Table 3 Primers used in this study

Cm cassette

pKD3 forward 1

GTGTAGGCTGGAGCTGCTTC

pKD3 reverse 1

CATATGAATATCCTCCTTA

pKD3 forward 2

ACCTGTGACGGAAGATCACTTCG

pKD3 reverse 2

AGGAACTTCATTTAAATGGCGCG

flanking sequence of VP0220 (wbfF) gene

upstream forward*

CCCAGCCATAACTAACACTAACCCGT

upstream reverse

GAAGCAGCTCCAGCCTACACGATAATTCGCTATTTAAATCGAGAGTTAAA

downstream forward

TAAGGAGGATATTCATATGGGAACGACAAGATCATTCCAATCAG

downstream reverse*

TAGGCTAAGTTCTGAGAGGTTTCCG

flanking sequence of CPS region VP0219-0237

upstream forward

AATACTAGTGAGCTGTGTTCTTCATTATTAATCCT

upstream reverse

CGAAGTGATCTTCCGTCACAGGTGCAGTGAATGTCTGTTAACTCT

downstream forward

CGCGCCATTTAAATGAAGTTCCTCAGGCTCGTTACCAATGTGCT

downstream reverse

GCCAATTATCCTAGACTCACCACT

flanking sequence of VP0215-0218

upstream forward

CACCAGCATTGATCTGGTTATTCA

upstream reverse

CGCGCCATTTAAATGAAGTTCCTTATTTAAGGGAGCTTCGGCTCCCT

downstream forward

CGAAGTGATCTTCCGTCACAGGTAGAGCTGTGTTCTTCATTATTAATCC

downstream reverse

TCGGCATTAGAGTAGCTCACTAACG

flanking sequence of EPS genes VPA1403-1406

upstream forward ^$

CCACTACCCACAGAACCGCTTTGT

upstream reverse

CGAAGTGATCTTCCGTCACAGGTATGACCTAGTTTCCCTTCTAGCA

downstream forward

CGCGCCATTTAAATGAAGTTCCTAGCCAGGTTTAACCAACATATTGA

downstream reverse^$

ACCACTCCAAAGGGTAGTGGTGA

flanking sequence of wza, wzb, wzc genes

upstream forward

CAGGGAATCAAGCATACGTTGAA

upstream reverse

CGAAGTGATCTTCCGTCACAGGTATTCATCTGACGTAAAGAGCGA

downstream forward

CGCGCCATTTAAATGAAGTTCCTATCTAGATCGCTAATTTGACCAAA

downstream reverse

GAGCAGCAAAGCTGCAGATTGA