dnaJ: a New Approach to Identify Species within the Genus Enterobacter

Area of Science:

• Microbiology
• Genetics
• Clinical Diagnostics

Background:

• The taxonomy of the genus Enterobacter is complex and has undergone recent revisions.
• Accurate identification of Enterobacter species is crucial for clinical diagnostics and epidemiological studies.
• Existing methods for bacterial identification can be time-consuming or require specialized equipment.

Purpose of the Study:

• To develop and validate a novel PCR and amplicon sequencing technique for accurate Enterobacter species identification.
• To assess the utility of the dnaJ gene sequence for differentiating Enterobacter species.
• To apply the developed method to identify Enterobacter species in clinical specimens, particularly from neonatal sepsis cases.

Main Methods:

• A PCR and amplicon sequencing technique targeting a partial sequence of the dnaJ gene was developed.
• The method was validated by comparing results with DNA-DNA digital hybridization (dDDH) and average nucleotide identity (ANI) using type strains, database sequences, and clinical isolates.
• The dnaJ sequencing method was applied to a collection of 68 Enterobacter strains from neonatal blood cultures.

Main Results:

• The partial dnaJ gene sequence demonstrated sufficient polymorphism for reliable Enterobacter species identification.
• The method showed congruence with whole-genome sequencing (WGS) for species identification in 100 database strains.
• The study identified Enterobacter quasihormaechei in four neonatal sepsis cases, and revealed a high prevalence of E. bugandensis and E. xiangfangensis in neonatal blood cultures.

Conclusions:

• Sequencing a part of the dnaJ gene provides a rapid, economical, and highly discriminatory method for Enterobacter species identification.
• This dnaJ-based approach is a valuable tool for clinical practice and research, complementing existing methods like MALDI-TOF.
• The study highlights the importance of accurate Enterobacter species identification in neonatal sepsis and introduces a new diagnostic approach.