Table 5. Comparison of the number of TR units for each VNTR locus as obtained from MLVA capillary analysis, confirmed by Sanger sequencing in all cases, and in silico analysis of the corresponding WGS sequences deposited in Genbank.
| Strain ID | Genbankaccession | Psa-01 | Psa-03 | Psa-04 | Psa-05 | Psa-06 | Psa-07 | Psa-08 | Psa-09 | Psa-10 | GM-254 | GM-1553 | GM-1834 | GM-4076 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CFBP 7286 | GCA_000245415.1 | 9(7) | 10(7) | 3(2) | 6 | 4 | 2 | 3 | 6(n.a.) | 6 | 5 | 6 | 17(7) | 2 |
| CH2010-6 a | GCA_000245475.1 | 9 | 11(10) | 3 | 5 | 4 | 2 | 3 | 6 | 14(10) | 5(3) | 6 | 18(11) | 2 |
| M7 a | GCA_000344495.1 | 9 | 11(n.a.) | 3 | 5 | 4 | 2 | 3 | 6 | 14(n.a.) | 5(3) | 6 | 18(n.a.) | 2 |
| PA459 | GCA_000245455.1 | 4 | 4 | - | 5 | 3 | 2 | 4 | 7 | 16(10) | 12(n.a.) | 4 | 14(11) | 4 |
| KW41 b | GCA_000245435.1 | 4 | 3 | - | 4 | 3 | 3 | 10(7) | 7(n.a.) | 14(8) | 12 | 4 | 14(10) | 3 |
| ICMP 9855 b | GCA_000416665.1 | 4 | 3 | - | 4 | 3 | 3 | 10(36) | 7(n.a.) | 14(52) | 12(10) | 4 | 14(9) | 3 |
| NCPPB 3739 c | GCA_000233835.2 | 4 | 3 | - | 4 | 3 | 3 | 10(n.a.) | 7(n.a.) | 14(13) | 12 | 4 | 15(11) | 3 |
| ICMP 9617 c | GCA_000658965.1 | 4 | 3 | - | 4 | 3 | 3 | 10 | 7(n.a.) | 14 | 12 | 4 | 15 | 3 |
| NCPPB 3871 | GCA_000233795.2 | 3(4) | 3 | - | 4 | 3 | 3 | 10 | 7(n.a.) | 14 | 12 | 4 | 15(14) | 3 |
| ICMP 9853 | GCA_000344335.1 | 4 | 3 | - | 4 | 3 | 4(n.a.) | 10 | 7(n.a.) | 14 | 12 | 4 | 15 | 3 |
| ICMP 18804 d | GCA_000344395.1 | 3 | 3 | 1 | 2 | - | - | 2 | - | 2 | - | 3 | 7 | 2 |
| ICMP 18804 d | GCA_000416905.1 | 3 | 3 | 1(n.a.) | 2 | - | - | 2 | - | 2 | - | 3(n.a.) | 7 | 2 |
| ICMP 19439 | GCA_000344555.1 | 9 | 9 | 3 | 6 | 4 | 2 | 3 | 6 | 11 | 5(3) | 6 | 17(n.a.) | 2 |
| M228 | GCA_000344475.2 | 5 | 7 | 3 | 6 | 5 | 2 | 9 | 7(n.a.) | 9(8) | 4 | 4 | 16 | 2 |
Single numbers point out an exact correspondence between the two values, whilst incongruities are reported with a second number in brackets, e.g. 17(7) means that both MLVA capillary electrophoresis and Sanger sequencing indicate a value of 17 whereas the WGS assembly indicates a value of 7 repeats. In most cases, the MLVA/Sanger result is longer than the WGS result, as expected from the assembly of perfect tandem repeats when the WGS sequencing reads are too short. The lettering n.a. means the lack of the complete corresponding sequence on a single WGS scaffold or contig. In four among ten strains, two independent WGS sequence assemblies are available.
b these are the same strain that was independently sequenced as KW41 in [35] and as ICMP 9855 in [37].