CRISPR Typing and Subtyping for Improved Laboratory Surveillance of Salmonella Infections

Laboratory surveillance systems for salmonellosis should ideally be based on the rapid serotyping and subtyping of isolates. However, current typing methods are limited in both speed and precision. Using 783 strains and isolates belonging to 130 serotypes, we show here that a new family of DNA repeats named CRISPR (clustered regularly interspaced short palindromic repeats) is highly polymorphic in Salmonella. We found that CRISPR polymorphism was strongly correlated with both serotype and multilocus sequence type. Furthermore, spacer microevolution discriminated between subtypes within prevalent serotypes, making it possible to carry out typing and subtyping in a single step. We developed a high-throughput subtyping assay for the most prevalent serotype, Typhimurium. An open web-accessible database was set up, providing a serotype/spacer dictionary and an international tool for strain tracking based on this innovative, powerful typing and subtyping tool

Supplement 2003–2007 (No. 47) to the White-Kauffmann-Le Minor scheme

International audienceThis supplement reports the characterization of 70 new Salmonella serovars recognized between 2003 and 2007 by the WHO Collaborating Center for Reference and Research on Salmonella: 44 were assigned to Salmonella enterica subspecies enterica, 11 to subspecies salamae, 5 to subspecies arizonae, 8 to subspecies diarizonae, one to subspecies houtenae and one to Salmonella bongori. One new serovar, Mygdal, displayed a new H factor, H:z(91)

Supplement 2008-2010 (no. 48) to the White-Kauffmann-Le Minor scheme.

International audienceThis supplement (no. 48) of the White-Kauffmann-Le Minor scheme reports on the characterization of 63 new Salmonella serovars and 25 new variants of previously described Salmonella serovars recognized by the WHO Collaborating Centre for Reference and Research on Salmonella between 2008 and 2010. Forty-four new serovars were assigned to Salmonella enterica subspecies enterica, 12 to subspecies salamae, two to subspecies arizonae, two to subspecies diarizonae and three to subspecies houtenae. All these new serovars or new variants are described with their multilocus sequence type

CRISPR sizing by PCR for the rapid comparison of <i>Salmonella</i> spp isolates.

<p>Results of PCR amplification for 8 <i>S. enterica</i> serotype Typhimurium isolates collected from the same city during a single week (cluster E in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036995#pone.0036995.s009" target="_blank">Table S7</a>). Three cases were from the same food poisoning cluster (the food isolate was also tested), whereas the other cases were unrelated.</p

Comparison of CRISPR1 spacer content with the population structure of <i>S. enterica</i> serotype Newport, as assessed by MLST.

1<p>ND, Not done.</p>2<p>The deletions are named according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036995#pone-0036995-t003" target="_blank">Table 3</a>.</p>3<p>Due to space constraints, the spacer names Newp and Had are abbreviated to N and H, respectively.</p

Dendrogram presentation of the 245 distinct CRISPOL types detected among 2,200 isolates of <i>S. enterica</i> serotype Typhimurium or its monophasic variant of antigenic formula 1,4,[<b>5</b>],12:i:-.

<p>Black squares indicate presence of the spacer, as detected by the corresponding probe, whereas white indicates an absence of the spacer. For the determination of CRISPOL types (CTs), each of the 68 spacers was treated as a numerical character indicating absence (0) or presence (1 for all spacers except BraB14, for which an arbitrary value of 10 was assigned) in BioNumerics 6.5 software (Applied Maths, Sint-Martens-Latem, Belgium). Similarities between CTs were assessed by calculating the Pearson product-moment, and a dendrogram was constructed by the unweighted pair group method with arithmetic mean (UPGMA). The four SNP-variant spacers targeted by probes 69 to 72 are shown but were excluded from the phylogenetic analysis, as they were not independent. A indicates a group of profiles derived from CT1, the main type of emerging monophasic isolates. B indicates a group of profiles derived from CT21, which is associated with multidrug-resistant DT104 serotype Typhimurium isolates. C indicates a group of serotype Typhimurium isolates of ST36 that may have one or two specific spacers on the leader side of CRISPR1 (BraB14) and CRISPR2 (STMB35).</p

CRISPR1 spacer content in various O:9 and O:2 serotypes.

1<p>ST (sequence type) 11 group consists of ST11 and its single-locus variants (SLV).</p>2<p>Includes the 5 ST136 “Danysz”» strains used as rodenticides.</p>3<p>Ent20−//−Ent35, 15 unique spacers are located between Ent20 and Ent35 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036995#pone.0036995.s004" target="_blank">Table S2</a>).</p>4<p>Serotype Gallinarum biovar Duisburg is different from serotype Duisburg.</p