The combination of CRISPR-MVLST and PFGE provides increased discriminatory power for differentiating human clinical isolates of Salmonella enterica subsp. enterica serovar Enteritidis

• Published in: Food microbiology 2013-05, Vol.34 (1), p.164-173
• Main Authors: Shariat, Nikki, DiMarzio, Michael J., Yin, Shuang, Dettinger, Lisa, Sandt, Carol H., Lute, James R., Barrangou, Rodolphe, Dudley, Edward G.
• Format: Article
• Language: English
• Subjects: alleles; bacteria; Bacterial Typing Techniques - methods; Biological and medical sciences; Clinical isolates; CRISPR-MVLST; Electrophoresis, Gel, Pulsed-Field - methods; evolution; farms; Feces - microbiology; Food industries; Food microbiology; food supply chain; Fundamental and applied biological sciences. Psychology; genotype; Humans; Inverted Repeat Sequences; loci; Molecular Sequence Data; Molecular subtyping; Phylogeny; Polymerase Chain Reaction - methods; Salmonella enterica; Salmonella enterica subsp. enterica serovar Enteritidis; Salmonella Enteritidis; Salmonella enteritidis - classification; Salmonella enteritidis - genetics; Salmonella enteritidis - isolation & purification; Salmonella Infections - microbiology; salmonellosis; Urine - microbiology; virulence
• ISSN: 0740-0020; 1095-9998
• DOI: 10.1016/j.fm.2012.11.012

Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is a major cause of foodborne salmonellosis. Rapid, efficient and accurate methods for identification are required to track specific strains of S. Enteritidis during outbreaks of human salmonellosis. By exploiting the hypervariable nature of virulence genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs), we previously developed a powerful sequence-based subtyping approach, designated CRISPR-MVLST. To substantiate the applicability of CRISPR-MVLST, we analyzed a broad set of S. Enteritidis isolates collected over a six-year period. Among 141 isolates we defined 22 Enteritidis Sequence Types (ESTs), the majority of which were novel. Notably, strains exhibiting the common PFGE pattern, JEGX01.0004 (characteristic of ∼40% of S. Enteritidis isolates in the United States), were separated into twelve distinct sequence types. Conversely, isolates of EST4, the most predominant EST we observed, comprised eight different PFGE patterns. Importantly, we showed that some genotypes that were previously associated with the food supply chain at the farm level have now been identified in clinical samples. CRISPR sequence data shows subtle but distinct differences among different alleles of S. Enteritidis, suggesting that evolution of these loci occurs vertically, as opposed to previously reported evolution by spacer acquisition in other bacteria. ► CRISPR-MVLST identifies several unique Salmonella Enteritidis Sequence Types. ► Combination of CRISPR-MVLST and PFGE provides a high discriminatory power. ► Subtle differences among different CRISPR alleles, suggesting vertical evolution.