The members of the genus Shigella are Gram-negative pathogens that are closely related to Escherichia coli (Pupo et al., 2000) and cause dysenteric diarrhoea (stools containing blood and/or mucus) via a cascade of virulence factors encoded principally on a large signature virulence plasmid (Sansonetti et al., 1982). The genus contains four species: Shigella sonnei, Shigella flexneri, Shigella boydii and Shigella dysenteriae, with S. sonnei and S. flexneri dominating in developed and developing countries, respectively. However, this pattern is changing, as S. sonnei is currently replacing S. flexneri in countries undergoing economic transition (Vinh et al., 2009; Thompson et al., 2015). This species replacement has positive and negative ramifications. By replacing S. flexneri, which is very diverse with multiple serotypes with respect to the single serotype S. sonnei (Connor et al., 2015), as the leading cause of dysentery means that it may be possible to control disease through vaccination (Levine et al., 2007). However, S. sonnei is also highly adept at acquiring antimicrobial resistance genes and resistance-associated mutations (Huang et al., 2005; Seol et al., 2006; Nguyen et al., 2010), limiting treatment options and making control through antimicrobial treatment alone improbable.