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

Enhanced virulence and stress tolerance are signatures of epidemiologically successful Shigella sonnei

Sydney L. Miles, Dilys Santillo, Hannah Painter, Kathryn Wright, Vincenzo Torraca, Ana T. López-Jiménez, Mollie Virgo, Xosé M. Matanza, Abigail Clements, Claire Jenkins, Stephen Baker, Kate S. Baker, David A. Cisneros, Andrea Puhar, Vanessa Sancho‐Shimizu, , Serge Mostowy

This study identifies enhanced virulence and stress tolerance as factors contributing to the epidemiological success of Shigella sonnei, using zebrafish models and genomic analysis.

Nature Communications · Oct 9, 2025Peer-reviewedMicrobiology

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

Recent emergence of cephalosporin resistant Salmonella Typhi in India due to the endemic clone acquiring IncFIB(K) plasmid encoding blaCTX-M-15 gene

Tharani Priya Thirumoorthy, Jobin John Jacob, Aravind Velmurugan, Monisha Priya Teekaraman, Bhavini Sandip Shah, Veena J Iyer, Geeti Maheshwari, Urmi H. Trivedi, Anand Shah, Pooja R. Patel, Anushree S. Gaigawale, M Yesudoss, Pavithra Sathya Narayanan, Ankur Mutreja, Megan E. Carey, , Balaji Veeraraghavan

Microbiology Spectrum · Apr 10, 2025Peer-reviewedGenomics

Spontaneous emergence of azithromycin resistance in independent lineages of Salmonella Typhi in Northern India

Megan E. Carey, Ruby Jain, Mohammad A. Yousuf, Mailis Maes, Zoe A. Dyson, Trang Nguyen Hoang Thu, To Nguyen Thi Nguyen, Thanh Ho Ngoc Dan, Quynh Nhu Pham Nguyen, Jaspreet Mahindroo, Duy Pham Thanh, Kawaljeet Singh Sandha, Stephen G. Baker, Neelam Taneja

The paper identifies azithromycin-resistant Salmonella Typhi in Northern India, showing independent emergence of resistance and highlighting the need for typhoid conjugate vaccines.

Clinical Infectious Diseases · Dec 14, 2020Peer-reviewedGenomics