Phenotypic and Molecular Characterization of ESBL-Producing Enterobacterales from Intestinal Colonization in Loja, Ecuador

Background/Objectives: Extended-spectrum β-lactamase (ESBL)-producing Enterobacterales pose a significant threat to public health due to increasing antimicrobial resistance. In Ecuador, molecular characterization of these microorganisms remains limited. The objective of this study was to phenotypically and molecularly characterize ESBL-producing Enterobacterales in patients treated at a referral hospital in Loja, Ecuador. Methods: A descriptive cross-sectional study was conducted between November 2022–October 2023. 862 intestinal samples (stool samples and rectal swabs) were analyzed: 799 obtained from outpatient clinics, 34 from medical/surgical hospitalization wards, and 29 from the intensive care unit (ICU). Bacterial identification was performed using MALDI-TOF MS. Detection of ESBL and carbapenemase genes was performed using multiplex PCR. Phenotypic clustering was assessed by Fourier transform infrared spectroscopy (FT-IR). Results: A total of 195 (22.6%) ESBL-producing Enterobacterales were identified, of which 89 were molecularly characterized. Escherichia coli was the predominant species (79.8%), followed by Klebsiella pneumoniae (15.7%). High resistance rates to ciprofloxacin (57.1–100%) were observed being lower resistance to aminoglycosides (amikacin 1.5–57.1%; gentamicin 10.3–100%). The gene blaCTX-M was the most frequent, detected in 79.8% of isolates, mainly in combination with blaTEM-1 (59.6%). Among the CTX-M family, the blaCTX-M-1 group was predominant (87.3%). Two isolates carried blaKPC. FT-IR analysis revealed species-dependent phenotypic clusters, particularly in K. pneumoniae, whereas E. coli showed greater spectral heterogeneity. Conclusions: ESBL-producing Enterobacterales were frequently identified among analyzed samples and exhibited a marked pattern of multidrug resistance, with a predominance of blaCTX-M genes. These findings support the strengthening of molecular surveillance that might impact antimicrobial use.