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Investigators Use WGS, Mutational Analysis to Characterize Drug-Resistant Salmonella Epidemiology

NEW YORK (GenomeWeb) – An international research team has sequenced samples of multidrug-resistant Salmonella enterica strain sourced from different species and countriesand characterized the epidemiology of the bacteria to better understand why the strain has been so successful.

In the US alone, Salmonella is estimated to cause 1 million cases resulting in 19,000 hospitalizations and 380 deaths each year, according to the US Centers for Disease Control and Prevention.

The multidrug resistant strain of Salmonella (serovar Typhimurium phage type DT104) emerged during the last three decades and has been previously studied because of its rapid global dissemination, the researchers state in the study.

DT104's success was due in no small part to its resistance to at least five antibiotics, including ampicillin, chloramphenicol, streptomycin, sulphonamide, and tetracycline, Pimlapas Leekitcharoenphon, corresponding author and researcher at the Technical University of Denmark, said in a statement.

This bacterium was also ideally situated to be successful because it was able to infect numerous livestock species, including cattle, poultry, pigs, and sheep, Leekitcharoenphon said. This isn't the case with other strains of DT Salmonella. "Having multiple hosts increases the chances of dissemination," she explained.

In order to gain a more comprehensive understanding of the bacteria, the researchers sequenced 315 samples collected from patients over a period of 40 years in 21 countries. They published their study today in the journal Applied and Environmental Microbiology.

The research team sequenced the isolates on either Illumina HiSeq or MiSeq platforms. They submitted the raw sequence data to the European Nucleotide Archive, and de novo assembled raw reads using a pipeline available from the Center for Genomic Epidemiology (CGE).

The researchers then used various informatics resources to cluster protein sequence similarities and determine single nucleotide polymorphisms. They also detect SNP alignments for significant recombination sites in order to construct a phylogenetic tree with Bayesian Evolutionary Analysis Sampling Trees (BEAST).

After sequencing, the researchers found that about 96 percent of the total genes in a DT104 genome (approximately 4,635 genes) are common among other DT104 strains.

Using the BEAST program, which took into account the rate of mutations in DT104, the investigators estimated that the strain first emerged in 1948 as an antibiotic-susceptible pathogen. Then, the researchers observed that the DT104 strain later acquired resistance by acquiring a multidrug resistance-containing transposon.

It is not clear exactly when DT104 first acquired the transposon, but the study suggests that the first acquisition of antibiotic resistance may have happened in 1972. They also noted one case where the bacteria independently acquired resistance genes around 1975 in Thailand.  However, multidrug-resistance in DT104 was first reported in 1984, in the UK.

Additionally, the researchers were able to determine that there had been multiple transmission events, initially from central Europe and later between several European countries. They also found that there had been independent transmission to the United States and another to Japan, which they believe led to the spread of the bacteria into Taiwan and Canada.

Finally, after looking closely at WGS analysis in Denmark, they found evidence that the organism had been transmitted between herds. However, they also noted that there was evidence that a program previously instituted in Denmark to eradicate all pigs infected with DT104 ultimately proved successful, even though the program was stopped in 2000 due to financial pressures.

The researchers believe that this indicates that WGS may be a useful monitoring tool to observed emerging outbreaks and devising prevention strategies for Salmonella infections.

"If we know and understand the past, we might be able to solve the current resistance problems and prevent future ones," Leekitcharoenphon said.