Identification of putative ancestors of the multidrug-resistant Salmonella enterica serovar typhimurium DT104 clone harboring the Salmonella genomic island 1

Abstract

The origin of multidrug-resistant Salmonella enterica serovar typhimurium (S. typhimurium) harboring the Salmonella Genomic Island 1 (SGI1), which was detected for the first time in the mid-1980s is unknown. In this study, we performed microarray genomotyping of four multidrug-resistant SGI1 positive strains and found that unlike the S. typhimurium LT2 strain, the multidrug-resistant strains lacked genes STM0517-0529 allowing the utilization of allantoin as a sole nitrogen source. We extended this observation by PCR screening of additional 120 S. typhimurium field strains and found that this locus was absent in all SGI1 positive and also in 24% of SGI1 negative strains, which were proposed to be the original recipients of SGI1. To prove this hypothesis, we compared the STM0517-0529 negative strains (with or without the SGI1) by PFGE and PCR prophage typing and found that 8 out of 11 of the SGI1 negative strains and 17 out of 22 SGI1 positive strains were of identical PFGE pattern and PCR prophage pattern, while this specific pattern was never observed among STM0517-0529 positive strains. We therefore propose that a lineage of the S. typhimurium DT104 sensitive strain first lost the ability to metabolize allantoin and then acquired SGI1.

The Importance of Mobile Genetic Elements in the Evolution of Salmonella: Pathogenesis, Antibiotic Resistance and Host Adaptation

“…Recent population studies are supporting the notion that the prophage content is one the most dynamic part of the genome, indicating that phage integration/excision are frequent events shaping Salmonella genome evolution (Hermans et al, 2006;Cooke et al, 2007;Drahovska et al, 2007;Matiasovicova et al, 2007;Cooke et al, 2008;Litrup et al, 2010). These observations are in agreement with the phage remnants found in the genomes of Salmonella (McClelland et al, 2001;Parkhill et al, 2001;Porwollik et al, 2002;Chan et al, 2003;Porwollik and McClelland 2003;Matiasovicova et al, 2007).…”

Salmonella enterica serovar Typhimurium typing by prophage-specific PCR

“…When we analysed genomes of three S. Typhimurium strains, we found that almost all of the variation in their XbaI-generated PFGE profiles could be attributed to the presence of prophages. The fact that prophages are major sources of genomic variation in different S. Typhimurium strains has been shown by several studies using microarray genomotyping (Porwollik et al, 2004;Reen et al, 2005;Matiasovicova et al, 2007); these studies have indicated that Fels1 and Fels2 prophages are relatively specific for the LT2 strain. Other studies, using conventional PCR, have found that sopE, encoded by a Fels-like prophage, is quite uncommon to S. Typhimurium (Mirold et al, 1999).…”

“…This information has led to studies that have used the detection of prophage sequences for strain characterization (Mikasova et al, 2005;Hermans et al, 2005;Ross & Heuzenroeder, 2005); however, the approach in those studies was rather arbitrary. In this study, we used accumulated genomic data, either from genome sequencing (McClelland et al, 2001) or from microarray genomotyping (Porwollik et al, 2004;Reen et al, 2005;Matiasovicova et al, 2007), for rational design of a PCRtyping system based on the presence or absence of mobile DNA sequences. Multiplexing of the specific PCR further simplified the protocol, and made it user friendly.…”

“…Based on the identification of variable DNA sequences in the genomes of three strains, and data originating from microarray genomotyping (Porwollik et al, 2004;Reen et al, 2005;Matiasovicova et al, 2007), 22 individual PCRs specific for the potentially variable DNA sequences were designed. These included the STM0517-0529 deletion, the left junction of SGI1, and STM908, STM2619, STM2697, STM2705, gipA, artA, sodCI, bim2, eac, sieB, g8, gtrA, hldD, sopE, Fels Sop, gp36, rrtT, spvB, oafA and fljB (for primer sequences and the results of these PCRs, see supplementary material, available with the online version of this paper).…”

“…Although not annotated in GenBank, two additional S. Typhimurium genomes, specifically those of SL1344 and the pentadrug-resistant DT104 strain, are publicly available on the website of the institution that performed the sequencing. When we searched for the XbaI sites in the sequenced genomes to verify the PFGE profiles (Van Immerseel et al, 2004;Hradecka et al, 2006;Matiasovicova et al, 2007), we observed that the XbaI sites frequently overlapped with the prophage sequences. In other cases, the presence of a prophage was shown to have led to an increase in the size of DNA fragments generated by XbaI restriction endonuclease.…”