Comparative analysis of using CRISPR-1 locus, 16S rRNA and rrnH as identification systems for clinical strains of Salmonella enterica species
Keywords:
CRISPR-1 locus, 16S rRNA, rrnH, Salmonella entericaAbstract
Salmonella enterica species are major global foodborne pathogensthat are divided into six distinct subspecies. Proper identification of Salmonella species is a challenge for many laboratories. In Salmonella, CRISPR loci were found to be conserved in all Salmonella species and also very diverse. Therefore, it could be potentially used as a promising target region for Salmonella identification. Henceforth,we aimed tointroduce a new subtyping genetic system for genotyping someclinical Zoonotic Salmonella isolates using a PCR assay that is targeting the CRISPR-1 region. About total 30 isolates were analysed in this study (human isolates n=10, camel isolates n=10 and poultry isolates n=10). All these isolates were previously identified at the genus and species level following an analysis of DNA sequences of 16S rRNA and rrnH.
At PCR amplification level, the system was able to amplifyall 10 human isolates (33.3%) and 7 camel-isolates (23.3%) 10 chicken isolates (33.3%).
Finally, due to the fact that the tested isolates were previously identified and serotyped by two different systems (16S rRNA and rrnH), this identification and serotyping was also validated by our new CRISPR-1 sequence system. The validation showed non-confirmative results as CRISPR-1 system identified the human and camel isolates as Salmonella enterica sp. enterica serovar Enteritidis and the chicken isolate as Salmonella enterica sp. enterica serovar Anatum. On the other hand, 16S rRNA identified the chicken isolate as Salmonella enterica sp. enterica serovar Typhimurium while the rrnH system identified the camel isolate as Salmonella enterica sp. enterica serovar Indiana. Therefore, these results showed that a definitive identification requires using multiple genomic regions instead of sequencing a one region for bacteria.
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