Small-colony variants (SCVs) of bacteria are subpopulations with a small colony size, low growth rate, and atypical colony morphology. The purpose of this study was to comprehensively elucidate the characteristics and underlying mechanism of the development of a glutamine-dependent SCV of E. coli, GU-92SCV, isolated from the blood of a patient with pyelonephritis.

The GU-92SCV strain was tested for auxotrophy testing for glutamine. DNA mutations in genes related to glutamine synthesis were analysed by sequencing. The isolate's proliferation and antimicrobial susceptibility in Mueller-Hinton II medium supplemented with glutamine were examined.

The colony of the GU-92SCV strain did not grow on Mueller-Hinton II agar, but growth around the filter paper containing l-glutamine was enhanced on Mueller-Hinton II agar. The GU-92SCV strain had a single nucleotide substitution in glnA, c.193G>A, corresponding to p.Asp65Asn. Changing c.193G>A to the wild-type sequence in glnA restored these phenotypes. Because GU-92SCV did not grow in Mueller-Hinton II broth, antimicrobial susceptibility test results were not obtained; however, in the presence of 10 mg mL−1l-glutamine, the results were consistent with those of the revertant strain GU-92REV.

To the best of our knowledge, this is the first clinical isolation of a glutamine-dependent E. coli SCV from a patient blood culture. Our data showed that glnA was important for the growth of E. coli in Mueller-Hinton II medium, which also required the presence of glutamine when performing antimicrobial susceptibility testing for glutamine-dependent SCV strains.