Online Resource 1:The primers used for targeted disruption of S. enterica strains virulence genes.

Strain / Virulence gene / Insertion location (gene 5’ exon – gene 3’ exon) / Primers sequence (5’– 3’)
S. Typhimurium
(ATCC 14028) / sopB / 572|573sa
CCAAAGCCGAGCTTGAGCGC-intron- CAGCTCATTAACACC / IBS:
AAAAAAGCTTATAATTATCCTTAGAGCTCGAGCGCGTGCGCCCAGATAGGGTG
EBS1:
CAGATTGTACAAATGTGGTGATAACAGATAAGTCGAGCGCCATAACTTACCTTTCTTTGT
EBS2:
TGAACGCAAGTTTCTAATTTCGATTAGCTCTCGATAGAGGAAAGTGTCT
sopD / 69|70aa
AGGATATAAATAAAATTTAC - intron - GCCTTTAAACGGCTA / IBS:
AAAAAAGCTTATAATTATCCTTAAATAACATTTACGTGCGCCCAGATAGGGTG
EBS1:
CAGATTGTACAAATGTGGTGATAACAGATAAGTCATTTACGCTAACTTACCTTTCTTTGT
EBS2:
TGAACGCAAGTTTCTAATTTCGGTTTTATTCCGATAGAGGAAAGTGTCT
pipD / 353|354aa
ATAACGCCATGGGTGAAGCC - intron -GGTTTCAATTCGGCG / IBS:
AAAAAAGCTTATAATTATCCTTAATGGGCGAAGCCGTGCGCCCAGATAGGGTG
EBS1:
CAGATTGTACAAATGTGGTGATAACAGATAAGTCGAAGCCGGTAACTTACCTTTCTTTGT
EBS2:
TGAACGCAAGTTTCTAATTTCGGTTCCCATCCGATAGAGGAAAGTGTCT
S. Agona
(Ag1) / sopB / 563|564aa
ACGTTGCCGCATTTAATATG - intron - GGGGTTAATGAGCTG / IBS:
AAAAAAGCTTATAATTATCCTTAGCATTCAATATGGTGCGCCCAGATAGGGTG
EBS1:
CAGATTGTACAAATGTGGTGATAACAGATAAGTCAATATGGGTAACTTACCTTTCTTTGT
EBS2:
TGAACGCAAGTTTCTAATTTCGATTAATGCTCGATAGAGGAAAGTGTCT

Continue Online Resource 1

Strain / Virulence gene / Insertion location (gene 5’ exon – gene 3’ exon) / Primers sequence (5’– 3’)
sopD / 69|70aa
AGGATATAAATAAAATTTAC - intron - GCCTTTAAACGGCTA / IBS:
AAAAAAGCTTATAATTATCCTTAAATAACATTTACGTGCGCCCAGATAGGGTG
EBS1:
CAGATTGTACAAATGTGGTGATAACAGATAAGTCATTTACGCTAACTTACCTTTCTTTGT
EBS2:
TGAACGCAAGTTTCTAATTTCGGTTTTATTCCGATAGAGGAAAGTGTCT
pipD / 353|354aa
ATAACGCCATGGGTGAAGCC - intron -GGTTTCAATTCGGCG / IBS:
AAAAAAGCTTATAATTATCCTTAATGGGCGAAGCCGTGCGCCCAGATAGGGTG
EBS1:
CAGATTGTACAAATGTGGTGATAACAGATAAGTCGAAGCCGGTAACTTACCTTTCTTTGT
EBS2:
TGAACGCAAGTTTCTAATTTCGGTTCCCATCCGATAGAGGAAAGTGTCT

a Insertion direction: s, Sense; a, anti-sense

Online Resource 2: The primers used to identified the intron inserted S. enterica strains.

Virulence Gene / PCR Programme / Product Size without Intron Insertion
(bp) / Product Size with Intron Insertion
(bp) / Oligonucleotide Sequence 5’-3’
(Forward/Reverse)
sopB / 95oC : 5 min
94oC : 1 min
55oC : 1 min
72oC : 1 min
72oC : 3 min / 1170 / ~ 2170 / sopB1: GATGTGATTAATGAAGAAATGCC
sopB2:
GCAAACCATAAAAACTACACTCA
sopD / 95oC : 5 min
94oC : 1 min
58oC : 1 min
72oC : 1 min
72oC : 5 min / 310 / ~1310 / sopD1: CTTTAAGCTTCGGTAATCATCAAAA
sopD2:
AAGCGTCCATCTTGATAGTAAACAG
pipD / 405 / ~1405 / pipD1:
CGGCGATTCATGACTTTGAT
pipD2:
CGTTATCATTCGGATCGTAA

Online Resource 3: S. entericaand nematode strains used in this study.

Strain/ Code / Relevant Genotype / Sources/ Reference
S. Agona (Ag 1) / Wild-type food strain / Vegetable: Polygonum minus
S. Agona ∆sopB / Intron-inserted mutant strain; sopB gene disrupted
S. Agona ∆sopD / Intron-inserted mutant strain; sopD gene disrupted
S. Agona ∆pipD / Intron-inserted mutant strain; pipD gene disrupted
S. Agona ∆sopB∆sopD / Intron-inserted mutant strain; sopB and sopD gene disrupted
S. Agona ∆sopB∆sopD∆pipD / Intron-inserted mutant strain; sopB, sopD and pipD gene disrupted
S. Typhimurium (ATCC 14028) / References strain / American Type Culture Collection
S. Typhimurium ∆sopB / Intron-inserted mutant strain; sopB gene disrupted
S. Typhimurium ∆sopD / Intron-inserted mutant strain; sopD gene disrupted
S. Typhimurium ∆pipD / Intron-inserted mutant strain; pipD gene disrupted
S. Typhimurium ∆sopB∆sopD / Intron-inserted mutant strain; sopB and sopD gene disrupted
S. Typhimurium ∆sopB∆sopD∆pipD / Intron-inserted mutant strain; sopB, sopD and pipD gene disrupted
E. coli OP 50 / Uracil auxotrophy strain / CaenorhabditisGeneticsCenter
C. elegans / glp-4 (temperature sensitive strain) / CaenorhabditisGeneticsCenter

Online Resource 4: Strains of S. enterica used in Phenotypic Microarray analysis.

Strain / Genotype / Origin/ Source
S. Agona
(Ag 1) / Wild-type food isolate strain / Vegetable: Polygonum minus
S. Agona ∆sopB∆sopD∆pipD / Triple mutant strain of S. Agona(Ag 1) / Wild-type strain of S. Agona (Ag 1)
S. Typhimurium
(ATCC 14028) / Wild-type pathogenic
reference strain / American Type Culture Collection
S. Typhimurium ∆sopB∆sopD∆pipD / Triple mutant strain of S. Typhimurium (ATCC 14028) / Wild-type strain of S. Typhimurium (ATCC 14028)