Whole-Genome Characterization of Pediatric Urinary E. coli Isolates from a Tertiary Care Pediatric Hospital in Guayaquil, Ecuador: Identification of the High-Risk ST1193 Clone.
- 1Laboratorio de Ciencias Ómicas, Facultad de Ciencias de La Salud, Universidad Espíritu Santo, Samborondón 092301, Ecuador.
- 2Hospital de Niños Dr. Roberto Gilbert E. Junta de Beneficencia de Guayaquil, Guayaquil 090514, Ecuador.
- 3Facultad de Ciencias de la Salud y Desarrollo Humano, Universidad Ecotec, Km. 13.5 Samborondón, Samborondón EC092302, Ecuador.
Abstract
Background
Escherichia coli is a leading cause of urinary tract infections (UTIs) in children, and increasing antimicrobial resistance complicates empirical treatment. However, genomic information on pediatric urinary E. coli associated with urinary tract infection in Ecuador remains limited.Objective
This exploratory study analyzed four E. coli isolates obtained from urine samples of pediatric patients at a tertiary hospital in Guayaquil, Ecuador.Methods
Whole-genome sequencing (WGS) was performed to determine sequence types (STs), serotypes, antimicrobial resistance genes (ARGs) virulence factors (VFs), and phylogenetic relationships.Results
Two isolates were assigned to the globally disseminated high-risk clone ST1193 and carried extended-spectrum β-lactamase (ESBL) genes, including blaCTX-M-27, whereas one isolate was assigned to ST162 and carried blaCTX-M-65. The remaining isolate could not be assigned to a complete ST because of missing MLST loci, but it harbored blaCTX-M-15, blaOXA-1, and blaTEM-1. Fluoroquinolone resistance-associated substitutions were detected in gyrA, parC, and parE in three isolates. The isolates shared a conserved set of VFs involved in adhesion, iron acquisition, and secretion systems. ARGs were frequently associated with insertion sequences and IncF plasmid replicons, indicating a potential contribution of mobile genetic elements (MGEs) to the dissemination of antimicrobial resistance.Conclusions
Despite the limited number of isolates, these findings provide preliminary genomic evidence of the presence of ST1193 and diverse ESBL-producing urinary E. coli lineages among pediatric patients in Guayaquil, supporting the need for expanded genomic surveillance and antimicrobial stewardship efforts at the hospital level.
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BibTeX
@article{lapocalle2026wholegenome,
title = {{Whole-Genome Characterization of Pediatric Urinary E. coli Isolates from a Tertiary Care Pediatric Hospital in Guayaquil, Ecuador: Identification of the High-Risk ST1193 Clone.}},
author = {Laura Lapo-Calle and Isaías Mejía-Limones and Ricardo David Avellán-Llaguno and Julio Cesar Hidalgo-Olmedo and Juan Gregorio Chang-Asinc and Gabriel Morey-León and Derly Andrade-Molina},
journal = {Antibiotics (Basel, Switzerland)},
year = {2026},
month = oct,
doi = {10.3390/antibiotics15100996},
url = {https://europepmc.org/article/MED/42938737},
note = {CC BY},
}
RIS
TY - JOUR
TI - Whole-Genome Characterization of Pediatric Urinary E. coli Isolates from a Tertiary Care Pediatric Hospital in Guayaquil, Ecuador: Identification of the High-Risk ST1193 Clone.
AU - Laura Lapo-Calle
AU - Isaías Mejía-Limones
AU - Ricardo David Avellán-Llaguno
AU - Julio Cesar Hidalgo-Olmedo
AU - Juan Gregorio Chang-Asinc
AU - Gabriel Morey-León
AU - Derly Andrade-Molina
PY - 2026
DA - 2026/10/08
JO - Antibiotics (Basel, Switzerland)
DO - 10.3390/antibiotics15100996
UR - https://europepmc.org/article/MED/42938737
AB - Background Escherichia coli is a leading cause of urinary tract infections (UTIs) in children, and increasing antimicrobial resistance complicates empirical treatment. However, genomic information on pediatric urinary E. coli associated with urinary tract infection in Ecuador remains limited.Objective This exploratory study analyzed four E. coli isolates obtained from urine samples of pediatric patients at a tertiary hospital in Guayaquil, Ecuador.Methods Whole-genome sequencing (WGS) was performed to determine sequence types (STs), serotypes, antimicrobial resistance genes (ARGs) virulence factors (VFs), and phylogenetic relationships.Results Two isolates were assigned to the globally disseminated high-risk clone ST1193 and carried extended-spectrum β-lactamase (ESBL) genes, including blaCTX-M-27, whereas one isolate was assigned to ST162 and carried blaCTX-M-65. The remaining isolate could not be assigned to a complete ST because of missing MLST loci, but it harbored blaCTX-M-15, blaOXA-1, and blaTEM-1. Fluoroquinolone resistance-associated substitutions were detected in gyrA, parC, and parE in three isolates. The isolates shared a conserved set of VFs involved in adhesion, iron acquisition, and secretion systems. ARGs were frequently associated with insertion sequences and IncF plasmid replicons, indicating a potential contribution of mobile genetic elements (MGEs) to the dissemination of antimicrobial resistance.Conclusions Despite the limited number of isolates, these findings provide preliminary genomic evidence of the presence of ST1193 and diverse ESBL-producing urinary E. coli lineages among pediatric patients in Guayaquil, supporting the need for expanded genomic surveillance and antimicrobial stewardship efforts at the hospital level.
SN - 2079-6382
ER -