Genomic characterization of a WHO critical priority isolate Enterobacter kobei ST2070 harboring OXA-10, KPC-2, and CTX-M-12 recovered from a water irrigation channel in Ecuador
Joselyn Corrales-Martínez,
Katherine Jaramillo,
Daniel A. Tadesse,
Carolina Satán,
Fernando X. Villavicencio,
Lissette Sánchez-Gavilanes,
Brenda Rivadeneira-Cueva,
José Luis Balcázar,
William Calero-Cáceres
Affiliations
Joselyn Corrales-Martínez
UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
Katherine Jaramillo
Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador; Facultad de Ciencias de la Salud, Universidad Técnica de Ambato, Ambato, Ecuador
Daniel A. Tadesse
U.S. Food &Drug Administration, Center for Veterinary Medicine, Office of Applied Science Laurel, MD 20708, USA
Carolina Satán
Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador
Fernando X. Villavicencio
Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador; Veterinary Medicine, Eugenio Espejo Faculty of Health Sciences, Universidad UTE, Quito, Ecuador
Lissette Sánchez-Gavilanes
UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
Brenda Rivadeneira-Cueva
UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
José Luis Balcázar
Catalan Institute for Water Research (ICRA), 17003 Girona, Spain; University of Girona, 17004 Girona, Spain
William Calero-Cáceres
UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador; Corresponding author.
The discharge of untreated or partially treated wastewater can have detrimental impacts on the quality of water bodies, posing a significant threat to public health and the environment. In Ecuador, previous research indicates a high prevalence of antimicrobial resistant (AMR) bacteria in surface waters affected by human activities, including irrigation channels. In this study, we analyzed sediment samples collected from an irrigation channel utilized for agricultural purposes in northern Ecuador, using microbiological techniques and whole-genome sequencing (WGS). Our investigation revealed the first documented occurrence of E. kobei in Ecuador and the initial report of environmental E. kobei ST2070. Furthermore, we identified the coexistence of OXA-10-type class D β-lactamase and KPC-2-type class A β-lactamase in the E. kobei isolate (UTA41), representing the first report of such a phenomenon in this species. Additionally, we detected various antibiotic resistance genes in the E. kobei UTA41 isolate, including blaCTX-M-12, fosA, aac(6′)-lb, sul2, msr(E), and mph(A), as well as virulence genes such as bacterial efflux pump and siderophore biosynthesis genes. We also identified two intact prophage regions (Entero_186 and Klebsi_phiKO2) in the isolate. Our study presents the first evidence of E. kobei isolate containing two carbapenemase-encoding genes in environmental samples from Latin America. This finding indicates the potential spread of critical-priority bacteria in water samples originating from anthropogenic sources, such as urban wastewater discharges and livestock facilities.
