2026

Genetic context drives evolution of divergent antibiotic survival phenotypes in Staphylococcus epidermidis

Carolin M Kobras, Carlota Losa-Mediavilla, James C Littlefair, Elizabeth A Cummins, Charlotte Woolley, Seungwon Ko, Priyanshu Singh Raikwar, Keith A Jolley, Samuel K Sheppard, Mathew Stracy

bioRxiv, 2026.05. 29.728712 (2026)

Infant gut bacterial Study in Nigeria (INBUGS-NG).

Chinenye Pascaline Akpulu, Hafsat Maikudi Sada, Hafsat Ahmed, Hassana B Idris, Rashida Yakubu, Aliyu Aminu, Kenneth Iregbu, Jared Oduwo, Edward Owinoh, Aditya K Lankapalli, Laura de Nies, Chioma R Achi, Kathryn Thomson, Mathew Stracy, Timothy R Walsh, Kirsty Sands

BMJ Open 16:e111007 (2026)

Insertion sequence elements associated with Staphylococcus epidermidis evolution in persistent orthopaedic device-related infections

James C Littlefair, Carolin M Kobras, Virginia Post, Ben Pascoe, David J Baker, Christoph Erichsen, Mathew Stracy, Fintan Moriarty, Samuel K Sheppard

BMC Genomics, 27, 818 (2026)

2024

Covalent penicillin-protein conjugates elicit anti-drug antibodies that are clonally and functionally restricted

Deimel LP, Moynié L, Sun G, Lewis V, Turner A, Buchanan CJ, Burnap SA, Kobras CA, Stracy M, Struwe WB, Baldwin AJ, Naismith J, Davis BG and Sattentau QJ.

Nature Communications, 15, 6851 (2024).

Comparing Mfd-and UvrD-dependent models of transcription coupled DNA repair in live Escherichia coli using single-molecule tracking

Kaja E, Vijande D, Kowalczyk, J Michalak M, Gapiński J, Kobras C, Rolfe P, Stracy M.

DNA Repair, 137, 103665 (2024).

Single-molecule tracking reveals the functional allocation, in vivo interactions, and spatial organization of universal transcription factor NusG

El Sayyed H, Pambos OJ, Stracy M, Gottesman ME, Kapanidis AN.

Molecular Cell, 85 (5), 926-937 (2024).

2023

Antibiotic-induced collateral damage to the microbiota and associated infections

de Nies L, Kobras CM, Stracy M

Nature Reviews Microbiology, 21, 789–804 (2023). PDF

Deep Learning and Single Cell Phenotyping for Rapid Antimicrobial Susceptibility Testing

Zagajewski A , Turner P, Feehily C, El Sayyed H, Andersson M, Barrett L , Oakley S, Stracy M, Crook D, Nellaker C, Stoesser N, Kapanidis AN.

Communications Biology 6 (1), 1164, (2023).

2022

Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections

Stracy M, Snitser O, Yelin I, Amer Y, Parizade M, Rimler G, Wolf T, Herzel E, Koren G, Kuint J, Foxman B, Chodick G, Shalev V, Kishony R.

Science 375, 889 (2022). PDF

• See the perspectives on this article here and here. See some of the news features on the work here, here and here.

RNA polymerase redistribution supports growth in E. coli strains with a minimal number of ribosomal RNA operons

Fan J, El Sayyed H, Pambos OJ, Stracy M, Kyropoulos J, Kapanidis AN.

Nucleic Acids Research, gkad511 (2022).

Microbiome cartography

Stracy, M.

Nature Reviews Microbiology (2022). PDF

2021

Competitive binding of MatP and topoisomerase IV to the MukB dimerization hinge

Fisher GLM, Bolla JR, Rajasekar KV, Mäkelä J, Baker R, Zhou M, Prince JP, Stracy M, Robinson CV, Arciszewska LK, Sherratt DJ.

eLife, 10, e70444 (2021).

Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

Stracy M*, Schweizer J, Sherratt D, Kapanidis AN, Uphoff S, Lesterlin C. *corresponding author.

Molecular Cell, 81, 1–16. (2021).

2019

Single-molecule imaging of DNA gyrase activity in living Escherichia coli

Stracy M, Wollman AJM, Kaja E, Gapinski J, Lee JE, Leek VA, McKie SJ, Mitchenall LA, Maxwell A, Sherratt DJ, Leake MC, Zawadzki P.

Nucleic Acid Research, 47, 210–220. (2019).

2018

Tracking tRNA packages

Kapanidis AN, Stracy M.

Nature Chemical Biology, 14, 528–529. (2018).

Understanding protein mobility in bacteria by tracking single molecules

Kapanidis AN, S Uphoff, Stracy M

Journal of Molecular Biology. 430(22), 4443-4455. (2018).

2017

Single-molecule and super-resolution imaging of transcription in living bacteria

Stracy M, Kapanidis AN,

Methods, 120, 103–114. (2017).

Tracking low-copy transcription factors in living bacteria: the case of lac repressor.

Garza de Leon F, Sellars L, Stracy M, Busby SJW, Kapanidis AN

Biophysical Journal. 112(7), 1316–1327. (2017).

Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase  

Lamberte LE, Baniulyte G, Singh SS, Stringer AM, Bonocora R, Stracy M, Kapanidis AN, Wade JT, Grainger DC.

Nature Microbiology. 2, 16249. (2017).

2016 

Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia Coli

Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P

Nature Communications. 7, 12568. (2016).

2015

The localization and action of topoisomerase IV in Escherichia coli chromosome segregation is coordinated by the SMC complex, MukBEF

Zawadzki P*, Stracy M*, Ginda K, Zawadzka K, Lesterlin C, Kapanidis AN, Sherratt DJ.

Cell Reports. 13(11), 2587-2596. (2015).

Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid.

Stracy M, Lesterlin C, Garza de Leon F, Uphoff S, Zawadzki P, Kapanidis AN (2015).

Proceedings of the National Academy of Science. 112(32), 201507592.

2014

In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair

Stracy M, Uphoff S, Garza de Leon F, Kapanidis AN

FEBS Letters. 588(19), 3585–3594. (2014)