Publications
2024
A description of lineage 1 Mycobacterium tuberculosis from papua, Indonesia.
Djunaedy, H. A. K., Febinia, C. A., Hamers, R. L., Baird, K., Elyazar, I., Thuong, N. T. T., . . . Ashton, P. M. (2024). A description of lineage 1 Mycobacterium tuberculosis from papua, Indonesia.. Tuberculosis (Edinburgh, Scotland), 149, 102568. doi:10.1016/j.tube.2024.102568
Enterotoxigenic Escherichia coli in Blantyre, Malawi
Ashton, P. M., Katuah, Z. J., Botomani, A., Kutambe, B. M., Cunliffe, N. A., von Mentzer, A., . . . Jere, K. C. (2024). Enterotoxigenic Escherichia coli in Blantyre, Malawi. Access Microbiology, 6(11). doi:10.1099/acmi.0.000885.v3
Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent<i>Salmonella</i>Typhi
Enterotoxigenic Escherichia coli in Blantyre, Malawi
Interplay Between the Gut Microbiome and Typhoid Fever: Insights from Endemic Countries and a Controlled Human Infection Model
Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study.
Dyson, Z. A., Ashton, P. M., Khanam, F., Chunga Chirambo, A., Shakya, M., Meiring, J. E., . . . STRATAA Study Group. (2024). Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study.. The Lancet. Microbe, 5(8), 100841. doi:10.1016/s2666-5247(24)00047-8
Enterotoxigenic Escherichia coli in Blantyre, Malawi
A description of Lineage 1<i>Mycobacterium tuberculosis</i>from Papua, Indonesia
Evaluating the relationship between ciprofloxacin prescription and non-susceptibility in Salmonella Typhi in Blantyre, Malawi: an observational study.
Ashton, P. M., Chunga Chirambo, A., Meiring, J. E., Patel, P. D., Mbewe, M., Silungwe, N., . . . Gordon, M. A. (2024). Evaluating the relationship between ciprofloxacin prescription and non-susceptibility in Salmonella Typhi in Blantyre, Malawi: an observational study.. The Lancet. Microbe, 5(3), e226-e234. doi:10.1016/s2666-5247(23)00327-0
<i>Salmonella enterica</i> serovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage.
Kumwenda, B., Canals, R., Predeus, A. V., Zhu, X., Kröger, C., Pulford, C., . . . Hinton, J. C. D. (2024). <i>Salmonella enterica</i> serovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage.. microLife, 5, uqae005. doi:10.1093/femsml/uqae005
2023
Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems.
Barnes, K. G., Levy, J. I., Gauld, J., Rigby, J., Kanjerwa, O., Uzzell, C. B., . . . Feasey, N. (2023). Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems.. Nature communications, 14(1), 7883. doi:10.1038/s41467-023-43047-y
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 <i>Salmonella</i> Typhi genomes.
Carey, M. E., Dyson, Z. A., Ingle, D. J., Amir, A., Aworh, M. K., Chattaway, M. A., . . . Global Typhoid Genomics Consortium Group Authorship. (2023). Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 <i>Salmonella</i> Typhi genomes.. eLife, 12, e85867. doi:10.7554/elife.85867
Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam
Sephton-Clark, P., Nguyen, T., Hoa, N. T., Ashton, P., van Doorn, H. R., Ly, V. T., . . . Cuomo, C. A. (2023). Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam. GENETICS. doi:10.1093/genetics/iyad100
Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems.
FLASH-TB: an Application of Next-Generation CRISPR to Detect Drug Resistant Tuberculosis from Direct Sputum
Tram, T. T. B., Ha, V. T. N., Trieu, L. P. T., Ashton, P. M., Crawford, E. D., Thu, D. D. A., . . . Thuong, N. T. T. (2023). FLASH-TB: an Application of Next-Generation CRISPR to Detect Drug Resistant Tuberculosis from Direct Sputum. JOURNAL OF CLINICAL MICROBIOLOGY, 61(4). doi:10.1128/jcm.01634-22
Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam.
Sephton-Clark, P., Nguyen, T., Hoa, N. T., Ashton, P., van Doorn, H. R., Ly, V. T., . . . Cuomo, C. A. (2023). Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam.. bioRxiv. doi:10.1101/2023.03.30.534926
What is the Source of Infections Causing Invasive Nontyphoidal <i>Salmonella</i> Disease?
Chirwa, E. B., Dale, H., Gordon, M. A., & Ashton, P. M. (2023). What is the Source of Infections Causing Invasive Nontyphoidal <i>Salmonella</i> Disease?. Open forum infectious diseases, 10(3), ofad086. doi:10.1093/ofid/ofad086
Different clinical features in Malawian outpatients presenting with COVID-19 prior to and during Omicron variant dominance: A prospective observational study.
Chibwana, M. G., Thole, H. W., Anscombe, C., Ashton, P. M., Green, E., Barnes, K. G., . . . Jambo, K. C. (2023). Different clinical features in Malawian outpatients presenting with COVID-19 prior to and during Omicron variant dominance: A prospective observational study.. PLOS global public health, 3(3), e0001575. doi:10.1371/journal.pgph.0001575
A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study
Anscombe, C., Lissauer, S., Thole, H., Rylance, J., Dula, D., Menyere, M., . . . Ashton, P. M. (2023). A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study. BMC INFECTIOUS DISEASES, 23(1). doi:10.1186/s12879-022-07941-y
Distribution and origins of <i>Mycobacterium tuberculosis</i> L4 in Southeast Asia.
Ashton, P. M., Cha, J., Anscombe, C., Thuong, N. T. T., Thwaites, G. E., & Walker, T. M. (2023). Distribution and origins of <i>Mycobacterium tuberculosis</i> L4 in Southeast Asia.. Microbial genomics, 9(2). doi:10.1099/mgen.0.000955
2022
Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission.
Koolman, L., Prakash, R., Diness, Y., Msefula, C., Nyirenda, T. S., Olgemoeller, F., . . . Gordon, M. A. (2022). Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission.. PLoS neglected tropical diseases, 16(12), e0010982. doi:10.1371/journal.pntd.0010982
What is the source of infections causing invasive non-typhoidal Salmonella disease?
Distribution and origins of <i>Mycobacterium tuberculosis</i> L4 in Southeast Asia
Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission
Koolman, L., Prakash, R., Diness, Y., Msefula, C., Nyirenda, T., Olgemoeller, F., . . . Gordon, M. (2022). Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission. doi:10.1101/2022.01.31.22270114
2020
Sources of Multidrug Resistance in Patients With Previous Isoniazid-Resistant Tuberculosis Identified Using Whole Genome Sequencing: A Longitudinal Cohort Study
Srinivasan, V., Ha, V. T. N., Vinh, D. N., Thai, P. V. K., Ha, D. T. M., Lan, N. H., . . . Thuong, N. T. T. (2020). Sources of Multidrug Resistance in Patients With Previous Isoniazid-Resistant Tuberculosis Identified Using Whole Genome Sequencing: A Longitudinal Cohort Study. CLINICAL INFECTIOUS DISEASES, 71(10), E532-E539. doi:10.1093/cid/ciaa254
Carriage of the zoonotic organism Streptococcus suis in chicken flocks in Vietnam.
Nhung, N. T., Yen, N. T. P., Cuong, N., Kiet, B. T., Hien, V. B., Campbell, J., . . . Carrique-Mas, J. (2020). Carriage of the zoonotic organism Streptococcus suis in chicken flocks in Vietnam.. Zoonoses and public health, 67(8), 843-848. doi:10.1111/zph.12711
Assessing the virulence of Cryptococcus neoformans causing meningitis in HIV infected and uninfected patients in Vietnam.
Thanh, L. T., Toffaletti, D. L., Tenor, J. L., Giamberardino, C., Sempowski, G. D., Asfaw, Y., . . . Day, J. N. (2020). Assessing the virulence of Cryptococcus neoformans causing meningitis in HIV infected and uninfected patients in Vietnam.. Medical mycology, 58(8), 1149-1161. doi:10.1093/mmy/myaa013
The virulence of the<i>Cryptococcus neoformans</i>VNIa-5 lineage is highly plastic and associated with isolate background
Complete Genome Sequences for Two <i>Talaromyces marneffei</i> Clinical Isolates from Northern and Southern Vietnam.
Cuomo, C. A., Shea, T., Nguyen, T., Ashton, P., Perfect, J., & Le, T. (2020). Complete Genome Sequences for Two <i>Talaromyces marneffei</i> Clinical Isolates from Northern and Southern Vietnam.. Microbiology resource announcements, 9(2), e01367-e01319. doi:10.1128/mra.01367-19
2019
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.
Meehan, C. J., Goig, G. A., Kohl, T. A., Verboven, L., Dippenaar, A., Ezewudo, M., . . . Van Rie, A. (2019). Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.. Nature reviews. Microbiology, 17(9), 533-545. doi:10.1038/s41579-019-0214-5
Multilocus sequence typing of Cryptococcus neoformans var. grubii from Laos in a regional and global context.
Thanh, L. T., Phan, T. H., Rattanavong, S., Nguyen, T. M., Duong, A. V., Dacon, C., . . . Day, J. N. (2019). Multilocus sequence typing of Cryptococcus neoformans var. grubii from Laos in a regional and global context.. Medical mycology, 57(5), 557-565. doi:10.1093/mmy/myy105
Three phylogenetic groups have driven the recent population expansion of <i>Cryptococcus neoformans</i>
Ashton, P. M., Thanh, L. T., Trieu, P. N., Van Anh, D., Trinh, N. M., Beardsley, J., . . . Day, J. N. (2019). Three phylogenetic groups have driven the recent population expansion of <i>Cryptococcus neoformans</i>. NATURE COMMUNICATIONS, 10. doi:10.1038/s41467-019-10092-5
Informal genomic surveillance of regional distribution of <i>Salmonella</i> Typhi genotypes and antimicrobial resistance via returning travellers
Informal genomic surveillance of regional distribution of <i>Salmonella</i> Typhi genotypes and antimicrobial resistance via returning travellers
Ingle, D. J., Nair, S., Hartman, H., Ashton, P. M., Dyson, Z. A., Day, M., . . . Dallman, T. J. (2019). Informal genomic surveillance of regional distribution of <i>Salmonella</i> Typhi genotypes and antimicrobial resistance via returning travellers. PLOS NEGLECTED TROPICAL DISEASES, 13(9). doi:10.1371/journal.pntd.0007620
2018
Virulence of <i>Mycobacterium tuberculosis</i> Clinical Isolates Is Associated With Sputum Pre-treatment Bacterial Load, Lineage, Survival in Macrophages, and Cytokine Response.
Tram, T. T. B., Nhung, H. N., Vijay, S., Hai, H. T., Thu, D. D. A., Ha, V. T. N., . . . Thuong, N. T. T. (2018). Virulence of <i>Mycobacterium tuberculosis</i> Clinical Isolates Is Associated With Sputum Pre-treatment Bacterial Load, Lineage, Survival in Macrophages, and Cytokine Response.. Frontiers in cellular and infection microbiology, 8, 417. doi:10.3389/fcimb.2018.00417
SnapperDB: a database solution for routine sequencing analysis of bacterial isolates.
Dallman, T., Ashton, P., Schafer, U., Jironkin, A., Painset, A., Shaaban, S., . . . Grant, K. (2018). SnapperDB: a database solution for routine sequencing analysis of bacterial isolates.. Bioinformatics (Oxford, England), 34(17), 3028-3029. doi:10.1093/bioinformatics/bty212
Genomics of<i>Cryptococcus neoformans</i>
Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014.
Waldram, A., Dolan, G., Ashton, P. M., Jenkins, C., & Dallman, T. J. (2018). Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014.. Food microbiology, 71, 39-45. doi:10.1016/j.fm.2017.02.012
Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015.
Kanagarajah, S., Waldram, A., Dolan, G., Jenkins, C., Ashton, P. M., Carrion Martin, A. I., . . . Elson, R. (2018). Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015.. Food microbiology, 71, 32-38. doi:10.1016/j.fm.2017.04.005
Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal <i>Salmonella enterica</i>
Neuert, S., Nair, S., Day, M. R., Doumith, M., Ashton, P. M., Mellor, K. C., . . . Dallman, T. J. (2018). Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal <i>Salmonella enterica</i>. FRONTIERS IN MICROBIOLOGY, 9. doi:10.3389/fmicb.2018.00592
<i>Salmonella</i> Enteritidis ST183: emerging and endemic biotypes affecting western European hedgehogs (<i>Erinaceus europaeus</i>) and people in Great Britain
Lawson, B., Franklinos, L. H. V., Fernandez, J. R. -R., Wend-Hansen, C., Nair, S., Macgregor, S. K., . . . de Pinna, E. M. (2018). <i>Salmonella</i> Enteritidis ST183: emerging and endemic biotypes affecting western European hedgehogs (<i>Erinaceus europaeus</i>) and people in Great Britain. SCIENTIFIC REPORTS, 8. doi:10.1038/s41598-017-18667-2
Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi.
Day, M. R., Doumith, M., Do Nascimento, V., Nair, S., Ashton, P. M., Jenkins, C., . . . Godbole, G. (2018). Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi.. The Journal of antimicrobial chemotherapy, 73(2), 365-372. doi:10.1093/jac/dkx379
2017
Investigation using whole genome sequencing of a prolonged restaurant outbreak of <i>Salmonella</i> Typhimurium linked to the building drainage system, England, February 2015 to March 2016.
Mair-Jenkins, J., Borges-Stewart, R., Harbour, C., Cox-Rogers, J., Dallman, T., Ashton, P., . . . Puleston, R. (2017). Investigation using whole genome sequencing of a prolonged restaurant outbreak of <i>Salmonella</i> Typhimurium linked to the building drainage system, England, February 2015 to March 2016.. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 22(49). doi:10.2807/1560-7917.es.2017.22.49.17-00037
Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa
Ashton, P. M., Owen, S. V., Kaindama, L., Rowe, W. P. M., Lane, C. R., Larkin, L., . . . Dallman, T. J. (2017). Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa. GENOME MEDICINE, 9. doi:10.1186/s13073-017-0480-7
Multilocus Sequence Typing Reveals A Unique Co-Dominant Population Structure of<i>Cryptococcus Neoformans</i>Var.<i>Grubii</i>in Vietnam
Assessing the virulence of<i>Cryptococcus neoformans</i>causing meningitis in HIV infected and uninfected patients in Vietnam
SnapperDB: A database solution for routine sequencing analysis of bacterial isolates
Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam.
Day, J. N., Qihui, S., Thanh, L. T., Trieu, P. H., Van, A. D., Thu, N. H., . . . Baker, S. (2017). Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam.. PLoS neglected tropical diseases, 11(6), e0005628. doi:10.1371/journal.pntd.0005628
<i>Salmonella enterica</i> serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in Africa
Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015.
Fonteneau, L., Jourdan Da Silva, N., Fabre, L., Ashton, P., Torpdahl, M., Müller, L., . . . Le Hello, S. (2017). Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015.. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 22(7). doi:10.2807/1560-7917.es.2017.22.7.30463
Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis
Inns, T., Ashton, P. M., Herrera-Leon, S., Lighthill, J., Foulkes, S., Jombart, T., . . . Vivancos, R. (2017). Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis. EPIDEMIOLOGY AND INFECTION, 145(2), 289-298. doi:10.1017/S0950268816001941
2016
WGS for surveillance of antimicrobial resistance: a pilot study to detect the prevalence and mechanism of resistance to azithromycin in a UK population of non-typhoidal Salmonella.
Nair, S., Ashton, P., Doumith, M., Connell, S., Painset, A., Mwaigwisya, S., . . . Day, M. (2016). WGS for surveillance of antimicrobial resistance: a pilot study to detect the prevalence and mechanism of resistance to azithromycin in a UK population of non-typhoidal Salmonella.. The Journal of antimicrobial chemotherapy, 71(12), 3400-3408. doi:10.1093/jac/dkw318
Phylogenetic structure of European <i>Salmonella</i> Enteritidis outbreak correlates with national and international egg distribution network
Dallman, T., Inns, T., Jombart, T., Ashton, P., Loman, N., Chatt, C., . . . Cleary, P. (2016). Phylogenetic structure of European <i>Salmonella</i> Enteritidis outbreak correlates with national and international egg distribution network. MICROBIAL GENOMICS, 2(8). doi:10.1099/mgen.0.000070
Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales.
Doumith, M., Godbole, G., Ashton, P., Larkin, L., Dallman, T., Day, M., . . . Woodford, N. (2016). Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales.. The Journal of antimicrobial chemotherapy, 71(8), 2300-2305. doi:10.1093/jac/dkw093
Evaluation of Molecular Methods for Serotyping Shigella flexneri.
Gentle, A., Ashton, P. M., Dallman, T. J., & Jenkins, C. (2016). Evaluation of Molecular Methods for Serotyping Shigella flexneri.. Journal of clinical microbiology, 54(6), 1456-1461. doi:10.1128/jcm.03386-15
MOST: A modified MLST typing tool based on short read sequencing
MOST: A modified MLST typing tool based on short read sequencing
Association between use of proton pump inhibitors and non-typhoidal salmonellosis identified following investigation into an outbreak of Salmonella Mikawasima in the UK, 2013.
Freeman, R., Dabrera, G., Lane, C., Adams, N., Browning, L., Fowler, T., . . . Adak, G. K. (2016). Association between use of proton pump inhibitors and non-typhoidal salmonellosis identified following investigation into an outbreak of Salmonella Mikawasima in the UK, 2013.. Epidemiology and infection, 144(5), 968-975. doi:10.1017/s0950268815002332
Whole Genome Sequencing for Public Health Surveillance of Shiga Toxin-Producing Escherichia coli Other than Serogroup O157.
Chattaway, M. A., Dallman, T. J., Gentle, A., Wright, M. J., Long, S. E., Ashton, P. M., . . . Jenkins, C. (2016). Whole Genome Sequencing for Public Health Surveillance of Shiga Toxin-Producing Escherichia coli Other than Serogroup O157.. Frontiers in microbiology, 7, 258. doi:10.3389/fmicb.2016.00258
Identification of Salmonella for public health surveillance using whole genome sequencing.
Ashton, P. M., Nair, S., Peters, T. M., Bale, J. A., Powell, D. G., Painset, A., . . . Salmonella Whole Genome Sequencing Implementation Group. (2016). Identification of Salmonella for public health surveillance using whole genome sequencing.. PeerJ, 4, e1752. doi:10.7717/peerj.1752
MOST: a modified MLST typing tool based on short read sequencing.
Tewolde, R., Dallman, T., Schaefer, U., Sheppard, C. L., Ashton, P., Pichon, B., . . . Underwood, A. (2016). MOST: a modified MLST typing tool based on short read sequencing.. PeerJ, 4, e2308. doi:10.7717/peerj.2308
2015
Revolutionising Public Health Reference Microbiology using Whole Genome Sequencing:<i>Salmonella</i>as an exemplar
Identification and typing of Salmonella for public health surveillance using whole genome sequencing
Identification and typing of Salmonella for public health surveillance using whole genome sequencing
Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.
Strachan, N. J. C., Rotariu, O., Lopes, B., MacRae, M., Fairley, S., Laing, C., . . . Forbes, K. J. (2015). Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.. Scientific reports, 5, 14145. doi:10.1038/srep14145
Applying phylogenomics to understand the emergence of Shiga-toxin-producing <i>Escherichia coli</i> O157:H7 strains causing severe human disease in the UK.
Dallman, T. J., Ashton, P. M., Byrne, L., Perry, N. T., Petrovska, L., Ellis, R., . . . Jenkins, C. (2015). Applying phylogenomics to understand the emergence of Shiga-toxin-producing <i>Escherichia coli</i> O157:H7 strains causing severe human disease in the UK.. Microbial genomics, 1(3), e000029. doi:10.1099/mgen.0.000029
Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study
Baker, K. S., Dallman, T. J., Ashton, P. M., Day, M., Hughes, G., Crook, P. D., . . . Thomson, N. R. (2015). Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. Lancet Infectious Diseases, 15(8), 913-921. doi:10.1016/S1473-3099(15)00002-X
Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.
Dallman, T. J., Byrne, L., Ashton, P. M., Cowley, L. A., Perry, N. T., Adak, G., . . . Wain, J. (2015). Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 61(3), 305-312. doi:10.1093/cid/civ318
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.
Quick, J., Ashton, P., Calus, S., Chatt, C., Gossain, S., Hawker, J., . . . Loman, N. J. (2015). Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.. Genome biology, 16, 114. doi:10.1186/s13059-015-0677-2
A multi-country <i>Salmonella</i> Enteritidis phage type 14b outbreak associated with eggs from a German producer: 'near real-time' application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014
Inns, T., Lane, C., Peters, T., Dallman, T., Chatt, C., McFarland, N., . . . Cleary, P. (2015). A multi-country <i>Salmonella</i> Enteritidis phage type 14b outbreak associated with eggs from a German producer: 'near real-time' application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014. EUROSURVEILLANCE, 20(16), 15-22. doi:10.2807/1560-7917.ES2015.20.16.21098
Whole Genome Sequencing for the Retrospective Investigation of an Outbreak of Salmonella Typhimurium DT 8.
Ashton, P. M., Peters, T., Ameh, L., McAleer, R., Petrie, S., Nair, S., . . . Dallman, T. (2015). Whole Genome Sequencing for the Retrospective Investigation of an Outbreak of Salmonella Typhimurium DT 8.. PLoS currents, 7, ecurrents.outbreaks.2c05a47d292f376afc5a6fcdd8a7a3. doi:10.1371/currents.outbreaks.2c05a47d292f376afc5a6fcdd8a7a3b6
Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing.
Ashton, P. M., Perry, N., Ellis, R., Petrovska, L., Wain, J., Grant, K. A., . . . Dallman, T. J. (2015). Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing.. PeerJ, 3, e739. doi:10.7717/peerj.739
MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island.
Ashton, P. M., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., . . . O'Grady, J. (2015). MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island.. Nature biotechnology, 33(3), 296-300. doi:10.1038/nbt.3103
2014
Insight into Shiga toxin genes encoded by <i>Escherichia coli </i>O157 from whole genome sequencing
Insight into Shiga toxin genes encoded by <i>Escherichia coli </i>O157 from whole genome sequencing
Draft genome sequences of the type strains of <i>Shigella flexneri</i> held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence
Ashton, P. M., Baker, K. S., Gentle, A., Wooldridge, D. J., Thomson, N. R., Dallman, T. J., & Jenkins, C. (2014). Draft genome sequences of the type strains of <i>Shigella flexneri</i> held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence. GUT PATHOGENS, 6. doi:10.1186/1757-4749-6-7
Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England.
Byrne, L., Elson, R., Dallman, T. J., Perry, N., Ashton, P., Wain, J., . . . Jenkins, C. (2014). Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England.. PloS one, 9(1), e85901. doi:10.1371/journal.pone.0085901