Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever

The most recent common ancestor of Paratyphi A, one of the most common causes of enteric fever, existed approximately 450 y ago, centuries before that disease was clinically recognized. Subsequent changes in the genomic sequences included multiple mutations and acquisitions or losses of genes, including bacteriophages and genomic islands. Some of those evolutionary changes were reliably attributed to Darwinian selection, but that selection was only transient, and many genetic changes were subsequently lost because they rendered the bacteria less fit (purifying selection). We interpret the history of Paratyphi A as reflecting drift rather than progressive evolution and suggest that most recent increases in frequencies of bacterial diseases are due to environmental changes rather than the novel evolution of pathogenic bacteria.

Multiple epidemic diseases have been designated as emerging or reemerging because the numbers of clinical cases have increased. Emerging diseases are often suspected to be driven by increased virulence or fitness, possibly associated with the gain of novel genes or mutations. However, the time period over which humans have been afflicted by such diseases is only known for very few bacterial pathogens, and the evidence for recently increased virulence or fitness is scanty. Has Darwinian (diversifying) selection at the genomic level recently driven microevolution within bacterial pathogens of humans? Salmonella enterica serovar Paratyphi A is a major cause of enteric fever, with a microbiological history dating to 1898. We identified seven modern lineages among 149 genomes on the basis of 4,584 SNPs in the core genome and estimated that Paratyphi A originated 450 y ago. During that time period, the effective population size has undergone expansion, reduction, and recent expansion. Mutations, some of which inactivate genes, have occurred continuously over the history of Paratyphi A, as has the gain or loss of accessory genes. We also identified 273 mutations that were under Darwinian selection. However, most genetic changes are transient, continuously being removed by purifying selection, and the genome of Paratyphi A has not changed dramatically over centuries. We conclude that Darwinian selection is not responsible for increased frequency of enteric fever and suggest that environmental changes may be more important for the frequency of disease.