Table 2.
Summary of bioinformatic tools used for species identification and detecting AMR by each participant
|
Method step |
Lab_1a* |
Lab_1b* |
Lab_2 |
Lab_3 |
Lab_4 |
Lab_5 |
Lab_6 |
Lab_7 |
Lab_8 |
Lab_9 |
Reference |
|---|---|---|---|---|---|---|---|---|---|---|---|
|
Species ID |
Kraken-HLL |
Kraken-HLL |
blast |
mash and wgsa |
Kraken |
KmerFinder (assembled contigs) |
KmerFinder (raw reads) |
Centrifuge |
Kraken |
Kmerid |
[28–31] |
|
Read assembly |
Shovill (SPAdes) |
Shovill (SPAdes) |
SPAdes |
Unicycler (SPAdes) |
No assembly |
A5-MiSeq |
Bionumerics |
No assembly |
Unicycler (SPAdes) |
No assembly |
[32–34] |
|
AMR identifier |
rgi |
c-SSTAR |
ABRicate |
rgi and Resfinder |
ariba |
rgi |
Bionumerics Escherichia coli genotyping plugin (blast) |
srst2 |
ABRicate |
Genefinder |
|
|
Reference database |
card |
Resfinder and arg-annot |
card |
card and Resfinder |
card and arg-annot |
card |
Resfinder |
arg-annot |
Resfinder |
card and Resfinder (manually curated) |
|
|
Sequence identity cut-off |
80% |
95% |
75% |
80 % (card) and 90 % (Resfinder) |
90% |
80% |
90% |
90% |
75% |
90% |
|
|
Breadth of coverage cut-off |
0% |
0% |
0% |
0 % (card) and 80 % (Resfinder) |
20% |
0% |
60% |
90% |
0% |
100% |
|
*Lab_1 provided two sets of results with two separate methods for AMR detection; these are referred to as Lab_1a and Lab_1b.