Isolation of carbon-dioxide-dependent Escherichia coli from urine of a patient with uncomplicated cystitis

Abstract

We report a case of uncomplicated cystitis caused by CO₂-dependent Escherichia coli small colony variants (SCVs). The initial E. coli isolate came from a midstream urine specimen containing large numbers of Gram-negative rod-shaped organisms that failed to grow on both Drigalski agar and sheep blood agar incubated in ambient air. The isolate grew when the urine was cultured overnight on GAM agar under anaerobic conditions and on chocolate agar under 5% CO₂ atmosphere. Further investigation revealed that the isolate grew on both Drigalski agar and sheep blood agar under 5% CO₂ atmosphere. Initially, we failed to identify the isolate or determine its antimicrobial susceptibilities using the MicroScan WalkAway System because the isolate did not grow in the system. However, the isolate was subsequently identified as E. coli on the basis of its morphological, cultural, and biochemical properties using a commercially available kit, rapid ID 32 E API. The identification of this isolate was confirmed by sequencing the 16S rRNA gene of the organism and MALDI-TOF MS. Cefdinir or fosfomycin was administered, and the patient’s condition improved. CO₂-dependent SCVs should be suspected when samples show positive Gram staining and negative culture test results under ambient air.