Figure 1.
General overview of the current classification of Salmonella enterica.
Figure 2.
Minimal spanning tree (MSTree) of MLST data on 4257 isolates of S. enterica subspecies enterica.
Each circle corresponds to one of 1,095 STs, whose size is proportional to the number of isolates. The topological arrangement within the MSTree is dictated by its graphic algorithm, which uses an iterative network approach to identify sequential links of increasing distance (fewer shared alleles), beginning with central STs that contain the largest numbers of isolates. As a result, singleton STs are scattered throughout the MSTree proximal to the first node that was encountered with shared alleles, even if equal levels of identity exist to other nodes that are distant within the MSTree. The figure only show links of six identical gene fragments (SLVs; thick black line) and five identical gene fragments (DLVs; thin black line) because these correlate with eBGs, which are indicated by grey shading. The serovar associated with most of the isolates in each eBG or singleton ST is indicated by color coding for the 28 most frequent serovars (see legend at lower right). Within each ST, isolates of a different serovar or for which information is lacking are shown in white, except for monophasic variants.
Figure 3.
Venn diagram of numbers of eBGs whose STs were assigned to a single cluster by ClonalFrame, BAPS and gene by gene bootstrapping.
Other details are in Table 1.
Table 1.
Comparison of groupings according to eBGs versus groupings by other algorithms.
Figure 4.
MSTree of Typhimurium plus its serological variants.
Each circle represents one ST, subdivided into one sector per isolate, flanked by the ST number in small print. The primary links between STs within the MSTree are indicated by straight lines and additional cross-links at the same level of identity are indicated by lines that are terminated by bars. eBG designations are indicated by rounded white boxes. White sectors indicate a lack of serological information. Serological formulas are summarized in Table S3. Other details are as in Fig. 2.
Figure 5.
MSTree of Enteritidis, Dublin, Paratyphi B and their serological variants.
Serological formulas are summarized in Tables S4 and S5. Other details are as in Fig. 4. Additional information on Paratyphi B and Java isolates can be found in Tables 2 and S6.
Table 2.
Comparison of assignments by MLST, MLEE, and molecular properties of Paratyphi B and Java isolates.
Table 3.
Biotypes associated with serovars within 6,7:c:1,5 S. enterica.
Figure 6.
Details are as in Fig. 4 and additional information can be found in Tables 3 and S7.
Figure 7.
Variant nucleotides in the fliC gene and variant amino acids in the FliC protein.
Sequences of fliC (Table S8) from isolates investigated here and additional sequences from GenBank with ≥97% BLAST identity and ≥97% coverage were trimmed to a length of 1344 bp, beginning at nucleotide 73 of the fliC gene of strain LT-2. The translated 448 amino acid sequences begin at amino acid 24. The figure shows all differences relative to the uppermost sequence (strain 6631/88), with nucleotide differences at the left and amino acid differences at the right. FliC protein groups were assigned with the help of a UPGMA tree (Fig. S4) and are indicated at the far right. Strain and serovar designations are in the center, followed by MLST ST and eBG designations for the strains investigated here.
Figure 8.
Variant amino acids in the FljB protein.
Sequences of FljB (Table S8) from isolates investigated here and additional sequences from GenBank with ≥95% BLAST identity and 100% coverage were trimmed to a length of 440 amino acids, beginning at amino acid 36 in the FljB protein from strain LT-2. The figure shows all differences relative to the uppermost sequence (strain SL3261). FljB protein groups were assigned with the help of a UPGMA tree (Fig. S7) and are indicated at the right, together with the serological factors in the phase 2 flagellar antigen. Strain and serovar designations are at the left, followed by MLST ST and eBG designations for the strains investigated here.
Table 4.
Relative frequencies of synonymous and non-synonymous polymorphisms.