New research co-authored by BIIE's Emma Slack charts the hidden diversity of E. coli surface structures
BIIE faculty member Emma Slack, together with Prof. Shinichi Sunagawa's group at ETH Zurich and an international team, has catalogued 85 distinct types of E. coli capsules - more than doubling what was previously known - laying essential groundwork for the precision vaccines and phage therapies that BIIE is working to bring to children worldwide.
Many E. coli strains that cause serious infections in children are shielded by a sugar capsule that blocks antibodies and immune attack. Developing capsule-targeted treatments requires knowing which capsule type a strain carries - but the field has been working from an incomplete map since classical typing methods were abandoned in the 1990s.
A new study co-led by BIIE faculty Emma Slack and Dr. Tim Keys, previously a senior scientist in the Slack group and now CEO of Baxiva Ag, alongside the group of Prof. Shinichi Sunagawa , addresses this directly. By sequencing a reference strain collection and surveying more than 37,000 E. coli genomes, the team assembled a catalogue of 85 transporter-dependent capsule types, 55 of which had not been described before. They also developed kTYPr, a free open-source tool that can identify capsule types from genome sequences, and applied it to a globally distributed collection of 24,000 genomes. Six newly described types were significantly associated with invasive disease in humans. Mass spectrometry analysis additionally corrected long-standing errors in published capsule structures.
For researchers developing vaccines or phage therapies against E. coli infections in children - particularly in settings where diagnostic and sequencing resources are limited - this freely available catalogue and tool represent a significant step forward.
The full article can be accessed in Nature Microbiology.
Supported by the Basel Research Centre for Child Health (BRCCH), the Swiss National Science Foundation, and the European Research Council.