Table 2.
List of the target pathogen species, abbreviations of their names used in the manuscript, and the numbers of times lineages of each species were identified reliably in the metagenomics data using the mGEMS pipeline
| Full name | Abbreviation | Reliably identified colonisations |
|---|---|---|
| Acinetobacter baumannii | A. bau | 0 |
| Escherichia coli | E. col | 1124 |
| Enterococcus faecalis | E. fcs | 690 |
| Enterococcus faecium | E. fcm | 38 |
| Klebsiella aerogenes | K. aer | 12 |
| Klebsiella grimontii | K. gri | 100 |
| Klebsiella huaxiensis | K. hua | 1 |
| Klebsiella michiganensis | K. mic | 86 |
| Klebsiella ornithinolytica | K. orn | 9 |
| Klebsiella oxytoca | K. oxy | 27 |
| Klebsiella pasteurii | K. pas | 0 |
| Klebsiella planticola | K. pla | 4 |
| Klebsiella pneumoniae | K. pne | 186 |
| Klebsiella quasipneumoniae subsp. quasipneumoniae | K. qpq | 0 |
| Klebsiella quasipneumoniae subsp. similipneumoniae | K. qps | 1 |
| Klebsiella spallanzanii | K. spa | 0 |
| Klebsiella variicola | K. var | 23 |
| Pseudomonas aeruginosa | P. aer | 6 |
| Staphylococcus aureus | S. aur | 76 |
| Streptococcus pneumoniae | S. pne | 0 |