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Published on: December 23, 2022
Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages
Elizabeth A Cummins1, Robert A Moran1, Ann E Snaith1
1Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
Abstract:
The repeated emergence of multi-drug-resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug-resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonization observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug-resistant E. coli clones. We employed large-scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20 000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterized the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones.
Insights
Multi-drug-resistant Escherichia coli clones pose a global health threat. This study investigated if the type VI secretion system (T6SS) aids their gut colonization, finding MDR clones often lack essential T6SS genes.
Area of Science:
- Microbiology
- Genomics
- Public Health
Background:
- Multi-drug-resistant (MDR) *Escherichia coli* clones are an increasing global public health concern.
- Drug-resistant *E. coli* can displace commensal bacteria in the human gut, suggesting a competitive advantage.
- The type VI secretion system (T6SS) is a potential mechanism for this competitive advantage, particularly in rapid colonization scenarios.
Purpose of the Study:
- To investigate the role of the type VI secretion system (T6SS) in the competitive advantage of multi-drug-resistant *Escherichia coli* (MDR *E. coli*).
- To determine if T6SS gene carriage is associated with MDR lineages within the *E. coli* phylogenetic diversity.
Main Methods:
- Large-scale genomic analysis of over 20,000 *E. coli* genomes.
- Phylogenetic analysis to assess the distribution of T6SS genes.
- Characterization of T6SS loci in specific MDR clones (ST410 and ST131).
Main Results:
- The presence of T6SS genes in *E. coli* showed significant non-phylogenetic variation.
- No direct association was found between T6SS gene carriage and MDR lineages.
- Multiple clades containing MDR clones exhibited the loss of essential structural T6SS genes.
- Specific genetic events, including recombination and insertion, were identified as responsible for the parallel loss of T6SS genes in MDR clones ST410 and ST131.
Conclusions:
- The type VI secretion system (T6SS) is not universally present in MDR *E. coli* and does not appear to confer a general competitive advantage through its presence.
- The loss of essential T6SS genes in certain MDR *E. coli* clades suggests alternative mechanisms for their success or adaptation.
- Understanding the genetic basis for T6SS gene loss in MDR *E. coli* is crucial for comprehending their epidemiology and public health impact.
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