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. Author manuscript; available in PMC: 2009 Sep 1.
Published in final edited form as: Infect Genet Evol. 2008 Apr 20;8(5):566–576. doi: 10.1016/j.meegid.2008.04.006

Table 1.

Descriptive analysis of the virulence gene cluster nt sequence among 40 L. monocytogenes isolates.

Fragment (length in nt)a Hb Sc PISd Substitutions NSSe NNSf πg π (NSS) π (NNS)
Cluster (8709), all 25 592 475 616 NA NA 0.0246 NA NA
  Lineage I 12 75 64 75 NA NA 0.0030 NA NA
  Lineage II 12 178 147 181 NA NA 0.0064 NA NA
prfA (711), all 9 25 23 25 23 2 0.0143 0.0684 0.0003
  Lineage I 4 6 6 6 6 0 0.0028 0.0129 0
  Lineage II 4 3 0 3 1 2 0.0004 0.0006 0.0003
plcA (951), all 18 66 55 67 50 17 0.0211 0.0729 0.0072
  Lineage I 8 7 6 7 5 2 0.0028 0.0098 0.0009
  Lineage II 9 35 33 35 25 10 0.0138 0.0431 0.0056
hly (1587), all 19 71 55 73 67 6 0.0160 0.0685 0.0020
  Lineage I 8 8 7 8 7 1 0.0017 0.0061 0.0004
  Lineage II 10 23 20 23 20 3 0.0042 0.0159 0.0008
mpl (1530), all 18 126 91 130 100 30 0.0293 0.1084 0.0096
  Lineage I 10 19 13 19 14 5 0.0035 0.0114 0.0013
  Lineage II 7 7 6 7 4 3 0.0015 0.0036 0.0009
actA (1917), all 20 184 161 197 98 90 0.0383 0.0977 0.0226
  Lineage I 9 24 23 24 13 10 0.0052 0.0123 0.0030
  Lineage II 10 82 74 85 47 35 0.0149 0.0371 0.0090
plcB (867), all 11 62 46 64 45 19 0.0254 0.0868 0.0097
  Lineage I 5 5 5 5 2 3 0.0017 0.0035 0.0012
  Lineage II 5 13 3 13 7 6 0.0023 0.0054 0.0015
a

the nt positions for the six coding regions in the alignment include: prfA, 1 – 711 (located in the opposite strand); plcA, 988 – 1938 (located in the opposite strand); hly, 2181 – 3767; mpl, 4105 – 5634; actA, 5837 – 7753; plcB, 7793 – 8659; data are shown for all 40 isolates as well as for lineage I and II separately (18 and 21 isolates, respectively; the data for the one lineage III isolate are not shown separately)

b

H: number of haplotypes

c

S: number of polymorphic sites (excluding polymorphic sites within indels)

d

PIS: number of parsimonious informative sites;

e

NSS: number of synonymous substitutions;

f

NNS: number of nonsynonymous substitutions;

g

π = nucleotide diversity (average pairwise differences per site); the π values for lineage I and II strains (for the whole cluster as well as for all genes) are statistically significantly different (P < 0.0001, T test).