Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

Genome Medicine · Oct 24, 2025Peer-reviewedMicrobiology✦ In-depth digest

The TyphiNET data visualisation dashboard: Unlocking Salmonella Typhi genomics data to support public health

Zoe A. Dyson, Louise Cerdeira, Vandana Sharma, Megan E. Carey, Kathryn E. Holt, David M. Aanensen, Ali H. Abbas, Antoine G. Abou Fayad, Ayorinde O. Afolayan, Niyaz Ahmed, Irshad Ahmed, Afreenish Amir, Saadia Andleeb, Silvia Argimón, Abraham Aseffa, , Jackie Wright

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

Genome Medicine · May 9, 2025Peer-reviewedMicrobiology

Genomic characteristics of recently recognized Vibrio cholerae El Tor lineages associated with cholera in Bangladesh, 1991-2017

Md Mamun Monir, Talal Hossain, Masatomo Morita, Makoto Ohnishi, Fatema‐Tuz Johura, Marzia Sultana, Shirajum Monira, Tahmeed Ahmed, Nicholas Robert Thomson, Haruo Watanabe, Anwar Huq, Rita R. Colwell, Kimberley D. Seed, Munirul Alam

The paper performs a genomic analysis of Vibrio cholerae El Tor strains from Bangladesh, identifying two lineages, BD-1 and BD-2, and their distinct genomic traits and epidemiological implications.

Microbiology Spectrum · Mar 22, 2022Peer-reviewedGenomics