Compositions and methods for identifying bacterial clonotypes and detecting antibiotic susceptibility

Inventors

Chattopdhyay, Sujay

Assignees

Id Genomics Inc

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. coli and predicting antibiotic susceptibility, comprising (a) providing forward primers and reverse primers for at least seven SNPs (single nucleotide polymorphisms) selected from the group consisting of fumC-63, fumC-248, fumC-380, fimH-162, fimH-233, fimH-483, and fimH-108, (b) measuring the presence or absence of each SNP, and (c) determining antibiotic susceptibility from Lookup Table 1.

Core Innovation

The disclosed invention relates to a method for determining antibiotic susceptibility of E. coli by amplifying polynucleotide fragments from an E. coli genome using forward and reverse primer pairs specific for at least seven different E. coli single nucleotide polymorphisms (SNPs). The SNPs comprise fumC-63, fumC-248, fumC-380, fimH-162, fimH-233, fimH-483, and fimH-108, and the primer pairs comprise one or more primer pair embodiments defined by nucleic acid sequences.

The method includes detecting the presence or absence of one or more of the at least seven SNPs in the E. coli genome to identify the E. coli clonotype. The identified clonotype is then compared to a Lookup Table to determine the E. coli's susceptibility to one or more antibiotics.

The invention further includes kits for carrying out this clonotype-identification and antibiotic-susceptibility workflow. The kit comprises forward and reverse primer pairs for at least seven SNPs, a Lookup Table, and an instruction for identifying an E. coli clonotype and determining E. coli susceptibility to one or more antibiotics.

The disclosure also describes a method for determining the presence or absence of one or more specified SNPs in E. coli by performing a nucleic acid amplification process on DNA isolated from E. coli obtained from a patient sample. Dependent claim language narrows the patient sample types, including urine from a patient suspected of having a urinary tract infection.

Claims Coverage

The document includes three independent claims that cover three inventive features: SNP amplification for clonotype-based antibiotic susceptibility, a kit for clonotype and susceptibility determination, and direct determination of SNP presence or absence from patient-derived DNA.

The claims define a workflow and supporting kit in which amplification and detection of specified fumC and fimH SNPs is used to identify an E. coli clonotype, and that clonotype is used with a Lookup Table to determine antibiotic susceptibility. A related claim independently covers determining SNP presence or absence from patient-sample-derived DNA using the same specified SNP-targeting primer pairs.

Stated Advantages

Documented Applications

No documented applications found