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Updated: Jul 2, 2026
Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples
Published on: October 25, 2018
Colonization of Salmonella Newport and Microbiome Analyses of Bulb Onions Grown in Artificially Contaminated Soil at
Bijay K Khajanchi1, John Grocholl1, Mohammad Alam1
1Office of Applied Microbiology and Technology, Human Foods Program, U. S. Food and Drug Administration, Laurel, Maryland, United States.
Introduction:
Several multistate Salmonella outbreaks in the United States have been linked to bulb onions. In this study, we investigated the extent of Salmonella colonization on bulb onions grown in contaminated soil.
Purpose:
The study evaluated the colonization potential and microbial community dynamics of Salmonella Newport on bulb onions grown in artificially spiked soil.
Methods:
Red bulb onions were grown from seed, and resultant seedlings were transplanted into pots containing soil. Soil surface was spiked with S. Newport at transplant and again two weeks before harvest. Three inoculum levels [102 (low), 104(medium), and 106 (high) CFU per 200 g soil] of Salmonella Newport were investigated in triplicate, with three unspiked controls. Three independent trials were conducted using two different soil types. Microbiome analyses were performed on the bulb onions and soil from the high inoculum group in Trial 1 (field topsoil) at 0, 1, and 24 h preenrichment.
Results:
Salmonella was detected in one high-inoculum bulb onion in Trial 1 (field topsoil) and in all high-inoculum onions in Trials 2 and 3 (Miracle-Gro soil). Among the medium inoculum groups, all onions in Trial 2, one in Trial 3, and none in Trial 1 were positive for Salmonella. No onions in the low inoculum group were Salmonella-positive. Microbiome analysis of control and Salmonella-spiked high inoculum field topsoil samples and associated bulb onions revealed that bacterial community composition remained stable at 0 and 1 h preenrichment but underwent notable shifts after 24 h. Bacterial diversity decreased following 24 h of preenrichment, with increased dominance of Proteobacteria and Firmicutes. However, Salmonella spiking had minimal or no effect on microbiome dynamics.
Significance:
These findings provide insights into the colonization capability of Salmonella Newport on bulb onions in different soil types and associated microbial community shifts after 24 h preenrichment.
