, M, Guan, Z, Castillo-Ramirez, S, America Cordoba-Castro, L, Lopez-Lara, I, Geiger, O, Sohlenkamp, C, Fenno, J. (2017). "1,2-Diacylglycerol choline phosphotransferase catalyzes the final step in the unique Treponema denticola phosphatidylcholine biosynthesis pathway". Molecular Microbiology. 103(5):896-912. [doi:10.1111/mmi.13596]28009086
2016Castillo-Ramirez, S, Fingerle, V, Jungnick, S, Straubinger, R, Krebs, S, Blum, H, Meinel, D, Hofmann, H, Guertler, P, Sing, A, Margos, G. (2016). "Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto". SCIENTIFIC REPORTS. 6():22794-22794. [doi:10.1038/srep22794]26955886
2016Aanensen, D, Feil, E, Holden, M, Dordel, J, Yeats, C, Fedosejev, A, Goater, R, Castillo-Ramirez, S, Corander, J, Colijn, C, Chlebowicz, M, Schouls, L, Heck, M, Pluister, G, Ruimy, R, Kahlmeter, G, Ahman, J, Matuschek, E, Friedrich, A, Parkhill, J, Bentley, S, Spratt, B, Grundmann, H, ESCMID Study Grp Mol Epidemiologic, European Staphylococcal Ref Lab Wo. (2016). "Whole-genome sequencing for routine pathogen surveillance in public health: A population snapshot of invasive Staphylococcus aureus in Europe". mBio. 7(3):e00444-16-. [doi:10.1128/mBio.00444-16]27150362
2016Bolanos, L, Rosenblueth, M, Castillo-Ramirez, S, Figuier-Huttin, G, Martinez-Romero, E. (2016). "Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota". Environmental Microbiology. 18(5):1364-1378. [doi:10.1111/1462-2920.12939]26058415
2016López-Leal G, Cevallos MA, Castillo-Ramírez S. (2016). "Evolution of a sigma factor: An All-In-One of Gene Duplication, Horizontal Gene Transfer, Purifying Selection, and Promoter Differentiation". Frontiers in Microbiology. 7(APR):581-581. [doi:10.3389/fmicb.2016.00581]27199915
2016Castro-Jaimes S., Salgado-Camargo A.D., Gra�a-Miraglia L., Lozano L., Bocanegra-Ibarias P., Volkow-Fern�ndez P., Silva-Sanchez J., Castillo-Ram�rez S., Cevallos M.A.. (2016). "Complete genome sequence of a multidrug-resistant Acinetobacter baumannii isolate obtained from a Mexican hospital (sequence type 422)". Genome Announcements. 4(3):e00583-16-. [doi:10.1128/genomeA.00583-16]
2016Graña-Miraglia L., Lozano L., Castro-Jaimes S., Cevallos M.A., Volkow P., Castillo-Ramírez S.. (2016). "First genome sequence of a mexican multidrug-resistant Acinetobacter baumannii isolate". Genome Announcements. 4(2):e00156-16-. [doi:10.1128/genomeA.00156-16]
2015Ezewudo, M, Joseph, S, Castillo-Ramirez, S, Dean, D, del Rio, C, Didelot, X, Dillon, J, Selden, R, Shafer, W, Turingan, R, Unemo, M, Read, T. (2015). "Population structure of Neisseria Gonorrhoeae based on whole genome data and its relationship with antibiotic resistance". Peerj. 2015(3):e806-. [doi:10.7717/peerj.806]25780762
2015Joseph, S, Marti, H, Didelot, X, Castillo-Ramirez, S, Read, T, Dean, D. (2015). "Chlamydiaceae genomics reveals interspecies admixture and the recent evolution of Chlamydia Abortus infecting lower mammalian species and humans". Genome Biology And Evolution. 7(11):3070-3084. [doi:10.1093/gbe/evv201]26507799
2014Lopez-Leal, G, Luisa Tabche, M, Castillo-Ramirez, S, Mendoza-Vargas, A, Ramirez-Romero, M, Davila, G. (2014). "RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock". Bmc Genomics. 15(1):770-770. [doi:10.1186/1471-2164-15-770]25201548
2014Castillo-Ramirez, S, Feil, E. (2014). "Towards a Synthesis of Population Genomics and Epidemiology: Next-Generation Sequencing of Bacterial Pathogens". Molecular Medical Microbiology: Second Edition. 1-3():337-345. [doi:10.1016/B978-0-12-397169-2.00018-4]
2013Castillo-Ramírez, S, Feil, E. (2013). "Population genetics". The Prokaryotes: Prokaryotic Biology And Symbiotic Associations. ():255-266. [doi:10.1007/978-3-642-30194-0_83]
2011Guerra-Crespo, M, Perez-Monter, C, Janga, S, Castillo Ramírez, S, Gutierrez-Ríos, R, Joseph-Bravo, P, Perez-Martinez, L, Charli, J. (2011). "Transcriptional profiling of fetal hypothalamic TRH neurons". Bmc Genomics. 12():222-222. [doi:10.1186/1471-2164-12-222]21569245
2010Castillo-Ramírez, S, L. Liu, D. Pearl, S. V. Edwards. (2010). "Bayesian estimation of species trees: a practical guide to optimal sampling and analysis.". Estimating Species Trees: Practical and Theoretical Aspects. ():15-33.
2008Crossman, L, Castillo-Ramirez, S, McAnnula, C, Lozano, L, Vernikos, G, Acosta, J, Ghazoui, Z, Hernandez-Gonzalez, I, Meakin, G, Walker, A, Hynes, M, Young, J, Downie, J, Romero, D, Johnston, A, Davila, G, Parkhill, J, Gonzalez, V. (2008). "A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria". Plos One. 3(7):e2567-. [doi:10.1371/journal.pone.0002567]18596979
2008Castillo-Ramirez, S, Gonzalez, V. (2008). "Factors affecting the concordance between orthologous gene trees and species tree in bacteria". Bmc Evolutionary Biology. 8(1):300-300. [doi:10.1186/1471-2148-8-300]18973688
2008González Zúñiga, V, Luis Lozano, Santiago Castillo-Ramírez, Hernández González, I, Bustos Arcos, V, Santamaria Gutiérrez, R, Fernandez Vázquez, J, Centro de Ciencias Genómicas CCG, Dávila Ramos, J. (2008). "Evolutionary Genomics of the Nitrogen Fixing Symbiotic Bacteria". Molecular Mechanisms of Plant-Microbe Coexistance Soil Biology Series. 15(0):183-198.
2007Guo, X, Castillo-Ramirez, S, Gonzalez, V, Bustos, P, Fernandez-Vazquez, J, Santamaria, R, Arellano, J, Cevallos, M, Davila, G. (2007). "Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts". Bmc Genomics. 8():228-228. [doi:10.1186/1471-2164-8-228]17623083
2006González Zúñiga, V, Santamaría, R, Bustos, P, Acosta, J, Fernández, J, Hernández-González, I, Lozano, L, Castillo, S, Dávila, G. (2006). "Genomic diversity of Rhizobium etli: The Complete Genome and its -intraspecific-variation". Revista Latinoamericana De Microbiologia. 48(2):132-134.
2009Castillo-Ramirez, S, Vazquez-Castellanos, J, Gonzalez, V, Cevallos, M. (2009). "Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: The repABC operon". Bmc Genomics. 10():536-536. [doi:10.1186/1471-2164-10-536]19919719
2009Martinez-Salazar, J, Sandoval-Calderon, M, Guo, X, Castillo-Ramirez, S, Reyes, A, Loza, M, Rivera, J, Alvarado-Affantranger, X, Sanchez, F, Gonzalez, V, Davila, G, Ramirez-Romero, M. (2009). "The Rhizobium etli RpoH1 and RpoH2 sigma factors are involved in different stress responses". MICROBIOLOGY-SGM. 155(2):386-397. [doi:10.1099/mic.0.021428-0]19202087
2018Challagundla, L, Reyes, J, Rafiqullah, I, Sordelli, D, Echaniz-Aviles, G, Velazquez-Meza, M, Castillo-Ramirez, S, Fittipaldi, N, Feldgarden, M, Chapman, S, Calderwood, M, Carvajal, L, Rincon, S, Hanson, B, Planet, P, Arias, C, Diaz, L, Robinson, D. (2018). "Phylogenomic classification and the evolution of Clonal complex 5 methicillin-resistant Staphylococcus aureus in the Western Hemisphere". Frontiers in Microbiology. 9():1901-. [doi:10.3389/fmicb.2018.01901]30186248
2016Becker, N, Margos, G, Blum, H, Krebs, S, Graf, A, Lane, R, Castillo-Ramirez, S, Sing, A, Fingerle, V. (2016). "Recurrent evolution of host and vector association in bacteria of the Borrelia burgdorferi sensu lato species complex". Bmc Genomics. 17(1):734-734. [doi:10.1186/s12864-016-3016-4]27632983
2016Joseph, S, Cox, D, Wolff, B, Morrison, S, Kozak-Muiznieks, N, Frace, M, Didelot, X, Castillo-Ramirez, S, Winchell, J, Read, T, Dean, D. (2016). "Dynamics of genome change among Legionella species". SCIENTIFIC REPORTS. 6():33442-33442. [doi:10.1038/srep33442]27633769
2017Graña-Miraglia L, Lozano LF, Velázquez C, Volkow-Fernández P, Pérez-Oseguera Á, Cevallos MA, Castillo-Ramírez S. (2017). "Rapid gene turnover as a significant source of genetic variation in a recently seeded population of a healthcare-associated pathogen". Frontiers in Microbiology. 8(SEP):1817-1817. [doi:10.3389/fmicb.2017.01817]28979253
2018Graña-Miraglia, L, Arreguín-Pérez, C, López-Leal, G, Muñoz, A, Pérez-Oseguera, A, Miranda-Miranda, E, Cossío-Bayúgar, R, Castillo-Ramírez, S. (2018). "Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus". Peerj. 2018(10):e5839-. [doi:10.7717/peerj.5839]30386709