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Mapping of all polymorphic sites within the core genome to ATCC 9150 identified only 4,584 SNPs (Table 1), which is comparable to the diversity found in (3), serovar Typhi (25), and other genetically monomorphic bacterial pathogens (26).

However, most genetic changes are transient, continuously being removed by purifying selection, and the genome of Paratyphi A has not changed dramatically over centuries.To strengthen dating estimates, we included 42 old strains (1917–1980) from the historical, global collection at the Institut Pasteur (Paris) (Dataset S1, tab 1).The remaining strains were isolated between 19 and represent the current global distribution of Paratyphi A, including isolates from India (42 genomes) and Pakistan (12), where Paratyphi A is now most common.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.

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