Dr Philip Ashton
Clinical Infection, Microbiology & Immunology
- Work email Philip.Ashton@liverpool.ac.uk
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2024
A description of Lineage 1<i>Mycobacterium tuberculosis</i>from Papua, Indonesia (Preprint)
Evaluating the relationship between ciprofloxacin prescription and non-susceptibility in Salmonella Typhi in Blantyre, Malawi: an observational study. (Journal article)
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. (Journal article)
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/uqae0052023
Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems. (Journal article)
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-yGlobal diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 <i>Salmonella</i> Typhi genomes. (Journal article)
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.85867Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam (Journal article)
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/iyad100Utilizing 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. (Preprint)
FLASH-TB: an Application of Next-Generation CRISPR to Detect Drug Resistant Tuberculosis from Direct Sputum (Journal article)
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.01634-22Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam. (Journal article)
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:10.1101/2023.03.30.534926What is the Source of Infections Causing Invasive Nontyphoidal <i>Salmonella</i> Disease? (Journal article)
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/ofad086Different clinical features in Malawian outpatients presenting with COVID-19 prior to and during Omicron variant dominance: A prospective observational study. (Journal article)
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.0001575A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study (Journal article)
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-yDistribution and origins of <i>Mycobacterium tuberculosis</i> L4 in Southeast Asia. (Journal article)
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.0.0009552022
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. (Journal article)
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.0010982What is the source of infections causing invasive non-typhoidal Salmonella disease? (Preprint)
Distribution and origins of <i>Mycobacterium tuberculosis</i> L4 in Southeast Asia (Preprint)
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 (Journal article)
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:10.1101/2022.01.31.222701142020
Sources of Multidrug Resistance in Patients With Previous Isoniazid-Resistant Tuberculosis Identified Using Whole Genome Sequencing: A Longitudinal Cohort Study (Journal article)
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/ciaa254Carriage of the zoonotic organism Streptococcus suis in chicken flocks in Vietnam. (Journal article)
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.12711Assessing the virulence of Cryptococcus neoformans causing meningitis in HIV infected and uninfected patients in Vietnam. (Journal article)
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/myaa013An Evaluation of Progress Towards the 2035 WHO End TB Targets in 40 High Burden Countries (Preprint)
The virulence of the <i>Cryptococcus neoformans</i> VNIa-5 lineage is highly plastic and associated with isolate background (Preprint)
Complete Genome Sequences for Two <i>Talaromyces marneffei</i> Clinical Isolates from Northern and Southern Vietnam. (Journal article)
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.01367-192019
Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. (Journal article)
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/s41579-019-0214-5Multilocus sequence typing of Cryptococcus neoformans var. grubii from Laos in a regional and global context. (Journal article)
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/myy105Three phylogenetic groups have driven the recent population expansion of <i>Cryptococcus neoformans</i> (Journal article)
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/s41467-019-10092-5Informal genomic surveillance of regional distribution of <i>Salmonella</i> Typhi genotypes and antimicrobial resistance via returning travellers (Preprint)
Informal genomic surveillance of regional distribution of <i>Salmonella</i> Typhi genotypes and antimicrobial resistance via returning travellers (Journal article)
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.00076202018
Virulence of <i>Mycobacterium tuberculosis</i> Clinical Isolates Is Associated With Sputum Pre-treatment Bacterial Load, Lineage, Survival in Macrophages, and Cytokine Response. (Journal article)
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.2018.00417SnapperDB: a database solution for routine sequencing analysis of bacterial isolates. (Journal article)
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/bty212Genomics of<i>Cryptococcus neoformans</i> (Preprint)
Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014. (Journal article)
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.2017.02.012Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015. (Journal article)
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.2017.04.005Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal <i>Salmonella enterica</i> (Journal article)
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 (Journal article)
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/s41598-017-18667-2Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi. (Journal article)
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/dkx3792017
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. (Journal article)
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.2017.22.49.17-00037Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa (Journal article)
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/s13073-017-0480-7Multilocus Sequence Typing Reveals A Unique Co-Dominant Population Structure of <i>Cryptococcus Neoformans</i> Var. <i>Grubii</i> in Vietnam (Preprint)
Assessing the virulence of<i>Cryptococcus neoformans</i>causing meningitis in HIV infected and uninfected patients in Vietnam (Preprint)
SnapperDB: A database solution for routine sequencing analysis of bacterial isolates (Preprint)
Comparative genomics of Cryptococcus neoformans var. grubii associated with meningitis in HIV infected and uninfected patients in Vietnam. (Journal article)
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 (Preprint)
Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015. (Journal article)
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.2017.22.7.30463Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis (Journal article)
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/S09502688160019412016
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. (Journal article)
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/dkw318Phylogenetic structure of European <i>Salmonella</i> Enteritidis outbreak correlates with national and international egg distribution network (Journal article)
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.0.000070Detection 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. (Journal article)
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/dkw093Evaluation of Molecular Methods for Serotyping Shigella flexneri. (Journal article)
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.03386-15MOST: A modified MLST typing tool based on short read sequencing (Preprint)
MOST: A modified MLST typing tool based on short read sequencing (Preprint)
Association between use of proton pump inhibitors and non-typhoidal salmonellosis identified following investigation into an outbreak of Salmonella Mikawasima in the UK, 2013. (Journal article)
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/s0950268815002332Whole Genome Sequencing for Public Health Surveillance of Shiga Toxin-Producing Escherichia coli Other than Serogroup O157. (Journal article)
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.2016.00258Identification of Salmonella for public health surveillance using whole genome sequencing. (Journal article)
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.1752MOST: a modified MLST typing tool based on short read sequencing. (Journal article)
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.23082015
Revolutionising Public Health Reference Microbiology using Whole Genome Sequencing: Salmonella as an exemplar (Preprint)
Identification and typing of Salmonella for public health surveillance using whole genome sequencing (Preprint)
Identification and typing of Salmonella for public health surveillance using whole genome sequencing (Preprint)
Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association. (Journal article)
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/srep14145Applying phylogenomics to understand the emergence of Shiga-toxin-producing <i>Escherichia coli</i> O157:H7 strains causing severe human disease in the UK. (Journal article)
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.0.000029Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study (Journal article)
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-XWhole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. (Journal article)
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/civ318Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. (Journal article)
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/s13059-015-0677-2A 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 (Journal article)
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.ES2015.20.16.21098Whole Genome Sequencing for the Retrospective Investigation of an Outbreak of Salmonella Typhimurium DT 8. (Journal article)
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.2c05a47d292f376afc5a6fcdd8a7a3b6DOI: 10.1371/currents.outbreaks.2c05a47d292f376afc5a6fcdd8a7a3b6