Salmonella enterica Serotype Typhi with Nonclassical Quinolone Resistance Phenotype

We report Salmonella enterica serotype Typhi strains with a nonclassical quinolone resistance phenotype (i.e., decreased susceptibility to ciprofloxacin but with susceptibility to nalidixic acid) associated with a nonsynonymous mutation at codon 464 of the gyrB gene. These strains, not detected by the nalidixic acid disk screening test, can result in fluoroquinolone treatment failure

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

Foodborne Outbreak and Nonmotile Salmonella enterica Variant, France

We report a food-related outbreak of salmonellosis in humans caused by a nonmotile variant of Salmonella enterica serotype Typhimurium in France in 2009. This nonmotile variant had been circulating in laying hens but was not considered as Typhimurium and consequently escaped European poultry flock regulations

Primers used for the spacer content inventory.

1<p>Degenerate positions: R = G or A; Y = T or C; M = A or C; K = G or T; D = G or A or T; B = G or T or C.</p>2<p>AE006468, serotype Typhimurium LT2 strain; AE014613, serotype Typhi Ty2 strain.</p>3<p>The primer pairs used for CRISPR1 amplification for each of the 744 strains are indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036995#pone.0036995.s004" target="_blank">Table S2</a>.</p

Serotypes with deletions of the Cas machinery.

1<p>The coordinates of the deleted regions of isolates with type A CRISPR structure and those of isolates with type F CRISPR structure are based on <i>S. enterica</i> serotype Typhimurium strain LT2 (GenBank AE006468) and serotype Typhi strain Ty2 (GenBank AE014613) genomes, respectively. The reverse primers used for these isolates are indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036995#pone-0036995-t002" target="_blank">Table 2</a>.</p>2<p>The <i>cas3</i> gene of serotype Typhimurium LT2 strain is 2663 bp in size, whereas that of serotype Typhi strain Ty2 is 2207 bp in size, due to a frameshift leading to a premature stop codon. The sizes of the <i>cas3</i> gene remnant are shown in brackets, not taking into account the serotype Typhi-specific frameshift.</p

Probe responses in the CRISPOL assay (data from 25 sequenced isolates).

1<p>MFI, median fluorescence intensity (raw data); SD, standard deviation.</p>2<p>The ratio is the positive average median fluorescence intensity (MFI) divided by the negative average MFI.</p>3<p>Due to partial identity with spacer STMB34, the signal of pSTMB26 is stronger in isolates containing spacer STMB34 (such as the emergent monophasic population). This has been taken into account by subtracting the MFI of control strain <b>#</b>02-7015 from that of pSTMB26 in each experiment. The corrected median is 183±46 with a ratio of 20.</p>4<p>Median calculated for 24 isolates.</p>5<p>Median calculated for 20 isolates.</p