Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2023

The Essential Genome of Enteroaggregative Escherichia coli strain 042 (#212)

Isabel Warner 1 , Emily Goodall 1 , Ian Henderson 1
  1. University of Queensland, Brisbane, QLD, Australia

Enteroaggregative Eschierchia coli (EAEC) are a major factor in acute and persistent diarrheal disease worldwide and remain one of the leading causes of mortality for children under 5 [1]. EAEC are defined by their ability to adhere to HEp-2 cells in a specific “stacked brick” pattern, facilitated by adhesins on the plasmid [2, 3]. They contain a range of endo- and cyto-toxins which can damage host intestines and cause chronic inflammation, particularly in children and immunocompromised individuals [4]. The current prototypical strain for EAEC is E. coli 042, which was isolated from a Chilean child with diarrhea and was shown to cause disease in adults in a challenge study [5, 6].

 

Here, we used Transposon Directed Insertion Site Sequencing (TraDIS or TIS) to identify genes in the E. coli strain 042 that are essential for its growth and survival. TraDIS couples random transposon mutagenesis with multi-parallel sequencing to identify transposon insertion sites on a high throughput scale. If the transposon inserts into a gene that is “essential” for growth and survival, the mutants will be non-viable, and no transposon insertions will be detected in that gene. An “essential” gene contains few or no insertions, while a “non-essential” gene is easily disrupted with no consequence for survival.

 

A transposon library of >1 million mutants was generated in the EAEC strain 042, with more than 380,000 unique insertion points, or a resolution of 1 insertion every 14 base pairs. We identified 375 essential genes, which corresponds to roughly 7% of the genome. We then compared this with other transposon mutant libraries to establish genes that are only essential in this strain. We found that it had several essential genes that were not present in other strains, which may be candidates for further study.

 

Because antibiotics target gene products that are essential for survival, examining the essential genome of E. coli strains provides insight into new targets for novel antimicrobials. Additionally, genes that are only essential in EAEC offer the exciting possibility of designing precision antimicrobials for pathogenic E. coli.

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