Dr Muhammad Yasir

Researcher

Contact via email

Investigating the evolution of antimicrobial resistance

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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

Acton L, Pye HV, Thilliez G, Kolenda R, Matthews M, Turner AK, Yasir M, Holden E, Al-Khanaq H, Webber M, Adriaenssens EM, Kingsley . (2024)

Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica

Journal of Virology


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Yasir M, Thomson N, Turner K, Webber M, Charles . (2024)

Overflow metabolism provides a selective advantage to Escherichia coli in mixed cultures

Annals of Microbiology, 74, 15


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Thomson N, Turner K, Bastkowski S, Yasir M, Lott M, Webber M, Charles I. (2022)

A whole-genome assay identifies four principal gene functions that confer tolerance of meropenem stress upon Escherichia coli

Frontiers in Antibiotics, 1:957942


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Volz E,Hill V,McCrone JT,Price A,Jorgensen D,O'Toole Á,Southgate J,Johnson R,Jackson B,Nascimento FF,Rey SM,Nicholls SM,Colquhoun RM,da Silva,Shepherd J,Pascall DJ,Shah R,Jesudason N,Li K,Jarrett R,Pacchiarini N,Bull M,Geidelberg L,Siveroni I,Goodfellow I,Loman NJ,Pybus OG,Robertson DL,Thomson EC,Rambaut A,Connor TR,Koshy C,Wise E,Cortes N,Lynch J,Kidd S,Mori M,Fairley DJ,Curran T,McKenna JP,Adams H,Fraser C,Golubchik T,Bonsall D,Moore C,Caddy SL,Khokhar FA,Wantoch M,Reynolds N,Warne B,Maksimovic J,Spellman K,McCluggage K,John M,Beer R,Afifi S,Morgan S,Marchbank A,Price A,Kitchen C,Gulliver H,Merrick I,Southgate J,Guest M,Munn R,Workman T,Connor TR,Fuller W,Bresner C,Snell LB,Charalampous T,Nebbia G,Batra R,Edgeworth J,Robson SC,Beckett A,Loveson KF,Aanensen DM,Underwood AP,Yeats CA,Abudahab K,Taylor BEW,Menegazzo M,Clark G,Smith W,Khakh M,Fleming VM,Lister MM,Howson-Wells HC,Berry L,Boswell T,Joseph A,Willingham I,Bird P,Helmer T,Fallon K,Holmes C,Tang J,Raviprakash V,Campbell S,Sheriff N,Loose MW,Holmes N,Moore C,Carlile M,Wright V,Sang F,Debebe J,Coll F,Signell AW,Betancor G,Wilson HD,Feltwell T,Houldcroft CJ,Eldirdiri S,Kenyon A,Davis T,Pybus O,du Plessis,Zarebski A,Raghwani J,Kraemer M,Francois S,Attwood S,Vasylyeva T,Torok ME,Hamilton WL,Goodfellow IG,Hall G,Jahun AS,Chaudhry Y,Hosmillo M,Pinckert ML,Georgana I,Yakovleva A,Meredith LW,Moses S,Lowe H,Ryan F,Fisher CL,Awan AR,Boyes J,Breuer J,Harris KA,Brown JR,Shah D,Atkinson L,Lee JCD,Alcolea-Medina A,Moore N,Cortes N,Williams R,Chapman MR,Levett LJ,Heaney J,Smith DL,Bashton M,Young GR,Allan J,Loh J,Randell PA,Cox A,Madona P,Holmes A,Bolt F,Price J,Mookerjee S,Rowan A,Taylor GP,Ragonnet-Cronin M,Nascimento FF,Jorgensen D,Siveroni I,Johnson R,Boyd O,Geidelberg L,Volz EM,Brunker K,Smollett KL,Loman NJ,Quick J,McMurray C,Stockton J,Nicholls S,Rowe W,Poplawski R,Martinez-Nunez RT,Mason J,Robinson TI,O'Toole E,Watts J,Breen C,Cowell A,Ludden C,Sluga G,Machin NW,Ahmad SSY,George RP,Halstead F,Sivaprakasam V,Thomson EC,Shepherd JG,Asamaphan P,Niebel MO,Li KK,Shah RN,Jesudason NG,Parr YA,Tong L,Broos A,Mair D,Nichols J,Carmichael SN,Nomikou K,Aranday-Cortes E,Johnson N,Starinskij I,da Silva,Robertson DL,Orton RJ,Hughes J,Vattipally S,Singer JB,Hale AD,Macfarlane-Smith LR,Harper KL,Taha Y,Payne BAI,Burton-Fanning S,Waugh S,Collins J,Eltringham G,Templeton KE,McHugh MP,Dewar R,Wastenge E,Dervisevic S,Stanley R,Prakash R,Stuart C,Elumogo N,Sethi DK,Meader EJ,Coupland LJ,Potter W,Graham C,Barton E,Padgett D,Scott G,Swindells E,Greenaway J,Nelson A,Yew WC,Resende Silva,Andersson M,Shaw R,Peto T,Justice A,Eyre D,Crooke D,Hoosdally S,Sloan TJ,Duckworth N,Walsh S,Chauhan AJ,Glaysher S,Bicknell K,Wyllie S,Butcher E,Elliott S,Lloyd A,Impey R,Levene N,Monaghan L,Bradley DT,Allara E,Pearson C,Muir P,Vipond IB,Hopes R,Pymont HM,Hutchings S,Curran MD,Parmar S,Lackenby A,Mbisa T,Platt S,Miah S,Bibby D,Manso C,Hubb J,Chand M,Dabrera G,Ramsay M,Bradshaw D,Thornton A,Myers R,Schaefer U,Groves N,Gallagher E,Lee D,Williams D,Ellaby N,Harrison I,Hartman H,Manesis N,Patel V,Bishop C,Chalker V,Osman H,Bosworth A,Robinson E,Holden MTG,Shaaban S,Birchley A,Adams A,Davies A,Gaskin A,Plimmer A,Gatica-Wilcox B,McKerr C,Moore C,Williams C,Heyburn D,De Lacy,Hilvers E,Downing F,Shankar G,Jones H,Asad H,Coombes J,Watkins J,Evans JM,Fina L,Gifford L,Gilbert L,Graham L,Perry M,Morgan M,Bull M,Cronin M,Pacchiarini N,Craine N,Jones R,Howe R,Corden S,Rey S,Kumziene-Summerhayes S,Taylor S,Cottrell S,Jones S,Edwards S,O'Grady J,Page AJ,Wain J,Webber MA,Mather AE,Baker DJ,Rudder S,Yasir M,Thomson NM,Aydin A,Tedim AP,Kay GL,Trotter AJ,Gilroy RAJ,Alikhan NF,de Oliveira,Le Viet T,Meadows L,Kolyva A,Diaz M,Bell A,Gutierrez AV,Charles IG,Adriaenssens EM,Kingsley RA,Casey A,Simpson DA,Molnar Z,Thompson T,Acheson E,Masoli JAH,Knight BA,Hattersley A,Ellard S,Auckland C,Mahungu TW,Irish-Tavares D,Haque T,Bourgeois Y,Scarlett GP,Partridge DG,Raza M,Evans C,Johnson K,Liggett S,Baker P,Essex S,Lyons RA,Caller LG,Castellano S,Williams RJ,Kristiansen M,Roy S,Williams CA,Dyal PL,Tutill HJ,Panchbhaya YN,Forrest LM,Niola P,Findlay J,Brooks TT,Gavriil A,Mestek-Boukhibar L,Weeks S,Pandey S,Berry L,Jones K,Richter A,Beggs A,Smith CP,Bucca G,Hesketh AR,Harrison EM,Peacock SJ,Palmer S,Churcher CM,Bellis KL,Girgis ST,Naydenova P,Blane B,Sridhar S,Ruis C,Forrest S,Cormie C,Gill HK,Dias J,Higginson EE,Maes M,Young J,Kermack LM,Hadjirin NF,Aggarwal D,Griffith L,Swingler T,Davidson RK,Rambaut A,Williams T,Balcazar CE,Gallagher MD,O'Toole Á,Rooke S,Jackson B,Colquhoun R,Ashworth J,Hill V,McCrone JT,Scher E,Yu X,Williamson KA,Stanton TD,Michell SL,Bewshea CM,Temperton B,Michelsen ML,Warwick-Dugdale J,Manley R,Farbos A,Harrison JW,Sambles CM,Studholme DJ,Jeffries AR,Darby AC,Hiscox JA,Paterson S,Iturriza-Gomara M,Jackson KA,Lucaci AO,Vamos EE,Hughes M,Rainbow L,Eccles R,Nelson C,Whitehead M,Turtle L,Haldenby ST,Gregory R,Gemmell M,Kwiatkowski D,de Silva,Smith N,Angyal A,Lindsey BB,Groves DC,Green LR,Wang D,Freeman TM,Parker MD,Keeley AJ,Parsons PJ,Tucker RM,Brown R,Wyles M,Constantinidou C,Unnikrishnan M,Ott S,Cheng JKJ,Bridgewater HE,Frost LR,Taylor-Joyce G,Stark R,Baxter L,Alam MT,Brown PE,McClure PC,Chappell JG,Tsoleridis T,Ball J,Gramatopoulos D,Buck D,Todd JA,Green A,Trebes A,MacIntyre-Cockett G,de Cesare,Langford C,Alderton A,Amato R,Goncalves S,Jackson DK,Johnston I,Sillitoe J,Palmer S,Lawniczak M,Berriman M,Danesh J,Livett R,Shirley L,Farr B,Quail M,Thurston S,Park N,Betteridge E,Weldon D,Goodwin S,Nelson R,Beaver C,Letchford L,Jackson DA,Foulser L,McMinn L,Prestwood L,Kay S,Kane L,Dorman MJ,Martincorena I,Puethe C,Keatley JP,Tonkin-Hill G,Smith C,Jamrozy D,Beale MA,Patel M,Ariani C,Spencer-Chapman M,Drury E,Lo S,Rajatileka S,Scott C,James K,Buddenborg SK,Berger DJ,Patel G,Garcia-Casado MV,Dibling T,McGuigan S,Rogers HA,Hunter AD,Souster E,Neaverson AS. (2021)

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Cell


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Sarwar MB, Yasir M, Alikhan NF, Afzal N, de Oliveira Martins L, Le Viet, Trotter AJ, Prosolek SJ, Kay GL, Foster-Nyarko E, Rudder S, Baker DJ, Muntaha ST, Roman M, Webber MA, Shafiq A, Shabbir B, Akram J, Page AJ, Jahan . (2021)

SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021.

Microbial genomics


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Snell LB, Fisher CL, Taj U, Stirrup O, Merrick B, Alcolea-Medina A, Charalampous T, Signell AW, Wilson HD, Betancor G, Kia Ik, Cunningham E, Cliff PR, Pickering S, Galao RP, Batra R, Neil SJD, Malim MH, Doores KJ, Douthwaite ST, Nebbia G, Edgeworth JD, Awan AR, Connor TR, Loman NJ, Robson SC, Golubchik T, Estee Torok, Hamilton WL, Bonsall D, Awan AR, Corden S, Goodfellow I, Smith DL, Curran MD, Parmar S, Logistics S, Curation M, Shepherd JG, Parker MD, Aggarwal D, Moore C, Fairley DJ, Loose MW, Watkins J, Bull M, Nicholls S, Aanensen DM, Glaysher S, Bashton M, Pacchiarini N, Underwood AP, de Silva, Wang D, Andersson M, Chauhan AJ, de Cesare, Ludden C, Mahungu TW, Dewar R, McHugh MP, Jesudason NG, Kathy KL, Shah RN, Taha Y, Templeton KE, Cottrell S, O'Grady J, Rambaut A, Smith CP, Holden MTG, Thomson EC, Moses S, Chand M, Constantinidou C, Darby AC, Hiscox JA, Paterson S, Unnikrishnan M, Page AJ, Volz EM, Houldcroft CJ, Jahun AS, McKenna JP, Meredith LW, Nelson A, Pandey S, Young GR, Price A, Re S, Roy S, Temperton B, Wyles M, Rooke S, Shaaban S, Adams H, Bourgeois Y, Loveson KF, O'Toole Á, Stark R, Harrison EM, Heyburn D, Peacock SJ, Buck D, John M, Jamrozy D, Quick J, Batra R, Bellis KL, Blane B, Girgis ST, Green A, Justice A, Kristiansen M, Williams RJ, Poplawski R, Scarlett GP, Todd JA, Fraser C, Breuer J, Castellano S, Michell SL, Gramatopoulos D, Edgeworth J, Kay GL, da Silva, Jeffries AR, Ott S, Pybus O, Robertson DL, Simpson DA, Williams C, Auckland C, Boyes J, Dervisevic S, Ellard S, Goncalves S, Meader EJ, Muir P, Osman H, Prakash R, Sivaprakasam V, Vipond IB, Masoli JA, Alikhan NF, Carlile M, Craine N, Haldenby ST, Holmes N, Lyons RA, Moore C, Perry M, Warne B, Williams T, Berry L, Bosworth A, Brown JR, Campbell S, Casey A, Clark G, Collins J, Cox A, Davis T, Eltringham G, Evans C, Graham C, Halstead F, Harris KA, Holmes C, Hutchings S, Iturriza-Gomara M, Johnson K, Jones K, Keeley AJ, Knight BA, Koshy C, Liggett S, Lowe H, Lucaci AO, Lynch J, McClure PC, Moore N, Mori M, Partridge DG, Madona P, Pymont HM, Randell PA, Raza M, Ryan F, Shaw R, Sloan TJ, Swindells E, Adams A, Asad H, Birchley A, Brooks TT, Bucca G, Butcher E, Caddy SL, Caller LG, Chaudhry Y, Coombes J, Cronin M, Dyal PL, Evans JM, Fina L, Gatica-Wilcox B, Georgana I, Gilbert L, Graham L, Groves DC, Hall G, Hilvers E, Hosmillo M, Jones H, Jones S, Khokhar FA, Kumziene-Summerhayes S, MacIntyre-Cockett G, Martinez Nunez, McKerr C, McMurray C, Myers R, Panchbhaya YN, Pinckert ML, Plimmer A, Stockton J, Taylor S, Thornton A, Trebes A, Trotter AJ, Tutill HJ, Williams CA, Yakovleva A, Yew WC, Alam MT, Baxter L, Boyd O, Nascimento FF, Freeman TM, Geidelberg L, Hughes J, Jorgensen D, Lindsey BB, Orton RJ, Ragonnet-Cronin M, Southgate J, Vattipally S, Starinskij I, Singer JB, Abudahab K, de Oliveira, Le-Viet T, Menegazzo M, Taylor Meng, Yeats CA, Palmer S, Churcher CM, Davies A, De Lacy, Downing F, Edwards S, Smith N, Coll F, Hadjirin NF, Bolt F, Alderton A, Berriman M, Charles IG, Cortes N, Curran T, Danesh J, Eldirdiri S, Elumogo N, Hattersley A, Holmes A, Howe R, Jones R, Kenyon A, Kingsley RA, Kwiatkowski D, Langford C, Mason J, Mather AE, Meadows L, Morgan S, Price J, Robinson TI, Shankar G, Wain J, Webber MA, Bradley DT, Chapman MR, Crooke D, Eyre D, Guest M, Gulliver H, Hoosdally S, Kitchen C, Merrick I, Mookerjee S, Munn R, Peto T, Potter W, Sethi DK, Smith W, Snell LB, Stanley R, Stuart C, Wastenge E, Acheson E, Afifi S, Allara E, Amato R, Angyal A, Aranday-Cortes E, Ariani C, Ashworth J, Attwood S, Aydin A, Baker DJ, Balcazar CE, Beckett A, Beer R, Betancor G, Betteridge E, Bibby D, Bradshaw D, Bresner C, Bridgewater HE, Broos A, Brown R, Brown PE, Brunker K, Carmichael SN, Cheng JKJ, Colquhoun R, Dabrera G, Debebe J, Drury E, du Plessis, Eccles R, Ellaby N, Farbos A, Farr B, Findlay J, Fisher CL, Forrest LM, Francois S, Frost LR, Fuller W, Gallagher E, Gallagher MD, Gemmell M, Gilroy RA, Goodwin S, Green LR, Gregory R, Groves N, Harrison JW, Hartman H, Hesketh AR, Hill V, Hubb J, Hughes M, Jackson DK, Jackson B, James K, Johnson N, Johnston I, Keatley JP, Kraemer M, Lackenby A, Lawniczak M, Lee D, Livett R, Lo S, Mair D, Maksimovic J, Manesis N, Manley R, Manso C, Marchbank A, Martincorena I, Mbisa T, McCluggage K, McCrone JT, Miah S, Michelsen ML, Morgan M, Nebbia G, Nelson C, Nichols J, Niola P, Nomikou K, Palmer S, Park N, Parr YA, Parsons PJ, Patel V, Patel M, Pearson C, Platt S, Puethe C, Quail M, Raghwani J, Rainbow L, Rajatileka S, Ramsay M, Resende Silva, Rudder S, Ruis C, Sambles CM, Sang F, Schaefer U, Scher E, Scott C, Shirley L, Signell AW, Sillitoe J, Smith C, Smollett KL, Spellman K, Stanton TD, Studholme DJ, Taylor-Joyce G, Tedim AP, Thompson T, Thomson NM, Thurston S, Tong L, Tonkin-Hill G, Tucker RM, Vamos EE, Vasylyeva T, Warwick-Dugdale J, Weldon D, Whitehead M, Williams D, Williamson KA, Wilson HD, Workman T, Yasir M, Yu X, Zarebski A, Evelien M, Ahmad SSY, Alcolea-Medina A, Allan J, Asamaphan P, Atkinson L, Baker P, Ball J, Barton E, Beale MA, Beaver C, Beggs A, Bell A, Berger DJ, Berry L, Bewshea CM, Bicknell K, Bird P, Bishop C, Boswell T, Breen C, Buddenborg SK, Burton-Fanning S, Chalker V, Chappell JG, Charalampous T, Cormie C, Cortes N, Coupland LJ, Cowell A, Davidson RK, Dias J, Diaz M, Dibling T, Dorman MJ, Duckworth N, Elliott S, Essex S, Fallon K, Feltwell T, Fleming VM, Forrest S, Foulser L, Garcia-Casado MV, Gavriil A, George RP, Gifford L, Gill HK, Greenaway J, Griffith L, Gutierrez AV, Hale AD, Haque T, Harper KL, Harrison I, Heaney J, Helmer T, Higginson EE, Hopes R, Howson-Wells HC, Hunter AD, Impey R, Irish-Tavares D, Jackson DA, Jackson KA, Joseph A, Kane L, Kay S, Kermack LM, Khakh M, Kidd SP, Kolyva A, Lee JC, Letchford L, Levene N, Levett L, Lister MM, Lloyd A, Loh J, Macfarlane-Smith LR, Machin NW, Maes M, McGuigan S, McMinn L, Mestek-Boukhibar L, Molnar Z, Monaghan L, Moore C, Naydenova P, Neaverson AS, Nelson R, Niebel MO, O'Toole E, Padgett D, Patel G, Payne BA, Prestwood L, Raviprakash V, Reynolds N, Richter A, Robinson E, Rogers HA, Rowan A, Scott G, Shah D, Sheriff N, Sluga G, Souster E, Spencer-Chapman M, Sridhar S, Swingler T, Tang J, Taylor GP, Tsoleridis T, Turtle L, Walsh S, Wantoch M, Watts J, Waugh S, Weeks S, Williams R, Willingham I, Wise EL, Wright V, Wyllie S, Young J, Amy Gaskin, Rowe W, Siveroni I, Johnson R. (2021)

Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases


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