NDtree

NDtree constructs phylogenetic trees from whole-genome sequencing (WGS) data by computing nucleotide differences to enable high-resolution sub-typing and epidemiological analysis of bacterial pathogens.

Key Features:

• Nucleotide difference methodology: Employs a nucleotide difference approach to construct phylogenetic trees and has been reported to cluster 100% of S. Typhimurium isolates according to their epidemiological associations, outperforming pulsed-field gel electrophoresis (PFGE).
• Integration with WGS data: Optimized for use with WGS data and supports comparative approaches including pan-genome trees, k-mer trees, SNP trees, and nucleotide difference trees.
• Real-time analysis capability: Facilitates real-time identification and typing of pathogens, demonstrated in analyses of verocytotoxin-producing Escherichia coli (VTEC) to accelerate outbreak detection versus conventional methods.
• Epidemiological relevance: Integrates genomic analysis with epidemiological data to distinguish sporadic from outbreak-related isolates for public health investigations.
• Cost-effectiveness: Enables WGS-based typing as a cost- and time-efficient alternative to traditional typing strategies for pathogen surveillance.

Scientific Applications:

• Epidemiological typing of bacterial pathogens: Accurate clustering and sub-typing of organisms such as Salmonella enterica serovar Typhimurium and verocytotoxin-producing Escherichia coli for outbreak investigation.
• Outbreak detection and routine surveillance: High-resolution differentiation of closely related strains to support foodborne outbreak monitoring and ongoing surveillance programs.

Methodology:

WGS data acquisition from bacterial isolates; construction of phylogenetic trees using the nucleotide difference method; evaluation of resulting phylogenies in conjunction with epidemiological data to determine outbreak associations.