Genomic surveillance uncovers high-risk resistance profiles in Escherichia coli and Klebsiella spp. from Central Mexico
6 affiliations
- 1Laboratorio Estatal de Salud Pública del Estado de Aguascalientes (LESPA), Aguascalientes, Mexico
- 2Microbiology Laboratory, Department of Natural Products Chemistry, Institute of Chemistry, National Autonomous University of Mexico (UNAM), CDMX, Mexico
- 3Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- 4European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
- 5Public Health Intelligence Unit, National Institute of Public Health, Cuernavaca, Morelos, Mexico
- 6School of Medicine, Cuauhtemoc University, Aguascalientes Campus, Aguascalientes, Mexico
Abstract
Objective: To generate actionable genomic evidence for antimicrobial-resistance (AMR) surveillance in Central Mexico by characterizing the diversity, resistome, and mobilome of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Escherichia coli, Klebsiella pneumoniae, and K. michiganensis belonging to the K. oxytoca complex (KoxSC) circulating between 2021 and 2023, and by contextualizing these findings within national genomic data.
Design/Methods: We sequenced 65 MDR/XDR isolates referred to the State Public Health Laboratory of Aguascalientes (LESPA) and compared them with 268 publicly available Mexican genomes. Phenotypic susceptibility profiles (BD Phoenix M50) were integrated with genomic predictions to assess concordance. Phylogenomics, pangenomics, resistome and mobilome profiling, and virulence analyses were performed using standardized pipelines. Because LESPA receives referral cases from severe or treatment-refractory infections, this dataset represents a high-risk clinical subset rather than a population-level sample.
Results: The sequenced isolates displayed substantial lineage diversity (34 sequence types across E. coli and Klebsiella spp.) and more than 100 distinct antimicrobial-resistance gene combinations. Several determinants not previously reported in Mexican resistant microorganisms—such as TEM-116, aadA22, ermB, and uhpA—were identified. Carbapenemase NDM-1 and colistin-associated MCR-9.1 were widespread, and resistance genes frequently co-localized with mobile genetic elements, suggesting active horizontal gene-transfer dynamics. Post-2020 isolates exhibited increased resistome richness, higher XDR rates, and more frequent coinfections, particularly in critical-care settings. The K. michiganensis isolates represent the first MDR genomes of this species from Aguascalientes and contribute to the expanding genomic characterization of this underrepresented member of the K. michiganensis (KoxSC) in Mexico.
Conclusions: This study provides the first genomic baseline for MDR E. coli and Klebsiella spp. in Central Mexico and documents an increasingly complex resistome likely shaped by clinical practices, referral patterns, and structural limitations in microbiological capacity. Embedding real-time whole-genome sequencing into routine diagnostics and public-health workflows is essential to strengthen stewardship, guide infection control, and support equitable AMR surveillance across Mexico.
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BibTeX
@article{gamboa2026genomic,
title = {{Genomic surveillance uncovers high-risk resistance profiles in Escherichia coli and Klebsiella spp. from Central Mexico}},
author = {Miriam Sarahi Lozano Gamboa and Brian Muñoz Gomez and Andrea Yaxiri Maldonado Gonzaga and Moisés Alejandro Alejo Hernández and Adrian Cazares and Daniel Diaz and Anastacio Palacios Marmolejo and Corina Diana Ceapă},
journal = {Frontiers in Cellular and Infection Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fcimb.2026.1939440},
url = {https://doi.org/10.3389/fcimb.2026.1939440},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Genomic surveillance uncovers high-risk resistance profiles in Escherichia coli and Klebsiella spp. from Central Mexico
AU - Miriam Sarahi Lozano Gamboa
AU - Brian Muñoz Gomez
AU - Andrea Yaxiri Maldonado Gonzaga
AU - Moisés Alejandro Alejo Hernández
AU - Adrian Cazares
AU - Daniel Diaz
AU - Anastacio Palacios Marmolejo
AU - Corina Diana Ceapă
PY - 2026
DA - 2026/10/21
JO - Frontiers in Cellular and Infection Microbiology
DO - 10.3389/fcimb.2026.1939440
UR - https://doi.org/10.3389/fcimb.2026.1939440
AB - Objective: To generate actionable genomic evidence for antimicrobial-resistance (AMR) surveillance in Central Mexico by characterizing the diversity, resistome, and mobilome of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Escherichia coli, Klebsiella pneumoniae, and K. michiganensis belonging to the K. oxytoca complex (KoxSC) circulating between 2021 and 2023, and by contextualizing these findings within national genomic data. Design/Methods: We sequenced 65 MDR/XDR isolates referred to the State Public Health Laboratory of Aguascalientes (LESPA) and compared them with 268 publicly available Mexican genomes. Phenotypic susceptibility profiles (BD Phoenix M50) were integrated with genomic predictions to assess concordance. Phylogenomics, pangenomics, resistome and mobilome profiling, and virulence analyses were performed using standardized pipelines. Because LESPA receives referral cases from severe or treatment-refractory infections, this dataset represents a high-risk clinical subset rather than a population-level sample. Results: The sequenced isolates displayed substantial lineage diversity (34 sequence types across E. coli and Klebsiella spp.) and more than 100 distinct antimicrobial-resistance gene combinations. Several determinants not previously reported in Mexican resistant microorganisms—such as TEM-116, aadA22, ermB, and uhpA—were identified. Carbapenemase NDM-1 and colistin-associated MCR-9.1 were widespread, and resistance genes frequently co-localized with mobile genetic elements, suggesting active horizontal gene-transfer dynamics. Post-2020 isolates exhibited increased resistome richness, higher XDR rates, and more frequent coinfections, particularly in critical-care settings. The K. michiganensis isolates represent the first MDR genomes of this species from Aguascalientes and contribute to the expanding genomic characterization of this underrepresented member of the K. michiganensis (KoxSC) in Mexico. Conclusions: This study provides the first genomic baseline for MDR E. coli and Klebsiella spp. in Central Mexico and documents an increasingly complex resistome likely shaped by clinical practices, referral patterns, and structural limitations in microbiological capacity. Embedding real-time whole-genome sequencing into routine diagnostics and public-health workflows is essential to strengthen stewardship, guide infection control, and support equitable AMR surveillance across Mexico.
SN - 2235-2988
ER -