Table 2.
Genetic diversity, phylogenetic discrepancies in single locus phylogeny (SLP) analysis and ClonalFrame analysis of bacteria in the Media SC according to the population structure observed in multi-locus phylogeny analysis.
| Clade A (n = 21) | Clade B (n = 18) | Clades A, B, and C (n = 41) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standardized index of association (IsA) | 0.019 (P-value = 0.005) | 0.310 (P-value < 0.0001) | 0.222 (P-value < 0.0001) | |||||||||
| Mean genetic diversity (H) | 0.9702 ± 0.0172 | 0.9085 ± 0.0132 | 0.9730 ± 0.0053 | |||||||||
| No of alleles | Poly-morphic sites % | h, genetic diversity | Strains with phylogenetic discrepancies in SLP (most closely related clade) | No of alleles | Poly-morphic sites % | h, genetic diversity | Strains with phylogenetic discrepancies in SLP (most closely related clade) | No of alleles | Polymorphic sites (%) | h, genetic diversity | ||
| Genetic diversity and phylogenetic discrepancies at each locus | atpD (501 bp) | 18 | 7 | 0.9810 | AH31 (clade A. encheleia) | 10 | 2 | 0.9020 | − | 30 | 8 | 0.9768 |
| dnaJ (785–794 bp) | 20 | 6 | 0.9952 | − | 13 | 7 | 0.9477 | BVH83, CECT 4232T, RT10-17Ga, CECT 7111, LL4.4-18D (clade A) | 34 | 13 | 0.9866 | |
| dnaK (812 bp) | 20 | 5 | 0.9905 | − | 12 | 16 | 0.9739 | − | 34 | 19 | 0.9902 | |
| dnaX (496 bp) | 20 | 12 | 0.9952 | AK202 (clade A. caviae) | 12 | 9 | 0.9150 | − | 34 | 16 | 0.9829 | |
| gltA (433 bp) | 19 | 10 | 0.9905 | LMG 26323 (clade B) | 8 | 3 | 0.7516 | − | 29 | 12 | 0.9512 | |
| groL (510 bp) | 18 | 7 | 0.9810 | − | 12 | 4 | 0.9346 | − | 31 | 11 | 0.9817 | |
| gyrA (469 bp) | 8 | 6 | 0.7190 | R100 (clade A. caviae) | 12 | 3 | 0.9346 | − | 22 | 8 | 0.9159 | |
| gyrB (753 bp) | 21 | 7 | 1.0000 | − | 12 | 6 | 0.9346 | − | 35 | 12 | 0.9878 | |
| metG (504 bp) | 21 | 7 | 1.0000 | − | 10 | 8 | 0.8954 | − | 33 | 12 | 0.9805 | |
| ppsA (537 bp) | 21 | 14 | 1.0000 | − | 12 | 11 | 0.9346 | − | 35 | 19 | 0.9878 | |
| radA (405 bp) | 20 | 12 | 0.9952 | AK202 (clade B) | 10 | 3 | 0.9150 | − | 32 | 14 | 0.9829 | |
| recA (598 bp) | 19 | 7 | 0.9905 | − | 10 | 6 | 0.9216 | LL4.4-18D (clade A) | 31 | 11 | 0.9829 | |
| rpoB (426 bp) | 16 | 3 | 0.9667 | − | 8 | 4 | 0.8301 | − | 23 | 6 | 0.9415 | |
| rpoD (503 bp) | 19 | 8 | 0.9905 | − | 11 | 5 | 0.9085 | − | 32 | 12 | 0.9805 | |
| tsf (686 bp) | 14 | 4 | 0.9381 | AK202, BVH17 (clade B) | 9 | 4 | 0.8889 | RT10-17Ga* (clade A) | 24 | 7 | 0.9512 | |
| zipA (423-438 bp) | 19 | 29 | 0.9905 | ADV137a (clade A. popoffii/ A.bestiarum/ A. piscicola); CCM 4242 (clade A. veronii) | 12 | 22 | 0.9477 | LL4.4-18D*, AK207*, AK211* (clade A); CECT 4232T (clade A. enteropelogenes) | 33 | 34 | 0.9878 | |
| Clonal-Frame analysis | Mutation events† | 55 | 3 | 9 | ||||||||
| Recombination events† | 10 | 33 | 56 | |||||||||
| Substitutions introduced by recombination† | 95 | 126 | 216 | |||||||||
| No of sites without recombination† | 7364 (83.1% of the sequence length) | 2880 (32.5% of the sequence length) | 1744 (19.7% of the sequence length) | |||||||||
| ρ/θ‡ | 0.097 (0.094–0.099) | 9.4 (9.4–9.4) | 6.5 (6.5–6.5) | |||||||||
| r/m‡ | 0.89 (0.87–0.90) | 37 (36–40) | 23 (23–24) | |||||||||
ρ/θ, relative rate of recombination and mutation;
r/m, relative effect of recombination and mutation;
*
Phylogenetic discrepancy without horizontal gene transfer event detected by RDP software.
†
Measured between each isolate of each lineage (or the whole population) and their most recent common ancestor.
‡
The numbers in brackets are 95% confidence intervals.