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Table 1 Studies analyzed

From: Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability

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Mozambique Unpublished 138 Clinical isolates MTB dataset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
  1. *This study included sequencing samples from non-MTB organisms. We analyzed the 168 reported as MTB by the authors
  2. This study included sequencing samples from 2 species (E. faecalis and E. faecium)
  3. This study included sequencing samples from different Vibrio species. We only analyzed the 152 reported as V. cholerae by the authors