Dr Muhammad Yasir


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Investigating the evolution of antimicrobial resistance

I am interested in the study of the molecular mechanisms of microorganisms. I started my career in microbiology by studying antimicrobial resistance during my masters. Then, I became interested in understanding the molecular basis of bacterial pathogenicity, and how bacteria adapt to stress conditions. I was accepted for a Darwin Trust PhD studentship at the University of Birmingham, UK, to study gene expression regulation in pathogenic bacteria. A part of my PhD research aimed to understand regulation of genes involved in pathogenicity in a pathogenic Escherichia coli and how, the alteration in expression of these genes directly relates to the ability to cause disease. My PhD work shows that inactivation of the virulence gene’s regulator can change the phenotype of bacteria related to pathogenicity. The development of understanding of bacterial genes and promoters during my PhD increased my curiosity in the field of bacterial genomics and I became interested in genomic tools to understand various other bacterial mechanisms.

I joined Quadram Institute as a research scientist with the aim of developing and implementing an advanced version of Transposon Directed Insertion site Sequencing (TraDIS), which we have called TraDIS-Xpress. TraDIS-Xpress overcomes the limitation of TraDIS as it includes essential genes in the assay as well by measuring the changes in gene expression. TraDIS-Xpress technology enables us to assay the whole bacterial genome in any certain stress condition, down to sub-gene level resolution. We are using TraDIS-Xpress to study bacteria in the food chain.

Key Publications

Yasir M, Turner AK, Bastkowski S, Page AJ, Telatin A, Phan M, Monahan LG, Darling AE, Webber MA*, Charles IG. TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance  doi: 10.1101/gr.254391.119

Page AJ, Bastkowski S, Yasir M, Turner, AK, Le Viet T, Savva GM, Webber MA, Charles IG. AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments. bioRxiv 2019 https://doi.org/10.1101/593624.

Yasir, M., Icke, C., Abdelwahab, R., Haycocks, J.R., Godfrey, R.E., Sazinas, P., Pallen, M.J., Henderson, I.R., Busby, S.J.W., and Browning, D.F. (2019). Organization and architecture of AggR-dependent promoters from enteroaggregative Escherichia coli. Mol Microbiol 111, 534-551. https://doi.org/10.1111/mmi.14172

Ellis, S.J., Yasir, M., Browning, D.F., Busby, S.J.W., and Schuller, S. (2019). Oxygen and contact with human intestinal epithelium independently stimulate virulence gene expression in enteroaggregative Escherichia coli. Cell Microbiol 21, e13012. https://doi.org/10.1111/cmi.13012

Hannan A, Humayun T, Barkaat M, Yasir M, Sikandar S. In vitro antibacterial activity of Allium cepa extract against clinical isolates of Vibrio cholerae. J Ayub Med Coll. 2010; 22(2):160-3

Webber M., Yasir M., Turner K., Bastkowski S., Baker D., Page A., Telatin A., Savva G., Charles I.. (2020)

TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance.

Genome Research, 30, 239-249

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Rasheed F,Saeed M,Alikhan NF,Baker D,Khurshid M,Ainsworth EV,Turner AK,Imran AA,Rasool MH,Saqalein M,Nisar MA,Fayyaz Ur,Wain J,Yasir M,Langridge GC,Ikram A. (2020)

Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan.


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