INSTITUTO POLITÉCNICO NACIONAL CENTRO DE BIOTECNOLOGÍA GENÓMICA Isolation and Genomic Characterization of Stenotrophomonas spp in Mexico” “Aislamiento y caracterización genómica de Stenotrophomonas spp en México” Submitted as a fulfillment for obtaining Doctor en Ciencias en Biotecnología BY ELUFISAN TEMIDAYO OLUYOMI B. Tech (Microbiology), LAUTECH, Ogbomosho, Nigeria MSc. (Pharmaceutical Microbiology), University of Ibadan, Nigeria INSTITUTO POLITÉCNICO NACIONAL CENTRO DE BIOTECNOLOGÍA GENÓMICA “Isolation and Genomic Characterization of Stenotrophomonas spp in Mexico” “Aislamiento y caracterización genómica de Stenotrophomonas spp en México” Submitted as a fulfillment for obtaining Doctor en Ciencias en Biotecnología BY ELUFISAN TEMIDAYO OLUYOMI B. Tech (Microbiology), LAUTECH, Ogbomosho, Nigeria MSc. (Pharmaceutical Microbiology), University of Ibadan, Nigeria ii iii DEDICATION I dedicate this work to the God Almighty for providing me the privilege to complete the doctoral dissertation in good health. Also, to my late uncles (Mr. Tunde Adufe Oyesanmi and Mr. Patrice Babatunde Adewoyin) who provided the stair on which I rode to this academic ladder and finally to all my family and friends who contributed immensely to the success of this work. iv ACKNOWLEDGEMENT I want to sincerely appreciate my thesis directors, Dr. Xianwu Guo and Dr. Miguel Villalobos López for their unceasing effort in ensuring that this research studies became a success. I want to thank them for their fatherly counsel, correction and criticisms when necessary. I also want to appreciate the members of my thesis committee – Dr. Jose, Narvaez, Dr. Virgillo Bocanegra, Dr. Miguel Angel, Dr. Juan Manuel Gonzalez Prieto (of blessed memory) for their constructive criticisms in ensuring that this work comes out better. I want to say a big thank you to Maestro en Ciencias Alejandro Sánchez-Varela and Isabel Cristina Rodriguez for being my great pillar of supports while working in the laboratory (Muchísimas gracias a ustedes). I also thank Consejo Nacional de Ciencia y Tecnología (Conacyt), Secretaría de Investigación del IPN (SIP), Programa Institutional de Formación de Investigadores – PIFI-IPN (BEIFI) and Comisión deOperación and Promoción de Actividades Academicas del IPN (COFAA) for proving grants and scholarship for this project. My sincere appreciation also goes to the Director General of National Centre for Technology Management (Federal Ministry of Science and Technology, Nigeria) (Prof. Okechukwu F. Ukwuoma) and the management team for granting me the needed leave for this study. I also want to appreciate the immense contributions made by Dra. Samantha Flores Treviño (Laboratorio de Diagnóstico Microbiológico de Alta Especialidad Servicio de Gastroenterología Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León), Dra. Patricia Bustos, Dr. Luis Lozano (Centro de Ciencia Genómicas, Universidad Nacional Autónoma de México (UNAM)), Dra. Ana Verónica Martínez Vázquez towards ensuring that this study is a success. I want to thank Dra. María del Rayo Morfín Otero of the Institute of infectious and Experimental Pathology, University Center for Health Science, University of Guadalajara, Guadalajara, Jalisco, Mexico for providing me with the reference and clinical strains for this study. Similarly, I want to acknowledge the contribution of Dr. Gildardo Rivera Sánchez for his time and the permission to use his lab for the analytics part of my study. I want to say a heartfelt appreciation to Lic. Alma Paz for her assistant while working in her laboratory. Special thanks to Dr. Victor González of the Centro de Ciencias Genómicas, UNAM for giving such a wonderful opportunity to learn about genomic analysis in his Laboratory. My Sincere appreciation goes to Dr. Erick de Jesús Luna Santillana for not just being a professor to me but also a brother (Thanks so much sir). Thanks, so much Kashif, and Alonzo for your assistance. I want to sincerely appreciate all my laboratory colleagues (Maria López (My big aunt as I fondly call her), Dra. Cristina Reyna, Martin Daniel, Ivan, Yewande Olajumoke Ajao, José Antonio Carmona Vilches (My only Hermano Mexicano), Aranza and Ana for their kindness and assistances rendered in the course of my study. v I want to sincerely appreciate the out gone DG of NACETEM (Prof Willie O Siyanbola) for giving me the opportunity to complete my master’s degree program at a time when official duties could have led to the termination of my master´s program. I want to sincerely appreciate my friend and brother Dr. Omotayo Oyedara for his encouraging words and supports during this program. To Olatunde Victor Taiwo, My gratitude knows no bound, Thank you for not just being a friend but my brother, in you I found the scripture truth that there is a friend which is closer than a brother. Sincere appreciation goes to my Nigerian colleagues – Mr AbdulHakeem Adebiyi Adeniran, Mr Ezekiel Onaleye, Mr. Ibrahim Olushi, Mr. Bimbo, Almustapha, Mr. Osas and Miss Yewande Olajumoke Ajao in Mexico for their unflinching support for me. Many thanks to you all. Special thanks to my wife Nurse Sarah Udeme Elufisan and My son Oreoluwa Zion Elufisan for their sacrifices in the course of this study. I also want to appreciate Mr Patric Adewoyin (RIP) for all his effort in ensuring this dream come to pass, though you are no more here with us in the world Daddy, I am happy that this is another result of your many good efforts in their life of the people around you. Special thanks to my all my uncle Mr Mich Olusegun Fabusoro, my sister in law turn aunt, Mrs Bose Oyesanmi and Uncle Lawrence Fayemi for their supports in the course of this study. Thanks to My siblings. Mr. Olusegun Elufisan, Mrs. Omotayo Akindeji, Mr Ayodeji Elufisan, Tosin Elufisan and Iyanuloluwa Elufisan for all their support while undergoing this training. My appreciation will not complete without mentioning my wonderful parents Dr. and mrs Isaiah and Julaiana Ekwerem Udom for their spiritual financial and moral supports. Specials thanks to my Parents Elder and Mrs. Elufisan for always supporting my dream and making sure they come to fruition. My Final appreciation goes to God who is the creator Preserver and Governor of all things for giving me life wisdom and understanding to go through this program. vi Table of Content ..................................................................................................................................................................... iii DEDICATION............................................................................................................................................ iv ACKNOWLEDGEMENT .......................................................................................................................... v List of Table ................................................................................................................................................. x Resumen ...................................................................................................................................................... xi Abstract ..................................................................................................................................................... xiii CHAPTER ONE ......................................................................................................................................... 1 1.1 Introduction ........................................................................................................................................ 1 1.1.1 The Dual Nature of Bacteria ......................................................................................................... 1 1.2 History and Significance of Stenotrophomonas .................................................................................. 2 1.3 The Microbiology of Stenotrophomonas species ................................................................................ 9 1.3.1. The Pathogenic nature of the genus Stenotrophomonas species ............................................. 15 1.3.2 Quorum Sensing and biofilm formation ..................................................................................... 17 1.3.3 Disruption of Actin Cytoskeletal Structure by Ankyrin-Repeat Protein ...................................... 20 1.3.4 Antibiotic resistance in Stenotrophomonas spp. ........................................................................ 20 1.4 The beneficial nature of Stenotrophomonas ................................................................................. 27 1.5 Genome sequencing and analysis of Stenotrophomonas ............................................................. 30 1.6 Justification of the Studies ............................................................................................................ 33 1.7 Objective of the Study ................................................................................................................... 33 CHAPTER 2 .............................................................................................................................................. 34 Material and Method .............................................................................................................................. 34 2.1 Antimicrobial agents ..................................................................................................................... 34 2.2 Chemical products .......................................................................................................................