TABLE 3.
Number of antimicrobial resistance genes (ARGs) identified with three sequencing methods from four human samples.
| Method | ST5-1mo | HS21 | HS24 | HS26 | |
| Number of ARGs identified with each method | AMR Research panel * | 29 (14) | 39 (33) | 34 (28) | 54 (44) |
| Pan-Bacterial panel | 14 | 26 | 23 | 30 | |
| SMS + BLAST ** | 9 (7) | 17 (10) | 20 (16) | 28 (15) | |
| Number of unique ARGs identified when overlapping all three methods | 34 | 45 | 39 | 64 | |
| Number of ARGs identified exclusively with one method *** | AMR Research panel only | 24 (66.7%) | 27 (55.1%) | 21 (50.0%) | 38 (55.9%) |
| Pan-Bacterial panel only | 2 (5.6%) | 3 (6.1%) | 3 (7.1%) | 3 (4.4%) | |
| SMS + BLAST only | 5 (13.9%) | 6 (12.2%) | 5 (11.9%) | 11 (16.2%) | |
Reads obtained from the shotgun metagenomics sequencing (SMS) were queried against the NCBI “Bacterial Antimicrobial Resistance Reference Gene Database” (BioProject PRJNA313047) using MagicBLAST. Targeted sequencing used the Ion AmpliSeqTM AMR Research panel and the Ion AmpliSeqTM Pan-Bacterial Research panel.
*The number of genes with a depth > 1 is in brackets; depth is defined as the average number of reads piled up across the entire gene.
**The number of genes with a mean base depth per 5 million reads > 1 is in brackets.
***The percentage of ARGs identified with one method only (compared to the total number of ARGs identified with any method) is in brackets.