Microbial Genomics

EnteroBase

Since 2021, Prof. Sascha Ott (as director of Bioinformatics RTP) is responsible for the maintenance and development of the EnteroBase system which provides phylogenomic analyses of over one million bacterial genomes for more than 4,200 registered users. The system is used routinely by a large community of scientists and reference laboratories including those in England, Scotland, Ireland, France, Belgium, Denmark, Canada, China and South Africa, with 20,000 page views from 1,500 independent IP addresses per month. Recent work led includes the integration of EnteroBase into the PATH-SAFE infrastructure, addition of antimicrobial resistance predictions (to be released March 2024), and addition of plasmid annotations. A related system called PhytoBacExplorer is being developed for phytobacteria.

BactDating

The goal of BactDating is to perform Bayesian dating of the nodes of a bacterial phylogenetic tree. This typically involves simultaneous Bayesian estimation of the molecular clock rate and coalescent rate. Additional features include inference of root location, lost sampling dates and different evolutionary models. BactDating is available as a R package, for more details about how to install and use it, see here.

TransPhylo

TransPhylo is a software package that can reconstruct infectious disease transmission using genomic data. The input is a dated phylogeny, where leaves correspond to pathogens sampled from the known infected hosts. The main output is a transmission tree which indicates who infected whom, including the potential existence of unsampled individuals who may have acted as missing transmission links. TransPhylo works by colouring the branches of the phylogeny using a separate colour for each host, sampled or not. Each section of the tree coloured in a unique colour represents the pathogen evolution happening within a distinct host. Changes of colours on branches therefore correspond to transmission events from one host to another. TransPhylo is available as a R package, for more details on installation and usage see here.