Genomic and epidemiological characteristics of <i>Shigella boydii</i> in Australia, 1991–2022

Shigellosis is a leading cause of diarrheal mortality worldwide. <i>Shigella boydii</i> is one of four <i>Shigella</i> species that contributes to this burden, however studies on <i>S. boydii</i> are limited. Here we combined epidemiological and genomic data to better understand <i>S. boydii</i> circulating both in Australia and globally. Between 1991 and 2019, there were 294 cases of <i>S. boydii</i> infections notified to the National Notifiable Diseases Surveillance System by Australian states and territories, with an increasing trend in notifications observed from 2013. Of cases whose place of acquisition was known, 54% (111/206) were acquired overseas, mainly from South-East Asia (57%; 63/111). Our genomic analysis included 250 <i>S. boydii</i> isolates: 44 from Victoria, Australia spanning 22 years (2001-2022) and 206 international isolates spanning 91 years (1930-2020). Phylogenomic analyses identified five major <i>S. boydii</i> phylogenetic lineages circulating globally. The Australian isolates were distributed across all five lineages, but the highest proportion was in Lineage 3. Antimicrobial resistance was common in both international and Australian isolates with > 60% of isolates classified as multi-drug-resistant. Resistance to the main clinically relevant antimicrobials was rare in <i>S. boydii</i>. Ciprofloxacin resistance was detected in seven <i>S. boydii</i>, however reduced susceptibility to ciprofloxacin was detected in 56 isolates and found in both Australian and international data. Importantly, resistance mechanisms to third-generation cephalosporins and macrolides were also detected. This study is the largest genomic analysis of <i>S. boydii</i> to date, providing insights into the population structure, epidemiology and emerging AMR threats in this neglected <i>Shigella</i> species.