ORIGINAL RESEARCH published: 21 December 2016 doi: 10.3389/fmicb.2016.02042 Frontiers in Microbiology | www.frontiersin.org 1 December 2016 | Volume 7 | Article 2042 Edited by: Yuji Morita, Aichi Gakuin University, Japan Reviewed by: Sebastian Guenther, Free University of Berlin, Germany Tatiana Amabile De Campos, Universidade de Brasília, Brazil *Correspondence: Juan Xicohtencatl-Cortes juanxico@yahoo.com Specialty section: This article was submitted to Infectious Diseases, a section of the journal Frontiers in Microbiology Received: 05 September 2016 Accepted: 05 December 2016 Published: 21 December 2016 Citation: Ochoa SA, Cruz-Córdova A, Luna-Pineda VM, Reyes-Grajeda JP, Cázares-Domínguez V, Escalona G, Sepúlveda-González ME, López-Montiel F, Arellano-Galindo J, López-Martínez B, Parra-Ortega I, Giono-Cerezo S, Hernández-Castro R, de la Rosa-Zamboni D and Xicohtencatl-Cortes J (2016) Multidrug- and Extensively Drug-Resistant Uropathogenic Escherichia coli Clinical Strains: Phylogenetic Groups Widely Associated with Integrons Maintain High Genetic Diversity. Front. Microbiol. 7:2042. doi: 10.3389/fmicb.2016.02042 Multidrug- and Extensively Drug-Resistant Uropathogenic Escherichia coli Clinical Strains: Phylogenetic Groups Widely Associated with Integrons Maintain High Genetic Diversity Sara A. Ochoa 1, 2, 3 , Ariadnna Cruz-Córdova 1 , Victor M. Luna-Pineda 1 , Juan P. Reyes-Grajeda 4 , Vicenta Cázares-Domínguez 1 , Gerardo Escalona 1 , Ma. Eugenia Sepúlveda-González 1 , Fernanda López-Montiel 1 , José Arellano-Galindo 5 , Briceida López-Martínez 6 , Israel Parra-Ortega 7 , Silvia Giono-Cerezo 3 , Rigoberto Hernández-Castro 8 , Daniela de la Rosa-Zamboni 9 and Juan Xicohtencatl-Cortes 1 * 1 Laboratorio de Investigación en Bacteriología Intestinal, Hospital Infantil de México Federico Gómez, Mexico City, Mexico, 2 Posgrado en Ciencias Químico-Biológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico, 3 Laboratorio de Bacteriología Médica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico, 4 Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica, Mexico City, Mexico, 5 Área de Virología, Laboratorio de Infectología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico, 6 Subdirección de Servicios Auxiliares de Diagnóstico, Hospital Infantil de México Federico Gómez, Mexico City, Mexico, 7 Laboratorio Clínico, Hospital Infantil de México Federico Gómez, Mexico City, Mexico, 8 Departamento de Ecología de Agentes Patógenos, Hospital General “Dr. Manuel Gea González,” Mexico City, Mexico, 9 Epidemiología Hospitalaria, Hospital Infantil de México Federico Gómez, Mexico City, Mexico In recent years, an increase of uropathogenic Escherichia coli (UPEC) strains with Multidrug-resistant (MDR) and Extensively Drug-resistant (XDR) profiles that complicate therapy for urinary tract infections (UTIs) has been observed and has directly impacted costs and extended hospital stays. The aim of this study was to determine MDR- and XDR-UPEC clinical strains, their virulence genes, their phylogenetic groups and to ascertain their relationship with integrons and genetic diversity. From a collection of 500 UPEC strains, 103 were selected with MDR and XDR characteristics. MDR-UPEC strains were mainly associated with phylogenetic groups D (54.87%) and B2 (39.02%) with a high percentage (≥70%) of several fimbrial genes (ecpA, fimH, csgA, and papGII), an iron uptake gene (chuA), and a toxin gene (hlyA). In addition, a moderate frequency (40–70%) of other genes (iutD, tosA, and bcsA) was observed. XDR-UPEC strains were predominantly associated with phylogenetic groups B2 (47.61%) and D (42.85%), which grouped with ≥80 virulence genes, including ecpA, fimH, csgA, papGII, iutD, and chuA. A moderate frequency (40–70%) of the tosA and hlyA genes was observed. The class 1 and 2 integrons that were identified in the MDR- and XDR-UPEC strains were associated with phylogenetic groups D, B2, and A, while the XDR-UPEC strains that were associated with phylogenetic groups B2, D, and A showed an extended-spectrum beta-lactamase (ESBL) phenotype. The modifying enzymes (aadA1, aadB, aacC, ant1, dfr A1, dfr A17, and aadA4) that