Table 1.
Studies analyzed
| Study name | Publication | Runs analyzed | Sample source | Dataset |
|---|---|---|---|---|
| Mozambique | Unpublished | 138 | Clinical isolates | MTB dataset |
| Kwazulu-Natal | Cohen et al. 2015 | 433 | Single colonies from clinical isolates | MTB dataset |
| Nigeria | Senghore et al. 2017 | 73 | Clinical isolates | MTB dataset |
| Belarus | Wollenberg et al. 2017 | 552 | Clinical isolates | MTB dataset |
| High-depth sequencing | Trauner et al. 2017 | 63 | Clinical isolates | MTB dataset |
| Sputum-capture sequencing | Brown et al. 2015 | 58 | Clinical respiratory specimens (culture-free sequencing with a bait capture strategy) | MTB dataset |
| Sputum-direct sequencing | Votintseva et al. 2017 | 68 | Clinical respiratory specimens (direct culture-free sequencing) | MTB dataset |
| MGIT sequencing* | Pankhurst et al. 2016 | 168 | Early-positive MGIT cultures (liquid) | MTB dataset |
| A. baumannii | Willems et al. 2016 | 36 | Single-colony recultured in broth | Bacterial dataset |
| C. difficile | Stone et al. 2016 | 54 | Pooled single-colony isolates | Bacterial dataset |
| Enterococcus† | Tyson et al. 2018 | 197 | Isolates from retail meats | Bacterial dataset |
| K. pneumoniae | Holt et al. 2015 | 285 | Human, animal, and environmental isolates | Bacterial dataset |
| L. monocytogenes | Halbedel et al. 2018 | 424 | Clinical isolates from human | Bacterial dataset |
| L. pneumophila | Timms et al. 2018 | 48 | Pure culture isolates from human and cooling towers | Bacterial dataset |
| N. gonorrhoeae | Yahara et al. 2018 | 272 | Pure culture isolates from human | Bacterial dataset |
| P. aeruginosa | Marvig et al. 2015 | 445 | Clinical isolates from human | Bacterial dataset |
| S. aureus | Aanensen et al. 2016 | 337 | Clinical isolates from 186 hospitals in 21 countries | Bacterial dataset |
| S. enterica | Gymoese et al. 2017 | 366 | Human, animal, and environmental isolates | Bacterial dataset |
| T. pallidum | Pinto et al. 2016 | 25 | Clinical specimens (culture-free sequencing with a bait capture strategy) | Bacterial dataset |
| Vibrio‡ | Greig et al. 2018 | 152 | Clinical isolates from human | Bacterial dataset |
*This study included sequencing samples from non-MTB organisms. We analyzed the 168 reported as MTB by the authors
†This study included sequencing samples from 2 species (E. faecalis and E. faecium)
‡This study included sequencing samples from different Vibrio species. We only analyzed the 152 reported as V. cholerae by the authors