TABLE 1.
Summary of isolate diversity within subject and within time pointsa
| Subject ID |
Treatment | Isolate phylogenomics |
Resistance |
Virulence |
Phylogroup |
MLST |
Serotype |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. of isolates from subject |
No. of clades in subjectb |
No. of resistance cladesb |
Isolates in single resistance superclade |
Similar distribution as phylogenyb |
No. of virulence gene cladesb |
Similar distribution as phylogenyb |
Similar distribution as resistance genesb |
No. of phylogroups in subjectb |
Similar distribution as phylogenyb |
No. of sequence types in subjectb |
Similar distribution as phylogenyb |
No. of serotypes in subjectb |
Similar distribution as phylogenyb |
||
| 1_110_08 | MDA | 9 | 5 | 5 | No | No | 5 | No | Yes | 3 | No | 3 | No | 5 | Yes |
| 1_176_05 | MDA | 8 | 4 | 4 | No | Yes | 4 | Yes | Yes | 2 | No | 3 | No | 4 | Yes |
| 1_182_04 | MDA | 9 | 3 | 5 | No | No | 3 | Yes | No | 2 | No | 3 | Yes | 3 | Yes |
| 1_250_04 | MDA | 7 | 3 | 2 | Yes | No | 3 | Yes | No | 3 | Yes | 3 | Yes | 3 | Yes |
| 1_392_07 | MDA | 8 | 4 | 5 | No | No | 4 | Yes | No | 3 | No | 4 | Yes | 4 | Yes |
| 3_020_07 | MDA | 8 | 4 | 4 | No | Yes | 4 | Yes | Yes | 3 | No | 4 | Yes | 4 | Yes |
| 3_073_06 | MDA | 7 | 5 | 5 | No | Yes | 4 | No | No | 3 | No | 5 | No | 5 | No |
| 3_105_05 | MDA | 9 | 7 | 6 | No | Yes | 7 | Yes | No | 2 | No | 7 | Yes | 7 | Yes |
| 3_267_03 | MDA | 7 | 6 | 6 | No | Yes | 6 | Yes | Yes | 3 | No | 6 | Yes | 6 | Yes |
| 3_373_03 | MDA | 9 | 4 | 4 | No | Yes | 3 | No | No | 1 | No | 3 | No | 4 | Yes |
| 3_475_03 | MDA | 6 | 6 | 5 | No | No | 6 | Yes | No | 2 | No | 6 | Yes | 6 | Yes |
| 4_203_08 | MDA | 8 | 3 | 5 | No | No | 3 | No | No | 1 | No | 2 | No | 3 | Yes |
| 6_175_07 | MDA | 9 | 4 | 5 | No | Yes | 5 | Yes | Yes | 3 | No | 4 | Yes | 4 | Yes |
| 6_319_05 | MDA | 8 | 3 | 5 | No | No | 3 | Yes | No | 3 | Yes | 4 | No | 3 | Yes |
| 6_537_08 | MDA | 8 | 3 | 5 | No | No | 3 | Yes | No | 2 | No | 3 | Yes | 3 | Yes |
| 2_005_03 | No MDA | 9 | 5 | 7 | No | No | 6 | Yes | No | 5 | Yes | 5 | Yes | 4 | No |
| 2_011_08 | No MDA | 8 | 6 | 5 | No | No | 6 | Yes | No | 3 | Yes | 6 | No | 7 | No |
| 2_052_05 | No MDA | 8 | 5 | 4 | No | Yes | 5 | No | No | 3 | No | 5 | Yes | 5 | Yes |
| 2_156_04 | No MDA | 7 | 7 | 5 | No | Yes | 6 | No | No | 2 | No | 6 | No | 7 | Yes |
| 2_177_06 | No MDA | 9 | 6 | 5 | No | No | 7 | No | No | 3 | No | 6 | Yes | 6 | Yes |
| 2_210_07 | No MDA | 8 | 6 | 6 | No | Yes | 5 | No | No | 2 | No | 6 | Yes | 6 | Yes |
| 2_222_05 | No MDA | 9 | 4 | 5 | No | No | 4 | Yes | No | 2 | No | 4 | Yes | 4 | Yes |
| 2_316_03 | No MDA | 8 | 6 | 7 | No | No | 5 | No | No | 3 | No | 6 | Yes | 5 | No |
| 2_427_07 | No MDA | 8 | 5 | 4 | No | Yes | 6 | No | No | 3 | No | 5 | No | 7 | No |
| 2_460_02 | No MDA | 9 | 4 | 4 | No | Yes | 4 | Yes | Yes | 3 | No | 4 | Yes | 5 | No |
| 2_474_04 | No MDA | 8 | 4 | 3 | No | No | 3 | No | Yes | 2 | No | 4 | Yes | 4 | Yes |
| 5_172_05 | No MDA | 6 | 4 | 3 | No | No | 4 | Yes | No | 1 | No | 4 | Yes | 4 | Yes |
| 5_366_08 | No MDA | 7 | 5 | 5 | No | Yes | 4 | No | No | 3 | No | 6 | No | 5 | Yes |
| 7_233_03 | No MDA | 8 | 5 | 5 | Yes | Yes | 5 | Yes | Yes | 1 | No | 4 | No | 6 | No |
| 8_415_05 | No-MDA | 8 | 2 | 3 | No | No | 2 | Yes | No | 2 | Yes | 3 | No | 2 | Yes |
a
Diversity is measured using phylogenomics, resistance gene profiles, virulence gene profiles, phylogroups, MLST, and serotype. Cladograms were used to determine the relationships in the resistance gene profiles and virulence gene profiles of isolates within a subject and the number of lineages within each subject. Lineages with similar distributions are those that comprise the same isolates across diversity measurements. Phylogroups, MLST, and serotype distributions are considered similar if they contain the same number of types as phylogenomic lineages.
b
Further details are provided in Table S3.