Whole-Genome Sequencing Reveals Heterogeneous Resistance Profiles and Selected Mobile Genetic Elements in Ecuadorian Clinical Enterobacter hormaechei subsp. xiangfangensis and subsp. hoffmannii.

Background

Enterobacter hormaechei, a member of the Enterobacter cloacae complex (ECC), is increasingly recognized as a multidrug-resistant (MDR) nosocomial pathogen. However, subspecies-level genomic data from Ecuador remain limited.

Methods

Four clinical E. hormaechei isolates from a hospital in northern Ecuador were analyzed using antimicrobial susceptibility testing and whole-genome sequencing (WGS). Genomic characterization included multilocus sequence typing (MLST), resistome profiling, plasmid replicon detection, integron screening, genomic island analysis, and phylogenetic comparison with publicly available Ecuadorian genomes.

Results

WGS identified three isolates as subsp. xiangfangensis (ST136 and ST337) and one as subsp. hoffmannii (ST145). Two ST136 isolates exhibited extensive MDR phenotypes associated with blaCTX-M-15, blaOXA-1, blaACT-16, and additional aminoglycoside and fluoroquinolone resistance genes. ST145 showed moderate resistance, whereas ST337 remained largely susceptible despite harboring blaACT-16. Multiple genomic islands and plasmid replicons (IncF/IncR or IncHI2) were detected. Phylogenetic analysis demonstrated clustering with previously reported Ecuadorian lineages.

Conclusions

This study provides subspecies-level genomic characterization of clinical E. hormaechei in Ecuador and describes heterogeneous resistance profiles and associated mobile genetic elements, contributing baseline data for regional surveillance.