Role of dndC gene in DNA degeneration in pulsed-field gel electrophoresis and treatment method

  Objective  To understand the carriage of dndC gene in Escherichia coli and E. fergusonii strains and the relationship between the dndC gene and the DNA degeneration phenotype, and explore the causes of DNA degeneration in pulsed-field gel electrophoresis (PFGE) and treatment methods.

  Methods  A total of 450 E. coli and E. fergusonii strains were analyzed by PFGE. The primers were designed to detect and sequence the dndC gene. The phylogenetic tree was constructed based on the dndC genes obtained from this study and NCBI database to analyze the genotype of dndC gene and the distribution of dndC gene in different types of E. coli. Addition of thiourea and disinfection of electrophoresis equipment were used to study the treatment methods of DNA degeneration.

  Results  There were 40 strains (8.89%) with the DNA degeneration phenotype by PFGE analysis and 33 strains of them were positive for dndC gene, accounting for 7.33% of 450 E. coli and E. fergusonii strains. The dndC genes of E. coli were divided into eight groups. There were positive strains carrying dndC gene in all eight types of E. coli strains, and the positive rates of dndC gene in eight types of E. coli strains were different. Addition of thiourea and disinfection of electrophoresis equipment could effectively improve the DNA degeneration phenotype.

  Conclusion  The dndC gene can cause DNA degradation of E. coli and E. fergusonii in PFGE analysis. Addition of thiourea was an effective method to ease the DNA degradation caused by dndC.