Salmonella enterica
can colonize all parts of the tomato plant. Tomatoes have been frequently implicated in salmonellosis outbreaks. In agricultural settings,
Salmonella
must overcome stress, nutritional and competition barriers to become established on plant surfaces. Knowledge of the genetic mechanisms underlying
Salmonella-
plant associations is limited, especially when growing epiphytically. A genome-wide transcriptomic analysis of
Salmonella
Typhimurium (
Se
T) was conducted with RNA-Seq to elucidate strategies for epiphytic growth on live, intact tomato shoot and root surfaces. Six plasmid-encoded and 123 chromosomal genes were significantly (using Benjamini-Hochberg adjusted
p-
values) up-regulated; 54 and 110 detected in
Se
T on shoots and roots, respectively, with 35 common to both. Key signals included NsrR regulon genes needed to mitigate nitrosative stress, oxidative stress genes and host adaptation genes, including environmental stress, heat shock and acid-inducible genes. Several amino acid biosynthesis genes and genes indicative of sulphur metabolism and anaerobic respiration were up-regulated. Some Type III secretion system (T3SS) effector protein genes and their chaperones from pathogenicity island-2 were expressed mostly in
Se
T on roots. Gene expression in
Se
T was validated against
Se
T and also the tomato outbreak strain
Salmonella
Newport with a high correlation (
R
2
= 0.813 and 0.874, respectively; both
p <
0.001). Oxidative and nitrosative stress response genes, T3SS2 genes and amino acid biosynthesis may be needed for
Salmonella
to successfully colonize tomato shoot and root surfaces.