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Study reveals the diversity of non-pathogenic E. coli strains

A study, recently published in Nature Communications, has uncovered the vast diversity between non-diarrheagenic Escherichia coli strains. The work highlights the striking similarity between disease-causing and non-disease-causing bacteria and asks whether non-diarrheagenic E. coli strains have the potential to become more virulent.

A ubiquitous species

E. coli is a ubiquitous species of bacteria, found everywhere from soil to untreated water to the human body. Many strains of the bacteria exist, each with their own unique characteristics. In humans, pathogenic strains of E. coli can cause a variety of unpleasant symptoms, namely vomiting and diarrhoea. However, non-pathogenic strains are also found in healthy human microbiomes, existing in harmony with their host.

These non-diarrheagenic strains of E. coli are thought to play some kind of protective role within the human gut. Able to more effectively obtain nutrients than their pathogenic counterparts, these commensal E. coli strains can outcompete more dangerous bacteria. Despite this critical role in human health, non-diarrheagenic E. coli strains are relatively understudied.

Close relations

The Global Enteric Multicentre Study (GEMS) was a three-year initiative to identify causes of diarrhoeal disease in children from south Asia and sub-Saharan Africa. Whilst the study was successful in identifying numerous pathogenic strains, around half of the children involved in the work harboured a subtype of E. coli that did not cause illness. These strains have not yet been robustly analysed. In the current study, researchers from University of Maryland School of Medicine chose to look into the genomic diversity of these strains, to further understand the features that allow them to remain harmless in the human body.

Figure 1: Phylogenetic tree showing the many strains of non-diarrheagenic E. coli in the GEMS study. The tree shows where the sample originated from and the reference genome used for analysis. Adapted from Hazen et al., 2023.

The team were shocked to discover that whilst there was a vast amount of diversity between the non-diarrheagenic strains, they were ultimately much more similar to their pathogenic cousins than expected. In many cases, pathogenic and non-pathogenic strains were part of the same lineage. These findings led the researchers to question the origins of these strains. Did non-diarrheagenic bacteria evolve to lose the genetic components responsible for virulence, or is there potential for them to inherit these traits from neighbouring pathogens?

Gut-wrenching questions

Diarrhoeal disease is a leading cause of death in children worldwide, and so research into the disease-causing pathogens is vital. In addition, given that E. coli seems to reside happily within the human gut, it is important that we understand the differences between the strains, and the risk of the spread of virulence or antimicrobial resistance genes. Further work is needed to assess why certain strains lack virulence genes, and to determine their true protective benefit. Speaking of the findings, author David Rasko stated: “This suggests that there is a dynamic relationship between the strains that may shift over time depending on what happens with the host immune response and the interaction with the microbiome — in this case, within the child’s gut.”

More on these topics

Genetic Diversity / Microbiology / Microbiome