Table 7.
Influence of antibiotic exposure (broad vs. narrow spectrum regimen after first week of life) on abundance of antibiotic resistance genes (ARGs) in all preterm infants.
| Antibiotic resistance gene (ARG) classes*** | ARGs at 28 days | ARGs at 4 months | ||||||
|---|---|---|---|---|---|---|---|---|
| Absolute counts/total abundance | Absolute counts/total abundance | |||||||
| Broad* | Narrow | P | FDR Q | Broad* | Narrow | P | FDR Q | |
| (n = 7**) | (n = 15**) | (n = 9**) | (n = 13**) | |||||
| Class A Beta lactamase | 0.00 | 0.00 | 0.447 | 0.731 | 5.00 | 3.01 | 0.324 | 0.864 |
| Class C Beta lactamase | 44.96 | 0.00 | 0.021 | 0.095 | 9.11 | 8.16 | 0.235 | 0.752 |
| Aminoglycoside phosphotransferase | 6.14 | 0.00 | 0.078 | 0.281 | – | – | – | – |
| Aminoglycoside nucleotidyltransferase | 0.93 | 0.00 | 0.008 | 0.072 | 0.00 | 0.00 | 0.794 | 0.851 |
| Tetracycline efflux | 52.29 | 0.00 | 0.014 | 0.084 | 7.92 | 0.00 | 0.235 | 0.94 |
| Tetracycline ribosomal protection | 5.97 | 0.00 | 0.210 | 0.540 | 11.68 | 2.17 | 0.393 | 0.886 |
| Quinolone resistance | 29.75 | 9.43 | 0.298 | 0.671 | 9.40 | 8.34 | 0.357 | 0.816 |
| ABC efflux pump | 3.23 | 1.07 | 0.392 | 0.784 | 0.70 | 0.64 | 0.471 | 0.814 |
| RND antibiotic efflux | 312.10 | 37.73 | 0.875 | 0.875 | 94.00 | 84.96 | 0.393 | 0.63 |
| MFS antibiotic efflux | 272.36 | 117.02 | 0.490 | 0.68 | 119.50 | 107.51 | 0.404 | 0.59 |
| Multidrug efflux pump activity | 22.08 | 26.53 | 0.581 | 0.70 | 19.08 | 13.63 | 0.647 | 0.69 |
| Multidrug resistance efflux pump | 0.00 | 0.00 | 0.162 | 0.486 | 3.02 | 0.00 | 0.017 | 0.272 |
| Gene modulating antibiotic efflux | 75.30 | 15.53 | 0.490 | 0.73 | 19.65 | 20.86 | 0.393 | 0.63 |
| SMR antibiotic efflux | 0.00 | 0.00 | 0.447 | 0.805 | – | – | – | – |
| Antibiotic target | 1.70 | 0.00 | 0.002 | 0.030 | 2.36 | 0.00 | 0.096 | 0.512 |
| Gene modulating resistance | 16.25 | 22.83 | 0.535 | 0.69 | 9.68 | 39.10 | 0.043 | 0.344 |
| rRNA methyltransferase | 8.59 | 9.07 | 0.581 | 0.65 | 8.41 | 5.56 | 0.601 | 0.67 |
| Other ARG | 24.40 | 12.15 | 0.680 | 0.72 | 7.21 | 7.36 | 0.601 | 0.74 |
*
We defined regimens including third-generation cephalosporins or carbapenems as a broad-spectrum regimen.
**
Number of fecal samples included in these analyses.
***
See Materials and Methods section for further explanation of which antibiotic resistance genes that are included in these groups.
FDR, false discovery rate.
Bold indicates significant differences in abundance of antibiotic resistance genes between broad- and narrow-spectrum regimens (P- and Q-value).