Delving into the genome of resurged Shigella dysenteriae Type 1

The Gram-negative enteric bacterium Shigella dysenteriae serotype 1 (Sd1) has historically caused several dysentery epidemics but has largely disappeared from the global epidemiological landscape, with the last reported isolate dating back to 2010. In this study, we have recently identified Sd1 from lamb meat in India in 2022, the first detection since 2010 and compared its genetic characteristics with the two clinical Sd1 isolates that were identified in Kolkata in 2010 and other global genomic sequences collected between 1951 and 2011.

As part of the National ICMR-FoodNet surveillance, this study isolated S. dysenteriae serotype 1 from lamb meat in Sikkim (2022; SKM-823) and compared it with two clinical isolates from Kolkata (2010). Characterization involved biochemical and serological tests, antimicrobial resistance (AMR) and whole genome sequencing. SNP-based phylogenetic analysis, MLST, ARGs, and toxin gene detection were conducted for the study isolates against 331 global Sd1 genomes.

Comparative analysis of Sd1 (SKM-823) with two clinical isolates (IDH-3116 and IDH-3161) exhibited resistance to quinolones, fluroquinolones, tetracycline, chloramphenicol, and sulfamethoxazole/trimethoprim, but were susceptible to azithromycin and cephalosporins. The two clinical Sd1 isolates were resistant to azithromycin. Multi locus sequence typing identified that the clinical isolates belonging to ST5159 and SKM-823 as ST146. Both these STs are mostly represented by the other Asian Sd1 isolates. Several antimicrobial resistance encoding genes (ARGs) have been identified in the Shigella resistance locus-pathogenicity island. Four key toxin genes such as the Shiga toxins-stx1A, stx1B; enteroaggregative heat-stable toxin-astA; and invasion plasmid associated-antigen-ipaH were also identified in SKM-823, IDH-3116 and IDH-3161. The phylogenetic analysis showed clustering of SKM-823 Sd1 isolate and the other clinical isolates (IDH-3116 and IDH-3161) from India within lineage IV, consistent with the other Asian isolates.

This study finding reveals genomic changes and rising AMR in Sd1, underscoring its potential epidemic implications and the need to strengthen systematic surveillance. With the increasing reports on the incidence of Shigella spp from animals, foods of animal origin and food handlers, Sd1 is becoming a significant concern within the global one health framework. The identification of an epidemic causing S. dysenteriae Type 1 calls for timely action from health authorities to implement targeted interventions and ensure updated medical and policy responses remain updated and responsive.