Santiago Castillo Ramírez | Center for Genomic Sciences

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 (MRSA), under the supervision of Ed Feil, at the University of Bath in England. Santiago is Associate Professor in the Evolutionary Genomics Research Program at the CCG. His research focuses on diverse aspects of the micro evolution of bacterial pathogens, including phylogeography and evolutionary genomics. Although his initial work concentrated on the molecular evolution and the phylogeography of MRSA 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 nosocomial pathogen) and closely related species.

To date Santiago has published 46 articles, which have more than 1650 citations and his has an h-index of 20 and i10-index of 28. He is Associate Editor of the journals Plos Neglected Tropical Diseases and Frontiers in Microbiology; he is also member of the editorial board of Applied Environmental Microbiology. He has served as reviewer for over 20 journals, among them PNAS, Genome Research, Molecular Biology and Evolution, and Lancet Infectious Diseases. Additionally, he has acted as a reviewer for grant agencies in Mexico (National Council for Science and Technology), Canada (NSERC Discovery grants) and United Kingdom (Medical Research Council, Fellowships scheme). He has supervised a couple of postdocs, graduated one PhD student and two undergraduate students. At the present time, he supervises one postdoc, one PhD student and one Master student.

Currently, together with Michael Gillings and Timothy Ghaly (from Mcquarie University), we are leading the special issue “One Health & Antimicrobial Drug Resistance” (see link below) for Environmental Microbiology. https://sfamjournals.onlinelibrary.wiley.com/pb-assets/assets/17582229/2020-one-health_EMI-EMIR-1608325039767.pdf

Recently, he was the Lead Editor of the research topic “Genomic Basis of Antibiotic Resistance and Virulence in Acinetobacter” for Frontiers in Microbiology. https://www.frontiersin.org/research-topics/12244/

He has several ongoing international collaborations, listed below:

1) Together with Scott V. Edwards at Harvard University, we are studying the evolutionary dynamics of Mycoplasma gallisepticum.

2) Along with Ben Evans from University of East Anglia, Ayush Kumar (University of Manitoba) and Izhar Kahn (Agriculture and Agri-Food Canada), we are studying environmental isolates of A. baumannii.

3) In collaboration with Gabrielle Margos from the German National Reference Centre for Borrelia, we have been describing the phylogeography of several Borrelia species.

Links

ResearchGate
Google Scholar
Thomson Reuters ResearcherID
OrcID
Scopus

Selected publications

1: Hernández-González IL, Castillo-Ramírez S. Antibiotic-resistant Acinetobacter baumannii is a One Health problem. The Lancet Microbe. Volume 1, Issue 7, November 2020. doi:https://doi.org/10.1016/S2666-5247(20)30167-1.

2: Castillo-Ramírez S, Mateo-Estrada V, Gonzalez-Rocha G, Opazo-Capurro A. Phylogeographical Analyses and Antibiotic Resistance Genes of Acinetobacter johnsonii Highlight Its Clinical Relevance. mSphere. 2020 Jul 1;5(4):e00581-20. doi:10.1128/mSphere.00581-20.

3: Castillo-Ramírez S, Graña-Miraglia L. Inaccurate Multilocus Sequence Typing of Acinetobacter baumannii. Emerg Infect Dis. 2019 Jan;25(1):186-187. doi:10.3201/eid2501.180374.

4: Mateo-Estrada V, Graña-Miraglia L, López-Leal G, Castillo-Ramírez S. Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter. Genome Biol Evol. 2019 Sep 1;11(9):2531-2541. doi:10.1093/gbe/evz178.

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 Biol. 2012 Dec 27;13(12):R126. doi:10.1186/gb-2012-13-12-r126.

Telephone: (777) 3133881
Email: iago@ccg.unam.mx

Publications

Year	Publication	PMID
2020	De la Rosa, C, Lozano, L, Castillo-Ramírez, S, Covarrubias, A, Reyes, J. (2020). "Origin and Evolutionary Dynamics of the miR2119 and ADH1 Regulatory Module in Legumes.". Genome Biology And Evolution. 12(12):2355-2369. [doi:10.1093/gbe/evaa205]	33045056
2020	Singh, M, De Silva, P, Al-Saadi, Y, Switala, J, Loewen, P, Hausner, G, Chen, W, Hernandez, I, Castillo-Ramirez, S, Kumar, A. (2020). *"Characterization of extremely drug-resistant and hypervirulent Acinetobacter* baumannii ab030".** ANTIBIOTICS-BASEL. 9(6):328-. [doi:10.3390/antibiotics9060328]	32560407
2020	Margos, G, Castillo-Ramirez, S, Cutler, S, Dessau, R, Eikeland, R, Estrada-Peña, A, Gofton, A, Graña-Miraglia, L, Hunfeld, K, Krause, A, Lienhard, R, Lindgren, P, Oskam, C, Rudolf, I, Schwartz, I, Sing, A, Stevenson, B, Wormser, G, Fingerle, V. (2020). "Rejection of the name Borreliella and all proposed species comb. nov. placed therein". International Journal Of Systematic And Evolutionary Microbiology. 70(5):3577-3581. [doi:10.1099/ijsem.0.004149]	32320380
2020	Castro-Jaimes, S, Bello-López, E, Velázquez-Acosta, C, Volkow-Fernández, P, Lozano-Zarain, P, Castillo-Ramírez, S, Cevallos, M. (2020). *"Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter* haemolyticus .".** Frontiers in Microbiology. 11():926-. [doi:10.3389/fmicb.2020.00926]	32670207
2020	Graña-Miraglia, L, Sikutova, S, Vancová, M, Bílý, T, Fingerle, V, Sing, A, Castillo-Ramírez, S, Margos, G, Rudolf, I. (2020). "Spirochetes isolated from arthropods constitute a novel genus Entomospira genus novum within the order Spirochaetales". SCIENTIFIC REPORTS. 10(1):17053-. [doi:10.1038/s41598-020-74033-9]	33051478
2020	Salgado-Camargo, A, Castro-Jaimes, S, Gutierrez-Rios, R, Lozano, L, Altamirano-Pacheco, L, Silva-Sanchez, J, Pérez-Oseguera, Á, Volkow, P, Castillo-Ramírez, S, Cevallos, M. (2020). *"Structure and Evolution of Acinetobacter* baumannii Plasmids".** Frontiers in Microbiology. 11():1283-. [doi:10.3389/fmicb.2020.01283]	32625185
2020	Castillo-Ramírez, S, Mateo-Estrada, V, Gonzalez-Rocha, G, Opazo-Capurro, A. (2020). *"Phylogeographical Analyses and Antibiotic Resistance Genes of Acinetobacter* johnsonii Highlight Its Clinical Relevance".** mSphere. 5(4):00581-. [doi:10.1128/mSphere.00581-20]	32611704
2020	Cornejo-Juárez, P, Cevallos, M, Castro-Jaimes, S, Castillo-Ramìrez, S, Velázquez-Acosta, C, Martìnez-Oliva, D, Pérez-Oseguera, A, Rivera-Buendìa, F, Volkow-Fernández, P. (2020). *"High mortality in an outbreak of multidrug resistant Acinetobacter* baumannii infection introduced to an oncological hospital by a patient transferred from a general hospital.".** Plos One. 15(7):e0234684-. [doi:10.1371/journal.pone.0234684]	32702006
2020	López-Leal, G, Santamaria, R, Cevallos, M, Gonzalez, V, Castillo-Ramírez, S. (2020). *"Letter to the Editor: Prophages Encode Antibiotic Resistance Genes in Acinetobacter* baumannii .".** MICROBIAL DRUG RESISTANCE. 26(10):1275-1277. [doi:10.1089/mdr.2019.0362]	32109174
2019	Mayoral-Teran, C, Flores-Moreno, K, Cevallos, M, Volkow-Fernandez, P, Castillo-Ramirez, S, Grana-Miraglia, L, Lopez-Vidal, Y. (2019). *"High Phenotypic and Genotypic Diversity of Enterococcus* faecium from Clinical and Commensal Isolates in Third Level Hospital".** MICROBIAL DRUG RESISTANCE. 26(3):227-237. [doi:10.1089/mdr.2019.0039]	31545121
2019	Lopez-Leal, G, Cesar Zuniga-Moya, J, Castro-Jaimes, S, Grana-Miraglia, L, Perez-Oseguera, A, Sarahi Reyes-Garcia, H, David Gough-Coto, S, Pavon-Madrid, R, Aurora Bejarano, S, Ferrera, A, Castillo-Ramirez, S, Cevallos, M. (2019). *"Unexplored Genetic Diversity of Multidrug- and Extremely Drug-Resistant Acinetobacter* baumannii Isolates from Tertiary Hospitals in Honduras".** MICROBIAL DRUG RESISTANCE. 25(5):690-695. [doi:10.1089/mdr.2018.0311]	30614762
2019	Mateo-Estrada, V, Grana-Miraglia, L, Lopez-Leal, G, Castillo-Ramirez, S. (2019). *"Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter.".* Genome Biology And Evolution. 11(9):2531-2541. [doi:10.1093/gbe/evz178]	31406982
2018	Graña-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
2018	Challagundla, 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
2018	Frisch 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
2017	Graña-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
2017	Pérez-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".** Microbiology Resource Announcements. 5(36):e00949-17-. [doi:10.1128/genomeA.00949-17]	28883144
2017	Angel 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
2016	López-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
2016	Castro-Jaimes S., Salgado-Camargo A.D., Graï¿½a-Miraglia L., Lozano L., Bocanegra-Ibarias P., Volkow-Fernï¿½ndez P., Silva-Sanchez J., Castillo-Ramï¿½rez S., Cevallos M.A.. (2016). *"Complete genome sequence of a multidrug-resistant Acinetobacter* baumannii isolate obtained from a Mexican hospital (sequence type 422)".** Microbiology Resource Announcements. 4(3):e00583-16-. [doi:10.1128/genomeA.00583-16]	27340065
2016	Graña-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".** Microbiology Resource Announcements. 4(2):e00156-16-. [doi:10.1128/genomeA.00156-16]	27013043
2016	Aanensen, 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
2016	Castillo-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
2016	Bolanos, 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
2016	Becker, 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
2016	Joseph, 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
2015	Joseph, 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
2015	Ezewudo, 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
2014	Lopez-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
2014	Castillo-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]
2013	Castillo-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]
2011	Guerra-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
2010	Castillo-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.
2009	Castillo-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
2009	Martinez-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
2008	Castillo-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
2008	Crossman, 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
2008	González 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.
2007	Guo, 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
2006	González, 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.