Abstract: The present disclosure provides methods and compositions for generating clonotypes from input nucleic acid sequences. Presently disclosed clonotype generating methods produce accurate and efficient indicators of genetic relatedness and diversity, including for example, of pathogenic organisms such as infectious bacteria. Also provided are primers, kits, and related methods for determining antibiotic susceptibility of a pathogenic organism, such as, for example, Klebsiella, and for treating an infection by one or more pathogenic Discard organisms on the basis of herein disclosed clonotypes and clonotype-generating methods.

Abstract: There is disclosed a PCR-based test kit and PCR process for identification of multiple clonal sub-species lineages of infectious bacteria, such as uropathogenic E. coli causing cystitis, pyelonephritis and urosepsis, for the purposes of predicting antibiotic resistance of the bacteria. More specifically, there is further disclosed a SNP (single nucleotide polymorphism) identification process that simultaneously detect compilations of the presence of absence of predictive SNPs within mutated loci of infectious bacterial clonal subspecies variants, such as the fumC/fimH loci of the E. coli bacterium. This disclosure provides a PCR detection kit incorporating a SNP compilation that forms a BFC (Binary Footprint Code) that allows for rapid identification of multiple infectious bacterial clonotypes based on their SNP footprint. More specifically there is disclosed a clonotyping method for clonal typing E.