Genomic epidemiology of Shigella in the United Kingdom shows transmission of pathogen sublineages and determinants of antimicrobial resistance

Abstract

Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with traditional typing methods, and has identified sublineages associated with specific geographical regions or patient groups. Genomic analyses reveal temporal increases in Shigella antimicrobial resistance (AMR) gene content, which is frequently encoded on mobile genetic elements. Here, we whole genome sequenced representative subsamples of S. flexneri 2a and S. sonnei (n = 366) from the United Kingdom from 2008 to 2014, and analysed these alongside publicly available data to make qualitative insights on the genomic epidemiology of shigellosis and its AMR within the broader global context. Combined phylogenetic, epidemiological and genomic anlayses revealed the presence of domestically-circulating sublineages in patient risk-groups and the importation of travel-related sublineages from both Africa and Asia, including ciprofloxacin-resistant sublineages of both species from Asia. Genomic analyses revealed common AMR determinants among travel-related and domestically-acquired isolates, and the evolution of mutations associated with reduced quinolone susceptibility in domestically-circulating sublineages. Collectively, this study provides unprecedented insights on the contribution and mobility of endemic and travel-imported sublineages and AMR determinants responsible for disease in a high-income nation.

Figure 1

Representative sampling of isolates for whole genome sequencing. The figure shows a graph of the number of isolates sequenced per year by travel and species (upper graph), overlaid with the number of domestically-acquired (non-travel) and travel-associated cases of shigellosis (for all ages). Non-travel isolates were overrepresented (see Methods).

Figure 2

Shigella flexneri 2a UK cross section in context. (A) The smaller tree shows the broad context of phylogroups (PG) 1–7 of S. flexneri and intercontinental MSM-associated (MSMA) S. flexneri 3a, with the relationships of three non-PG3 isolates from this study. PG3 is overlaid by a grey polygon in the smaller tree and is shown in full in the larger tree. (B) The larger tree is a mid-point rooted maximum likelihood tree and shows the detailed evolutionary relationships of UK cross section isolates (black branches) with reference isolates (coloured branches). Reference isolate branches are coloured by region of sample origin, and region of recent travel is overlaid for UK samples as coloured circles on tree tips (both coloured according to the inlaid region key). Two MSM-associated sublineages are highlighted by grey boxes, and the S. flexneri 2a Central Asia lineage is indicated at the defining internal node. AMR features are shown in adjacent tracks. The leftmost track shows the presence of QRDR mutations and one ‘Other’, which designates a quadruple mutant also carrying the qnrS1 gene. Subsequent gray scale tracks indicate the presence of antimicrobial resistance genes (ARGs, labelled above) associated with known Shigella MGEs. Specifically (from left to right), the Tn7/Int2, SRL-MDRE, Small R-plasmids, Minor clade plasmid, pKSR100 (Table 1).

Figure 3

Shigella sonnei UK cross section in context. The midpoint-rooted maximum likelihood phylogenetic tree shows isolates from this study in the context of five global lineages of S. sonnei. Lineage III has further relevant sublineages indicated at the internal nodes and MSM-associated sublineages are highlighted in grey. Isolates from patients recently returned from endemic regions are indicated by circles overlying the tree tips which are coloured according to the inlaid key. Reference isolates from previously described WGSA subtypes (lineages/sublineages) are indicated in the leftmost adjacent track, and tree branches for references isolates are also coloured according to the inlaid key. AMR features are shown in subsequent tracks. The second leftmost track shows the presence of QRDR mutations and two isolates containing ‘Other’ quinolone resistance determinants (including an isolate with a single QRDR mutation and a qepA gene, and an isolate containing a qnrB19 gene). Subsequent gray scale tracks indicate the presence of antimicrobial resistance genes (ARGs, labelled above) associated with known Shigella MGEs. Specifically (from left to right), the Tn7/Int2, SpA, MSM-associated sublineage 3 plasmid, pKSR100, SRL-MDRE (Table 1).