Profiling Antibiotic Resistance Genes in Leukemia

The quality-controlled, decontaminated forward and reverse paired sequences from the 127 leukemia and lymphoma samples were mapped to the pediatric-oncology-ARG-database created using bowtie2 (Langmead and Salzberg, 2012 (link)). Counts of sequence reads that mapped to each ARG in the database were obtained for each sample using samtools “sort”, “index” and “idxstat”. Mapped read counts were corrected by the number of sequence reads in each sample. While reads were mapped to all ARG sequences identified, only those ≥60% sequence identity were used in downstream analyses. Antibiotic classes were assigned to each ARGs using the CARD database designation, with two exceptions, 1) genes that occurred in an antibiotic class connected with β-lactam drugs were coded as β-lactam antibiotic class genes (i.e., carbapenem, penam, etc.), 2) genes that occurred in multiple antibiotic classes (i.e., penam, fluoroquinolone, glycopeptide), were coded as “multidrug” antibiotic class genes. Counts within samples assigned to the same gene were summed for downstream analysis. Only genes present in ≥5% of samples were used. Genes in four antibiotic classes were selected for closer analysis: β-lactam antibiotic class, glycopeptide antibiotic class, peptide antibiotic class, and multidrug antibiotic class. These classes were specifically selected as the β-lactam antibiotic class and multidrug antibiotic class potentially contains genes for resistance to β-lactam antibiotics, and the glycopeptide antibiotic class, peptide antibiotic class (a parent class to glycopeptide antibiotics), and multidrug antibiotic class potentially contains genes for resistance to vancomycin. All analyses were carried out on gene sequence data, no allele or SNP information was used.