Probe Sequence Panels for Rapid Bacteria and AMR Gene Detection
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Solution Overview
Problem
Current methods for differential diagnosis of bacterial infections are slow and do not provide insights into antimicrobial resistance (AMR) genes, leading to the inappropriate use of antibiotics and increased antibiotic resistance.
Innovation Solution
A database of probe sequences and a set of probes targeting species-specific or clade-specific gene sequences, 16S ribosomal RNA, virulence factors, and AMR genes, designed to enhance high-throughput sequencing for rapid detection and differentiation of bacteria and AMR genes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of information
If multiplex PCR methods are used for differential diagnosis of bacterial infections, then pathogen identification is achieved, but antimicrobial resistance (AMR) gene detection is not provided
Solution Approach 1:
The patent combines bacterial pathogen identification and AMR gene detection into a single multiplex PCR platform. The assay simultaneously targets multiple bacterial species and AMR genes using a unified primer and probe set design, enabling comprehensive diagnostic information acquisition in one test rather than requiring separate assays for different diagnostic needs.
Solution Approach 2:
The detection platform is designed with universal applicability to detect both bacterial pathogens and their associated AMR genes using the same assay system. The primer and probe sets are engineered to work across multiple bacterial species and gene types, making the platform multi-functional for both identification and resistance profiling without requiring separate specialized assays.
2Measurement precision
If culture-based methods are used to identify pathogens and provide antibiotic susceptibility profiles, then comprehensive bacterial characterization is achieved, but the time required is two to several days
Solution Approach 1:
The patent replaces the mechanical/culture-based identification system with a molecular detection system using multiplex PCR. Instead of relying on bacterial growth and phenotypic characterization in culture media, the assay directly detects bacterial DNA and AMR genes through amplification and hybridization, dramatically reducing the time from days to hours while maintaining or improving identification accuracy.
Solution Approach 2:
The assay performs preliminary molecular detection of bacterial DNA and AMR genes before culture results are available. By extracting and amplifying genetic material directly from clinical samples, the system obtains diagnostic information in advance of traditional culture-based methods, enabling earlier intervention and reducing overall diagnostic time.
3Reliability
If broad-spectrum antibiotics are administered pending acquisition of specific information, then patient safety is maintained, but inappropriate antibiotic use increases
Solution Approach 1:
The multiplex PCR platform provides rapid feedback on both bacterial pathogen identification and AMR gene presence, enabling clinicians to adjust antibiotic therapy based on real-time diagnostic information. This feedback mechanism allows transition from empirical broad-spectrum coverage to targeted therapy once specific pathogens and resistance profiles are detected, reducing inappropriate antibiotic use while maintaining patient safety through initial coverage.
Solution Approach 2:
The assay enables preliminary identification of pathogens and AMR genes before final antibiotic selection is made. By detecting resistance genes in advance, the system allows clinicians to pre-plan appropriate antibiotic therapy, avoiding the need for prolonged broad-spectrum coverage and reducing overall inappropriate antibiotic exposure.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enables rapid and accurate identification of bacteria and AMR genes, reducing morbidity and mortality by enabling precise antibiotic treatment.
Implementation Method 1
The sequences or probes described herein increase the sensitivity of high-throughput sequencing for detection, identification, and/or differentiation of bacteria and/or pathogenicity elements and/or AMR genes and/or 16S ribosomal RNA
Data Source
AI summary
Described herein is a database of probe sequences and a set of probes that enable the detection, identification and differentiation of bacteria, and one or more of 16S ribosomal RNA pathogenicity elements, and/or antimicrobial resistance (AMR) genes. These sequences or probes have many uses including but not limited to use in a sequence capture platform and other diagnostic assays. The sequences or probes described herein increase the sensitivity of high-throughput sequencing for detection, identification, and differentiation of bacteria, and one or more of 16S ribosomal RNA, pathogenicity elements, and AMR genes.