Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates

Abstract

BackgroundSalmonella enterica serovar Enteritidis (S. Enteritidis) has caused major epidemics of gastrointestinal infection in many different countries. In this study we investigate genome divergence and pathogenic potential in S. Enteritidis isolated before, during and after an epidemic in Uruguay.Results266 S. Enteritidis isolates were genotyped using RAPD-PCR and a selection were subjected to PFGE analysis. From these, 29 isolates spanning different periods, genetic profiles and sources of isolation were assayed for their ability to infect human epithelial cells and subjected to comparative genomic hybridization using a Salmonella pan-array and the sequenced strain S. Enteritidis PT4 P125109 as reference. Six other isolates from distant countries were included as external comparators.Two hundred and thirty three chromosomal genes as well as the virulence plasmid were found as variable among S. Enteritidis isolates. Ten out of the 16 chromosomal regions that varied between different isolates correspond to phage-like regions. The 2 oldest pre-epidemic isolates lack phage SE20 and harbour other phage encoded genes that are absent in the sequenced strain. Besides variation in prophage, we found variation in genes involved in metabolism and bacterial fitness. Five epidemic strains lack the complete Salmonella virulence plasmid. Significantly, strains with indistinguishable genetic patterns still showed major differences in their ability to infect epithelial cells, indicating that the approach used was insufficient to detect the genetic basis of this differential behaviour.ConclusionThe recent epidemic of S. Enteritidis infection in Uruguay has been driven by the introduction of closely related strains of phage type 4 lineage. Our results confirm previous reports demonstrating a high degree of genetic homogeneity among S. Enteritidis isolates. However, 10 of the regions of variability described here are for the first time reported as being variable in S. Enteritidis. In particular, the oldest pre-epidemic isolates carry phage-associated genetic regions not previously reported in S. Enteritidis. Overall, our results support the view that phages play a crucial role in the generation of genetic diversity in S. Enteritidis and that phage SE20 may be a key marker for the emergence of particular isolates capable of causing epidemics.

Cell invasion of poultry-associated Salmonella enterica serovar Enteritidis isolates is associated with pathogenicity, motility and proteins secreted by the type III secretion system

“…Regardless of phage types, geographical origins or source of isolation, S. Enteritidis is one of the most genetically homogeneous serotypes of Salmonella and as a result is poorly discriminated by the commonly used genetic subtyping methods, such as phage typing, pulsed field gel electrophoresis or comparative genomic hybridization microarrays (Betancor et al, 2009;Botteldoorn et al, 2010;Hudson et al, 2001;Liebana et al, 2001;Malorny et al, 2008;Morales et al, 2005;Olsen et al, 1999;Pan et al, 2009;Pang et al, 2006;Porwollik et al, 2005;Saeed et al, 2006;Swaminathan et al, 2001). Because of its greater discriminatory capacity, MLVA was used to assess the genetic similarity among S. Enteritidis isolates tested in this study Cho et al, 2007;Malorny et al, 2008).…”

“…Most other studies to characterize the pathogenic potential of S. Enteritidis strains have primarily focused on isolates recovered from either human clinical cases or nonpoultry-associated environmental sources (Betancor et al, 2009;Lu et al, 1999;Pan et al, 2009; Solano et al, 1998Solano et al, , 2001; Yim et al, 2010). Humphrey et al (1996) showed that human isolates of S. Enteritidis PT4 with enhanced heat and acid tolerance were more virulent in mice and more invasive in chickens compared with poultryassociated strains of S. Enteritidis.…”

Prevalence of Salmonella enterica in Poultry and Eggs in Uruguay during an Epidemic Due to Salmonella enterica Serovar Enteritidis

“…Normalization and filtering were performed using GeneSpring microarray analysis software V7.2 (Silicon Genetics). Data analysis was performed on Excel files, following criteria previously described (4).…”

Investigation of a food-borne Salmonella Oranienburg outbreak in a Mexican prison

“…Taken together, the high D values calculated in this study, despite the relative low number of Oranienburg outbreak related isolates analyzed, suggest this serotype has a high genetic variation potential; the reasons for this potential remain unknown. Using the genomic analysis approach, it has been shown that prophage-related genes are the main source of genetic variation among outbreak related strains of the serotypes Enteritidis [11] and Typhimurium [48]. It will be desirable to make a genomic analysis of Oranienburg strains in order to shed light on the genetic variation displayed by this serotype.Interestingly, despite deriving from the same outbreak, the studied isolates differed in antibiotic resistance profiles; also remarkable was that all isolates had multiple resistance profiles.…”

“…However, analysis of repetitive DNA elements has also been proven to be successful [5,6], and even equally or more effective than PFGE for that purpose [7,8]. Additionally, it has been reported that random amplified polymorphic DNA (RAPD) assays combined with other typing techniques are useful for monitoring outbreaks and clinical cases of gastroenteritis caused by serotypes of S. enterica [9][10][11]. Repetitive DNA elements and RAPD analyses are advantageous due to their speed, low cost, and easiness of interpretation [12], but the RAPD assay has been criticized for its lack of reproducibility in laboratories [13].…”