Comparison of probe hybridization array typing to multilocus sequence typing for pathogenic Escherichia coli

Area of Science:

• Microbiology
• Genetics
• Bioinformatics

Background:

• Probe Hybridization Array Typing (PHAT) is a validated, high-throughput method for genetic material presence/absence detection.
• Multilocus Sequence Typing (MLST) is a standard for bacterial strain typing, defining clonal groups (CGs).
• There is a need for efficient methods to group bacterial isolates, especially for large-scale studies.

Purpose of the Study:

• To refine the PHAT method by developing a probe set targeting virulence genes for classifying Escherichia coli.
• To assess the ability of the refined PHAT probe set to distinguish MLST clonal groups (CGs).
• To evaluate PHAT as a cost- and time-efficient tool for initial analysis of large bacterial collections.

Main Methods:

• A refined PHAT probe set of 24 virulence genes was designed.
• 1,132 Escherichia coli isolates, representing at least 62 MLST CGs, were typed using a "library-on-a-slide" microarray format.
• PHAT classifications were validated against MLST data.

Main Results:

• The 24-probe PHAT set successfully distinguished all 62 MLST CGs in the tested E. coli collection.
• Overall sensitivity and specificity for classifying major CGs were 80.4% and 98.7%, respectively.
• MLST validation of PHAT classification yielded overall sensitivities and specificities of 64.7% and 88.3%, respectively, with variations among individual CGs.

Conclusions:

• The refined PHAT probe set effectively classifies E. coli isolates into groups similar to MLST clonal complexes, suggesting coevolution.
• PHAT is a time- and cost-efficient method suitable for the first level of analysis in large bacterial collections.
• Further refinement of the PHAT probe set is necessary for distinguishing closely related bacterial groups.