ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Infectious Agents and Disease
Comparative genomic and ecological insights into Salmonella enterica serovar Kumasi ST2302 from the first Asian clinical isolate
Provisionally accepted
- 1Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- 2The Affiliated Hospital of Panzhihua University, Panzhihua, China
- 3Panzhihua City Center for Disease Control and Prevention, Sichuan, China
- 4Panzhihua University, Panzhihua, China
- 5Henan Agricultural University, Zhengzhou, China
- 6Minhang Center for Disease Prevention and Control, Shanghai, China
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Background: Salmonella enterica subspecies enterica serovar Kumasi (S. Kumasi) is an exceptionally rare non-typhoidal Salmonella (NTS) serovar that has been historically linked to plant- or environment-associated sources and only sporadically isolated from humans. Its genomic characteristics, ecological niche, and pathogenic potential remain poorly defined. Methods: The clinical isolate (XXB410) underwent antimicrobial susceptibility testing and whole-genome sequencing. Comparative phylogenomic, resistome, virulence, and pan-genome analyses were performed against all 20 publicly available S. Kumasi genomes. Results: We report the first human infection due to S. Kumasi in Asia, isolated from a 4-year-old child in China presenting with self-limiting diarrhea. XXB410 was identified as sequence type ST2302 and clustered within a lineage dominated by plant/botanical and non-human sources. The genome was plasmid-free and pansusceptible, carrying only the intrinsic aac(6’)-Iaa and parC(T57S) polymorphism, with no acquired antimicrobial resistance (AMR) genes. Genomic profiling confirmed the conservation of canonical invasion islands (SPI1/2) and determinants critical for environmental persistence and plant attachment (e.g., csg operon), yet revealed an atypical toxin architecture restricted to a divergent cdtB homolog without pltA/B subunits. Pairwise core-genome SNP distances between XXB410 and other ST2302 isolates fell well outside outbreak-level relatedness, supporting sporadic spillover from plant-associated reservoirs rather than sustained human transmission. Conclusions: These findings expand the clinical and geographic range of S. Kumasi and support a model of a plant-adapted lineage characterized by a scarcity of mobile genetic elements (MGEs), an incomplete toxin architecture, and limited clinical expansion. The benign, self-limiting clinical course aligns with the genomic profile. Collectively, we propose S. Kumasi as a genomic sentinel to monitor hygiene vulnerabilities in plant-based food supply chains.
Keywords: cytolethal distending toxin, Non-typhoidal Salmonella, plant-associated reservoir, Salmonella enterica serovar Kumasi, spillover infectiongenomic sentinel, ST2302, Whole-genome sequencing
Received: 14 Nov 2025; Accepted: 02 Feb 2026.
Copyright: © 2026 Liu, Peng, Chen, Chen, Wang, Lv, Wang, Xu and Zhou. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Yue Liu
Yibin Zhou
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