South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study

Abstract

Background: Antimicrobial resistance is a major issue in the Shigellae, particularly as a specific multidrug-resistant (MDR) lineage of Shigella sonnei (lineage III) is becoming globally dominant. Ciprofloxacin is a recommended treatment for Shigella infections. However, ciprofloxacin-resistant S. sonnei are being increasingly isolated in Asia and sporadically reported on other continents. We hypothesized that Asia is a primary hub for the recent international spread of ciprofloxacin-resistant S. sonnei.

Methods and findings: We performed whole-genome sequencing on a collection of 60 contemporaneous ciprofloxacin-resistant S. sonnei isolated in four countries within Asia (Vietnam, n = 11; Bhutan, n = 12; Thailand, n = 1; Cambodia, n = 1) and two outside of Asia (Australia, n = 19; Ireland, n = 16). We reconstructed the recent evolutionary history of these organisms and combined these data with their geographical location of isolation. Placing these sequences into a global phylogeny, we found that all ciprofloxacin-resistant S. sonnei formed a single clade within a Central Asian expansion of lineage III. Furthermore, our data show that resistance to ciprofloxacin within S. sonnei may be globally attributed to a single clonal emergence event, encompassing sequential gyrA-S83L, parC-S80I, and gyrA-D87G mutations. Geographical data predict that South Asia is the likely primary source of these organisms, which are being regularly exported across Asia and intercontinentally into Australia, the United States and Europe. Our analysis was limited by the number of S. sonnei sequences available from diverse geographical areas and time periods, and we cannot discount the potential existence of other unsampled reservoir populations of antimicrobial-resistant S. sonnei.

Conclusions: This study suggests that a single clone, which is widespread in South Asia, is likely driving the current intercontinental surge of ciprofloxacin-resistant S. sonnei and is capable of establishing endemic transmission in new locations. Despite being limited in geographical scope, our work has major implications for understanding the international transfer of antimicrobial-resistant pathogens, with S. sonnei acting as a tractable model for studying how antimicrobial-resistant Gram-negative bacteria spread globally.

Fig 1. The phylogenetic structure of ciprofloxacin-resistant Shigella sonnei in an international context.

A) Unrooted maximum likelihood phylogeny of 211 globally representative S. sonnei, including 60 sequences from ciprofloxacin-resistant isolates (highlighted by the blue branches). Major lineages are indicated by numbers (I, II, III, and IV) as defined in Holt et al. 2012, with clades Global III and Central Asia III within lineage III highlighted. Horizontal scale bar indicates the number of nucleotide substitutions per site. B) Unrooted maximum likelihood phylogeny of Central Asia III, composed of 97 S. sonnei sequences. Branch colours indicate region of isolation (where no travel history is confirmed) or region of recent travel (where travel history was confirmed) according to the keys. For isolates with confirmed recent travel, a coloured circle at the tip indicates the region where the isolate was collected (multiple coloured circles are indicative of multiple isolates). Labelled arrows indicate branches where the mutations gyrA-S83L, gyrA-D87N, gyrA-D87G, and parC-S80I have arisen. Blue background shading denotes isolates exhibiting ciprofloxacin resistance conferred by triple mutations (gyrA-S83L, parC-S80I, and gyrA-D87G [or gyrA-D87N]). Subpopulations A and B are highlighted in the darker blue shaded areas, denoting clonal expansions in Southeast Asia and Europe/America, respectively. Numbers above major branches indicate bootstrap support values, and horizontal scale bar denotes the number of nucleotide substitutions per site.