ArticleNature communications2022
Paratype: a genotyping tool for Salmonella Paratyphi A reveals its global genomic diversity.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
- Global transmission dynamics of antibiotic resistance genes: Foodborne pathways as the critical link to humans.One health (Amsterdam, Netherlands) · 2026Article
- Global genomic surveillance uncovers emergence and spatiotemporal patterns of World Health Organization priority antibiotic resistance in invasive Salmonella.Nature communications · 2026Article
- The typhoid Mary legacy: Genomic epidemiology uncovers contemporary carriage dynamics across two decades of enteric fever surveillance in England and Wales.PLoS neglected tropical diseases · 2026Article
- Evolution of pneumococcal serotype 19A in children in Bangladesh: insights from genomic analysis.BMC microbiology · 2025Article
- A contemporary genomic snapshot ofMicrobial genomics · 2025Article
- Paratyphoid fever and the genomics of Salmonella enterica serovar Paratyphi A in Taiwan.PLoS neglected tropical diseases · 2025Article
- Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing.PLoS neglected tropical diseases · 2025Article
- Outbreak of Ceftriaxone-Resistant Salmonella enterica Serovar Typhi, Bangladesh, 2024.Emerging infectious diseases · 2025Article
- Genomic perspective on the bacillus causing paratyphoid B fever.Nature communications · 2024Article
- Rapid and specific differentiation of Salmonella enterica serotypes typhi and Paratyphi by multicolor melting curve analysis.Gut pathogens · 2024Article
- A retrospective investigation of the population structure and geospatial distribution of Salmonella Paratyphi A in Kathmandu, Nepal.PLoS neglected tropical diseases · 2024Article
- Typhoid fever.Nature reviews. Disease primers · 2023Review
- Trends in antimicrobial resistance amongst Salmonella Paratyphi A isolates in Bangladesh: 1999-2021.PLoS neglected tropical diseases · 2023Article
- Article
- Genomic Surveillance ofOpen forum infectious diseases · 2023Article
- Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages.PLoS pathogens · 2023Article
- Phylogenomic investigation of an outbreak of fluoroquinolone-resistantMicrobial genomics · 2023Article
Corrections and comments
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Authors and funding
14 authors at 8 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Salmonella Paratyphi A, the primary etiology of paratyphoid, is estimated to cause 3.4 million infections annually, worldwide. With rising antimicrobial resistance and no licensed vaccines, genomic surveillance is key to track and monitor transmission, but there is currently no reliable genotyping framework for this pathogen. Here, we sequence 817 isolates from South Asia and add 562 publicly available genomes to build a global database representing 37 countries, covering 1917-2019. We develop a single nucleotide polymorphism-based genotyping scheme, Paratype, that segregates Salmonella Paratyphi A population into three primary and nine secondary clades, and 18 genotypes. Each genotype is assigned a unique allele definition located on an essential gene. Using Paratype, we identify spatiotemporal genomic variation and antimicrobial resistance markers. We release Paratype as an open-access tool that can use raw read files from both Illumina and Nanopore platforms, and thus can assist surveillance studies tracking Salmonella Paratyphi A across the globe.
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