The paper identifies a rapidly expanding multidrug-resistant M. tuberculosis clade originating from Russia and circulating in Moldova, posing a threat to MDR-TB control.

Nature Communications · Mar 31, 2026Peer-reviewedMicrobiology

e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology

Peiyu Xu, Shenni Liang, Andrew Warren Hahn, Vivian Zhao, Wai Tung ‘Jack’ Lo, Benjamin C. Haller, Benjamin Sobkowiak, Melanie H. Chitwood, Caroline Colijn, Ted Cohen, Kyu Young Rhee, Philipp W. Messer, Martin T. Wells, Andrew G. Clark, Jaehee Kim

The paper introduces e3SIM, a simulator that models epidemiological, ecological, and evolutionary processes in pathogens, demonstrating its use with SARS-CoV-2 and Mycobacterium tuberculosis.

Methods in Ecology and Evolution · Mar 5, 2026Peer-reviewedBioinformatics

A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission

Benjamin Sobkowiak, Patrick Cudahy, Melanie H. Chitwood, Taane Gregory Clark, Caroline Colijn, Louis Grandjean, Katharine S. Walter, Valeriu Crudu, Ted Cohen

MixInfect2 accurately detects mixed Mycobacterium tuberculosis infections and estimates strain proportions, improving upon previous methods.

bioRxiv · Apr 26, 2024 · PreprintGenomics