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Updated: Jul 12, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.

Madikay Senghore¹, Hannah Read², Priyali Oza²

¹Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA. msenghore@hsph.harvard.edu.

Nature Communications

|November 1, 2023

Summary

This summary is machine-generated.

Tracking pathogen diversity using deep sequencing helps identify infectious disease transmission pairs. Allelic frequency of within-host single nucleotide variants (iSNVs) precisely infers transmission links, revealing bottleneck effects.

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Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Area of Science:

Microbiology
Genomics
Epidemiology

Background:

Identifying infectious disease transmission chains is crucial for control.
Within-host pathogen variation is an underutilized marker for inferring transmission events.
Limited datasets exist capturing pathogen diversity in both donor and recipient hosts.

Purpose of the Study:

To assess the utility of deep-sequenced genomic surveillance for identifying transmission pairs.
To develop a model for inferring transmission likelihood based on pathogen genetic variation.
To investigate the role of within-host variation and transmission bottlenecks.

Main Methods:

Utilized a mouse model for controlled transmission of Citrobacter rodentium.
Employed deep-sequenced genomic surveillance to analyze pathogen diversity.
Examined within-host single nucleotide variants (iSNVs) and their allelic frequencies.

Main Results:

Within-host single nucleotide variants (iSNVs) were maintained across multiple transmission steps.
A model was developed to infer transmission pair likelihood using iSNV data.
Allelic frequency differences of iSNVs provided more precise inference of transmission pairs than presence/absence alone.
Transmission bottlenecks were shown to play a critical role in preserving within-host diversity.

Conclusions:

Deep-sequenced genomic surveillance is effective for identifying pathogen transmission pairs.
Allelic frequencies of within-host variants offer a precise method for inferring transmission links.
Understanding pathogen diversity dynamics during transmission is key for disease control strategies.