Comparison of Genotypes of Salmonella enterica Serovar Enteritidis Phage Type 30 and 9c Strains Isolated during Three Outbreaks Associated with Raw Almonds

Abstract

, three outbreaks of Salmonella enterica serovar Enteritidis were linked with the consumption of raw almonds. The S. Enteritidis strains from these outbreaks had rare phage types (PT), PT30 and PT9c. Clinical and environmental S. Enteritidis strains were subjected to pulsed-field gel electrophoresis (PFGE), multilocus variable-number tandem repeat analysis (MLVA), and DNA microarray-based comparative genomic indexing (CGI) to evaluate their genetic relatedness. All three methods differentiated these S. Enteritidis strains in a manner that correlated with PT. The CGI analysis confirmed that the majority of the differences between the S. Enteritidis PT9c and PT30 strains corresponded to bacteriophage-related genes present in the sequenced genomes of S. Enteritidis PT4 and S. enterica serovar Typhimurium LT2. However, PFGE, MLVA, and CGI failed to discriminate between S. Enteritidis PT30 strains related to outbreaks from unrelated clinical strains or between strains separated by up to 5 years. However, metabolic fingerprinting demonstrated that S. Enteritidis PT4, PT8, PT13a, and clinical PT30 strains metabolized L-aspartic acid, L-glutamic acid, L-proline, L-alanine, and D-alanine amino acids more efficiently than S. Enteritidis PT30 strains isolated from orchards. These data indicate that S. Enteritidis PT9c and 30 strains are highly related genetically and that PT30 orchard strains differ from clinical PT30 strains metabolically, possibly due to fitness adaptations.

Prevalence, Distribution, and Diversity of Salmonella enterica in a Major Produce Region of California

“…This also suggests that some strains can persist in the environment long enough to be transported by some process to different locations in the watershed. Salmonella has been reported to persist in the environment for several months to more than a year (35,50,55). Alternatively, there may be one or more sources that maintain the pathogen (e.g., colonization) and disseminate the organism continuously into the environment.…”

“…Salmonella strains that can persist in the environment for years, withstanding periods of stress and nutrient depletion, have been reported (35). Multiple vertebrate sources exist for this bacterium, including livestock, wildlife, poultry, and companion animals, with water functioning as a documented mode of dissemination in the environment (32,50,55).…”

Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

“…In 2010 a large S. Enteritidis outbreak was associated with consumption of shell eggs, with more than 1,800 reported cases (9). Another common food vehicle for S. Enteritidis is chicken meat (22,30); however, other food vehicles have also been reported (30,34,35).…”

“…This lack of adequate discriminatory power makes it difficult to track a specific clone of S. Enteritidis in the food system using PFGE. Besides occasional inadequate discriminatory power, PFGE does not provide appropriate information to infer phylogenetic relationships among subtypes (34). Another subtyping method, MLVA, was reported to have higher discriminatory power than PFGE for S. Enteritidis (3,5,12,37).…”

Detection of Salmonella and several common Salmonella serotypes in food by loop-mediated isothermal amplification method

“…As FliC gene encoding S. Choleraesuis flagellum protein is conservative at both ends, but multifarious in the middle area among Salmonella serotypes [12,16]. LygD gene exists only in S. Enteritidis genome [13] and in all the genomes of 39 S. Enteritidis phage types that isolated from clinical samples [17]. The region including genes STM4488 to STM4497 houses a putative type II restriction enzyme that is only present in S. Typhimurium [14].…”