Conobacter sakazakii represents a significant foodborne pathogen threatening susceptible populations, yet its molecular characteristics in powdered spices and instant cereals remain poorly characterized. This investigation analyzed 45 retail samples (20 spices, 25 cereals) collected from Nanning, China, through pathogen isolation, whole genome sequencing, and bioinformatics profiling to elucidate virulence determinants, antimicrobial resistance patterns, and genetic features. The study revealed an overall contamination rate of 22.2% (10/45), with contamination rates of 25.0% in spices and 20.0% in cereals. Predominant serotype O1 accounted for 70.0% of isolates, while multilocus sequence typing identified seven sequence types, including novel ST1008. Genomic analysis demonstrated high genetic diversity (allelic differences: 57–2678) and revealed 42 virulence-associated genes (including flgA, ompA, and rpoS) alongside multidrug resistance patterns (notably to selected β-lactams). Crucially, mobile genetic element-mediated mcr-9 (conferring colistin resistance) and astA (encoding heat-stable enterotoxin) were detected, indicating significant transmission risks. This study provides the first documentation of concurrent virulence-resistance characteristics in C. sakazakii from Chinese retail powdered foods, highlighting the need for enhanced surveillance throughout low-moisture food supply chains to mitigate infection risks in vulnerable populations.
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