TABLE 3.

Genetic background-associated SNPs or InDels in L. monocytogenes osmotic stress response systems encoding genes.

Stress response systema	Encoding geneb	Function/annotationa	Number of genetic background- based SNPs or InDelsc
BetL	lmo2092	Glycine betaine transporter	10
Gbu	lmo1014 – lmo1016	Glycine betaine transporter	5
OpuC	lmo1425 – lmo1428	Carnitine transporter	4
KdpED	lmo2678 – lmo2679	Kdp ATPase, two-component system for K+ uptake	36
KdpABC	lmo2680 – lmo2682	Potassium-transporting ATPase	21
ProBA	lmo1259 – lmo1260	Proline biosynthesis	31
OppA	lmo2196	Oligopeptide transporter	2
DtpT	lmo0555	Oligopeptide transporter	14
TreA	lmo1254	Phosphotrehalase	17
Lmo0501	lmo0501	Transcriptional regulator	4
Lmo1078	lmo1078	UDP-glucose phosphorylase	65
Lmo2085	lmo2085	LPXTG peptidoglycan bound protein	55
HtrA	lmo0292	General stress response serine protease	2
ClpC	lmo0232	General stress response protein ATPase	6
ClpP	lmo2468	General stress response protease	1
CspA	lmo1364	Cold shock protein	Conserved
CspB	lmo2016	Cold shock protein	Strain specificd
CspD	lmo1879	Cold shock protein	Conserved
RelA	lmo1523	(p)ppGpp synthetase	4
Ctc	lmo0211	General stress protein, L25 family of ribosomal protein	Strain specific
LisRK	lmo1377 – lmo1378	Two component regulatory system	1e*
Iap	lmo0582	Invasion associated protein	30
MrpABCDEFG	lmo2378 – lmo2384	Na+/H+ antiporter	15*
σB	lmo0895	Alternative sigma factor σB	1

^aInclusion and function/annotation based on review by Burgess et al. (2016).

^bBased on L. monocytogenes reference strain EGDe.

^cDifferences reported are SNPs resulting in amino acid changes in encoded protein enriched in a particular lineage/s or clonal complex/es.

^dOnly L. monocytogenes N11-2675 and N12-1608, contained an amino acid changing SNP in CspB.

^eLisRK is also important for virulence. For more details on SNPs and Indels annotations, see Supplementary Tables 34–65.

*All other genes in these operons have genetic background-based differences except for LisR, MprB, and MprF, conserved in all analyzed strains.