Comparative genomic and ecological insights into Salmonella enterica serovar Kumasi ST2302 from the first Asian clinical isolate

TL;DR

This paper reports the first Asian case of a rare Salmonella strain, S. Kumasi, isolated from a child with mild diarrhea, highlighting its plant-associated origin and limited human transmission.

Contribution

The study provides the first genomic and clinical characterization of S. Kumasi ST2302 in Asia, revealing its plant-adapted lineage and limited pathogenic potential.

Findings

The S. Kumasi isolate from China is the first clinical case in Asia and is sequence type ST2302.

The genome lacks mobile genetic elements and acquired resistance genes, showing a plant-adapted lineage.

The isolate's atypical toxin architecture and limited clinical expansion suggest sporadic spillover from plant sources.

Abstract

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.

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.

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.

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.

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