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Table 1 Studies analyzed

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

Study namePublicationRuns analyzedSample sourceDataset
MozambiqueUnpublished138Clinical isolatesMTB dataset
Kwazulu-NatalCohen et al. 2015433Single colonies from clinical isolatesMTB dataset
NigeriaSenghore et al. 201773Clinical isolatesMTB dataset
BelarusWollenberg et al. 2017552Clinical isolatesMTB dataset
High-depth sequencingTrauner et al. 201763Clinical isolatesMTB dataset
Sputum-capture sequencingBrown et al. 201558Clinical respiratory specimens (culture-free sequencing with a bait capture strategy)MTB dataset
Sputum-direct sequencingVotintseva et al. 201768Clinical respiratory specimens (direct culture-free sequencing)MTB dataset
MGIT sequencing*Pankhurst et al. 2016168Early-positive MGIT cultures (liquid)MTB dataset
A. baumanniiWillems et al. 201636Single-colony recultured in brothBacterial dataset
C. difficileStone et al. 201654Pooled single-colony isolatesBacterial dataset
EnterococcusTyson et al. 2018197Isolates from retail meatsBacterial dataset
K. pneumoniaeHolt et al. 2015285Human, animal, and environmental isolatesBacterial dataset
L. monocytogenesHalbedel et al. 2018424Clinical isolates from humanBacterial dataset
L. pneumophilaTimms et al. 201848Pure culture isolates from human and cooling towersBacterial dataset
N. gonorrhoeaeYahara et al. 2018272Pure culture isolates from humanBacterial dataset
P. aeruginosaMarvig et al. 2015445Clinical isolates from humanBacterial dataset
S. aureusAanensen et al. 2016337Clinical isolates from 186 hospitals in 21 countriesBacterial dataset
S. entericaGymoese et al. 2017366Human, animal, and environmental isolatesBacterial dataset
T. pallidumPinto et al. 201625Clinical specimens (culture-free sequencing with a bait capture strategy)Bacterial dataset
VibrioGreig et al. 2018152Clinical isolates from humanBacterial 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