Microarray-based comparative genomic indexing of the Cronobacter genus (Enterobacter sakazakii)

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Cronobacter is a genus of 6 species, including Cronobacter sakazakii, formerly known as Enterobacter sakazakii.
• Understanding the genetic relatedness among Cronobacter species is crucial for public health and food safety.
• Cronobacter species are opportunistic pathogens found in various environments, including infant formula.

Purpose of the Study:

• To investigate the genetic relationships between Cronobacter sakazakii and other Cronobacter species using microarray-based comparative genomic indexing (CGI).
• To identify genetic markers that differentiate species and strains within the Cronobacter genus.
• To compare the presence and absence of genes from a sequenced Cronobacter sakazakii genome across diverse Cronobacter isolates.

Main Methods:

• Microarray-based comparative genomic indexing (CGI) was performed on 78 Cronobacter strains representing six species and additional isolates.
• The study analyzed the presence or absence of genes from a reference Cronobacter sakazakii genome.
• Hierarchical clustering was applied to the CGI data to group strains based on genetic similarity.

Main Results:

• Hierarchical clustering of CGI data revealed distinct species clusters for Cronobacter dublinensis and Cronobacter muytjensii.
• Cronobacter sakazakii and some Cronobacter malonaticus strains formed a large, distinct cluster.
• The presence of 10 fimbrial-related genes uniquely identified Cronobacter sakazakii and a subset of C. malonaticus strains.
• Capsule and lipopolysaccharide (LPS) related glycosyltransferases helped differentiate individual Cronobacter sakazakii strains.

Conclusions:

• Comparative genomic indexing effectively delineates species boundaries within the Cronobacter genus.
• Specific genetic markers, such as fimbrial genes and glycosyltransferases, can be used for accurate identification and differentiation of Cronobacter species and strains.
• This genomic analysis provides valuable insights into the evolutionary relationships and genetic diversity of Cronobacter species, aiding in risk assessment and control strategies.