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 webcite

⁽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

Orsi et al. BMC Genomics 2008 9:539   doi:10.1186/1471-2164-9-539