CRISPR Typing Increases the Discriminatory Power of Streptococcus agalactiae Typing Methods

Abstract

We explored the relevance of a Clustered regularly interspaced short palindromic repeats (CRISPR)-based genotyping tool for Streptococcus agalactiae typing and we compared this method to current molecular methods [multi locus sequence typing (MLST) and capsular typing]. To this effect, we developed two CRISPR marker schemes (using 94 or 25 markers, respectively). Among the 255 S. agalactiae isolates tested, 229 CRISPR profiles were obtained. The 94 and 25 markers made it possible to efficiently separate isolates with a high diversity index (0.9947 and 0.9267, respectively), highlighting a high discriminatory power, superior to that of both capsular typing and MLST (diversity index of 0.9017 for MLST). This method has the advantage of being correlated with MLST [through analysis of the terminal direct repeat (TDR) and ancestral spacers] and to possess a high discriminatory power (through analysis of the leader-end spacers recently acquired, which are the witnesses of genetic mobile elements encountered by the bacteria). Furthermore, this “one-shot” approach presents the benefit of much-reduced time and cost in comparison with MLST. On the basis of these data, we propose that this method could become a reference method for group B Streptococcus (GBS) typing.

Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci

“…In addition, this review shows that, especially in streptococci but also in other bacteria, sequencing CRISPR loci is also a relatively easy way to characterize and classify isolates precisely. Indeed, many studies have demonstrated that using CRISPR as a typing method is a promising tool and must be developed (Pourcel et al, 2005;Brudey et al, 2006;Beauruelle et al, 2021). More than precisely classifying strains, it can give a lot of information about species evolution.…”

“…MLST is the current reference method used to distinguish S. agalactiae isolates, and more than 1,600 different sequence types (ST) are now described. This method has a good discriminating power but, with the discovery and research on CRISPR-Cas systems, recent studies propose CRISPR-typing as a promising alternative method (Beauruelle et al, 2017(Beauruelle et al, , 2021.…”

Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects

“…In GBS research, the native CRISPR-Cas9 system has become a focus of study and the basis of new tools for pathogenesis research, such as using the highly variable CRISPR array as a strain-level barcode for lineage tracking in models of disease 29 , 30 .…”

“…This same study showed that, as in GAS, the GBS Cas9 enzyme requires a NGG PAM next to the target recognition site at its 3′ end 28 . Subsequent work has further investigated lineage specificity of GBS CRISPR arrays and their use as barcodes for precision subtyping 29 , 30 .…”

Group B Streptococcus CRISPR1 Typing of Maternal, Fetal, and Neonatal Infectious Disease Isolates Highlights the Importance of CC1 in In Utero Fetal Death

“…Finally, Beauruelle et al explored the relevance of the CRISPR-based genotyping tool for GBS typing and compared it to current molecular methods, including MLST, by analyzing 255 GBS isolates. The authors demonstrated that the analysis of leader-end spacers, which vary more widely between strains, may offer stronger discriminating power than MLST ( 31 ). According to these data and previous studies, CRISPR1 typing has been proposed as a reference method for GBS typing ( 31 ).…”