Short-term genome evolution of Listeria monocytogenes in a non-controlled environment

BMC Genomics

Table 3 Confirmed single nucleotide polymorphisms found among clinical and food isolates associated with the 1988 sporadic listeriosis case and the 2000 listeriosis outbreak

SNP no.	Position⁽¹⁾	Locus (LMOf6854)⁽²⁾	Annotation	Nucleotide change	Amino acid change
SNPs unique to isolate F6900 (1988 human isolate)
1	1675779	1688 ↔ 1688.1	trpE, anthranilate synthase component I ↔ alcohol dehydrogenase, iron-containing	A → G	Noncoding
SNPs unique to isolate J0161 (2000 human isolate)
2	378489	0351 → 0352	nikkomycin biosynthesis domain protein → N-acetylmannosamine- 6-phosphate epimerase	C → T	Noncoding
3⁽³⁾	2053116	2071 ← 2072	ABC transporter ← DNA-binding response regulator	T → C	Noncoding
SNPs unique to isolate J2818 (2000 food isolate)
4	174721	0150 → 0150.1	oligopeptide ABC transporter → conserved hypothetical protein	T → C	Noncoding
5	392427	0365.1 → 0367	conserved hypothetical protein → inlI, cell wall surface anchor family protein	G → A	Noncoding
6	462089	0447	Phosphoenolpyruvate synthase	G → A	113Pro→113Ser ⁽⁴⁾
7	885898	0876 ↔ 0877	Membrane protein ↔ transposase OrfA, IS3	A → G	Noncoding
8	1193390	1203	pduP, CoA-dependent propionaldehyde dehydrogenase	C → A	359Pro→359Thr⁽⁵⁾
9	1625104	1635.1	RDD family	G → T	2Ala → 2Asp⁽⁵⁾
10	2327842	2332	addB, ATP-dependent nuclease, subunit B	C → A	388Trp→388Cys⁽⁵⁾
11	2401731	2435.1	Unknown function	G → A	Synonymous
SNP differentiating the two 1988 isolates from the two 2000 isolates
12	2635720	2659	Phage tail component, N-terminal domain	A → T	419Ile→419Leu⁽⁵⁾

⁽¹⁾Nucleotide position in the full alignment of F6854, F6900, J0161 and J2818; this alignment is available at http://www.foodscience.cornell.edu/cals/foodsci/research/labs/wiedmann/links/orsi_2008-bmc-genomics.cfm
⁽²⁾Arrows indicate direction of genes in the chromosome, e.g. 0351 → 0352 means that the polymorphism falls downstream to LMOf6854_0351 and upstream to LMOf6854_0352. ↔ means that the polymorphism falls upstream to both genes (possible of genes are transcribed divergently).
⁽³⁾SNP #3 is not present in FSL R2-499, the J0161 subculture sent from CDC to the Cornell Food Safety Laboratory (FSL), and is also not present in nine other human isolates linked to the 2000 listeriosis outbreak, which were also tested; this SNP thus appears to have arisen during laboratory passage of the J0161 clone sequenced at the Broad Institute.
⁽⁴⁾This nonsynonymous change falls within the phosphoenolpyruvate/pyruvate binding domain (aa 3 to aa 341)
⁽⁵⁾These nonsynonymous changes fall into regions that have no specific predicted domains

ISSN: 1471-2164