Referral-based genomic surveillance reveals diverse resistance in central Mexico

Whole-genome sequencing of 65 multidrug-resistant or extensively drug-resistant clinical isolates from Aguascalientes, Mexico, revealed a complex antimicrobial-resistance landscape spanning 34 sequence types and more than 100 resistance-gene combinations among Escherichia coli, Klebsiella pneumoniae and Klebsiella michiganensis. The collection comprised 30 E. coli, 33 K. pneumoniae and two K. michiganensis isolates obtained between March 2021 and December 2023. Resistance determinants not previously reported in Mexican resistant E. coli and Klebsiella included TEM-116, aadA22, ermB and uhpA, while the analysis also identified the carbapenemase NDM-1 and the colistin-associated determinant MCR-9.1.

The results establish a regional genomic baseline for a selected high-risk clinical subset, rather than a population-wide estimate of resistance prevalence. The State Public Health Laboratory of Aguascalientes processed 3,454 E. coli and Klebsiella isolates from regional hospitals during the study period, including 683 E. coli, 679 K. pneumoniae and 92 organisms initially identified by MALDI-TOF mass spectrometry and phenotypic testing as K. oxytoca. Whole-genome sequencing reclassified two of the latter isolates as K. michiganensis.

Of the processed isolates, 246 met the study definitions for multidrug resistance or extensive drug resistance, and 65 were selected for sequencing after confirmation of species identity, availability of pure clinically relevant cultures and satisfaction of DNA-quality requirements. Almost all the sequenced isolates—94%—were recovered from patients in critical-care units, and clinical records classified 97.1% of Klebsiella cases and 93.3% of E. coli cases as severe illness. This referral pattern is central to interpreting the findings: the dataset represents severe, treatment-refractory or otherwise difficult-to-manage infections and is enriched for highly resistant organisms rather than representing community circulation.

p>Phenotypic susceptibility testing showed broad resistance across major antibiotic classes, including several drugs commonly used for urinary, respiratory and inpatient infections. Every sequenced isolate carried extended-spectrum beta-lactamase genes, consistent with cephalosporin resistance reaching 97.1% among the 35 Klebsiella isolates and 100% among the 30 E. coli isolates. Resistance to ciprofloxacin and levofloxacin exceeded 90% in both groups, while trimethoprim-sulfamethoxazole resistance was 82.8% in Klebsiella and 90% in E. coli.

Carbapenem resistance occurred in 31.4% of Klebsiella isolates and 13.3% of E. coli isolates. Amikacin retained activity against more isolates than most tested agents, although resistance was present in 11.4% of the Klebsiella group. Among Klebsiella respiratory isolates, tigecycline resistance increased from 0% in 2022 to 40% in 2023.

The study also found that E. coli XDR phenotypes were confined to the 2023 collection, while later Klebsiella isolates showed more dynamic carbapenem and tigecycline resistance patterns. p>Integrating phenotypic susceptibility results with genomic predictions produced 78.9% overall concordance across 689 antibiotic-class comparisons. Agreement exceeded 90% for fluoroquinolones, sulfonamides and macrolides, whose resistance determinants are comparatively well characterized, and reached 100% for E. coli against cephalosporins and for both macrolide results in Klebsiella. Concordance was substantially lower for aminoglycosides and carbapenems.

Some Klebsiella isolates were phenotypically resistant to carbapenems without carrying canonical blaKPC, blaNDM or blaOXA-48 genes; combinations of OXA-type beta-lactamases, porin disruption and efflux systems were instead associated with the phenotype. These findings identify possible non-classical contributors but do not directly prove their causal effects. Genomic predictions can also be affected by gene expression, regulatory mutations, epistasis, promoter efficiency and laboratory conditions, so the authors emphasize that gene detection alone cannot replace phenotypic susceptibility testing. p>Phylogenomic analysis placed the Aguascalientes genomes within a broader but unevenly sampled Mexican genomic landscape.

The comparative dataset included 268 public genomes: 139 E. coli, 85 K. pneumoniae and 44 K. michiganensis, the last comprising three Mexican isolates and 41 international reference genomes. Mexico City and Puebla were relatively well represented, whereas more than half of Mexico’s states were under-represented or absent. The 30 E. coli isolates from Aguascalientes fell into 15 sequence types and were distributed across the phylogeny rather than forming one local cluster.

They were interspersed with genomes from other states, indicating that the lineages detected locally overlapped with broader national patterns. Because sampling was neither population-based nor geographically uniform, the national comparison cannot establish population prevalence or a continuous national transmission route. The E. coli collection included established high-risk lineages such as ST131 and ST69, which also occurred most frequently among the public Mexican E. coli genomes.

Six isolates could not be assigned to a recognized sequence type; these untyped genomes carried the largest resistance-gene burdens, averaging more than 100 antimicrobial-resistance genes per genome. The blaCTX-M-15 gene was present in 90% of the Aguascalientes isolates, compared with 18% of public Mexican E. coli genomes. Polymyxin-associated regulators, including arnA, eptA, mgrB and members of the pmrB, pmrC and pmrF family, also occurred at higher frequencies in the referral collection.

Detection of these genes establishes their genomic presence, not phenotypic colistin resistance or the transfer of a particular plasmid. Across 169 E. coli genomes, the researchers identified 345 mobile genetic elements in the LESPA isolates, including 26 plasmid-associated elements and 319 of uncertain chromosomal origin. MITEEc1 had the largest number of reported associations, including links with ompT and virulence-associated loci.

p>Resistance genes were frequently located in mobile contexts, a pattern consistent with possible horizontal gene-transfer dynamics in clinical environments. The analysis catalogued 211 mobile genetic elements among the sequenced K. pneumoniae isolates and identified associations involving plasmids, transposons and insertion sequences. K. pneumoniae served as a principal sharing hub in the cross-species network, linking genes including the CTX-M-15, sul1, sul2, tetA, mphA and dfrA families with both E. coli and Klebsiella.

The two K. michiganensis isolates carried NDM-7, VIM-1 and MCR-9.1, which were absent from the sequenced E. coli and K. pneumoniae mobilomes. These observations identify mobile contexts and candidate routes of dissemination, but the study did not perform long-read sequencing or reconstruct complete plasmids. Genomic proximity alone therefore does not demonstrate patient-to-patient transmission or prove that a particular element transferred between species. p>The K. michiganensis isolates expanded the limited genomic record for an undercharacterized member of the K. oxytoca complex in Mexico.

One belonged to ST180 and clustered with genomes from China and the United States, while the other had an unknown sequence type and grouped with Mexican and North American isolates. Their phylogenetic positions were consistent with separate introductions into the regional collection, but the sample of two was too small to establish the species’ broader epidemiology. They were also the first multidrug-resistant K. michiganensis genomes reported from Aguascalientes and occupied separate resistance-gene clusters.

Pangenome analysis showed open, accessory-rich genomes for all three species. Cloud genes, defined as genes present in fewer than 15% of genomes, accounted for 81.7% of the E. coli pangenome, 76.1% of K. pneumoniae and 63.8% of the K. oxytoca complex dataset, illustrating substantial genomic diversity without directly demonstrating its origin or rate of evolution. p>Clinical complexity accompanied the molecular findings. Coinfections were recorded in 60% of Klebsiella cases and 36.7% of E. coli cases, with Acinetobacter baumannii, Enterococcus faecalis and Pseudomonas aeruginosa among the most frequent co-occurring organisms.

Among E. coli, virulence analysis identified seven units found only in the LESPA collection, including a shu hemin-uptake operon, afaC-VIII and galU; no K. pneumoniae virulence units exclusive to the new isolates were found. Temporal comparisons showed richer resistomes, more XDR phenotypes and more frequent coinfections among post-2020 isolates than in the older public collection, including a rise in carbapenem resistance among Klebsiella respiratory isolates from 0% in 2022 to 83% in 2023. These observations cannot be attributed to the COVID-19 pandemic or antibiotic use from this referral-heavy dataset, and they do not demonstrate population-wide temporal change.

The study instead supports routine whole-genome sequencing, standardized metadata and continued phenotypic testing as components of more representative antimicrobial-resistance surveillance across Mexico.

Subject of Research: Genomic surveillance of multidrug-resistant E. coli and Klebsiella in Aguascalientes, Mexico

Article Title: Genomic surveillance uncovers high-risk resistance profiles in Escherichia coli and Klebsiella spp. from Central Mexico

Article References: Lozano Gamboa, M. S., Muñoz Gomez, B., Maldonado Gonzaga, A. Y., Alejo Hernández, M. A., Cazares, A., Diaz, D., Marmolejo, A. P., & Ceapă, C. D. (2026). Genomic surveillance uncovers high-risk resistance profiles in Escherichia coli and Klebsiella spp. from Central Mexico. Frontiers in Cellular and Infection Microbiology, 16, 1939440. https://doi.org/10.3389/fcimb.2026.1939440

Image Credits: AI Generated

DOI: 10.3389/fcimb.2026.1939440

Keywords: antimicrobial resistance, genomic surveillance, Escherichia coli, Klebsiella pneumoniae, Klebsiella michiganensis, whole-genome sequencing, resistome, mobile genetic elements, Mexico, clinical microbiology, Genomic, surveillance