Table 1.
Comparison of key features of Klebsiella genomes from South and Southeast Asian sites
| S Asia | SE Asia | p value (adj) | OR | LCI | UCI | ||
|---|---|---|---|---|---|---|---|
| Species assignment | 102 | 100 | |||||
| K. pneumoniae | 100 (98%) | 87 (87%) | 0.011 | 0.13 | 0.01 | 0.62 | * |
| K. variicola | 1 (1%) | 4 (4%) | 0.838 | 4.18 | 0.40 | 209.04 | |
| K. quasipneumoniae ssp. quasipneumoniae | 1 (1%) | 0 (0%) | na | na | na | na | |
| K. quasipneumoniae ssp. similipneumoniae | 0 (0%) | 9 (9%) | na | na | na | na | |
| Features of K. pneumoniae sensu stricto | |||||||
| Sequence type assignment | 100 | 87 | |||||
| ST15 | 11 (11%) | 15 (17%) | 1.158 | 1.68 | 0.67 | 4.32 | |
| ST14 | 16 (16%) | 2 (2%) | 0.008 | 0.12 | 0.01 | 0.56 | ** |
| ST23 | 2 (2%) | 12 (14%) | 0.015 | 7.76 | 1.65 | 73.39 | * |
| ST231 | 17 (17%) | 0 (0%) | 5.14 × 10−5 | 0.00 | 0.0 | 0.24 | ** |
| Capsular serotype prediction | 79 | 87 | |||||
| KL1 | 2 (2.5%) | 13 (15%) | 0.012 | 6.70 | 1.44 | 63.22 | * |
| KL2 | 4 (5.1%) | 11 (13%) | 0.216 | 2.70 | 0.76 | 12.15 | |
| Antimicrobial resistance prediction | 100 | 87 | |||||
| Multi-drug resistant (≥ 3 acquired classes) | 81 (81%) | 44 (51%) | 1.06 × 10−4 | 0.24 | 0.12 | 0.48 | ** |
| Aminoglycosides | 76 (76%) | 41 (47%) | 0.001 | 0.28 | 0.14 | 0.55 | ** |
| Fluoroquinolones | 80 (80%) | 39 (45%) | 7.13 × 10−6 | 0.21 | 0.10 | 0.41 | ** |
| Phenicols | 27 (27%) | 25 (29%) | 7.833 | 1.09 | 0.55 | 2.17 | |
| Sulfonamides | 63 (63%) | 42 (48%) | 0.493 | 0.55 | 0.29 | 1.02 | |
| Tetracyclines | 24 (24%) | 39 (45%) | 0.029 | 2.56 | 1.32 | 5.05 | * |
| Trimethoprim | 62 (62%) | 38 (44%) | 0.118 | 0.48 | 0.25 | 0.89 | |
| 3rd-generation cephalosporins (ESBL) | 60 (60%) | 41 (47%) | 0.949 | 0.60 | 0.32 | 1.11 | |
| Carbapenems | 47 (47%) | 1 (1%) | 7.13 × 10−13 | 0.01 | 0.0 | 0.08 | ** |
| Virulence prediction | 100 | 87 | |||||
| Yersiniabactin (ybt) | 65 (65%) | 46 (53%) | 0.205 | 0.61 | 0.32 | 1.13 | |
| Aerobactin (iuc) | 27 (27%) | 32 (37%) | 0.319 | 1.57 | 0.81 | 3.07 | |
| Iuc lineages | 100 | 87 | |||||
| iuc 1 | 13 (13%) | 27 (31%) | 0.012 | 2.99 | 1.36 | 6.86 | * |
| iuc 3 | 0 (0%) | 5 (6%) | 0.061 | na | 1.08 | inf | |
| iuc 5 | 12 (12%) | 0 (0%) | 0.001 | 0.00 | 0.0 | 0.8 | ** |
| AMR and virulence convergence | 100 | 87 | |||||
| ESBL and ybt | 45 (45%) | 26 (30%) | 0.144 | 0.52 | 0.27 | 0.99 | |
| ESBL and iuc | 16 (16%) | 1 (1%) | 0.001 | 0.06 | 0.0 | 0.41 | ** |
| CP and ybt | 37 (37%) | 1 (1%) | 1.79 × 10− 10 | 0.02 | 0.0 | 0.13 | ** |
| CP and iuc | 13 (13%) | 0 (0%) | na | na | 0.0 | 0.34 | |
*South (S) Asia is represented by the two sites in India and Nepal, isolated 2016–2017; Southeast (SE) Asia is represented by the sites in Cambodia, Laos, Thailand and Vietnam, isolated 2015–2016. p values were calculated using Fisher’s exact test for differences in the prevalence of each feature (in rows) for the S vs SE Asia samples and are adjusted using Bonferroni correction for the number of tests within each group of comparisons (as labelled in italics; sample size for each are also in italics). na test not applicable (one or more values equal to zero). Inf infinity, OR odds ratio, LCI and UCI, lower and upper bounds for 95% confidence interval, respectively. *p < 0·05, **p < 0·01