Genomic insights into the impact of typhoid conjugate vaccine introduction and the COVID-19 pandemic on Salmonella Typhi and Paratyphi A in Nepal

Background: Enteric fever, caused by Salmonellaenterica serovars Typhi and Paratyphi A, remains a major concern in low- and middle-income countries, with treatment increasingly complicated by antimicrobial resistance. Typhoid conjugate vaccines (TCVs) offer a promising intervention, but their impact on circulating lineages and population structure remains poorly understood. Nepal introduced a nationwide TCV programme in April 2022, shortly after the COVID-19 pandemic disrupted healthcare delivery and surveillance. Methods: We sequenced 350 S. Typhi and 114 S. Paratyphi A isolates collected in Nepal between 2018 and 2024 and analyzed them alongside1,797 previously published Nepal genomes (2005-2018). We characterized genotype distribution, antimicrobial resistance determinants, phylogenetic relationships and lineage-specific phylodynamics across three epidemiological periods: pre-pandemic (before 2020), pandemic/pre-vaccine (2020-2022), and post-vaccine introduction (2022-2024). Results: Sixteen S. Typhi genotypes were identified, dominated by 4.3.1.2 (28%), 3.3.2 (20.3%) and 3.3.1 (16.9%); S. Paratyphi A was dominated by genotypes 2.4.3 (57.0%) and 2.4.2 (25.4%). Multidrug resistance was rare, but fluoroquinolone non-susceptibility was widespread (70.6% of S. Typhi; 99.1% of S. Paratyphi A), with high-level resistance confined to a single S. Typhi 4.3.1.2.1 clade dating to 2008. Phylodynamic reconstruction revealed asymmetric lineage trajectories: S. Typhi H58 contracted sharply during the pandemic, lineage 3.3 contracted specifically post-TCV, and S. Paratyphi A (not vaccine-targeted) showed only a modest pandemic-era decline. Post-TCV, the age distribution of cases shifted older and the adult genotype mix shifted toward lineage 3.3. We found no evidence of vaccine-driven escape at the Vi capsule or O-antigen in Nepal or across a cross-country cohort. Conclusions: Both S. Typhi and S. Paratyphi A populations in Nepal underwent recent declines in effective population size, coinciding with the COVID-19 pandemic and TCV introduction. Persistent fluoroquinolone resistance, particularly among S. Paratyphi A, underscores ongoing AMR challenges and highlights the need for expanded vaccine strategies targeting both pathogens.