Efficacy of a typing scheme for Campylobacter based on the combination of true and questionable CRISPR

This study evaluates an improved scheme for Campylobacter genotyping based on the combination of true and questionable CRISPR (clustered regularly interspaced short palindromic repeats) elements. A total of 180 Campylobacter strains (Campylobacter jejuni n=93 and Campylobacter coli n=87), isolated from neck skin and caecal content of broilers, poultry meat and sewage water were analysed. Another 97 C. jejuni DNA samples from cases of human campylobacteriosis were assessed. Sixty-three genotypes were found in C. jejuni considering only true CRISPR, and 16 additional genotypes were identified when questionable CRISPR were also taken into account. Likewise in C. coli the number of genotypes increased from eight for only true CRISPR to 14 after including questionable CRISPR elements. The number of typeable C. jejuni and C. coli isolates was 115 (60.5%) and 17 (19.5%) respectively considering only true CRISPR. These percentages increased to 92.7% (n=176) and 39.1% (n=34) respectively when both true and questionable CRISPR were considered. 60.9% of the C. coli isolates were non-typeable by CRISPR due to the lack of any PCR amplifiable CRISPR loci, which raises questions about CRISPR analysis as an appropriate method for C. coli typing. However the assessment of true and questionable CRISPR has proved to be fairly useful for typing C. jejuni due to its high discriminatory power (Simpson's index=0.960) and typeability (92.7%) values. The results of the present work show that our genotyping method based on the combination of true and questionable CRISPR elements may be used as a suitable complementary tool to existing C. jejuni genotyping methods.