Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010

Emerg Infect Dis. 2016 Apr;22(4):617-24. doi: 10.3201/eid2204.150531.


Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success. To determine microevolution associated with monophasic Salmonella Typhimurium during an epidemic, we performed comparative whole-genome sequencing and phylogenomic analysis of isolates from the United Kingdom and Italy during 2005-2012. These isolates formed a single clade distinct from recent monophasic epidemic clones previously described from North America and Spain. The UK monophasic epidemic clones showed a novel genomic island encoding resistance to heavy metals and a composite transposon encoding antimicrobial drug resistance genes not present in other Salmonella Typhimurium isolates, which may have contributed to epidemiologic success. A remarkable amount of genotypic variation accumulated during clonal expansion that occurred during the epidemic, including multiple independent acquisitions of a novel prophage carrying the sopE gene and multiple deletion events affecting the phase II flagellin locus. This high level of microevolution may affect antigenicity, pathogenicity, and transmission.

Keywords: MDR; Salmonella; Salmonella Typhimurium; United Kingdom; antimicrobial resistance; bacteria; heavy metal resistance; microevolution; molecular epidemiology; monophasic.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / therapeutic use
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Bacterial Typing Techniques
  • Clonal Evolution / genetics*
  • Clone Cells
  • DNA Transposable Elements
  • Disease Outbreaks*
  • Drug Resistance, Multiple, Bacterial
  • Epidemiological Monitoring
  • Flagellin / genetics
  • Flagellin / metabolism
  • Gene Expression Regulation, Bacterial*
  • Genetic Variation
  • Genomic Islands
  • Humans
  • Italy / epidemiology
  • Phylogeny
  • Prophages / genetics
  • Prophages / isolation & purification
  • Salmonella Infections / drug therapy
  • Salmonella Infections / epidemiology*
  • Salmonella Infections / microbiology
  • Salmonella Infections / transmission
  • Salmonella typhimurium / classification
  • Salmonella typhimurium / drug effects
  • Salmonella typhimurium / genetics*
  • Salmonella typhimurium / virology
  • United Kingdom / epidemiology


  • Anti-Bacterial Agents
  • Bacterial Proteins
  • DNA Transposable Elements
  • SopE protein, Salmonella
  • Flagellin