Table 1.
Extent of Within-country Clustering by Ribotype
| Ribotype | Isolates, No. | Isolates Sequenced, No. (%) | Countries Where Ribotype Was Found, No. | SNPs Between Isolates, Overall Median (IQR) | TMRCA (95% HPD) | SNPacross Median (IQR) | SNPwithin Median (IQR) | SNPwithin/SNPacross Ratio | Expected Ratio, 95% CIb | Compatible With Random European Distribution | Distance Between Hospitals for Most Closely Related Isolates, Median (IQR), Milesa |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 020 | 37 | 33 (89) | 9 | 43 (34–64) | 1955 (1920–1986) | 52 (34–104) | 42 (34–60) | 1.25 | .84–1.24 | Yes | 542 (256–796) |
| 014 | 86 | 80 (93) | 13 | 146 (66–172) | 1963 (1924–1995) | 147 (59–173) | 146 (68–171) | 1.01 | .87–1.09 | Yes | 347 (198–608) |
| 002 | 48 | 44 (92) | 11 | 73 (61–97) | 1955 (1922–1986) | 69 (59–88) | 75 (62–100) | 0.92 | .88–1.05 | Yes | 443 (191–817) |
| 015 | 30 | 29 (97) | 7 | 298 (54–366) | 1857 (1757–1943) | 296 (29–364) | 346 (189–433) | 0.86 | .84–1.18 | Yes | 280 (176–574) |
| 078 | 37 | 31 (84) | 9 | 54 (34–148) | 1721 (1556–1872) | 56 (29–129) | 54 (35–152) | 1.04 | .74–1.43 | Yes | 424 (266–812) |
| 027 | 223 | 216 (97) | 10 | 71 (50–110) | 1949 (1913–1977) | 49 (17–71) | 82 (60–125) | 0.60 | .93–1.07 | No | 21 (0–189) |
| 001/072 | 134 | 119 (89) | 14 | 201 (41–273) | 1851 (1754–1934) | 37 (23–199) | 253 (173–322) | 0.15 | .70–1.31 | No | 184 (0–351) |
| 176 | 25 | 21 (84) | 3 | 15 (7–19) | 1993 (1977–2004) | 6 (4–8) | 19 (16–20) | 0.31 | .65–1.23 | No | 36 (0–198) |
| 018 | 36 | 34 (94) | 7 | 39 (22–88) | 1787 (1638–1910) | 28 (17–38) | 92 (83–285) | 0.30 | .40–1.56 | No | 189 (53–636) |
| 356 | 22 | 17 (77) | 1 | 9 (5–12) | 2008 (2004–2011) | 9 (5–12) | … | … | … | No | 133 (57–248) |
Abbreviations: CI, confidence interval; HPD, highest posterior density interval; IQR, interquartile range, SNP, single-nucleotide polymorphism; SNPacross, SNPs between isolates across different countries; SNPwithin, SNPs between isolates within a country; TMRCA, time of most recent common ancestor.
aTo calculate the number of miles between the most closely related isolates, within each ribotype, a minimum spanning tree was constructed using SNP distances as edge weights and isolates as nodes. The properties of the edges (SNPs and miles) of the minimum-spanning tree were analyzed, such that each isolate but 1 contributes 1 data point (see Figure 5).
bCIs were based on permutation tests (see Methods).