Genomic characterization of CTX-M-55-producing Escherichia coli ST219 and ST1011 from wildlife in remote austral...

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are globally recognized priority pathogens and are increasingly detected in wildlife and remote ecosystems. To date, the southernmost wildlife reports of ESBL-producing E. coli have been restricted to seagulls from the Chiloé archipelago in Chile.

To identify and genomically characterize ESBL-producing E. coli colonizing wildlife from remote islands in the Southern Cone of South America.

Samples collected during wildlife surveillance activities involving Culpeo foxes (Lycalopex culpaeus) on Riesco Island (2023) and wild birds on Navarino Island (2025) were screened on ceftriaxone-supplemented MacConkey agar. Isolates were identified using API 20E, and ESBL production was confirmed by DDST. Genomes were sequenced on Illumina platforms, assembled with Shovill/SKESA, and quality control and genomic characterization were performed using CheckM taxonomy_wf, QUAST, Prokka, and Bakta. Multilocus sequence type, serotype, virulome, and plasmid replicons were predicted using tools from the Center for Genomic Epidemiology and the resistome through AMRFinderPlus. Phylogenomic placement was assessed through EnteroBase using cgMLST and HierCC.

Two ESBL-producing E. coli were recovered: MVL009 (ST1011; O11:H16) from a Culpeo fox and IN25 (ST219; O53:H4) from a Kelp gull (Larus dominicanus). Both carried bla_CTX-M-55, additional antimicrobial resistance genes, and virulence determinants. Phylogenomic analysis placed MVL009 within an ST1011 cluster comprising retail meat- and swine-associated genomes from the Southern Cone, whereas IN25 was positioned within an ST219 subclade including farm animal- and human-derived genomes from multiple countries.

These findings expand the southern distribution of ESBL-producing E. coli in wildlife and support wildlife-based genomic surveillance in remote austral ecosystems.