Characteristics of a Capnophilic Small Colony Variant of Escherichia Coli Co-Isolated With Two Other Strains From a Patient With Bacteremia in China

Abstract Small colony variants (SCVs) are a slow-growing subpopulation of bacteria characterized by their atypical colony morphology and distinct biochemical properties, which are known to cause chronic persistent infections. Here, we investigated the characteristics of three phenotypes of Escherichia coli, including a capnophilic SCV, co-isolated from a 64-year-old patient with bacteremia in China. The three strains were identified as a capnophilic strain (EC1), a capnophilic SCV (EC2), and a wild-type strain (EC3). The EC1 and EC2 strains did not grow in the absence of CO2, while the EC2 colonies were pinpoint in appearance and had the ability to revert to the large-form phenotype. The growth of the SCV was slow and not enhanced in the presence of thymidine, hemin, thiamine, and menadione. The results of antimicrobial susceptibility showed similar sensitivity to cefoxitin and imipenem, but resistant to most of the other antimicrobials tested. Whole genome sequencing showed that no genetic mutational variations associated with SCVs were observed, while EC1, EC2 and the revertible strains of EC2 lacked the can gene. Multi-locus sequence typing showed that all strains belonged to ST457 and nucleotide similarity analysis indicated that they had high homology. In conclusion, we report rarely described co-isolated forms of three phenotypes of E. coli that included acapnophilic SCV in a patient with bacteremia. The capnophilic SCV strain had atypical morphology and biochemical characteristics with the absent of can gene. Based on our findings, we have discussed the laboratory identification, characterization, mechanisms, and clinical treatment of capnophilic SCV strains.