Pandemic SHV-106-producing Klebsiella pneumoniae ST231 isolated from Brazilian hedgehog (Coendou spinosus) reveals an emerging environmental circulation of a high-risk multidrug-resistant lineage

Abstract

Antimicrobial resistance (AMR) poses a major global health challenge, and wildlife has increasingly been recognized as an important sentinel for monitoring the environmental circulation of clinically relevant resistant bacteria. In this study, we report the phenotypic, genomic, and phylogenomic characterization of a multidrug-resistant (MDR) Klebsiella pneumoniae isolate recovered from a free-ranging wild porcupine ( Coendou spinosus ) in southern Brazil. An extended-spectrum β-lactamase (ESBL)-producing strain, designated UFRGS-ourico-23, was isolated during routine surveillance at a Wild Animals Care Unity. It exhibited resistance to β-lactams, quinolones, aminoglycosides, sulfonamides, and tetracycline. Whole-genome sequencing revealed a complex resistome, including bla SHV-106 , oqxAB , qnrB1 , aminoglycoside-modifying enzymes, sulfonamide, tetracycline, fosfomycin, and trimethoprim resistance genes, consistent with the MDR phenotype. Notably, ESBL production was mediated by the rare bla SHV-106 gene chromosomally located near the lactose operon. In addition, the UFRGS-ourico-23 strain belonged to the pandemic high-risk sequence type ST231. This is the first report of a bla SHV-106 in an animal-derived K. pneumoniae ST231 in Brazil. The strain also harbored a class 1 integron and conjugative IncFIB and Col440I plasmids carrying multiple resistance genes, as well as heavy-metal tolerance operons, suggesting co-selection pressures in anthropized environments. The phylogenomic analysis demonstrated close clustering with globally distributed, predominantly human-derived ST231 genomes, indicating limited core-genome divergence. Collectively, these findings document the emergence of a high-risk MDR K. pneumoniae ST231 clone in Brazilian wildlife and highlight the role of wild animals as reservoirs and sentinels of clinically relevant AMR lineages, reinforcing the need for integrated One Health genomic surveillance at the human–animal–environment interface.

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