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.

While the spread of Salmonella enterica serotype Kentucky resistant to ciprofloxacin across Africa and the Middle-East has been described recently, the presence of this strain in humans, food, various animal species (livestock, pets, and wildlife) and in environment is suspected in other countries of different continents. Here, we report results of an in-depth molecular epidemiological study on a global human and non-human collection of S. Kentucky (n = 70). We performed XbaI-pulsed field gel electrophoresis and multilocus sequence typing, assessed mutations in the quinolone resistance-determining regions, detected β-lactam resistance mechanisms, and screened the presence of the Salmonella genomic island 1 (SGI1). In this study, we highlight the rapid and extensive worldwide dissemination of the ciprofloxacin-resistant S. Kentucky ST198-X1-SGI1 strain since the mid-2000s in an increasingly large number of contaminated sources, including the environment. This strain has accumulated an increasing number of chromosomal and plasmid resistance determinants and has been identified in the Indian subcontinent, Southeast Asia and Europe since 2010. The second substitution at position 87 in GyrA (replacing the amino acid Asp) appeared helpful for epidemiological studies to track the origin of contamination. This global study provides evidence leading to the conclusion that high-level resistance to ciprofloxacin in S. Kentucky is a simple microbiological trait that facilitates the identification of the epidemic clone of interest, ST198-X1-SGI1. Taking this into account is essential in order to detect and monitor it easily and to take rapid measures in livestock to ensure control of this infection.

During 2002 to 2003, eight Salmonella enterica serotype Virchow poultry and poultry product isolates from various sources (chicken farms, poultry slaughterhouse, or retail store) and one S. enterica rough strain isolated from human feces were found to produce extended-spectrum ␤-lactamase CTX-M-9. Poultry and poultry product isolates were recovered from different locations in the southwest of France. The human rough isolate had sequences of flagellin genes (fliC and fljB) typical of serotype Virchow and ribotyping and pulsedfield gel electrophoresis (PFGE) patterns closely similar to those of serotype Virchow strains. PFGE confirmed the clonal relationship between the poultry isolates, while the human isolate displayed a pattern with 94% homology. The bla CTX-M-9 gene was located on a conjugative plasmid and was shown to be linked to orf513. Plasmid profiling found a very similar EcoRI restriction pattern in six transconjugants studied, including transconjugants obtained from the human isolate. A single hatchery, supplying chicks to the six farms, was identified. Emergence of extended-spectrum ␤-lactamase-producing S. enterica strains in food animals is a major concern, as such strains could disseminate on a large scale and lead to antibiotic therapy difficulties.

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Salmonella enterica serotype Typhi clinical isolates (n ‫؍‬ 91) resistant to nalidixic acid (Nal r ) were collected from sporadic cases and minor outbreaks throughout Vietnam between 1996 and 2004. These isolates were typed and compared by four methods: Vi phage typing, PstI ribotyping, XbaI and SpeI pulsed-field gel electrophoresis (PFGE), and single-nucleotide polymorphism (SNP) analysis. The results indicated that 65% of the isolates were not typeable by Vi phage typing. In contrast, the ribotyping and, with more accuracy, the SNP analysis methods indicated that all Nal r isolates belonged to a single clone (ribotype 3a, haplotype H58) that was found previously and that largely consisted of plasmid-encoded multidrug-resistant serotype Typhi isolates. PFGE demonstrated the occurrence of microevolution within this clone. We identified two major combined PFGE profiles: X1-S1 and X3-S6. X3-S6 predominated between 1996 and 2002 but was replaced by X1-S1 after 2002. Nevertheless, PFGE, with a Simpson's index of 0.78, was not considered an optimal discriminatory method for investigating typhoid fever outbreaks in Vietnam. The rate of quinolone resistance increased and the rate of multidrug resistance decreased during the study period. From 2002 to 2004, 80.6% of the isolates from South Vietnam were resistant only to Nal. The mechanism of Nal resistance in most of the isolates (94%) was a mutation in the quinolone resistance-determining chromosomal region of gyrA that led to the amino acid substitution Ser83Phe. No plasmid-located qnrA, qnrB, or qnrS was detected.

We report the emergence of Salmonella enterica isolates of serotype Concord (and its monophasic variant 6,7:l,v:-) producing the extended-spectrum ␤-lactamases (

A chromosomal genomic island called Salmonella genomic island 1 (SGI1) has been initially described in epidemic multidrugresistant Salmonella enterica serovar Typhimurium phage type DT104 strains (serovar Typhimurium DT104) (4). SGI1 contains an antibiotic resistance gene cluster conferring the common multidrug resistance profile ApCmFfSmSpSuTc (i.e., ampicillin [Ap] (1, 2, 4-7, 12, 13, 23, 24, 30, 31). Multidrug-resistant serovar Typhimurium DT104 emerged during the 1980s as a global health problem because of its involvement in diseases in animals and humans (7,12,13,23,24,30,31).The 43-kb SGI1 is located between the thdF and int2 genes of the chromosome of serovar Typhimurium. The int2 gene is part of a retron sequence, which has been reported to date only in serovar Typhimurium strains (4, 5). In other S. enterica serovars, SGI1 is located between the thdF and yidY genes (3, 4, 9-11, 17, 18). The antibiotic resistance gene cluster is located near the 3Ј end of SGI1 and constitutes a complex class 1 integron that belongs to the In4 group (3). The In4 group has a 3Ј conserved segment (3Ј-CS) that includes a copy of IS6100 but no transposition genes, and most members are bound by 25-bp inverted repeats IRi and IRt (20,21). The antibiotic resistance gene cluster of SGI1 is indeed bound by IRi and IRt and thus can be considered a complex In4-type integron (3). Further, the multidrug resistance region is surrounded by 5-bp direct repeats, strongly suggesting it was integrated by a transposition event (3,20,21). Interestingly, in SGI1 there is a duplication of a part of the 5Ј conserved segment (5Ј-CS) of the integron that leads to a second attI1 site, followed by a gene cassette. At the first attI1 site, the cassette carries the aadA2 gene, which confers resistance to Sm and Sp, and a 3Ј-CS with a truncated sul1 (sul1⌬) gene. At the second attI1 site, the cassette contains the ␤-lactamase gene pse-1 conferring resistance to Ap and a 3Ј-CS with a complete sul1 gene conferring resistance to Su. Flanked by the two cassettes are the floR gene, which confers cross-resistance to Cm and Ff, and the Tc resistance genes tetR and tet(G) (1,2,4,6).Variant SGI1 antibiotic resistance gene clusters have recently been described in the serovars Typhimurium DT104, Agona, and Albany. SGI1 variants were accordingly classified in SGI1-A to SGI1-G (3, 9, 11). These clusters of antibiotic resistance genes were likely generated, according to sequence analysis, after chromosomal recombinational events or by antibiotic resistance gene cassette replacement at one of the attI1 sites. In variants SGI1-A, -D, and -G, the 3Ј-CS, designated 3Ј-CS1, is followed by the orf513/dfrA10 region originally described in In6 and In7 (19,29). Following the orf513/dfrA10