Table 1.
Clinical characteristics of fecal sample donors.
Figure 1.
Antibiotic selections for which resistance was observed.
The percent of libraries from infants (N = 8) and children and adolescents (N = 12) generating colonies resistant to 14 antibiotics is plotted. Two libraries that were <0.1 GB in size were excluded, as they did not have enough genetic diversity to accurately represent the resistance in their source metagenome. Not shown are four antibiotics for which no resistance was found: ciprofloxacin, meropenem, colistin, and cefepime.
Figure 2.
Unrooted approximate maximum-likelihood phylogenetic tree constructed using the predicted amino acid sequences of all beta-lactamases in the study set.
Ambler classes are color-coded as indicated in the legend (upper right). At the terminus of each branch, the number of unique amino acid sequences in the terminal cluster is indicated. Branches with identity to extended-spectrum beta-lactamases (ESBLs) are numbered I–V and their putative ESBL classification is listed in the lower left legend of selected genes. A Class D beta-lactamase with high identity to a known OXA-10 is also numbered (VI) and included in the lower left legend. Genes included in the lower left legend that were syntenic with mobile genetic elements are bolded and marked with a §. Clusters of sequences with <55% ID to any known beta-lactamase are marked with a ‡. Nodes with a Shimodaira-Hasegawa (SH) value > = 0.7 are starred. The Shimodaira-Hasegawa score provides a measure of confidence in tree topology, with a maximum score (highest confidence) of 1.0 [52].
Figure 3.
Unrooted approximate maximum-likelihood phylogenetic tree constructed using the predicted amino acid sequences of all aminoglycoside aminotransferases and phosphotransferases in the study set.
Enzyme classes are color-coded as indicated in the legend. At the terminus of each branch, the name of the source contig is listed. Aminoglycoside phosphotransferases that were syntenic with aminoglycoside acetyltransferases are indicated with purple bold text and marked with a ‡. Genes syntenic with a mobile element are bolded and marked with a §. Nodes with a Shimodaira-Hasegawa (SH)-value > = 0.7 are starred.
Table 2.
Putative novel resistance genes.