Genetic characterization of clinical and agri-food isolates of multi drug resistant Salmonella enterica serovar Heidelberg from Canada

Abstract

Background: Salmonella enterica serovar Heidelberg ranks amongst the most prevalent causes of human salmonellosis in Canada and an increase in resistance to extended spectrum cephalosporins (ESC) has been observed by the Canadian Integrated Program for Antimicrobial Resistance Surveillance. This study examined the genetic relationship between S. Heidelberg isolates from livestock, abattoir, retail meat, and clinical human specimens to determine whether there was a link between the emergence of MDR S. Heidelberg in chicken agri-food sources and the simultaneous increase of MDR S. Heidelberg in human clinical samples.

Results: Chromosomal genetic homogeneity was observed by pulsed-field gel electrophoresis (PFGE), DNA sequence-based typing (SBT) and DNA microarray-based comparative genomic hybridization (CGH). Sixty one percent of isolates were indistinguishable by PFGE conducted using XbaI and BlnI restriction enzymes. An additional 15% of isolates had PFGE patterns that were closely related to the main cluster. SBT did not identify DNA polymorphisms and CGH revealed only genetic differences between the reference S. Typhimurium strain and S. Heidelberg isolates. Genetic variation observed by CGH between S. Heidelberg isolates could be attributed to experimental variation. Alternatively, plasmid content was responsible for differences in antimicrobial susceptibility, and restriction fragment length polymorphism (RFLP) analyses followed by replicon typing identified two divergent plasmid types responsible for ESC resistance.

Conclusion: Due to the overall limited genetic diversity among the isolates, it was not possible to identify variable traits that would be suitable for source tracking between human and agri-food isolates of S. Heidelberg in Canada.

Figure 1

Dendrogram of S. Heidelberg DNA macrorestriction patterns generated using XbaI. Strains were selected to present a diverse range of patterns. Dendrogram was created using Applied Maths Bionumerics version 4.0 using unweighted pair group method (UPGMA) with a dice coefficient of similarity, 1% band tolerance and 1.5% optimization. The scale bar indicates percent similarity.

Figure 2

DNA microarray-based comparative genomics of S. Heidelberg. Array probes represent the linear order of S. Typhimurium LT2 coding sequences from left to right, and with the Salmonella genomic island 1 (SGI1) present at the far-left side. White denotes similarity to LT2, green denotes putative divergence and red represents putative duplication or copy number change. The region STM0691–0704 which was putatively divergent between S. Heidelberg strains is represented by "A". Clusters of bacteriophage-related determinants that are divergent in S. Heidelberg compared to S. Typhimurium: B, STM0892–0929 (Fels-1 prophage); C, STM2584–2636 (Gifsy-1 prophage); D, STM2694–2739 (Fels-2 prophage).

Figure 3

RFLP of the bla_cmy-2 plasmid using BglII. Dendrogram created with Bionumerics version 4.0 using UPGMA with a fuzzy band coefficient of correlation, 2% optimization and 10% tolerance.A – indicates RFLP performed on the full plasmid profile isolated from resistant S. Heidelberg strains. B – indicates RFLP performed on the full plasmid profile from sensitive S. Heidelberg strains. No scale bar is reported due to the high band tolerance settings used in this analysis.