A novel hemA mutation is responsible for small colony variant phenotype in Escherichia coli.

We identified a small colony variant (SCV) of a clinical isolate of Escherichia coli from Malawi following sequential in vitro selection in sub-inhibitory concentrations of amoxicillin-clavulanic acid and gentamicin. The SCV was auxotrophic for hemin and had impaired biofilm formation compared to the ancestral isolates. A single novel nucleotide polymorphism (SNP) in hemA, which encodes a glutamyl-tRNA reductase responsible for the initial step of porphyrin biosynthesis leading to the production of haem, was responsible for the SCV phenotype. We showed this phenotype was stable over multiple generations and the SNP in hemA resulted in a significant fitness cost to the isolate which persisted even in the presence of hemin. As hemA is not found in mammalian cells, and disruption of the gene results in impaired biofilm formation and a significant fitness cost, it represents a potential target for novel drug development specifically for the treatment of catheter-associated urinary tract infections caused by biofilm-producing E. coli.