Table 1 Bacterial strains and plasmids used in this study

  NCK56 (NCFM)

Human intestinal isolate

[28]

  NCK1909 (Δupp)

NCFM with a 315 bp in-frame deletion within the upp gene (lba0770); background/parent strain for NCFM deletion mutants

[27]

  NCK1910

NCK1909 harboring the repA helper plasmid pTRK669; host for pORI-based counterselective integration vector

[27]

  NCK2439 (Δlba0864)

NCK1909 with a 1425 bp in-frame deletion within the lba0864 gene

This study

  NCK2441 (Δlba1426)

NCK1909 with a 717 bp in-frame deletion within the lba1426 gene

This study

  NCK2530 (Δlba0046)

NCK1909 with a 342 bp in-frame deletion within the lba0046 gene

This study

  NCK2608 (Δlba1539)

NCK1909 with a 498 bp in-frame deletion within the lba1539gene

This study

  EC101

RepA⁺ JM101; Km^r; repA from pWV01 integrated in chromosome; cloning host for pORI-based plasmids

[29]

  NCK1391

E. coli DH10B harboring pTRK669; cloning host for pORI-based plasmids

[27]

  NCK1911

EC101 host harboring pTRK935 integration vector

[27]

  NCK2438

EC101 host harboring pTRK1118 recombinant plasmid

This study

  NCK2440

EC101 host harboring pTRK1119 recombinant plasmid

This study

  NCK2529

EC101 host harboring pTRK1126 recombinant plasmid

This study

  NCK2607

DH10B host harboring pTRK1170 recombinant plasmid

This study

 pTRK669

Ori (pWV01), Cm^r, RepA⁺, thermosensitive

[30]

 pTRK935

pORI upp-based counterselective integration vector, Em^r

[27]

 pTRK1118

pTRK935 harboring a mutated copy of lba0864 gene cloned into HindIII/SacI site

This study

 pTRK1119

pTRK935 harboring a mutated copy of lba1426 gene cloned into HindIII/SacI site

This study

 pTRK1126

pTRK935 harboring a mutated copy of lba0046 gene cloned into HindIII/SacI site

This study

 pTRK1170

pTRK935 harboring a mutated copy of lba1426 gene cloned into BamHI/SacI site

This study