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Cambridge Public Health

 

Whole genome sequencing
multi-drug resistant organisms

Publications from Elements

Journal articles

2022

  • Illingworth, CJR., Hamilton, WL., Jackson, C., Warne, B., Popay, A., Meredith, L., Hosmillo, M., Jahun, A., Fieldman, T., Routledge, M., Houldcroft, CJ., Caller, L., Caddy, S., Yakovleva, A., Hall, G., Khokhar, FA., Feltwell, T., Pinckert, ML., Georgana, I., Chaudhry, Y., Curran, M., Parmar, S., Sparkes, D., Rivett, L., Jones, NK., Sridhar, S., Forrest, S., Dymond, T., Grainger, K., Workman, C., Gkrania-Klotsas, E., Brown, NM., Weekes, MP., Baker, S., Peacock, SJ., Gouliouris, T., Goodfellow, I., Angelis, DD. and Török, ME., 2022. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events. Mol Biol Evol, v. 39
    Doi: http://doi.org/10.1093/molbev/msac025
  • 2021 (Accepted for publication)

  • Peacock, S., Hamilton, W., Torok, ME., COG-UK Consortium, , Goodfellow, I. and Dougan, G., 2021 (Accepted for publication). Genomic epidemiology of COVID-19 in 1 care homes in the 2 East of England eLife,
    Doi: http://doi.org/10.7554/eLife.64618
  • Tonkin-Hill, G., Martincorena, I., Amato, R., Lawson, AR., Gerstung, M., Johnston, I., Jackson, DK., Park, N., Lensing, SV., Quail, MA., Gonçalves, S., Ariani, C., Spencer Chapman, M., Hamilton, WL., Meredith, LW., Hall, G., Jahun, AS., Chaudhry, Y., Hosmillo, M., Pinckert, ML., Georgana, I., Yakovleva, A., Caller, LG., Caddy, SL., Feltwell, T., Khokhar, FA., Houldcroft, CJ., Curran, MD., Parmar, S., COVID-19 Genomics UK (COG-UK) Consortium, , Alderton, A., Nelson, R., Harrison, EM., Sillitoe, J., Bentley, SD., Barrett, JC., Torok, ME., Goodfellow, IG., Langford, C., Kwiatkowski, D. and Wellcome Sanger Institute COVID-19 Surveillance Team, , 2021 (Accepted for publication). Patterns of within-host genetic diversity in SARS-CoV-2 eLife, v. 10
    Doi: http://doi.org/10.7554/eLife.66857
  • Snell, LB., Fisher, CL., Taj, U., Stirrup, O., Merrick, B., Alcolea-Medina, A., Charalampous, T., Signell, AW., Wilson, HD., Betancor, G., Kia Ik, MT., Cunningham, E., Cliff, PR., Pickering, S., Galao, RP., Batra, R., Neil, SJD., Malim, MH., Doores, KJ., Douthwaite, ST., Nebbia, G., COVID-19 Genomics UK (COG-UK) consortium, , Edgeworth, JD. and Awan, AR., 2021 (Accepted for publication). 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,
    Doi: http://doi.org/10.1016/j.cmi.2021.07.040
  • Peacock, S., Illingworth, C., Torok, ME. and Goodfellow, I., 2021 (Accepted for publication). Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections eLife, v. 10
    Doi: http://doi.org/10.7554/eLife.67308
  • Maes, M., Higginson, E., Pereira-Dias, J., Curran, MD., Parmar, S., Khokhar, F., Cuchet-Lourenço, D., Lux, J., Sharma-Hajela, S., Ravenhill, B., Hamed, I., Heales, L., Mahroof, R., Solderholm, A., Forrest, S., Sridhar, S., Brown, NM., Baker, S., Navapurkar, V., Dougan, G., Bartholdson Scott, J. and Conway Morris, A., 2021 (Accepted for publication). Ventilator-associated pneumonia in critically ill patients with COVID-19 Critical Care (UK),
  • 2021

  • Macleod, CK., Khokhar, FA., Warne, B., Wick, R., Butcher, R., Cassimon, B., Hayden, P., Holt, K. and Török, ME., 2021. Rapid Whole Genome Sequencing of Serotype K1 Hypervirulent Klebsiella pneumoniae from an Undocumented Chinese Migrant. Case Rep Infect Dis, v. 2021
    Doi: http://doi.org/10.1155/2021/6638780
  • Srivastava, S., Khokhar, F., Madhav, A., Pembroke, B., Shetty, V. and Mutreja, A., 2021. COVID-19 lessons for climate change and sustainable health Energies, v. 14
    Doi: http://doi.org/10.3390/en14185938
  • Clark, JA., Kean, IRL., Curran, MD., Khokhar, F., White, D., Daubney, E., Conway Morris, A., Navapurkar, V., Bartholdson Scott, J., Maes, M., Bousfield, R., Gouliouris, T., Agrawal, S., Inwald, D., Zhang, Z., Török, ME., Baker, S. and Pathan, N., 2021. Rapid Assay for Sick Children with Acute Lung infection Study (RASCALS): diagnostic cohort study protocol. BMJ Open, v. 11
    Doi: http://doi.org/10.1136/bmjopen-2021-056197
  • 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 Filipe, A., Shepherd, J., Pascall, DJ., Shah, R., Jesudason, N., Li, K., Jarrett, R., Pacchiarini, N., Bull, M., Geidelberg, L., Siveroni, I., COG-UK Consortium, , Goodfellow, I., Loman, NJ., Pybus, OG., Robertson, DL., Thomson, EC., Rambaut, A. and Connor, TR., 2021. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity Cell, v. 184
    Doi: http://doi.org/10.1016/j.cell.2020.11.020
  • 2020 (Accepted for publication)

  • Weekes, M., 2020 (Accepted for publication). Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19 eLife,
    Doi: http://doi.org/10.7554/eLife.59391
  • Weekes, M., rivett, L., Sridhar, S., sparkes, D., routledge, M., jones, N., forrest, S., young, J., Pereira-Dias, J., hamilton, W., torok, E., Meredith, L., curran, M., fuller, S., Samworth, R., Bradley, J., Dougan, G., Smith, K., Lehner, P., Matheson, N., Goodfellow, I. and Baker, S., 2020 (Accepted for publication). Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission eLife,
  • 2020

  • The COVID-19 Genomics UK (COG-UK) consortium, , 2020. An integrated national scale SARS-CoV-2 genomic surveillance network The Lancet Microbe, v. 1
    Doi: http://doi.org/10.1016/S2666-5247(20)30054-9
  • Peacock, S., Meredith, L., Dougan, G., Torok, ME., Baker, S., Brwon, N. and Gouliouris, T., 2020. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study Lancet Infectious Diseases,
    Doi: http://doi.org/10.1016/S1473-3099(20)30562-4
  • 2018

  • Wilson, HJ., Khokhar, F., Enoch, DA., Brown, NM., Ahluwalia, J., Dougan, G. and Török, ME., 2018. Point-prevalence survey of carbapenemase-producing Enterobacteriaceae and vancomycin-resistant enterococci in adult inpatients in a university teaching hospital in the UK. J Hosp Infect, v. 100
    Doi: http://doi.org/10.1016/j.jhin.2018.06.024