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Dingle KE, Freeman J, Didelot X, Quan TP, Eyre DW, Swann J, Spittal WD, Clark EV, Jolley KA, Walker AS, Wilcox MH, Crook DW. Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile. mBio 2023; 14:e0024323. [PMID: 37017518 PMCID: PMC10128037 DOI: 10.1128/mbio.00243-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Clostridioides difficile remains a key cause of healthcare-associated infection, with multidrug-resistant (MDR) lineages causing high-mortality (≥20%) outbreaks. Cephalosporin treatment is a long-established risk factor, and antimicrobial stewardship is a key control. A mechanism underlying raised cephalosporin MICs has not been identified in C. difficile, but among other species, this is often acquired via amino acid substitutions in cell wall transpeptidases (penicillin binding proteins [PBPs]). Here, we investigated five C. difficile transpeptidases (PBP1 to PBP5) for recent substitutions, associated cephalosporin MICs, and co-occurrence with fluoroquinolone resistance. Previously published genome assemblies (n = 7,096) were obtained, representing 16 geographically widespread lineages, including healthcare-associated ST1(027). Recent amino acid substitutions were found within PBP1 (n = 50) and PBP3 (n = 48), ranging from 1 to 10 substitutions per genome. β-Lactam MICs were measured for closely related pairs of wild-type and PBP-substituted isolates separated by 20 to 273 single nucleotide polymorphisms (SNPs). Recombination-corrected phylogenies were constructed to date substitution acquisition. Key substitutions such as PBP3 V497L and PBP1 T674I/N/V emerged independently across multiple lineages. They were associated with extremely high cephalosporin MICs; 1 to 4 doubling dilutions >wild-type, up to 1,506 μg/mL. Substitution patterns varied by lineage and clade, showed geographic structure, and occurred post-1990, coincident with the gyrA and/or gyrB substitutions conferring fluoroquinolone resistance. In conclusion, recent PBP1 and PBP3 substitutions are associated with raised cephalosporin MICs in C. difficile. Their co-occurrence with fluoroquinolone resistance hinders attempts to understand the relative importance of these drugs in the dissemination of epidemic lineages. Further controlled studies of cephalosporin and fluoroquinolone stewardship are needed to determine their relative effectiveness in outbreak control. IMPORTANCE Fluoroquinolone and cephalosporin use in healthcare settings has triggered outbreaks of high-mortality, multidrug-resistant C. difficile infection. Here, we identify a mechanism associated with raised cephalosporin MICs in C. difficile comprising amino acid substitutions in two cell wall transpeptidase enzymes (penicillin binding proteins). The higher the number of substitutions, the greater the impact on phenotype. Dated phylogenies revealed that substitutions associated with raised cephalosporin and fluoroquinolone MICs were co-acquired immediately before clinically important outbreak strains emerged. PBP substitutions were geographically structured within genetic lineages, suggesting adaptation to local antimicrobial prescribing. Antimicrobial stewardship of cephalosporins and fluoroquinolones is an effective means of C. difficile outbreak control. Genetic changes associated with raised MIC may impart a "fitness cost" after antibiotic withdrawal. Our study therefore identifies a mechanism that may explain the contribution of cephalosporin stewardship to resolving outbreak conditions. However, due to the co-occurrence of raised cephalosporin MICs and fluoroquinolone resistance, further work is needed to determine the relative importance of each.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jane Freeman
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
- Healthcare Associated Infections Research Group, The Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- Big Data Institute, Nuffield Department of Population Health, Oxford University of Oxford, Oxford, United Kingdom
| | - Jeremy Swann
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - William D Spittal
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
- Healthcare Associated Infections Research Group, The Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Emma V Clark
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
- Healthcare Associated Infections Research Group, The Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Keith A Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, United Kingdom
- Healthcare Associated Infections Research Group, The Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
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2
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Young BC, Bush SJ, Lipworth S, George S, Dingle KE, Sanderson N, Brankin A, Walker T, Sharma S, Leong J, Plaha P, Hofer M, Chiodini P, Gottstein B, Furrer L, Crook D, Brent A. Modern Solutions for Ancient Pathogens: Direct Pathogen Sequencing for Diagnosis of Lepromatous Leprosy and Cerebral Coenurosis. Open Forum Infect Dis 2022; 9:ofac428. [PMID: 36119959 PMCID: PMC9472670 DOI: 10.1093/ofid/ofac428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/21/2022] [Indexed: 11/26/2022] Open
Abstract
Microbes unculturable in vitro remain diagnostically challenging, dependent historically on clinical findings, histology, or targeted molecular detection. We applied whole-genome sequencing directly from tissue to diagnose infections with mycobacteria (leprosy) and parasites (coenurosis). Direct pathogen DNA sequencing provides flexible solutions to diagnosis of difficult pathogens in diverse contexts.
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Affiliation(s)
- Bernadette C Young
- Correspondence: Bernadette Young, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK ()
| | - Stephen J Bush
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sam Lipworth
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Sophie George
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Kate E Dingle
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nick Sanderson
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Alice Brankin
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Timothy Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Srilakshmi Sharma
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - James Leong
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Puneet Plaha
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Monika Hofer
- Department of Neuropathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Peter Chiodini
- Hospital of Tropical Diseases and the London School of Hygiene and Tropical Medicine London, London, United Kingdom
| | - B Gottstein
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Lavinia Furrer
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Derrick Crook
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Microbiology and Infectious Diseases Department, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
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3
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Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife 2021; 10:64325. [PMID: 34114561 PMCID: PMC8241443 DOI: 10.7554/elife.64325] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI–III. The emergence of these three novel genomospecies predates clades C1–5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.
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Affiliation(s)
- Daniel R Knight
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia
| | - Korakrit Imwattana
- School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Brian Kullin
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Enzo Guerrero-Araya
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile.,Department of Biology, Texas A&M University, College Station, United States
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V Riley
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
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4
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Ainsworth M, Andersson M, Auckland K, Baillie JK, Barnes E, Beer S, Beveridge A, Bibi S, Blackwell L, Borak M, Bown A, Brooks T, Burgess-Brown NA, Camara S, Catton M, Chau KK, Christott T, Clutterbuck E, Coker J, Cornall RJ, Cox S, Crawford-Jones D, Crook DW, D'Arcangelo S, Dejnirattsai W, Dequaire JMM, Dimitriadis S, Dingle KE, Doherty G, Dold C, Dong T, Dunachie SJ, Ebner D, Emmenegger M, Espinosa A, Eyre DW, Fairhead R, Fassih S, Feehily C, Felle S, Fernandez-Cid A, Fernandez Mendoza M, Foord TH, Fordwoh T, Fox McKee D, Frater J, Gallardo Sanchez V, Gent N, Georgiou D, Groves CJ, Hallis B, Hammond PM, Hatch SB, Harvala HJ, Hill J, Hoosdally SJ, Horsington B, Howarth A, James T, Jeffery K, Jones E, Justice A, Karpe F, Kavanagh J, Kim DS, Kirton R, Klenerman P, Knight JC, Koukouflis L, Kwok A, Leuschner U, Levin R, Linder A, Lockett T, Lumley SF, Marinou S, Marsden BD, Martinez J, Martins Ferreira L, Mason L, Matthews PC, Mentzer AJ, Mobbs A, Mongkolsapaya J, Morrow J, Mukhopadhyay SMM, Neville MJ, Oakley S, Oliveira M, Otter A, Paddon K, Pascoe J, Peng Y, Perez E, Perumal PK, Peto TEA, Pickford H, Ploeg RJ, Pollard AJ, Richardson A, Ritter TG, Roberts DJ, Rodger G, Rollier CS, Rowe C, Rudkin JK, Screaton G, Semple MG, Sienkiewicz A, Silva-Reyes L, Skelly DT, Sobrino Diaz A, Stafford L, Stockdale L, Stoesser N, Street T, Stuart DI, Sweed A, Taylor A, Thraves H, Tsang HP, Verheul MK, Vipond R, Walker TM, Wareing S, Warren Y, Wells C, Wilson C, Withycombe K, Young RK. Performance characteristics of five immunoassays for SARS-CoV-2: a head-to-head benchmark comparison. Lancet Infect Dis 2020; 20:1390-1400. [PMID: 32979318 PMCID: PMC7511171 DOI: 10.1016/s1473-3099(20)30634-4] [Citation(s) in RCA: 260] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic in 2020. Testing is crucial for mitigating public health and economic effects. Serology is considered key to population-level surveillance and potentially individual-level risk assessment. However, immunoassay performance has not been compared on large, identical sample sets. We aimed to investigate the performance of four high-throughput commercial SARS-CoV-2 antibody immunoassays and a novel 384-well ELISA. METHODS We did a head-to-head assessment of SARS-CoV-2 IgG assay (Abbott, Chicago, IL, USA), LIAISON SARS-CoV-2 S1/S2 IgG assay (DiaSorin, Saluggia, Italy), Elecsys Anti-SARS-CoV-2 assay (Roche, Basel, Switzerland), SARS-CoV-2 Total assay (Siemens, Munich, Germany), and a novel 384-well ELISA (the Oxford immunoassay). We derived sensitivity and specificity from 976 pre-pandemic blood samples (collected between Sept 4, 2014, and Oct 4, 2016) and 536 blood samples from patients with laboratory-confirmed SARS-CoV-2 infection, collected at least 20 days post symptom onset (collected between Feb 1, 2020, and May 31, 2020). Receiver operating characteristic (ROC) curves were used to assess assay thresholds. FINDINGS At the manufacturers' thresholds, for the Abbott assay sensitivity was 92·7% (95% CI 90·2-94·8) and specificity was 99·9% (99·4-100%); for the DiaSorin assay sensitivity was 96·2% (94·2-97·7) and specificity was 98·9% (98·0-99·4); for the Oxford immunoassay sensitivity was 99·1% (97·8-99·7) and specificity was 99·0% (98·1-99·5); for the Roche assay sensitivity was 97·2% (95·4-98·4) and specificity was 99·8% (99·3-100); and for the Siemens assay sensitivity was 98·1% (96·6-99·1) and specificity was 99·9% (99·4-100%). All assays achieved a sensitivity of at least 98% with thresholds optimised to achieve a specificity of at least 98% on samples taken 30 days or more post symptom onset. INTERPRETATION Four commercial, widely available assays and a scalable 384-well ELISA can be used for SARS-CoV-2 serological testing to achieve sensitivity and specificity of at least 98%. The Siemens assay and Oxford immunoassay achieved these metrics without further optimisation. This benchmark study in immunoassay assessment should enable refinements of testing strategies and the best use of serological testing resource to benefit individuals and population health. FUNDING Public Health England and UK National Institute for Health Research.
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5
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Adams ER, Ainsworth M, Anand R, Andersson MI, Auckland K, Baillie JK, Barnes E, Beer S, Bell JI, Berry T, Bibi S, Carroll M, Chinnakannan SK, Clutterbuck E, Cornall RJ, Crook DW, de Silva T, Dejnirattisai W, Dingle KE, Dold C, Espinosa A, Eyre DW, Farmer H, Fernandez Mendoza M, Georgiou D, Hoosdally SJ, Hunter A, Jefferey K, Kelly DF, Klenerman P, Knight J, Knowles C, Kwok AJ, Leuschner U, Levin R, Liu C, López-Camacho C, Martinez J, Matthews PC, McGivern H, Mentzer AJ, Milton J, Mongkolsapaya J, Moore SC, Oliveira MS, Pereira F, Perez E, Peto T, Ploeg RJ, Pollard A, Prince T, Roberts DJ, Rudkin JK, Sanchez V, Screaton GR, Semple MG, Slon-Campos J, Skelly DT, Smith EN, Sobrinodiaz A, Staves J, Stuart DI, Supasa P, Surik T, Thraves H, Tsang P, Turtle L, Walker AS, Wang B, Washington C, Watkins N, Whitehouse J. Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel. Wellcome Open Res 2020; 5:139. [PMID: 33748431 PMCID: PMC7941096 DOI: 10.12688/wellcomeopenres.15927.1] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2020] [Indexed: 01/26/2023] Open
Abstract
Background: The COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices. Methods: We tested plasma for COVID (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142). Results: ELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested ≥10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar. Conclusions: Currently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.
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Affiliation(s)
- Emily R. Adams
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Mark Ainsworth
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Rekha Anand
- NHS Blood and Transplant Birmingham, Vincent Drive, Birmingham, B15 2SG, UK
| | | | - Kathryn Auckland
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Sally Beer
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - John I. Bell
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Tamsin Berry
- Department of Health and Social Care, UK Government, London, UK
| | - Sagida Bibi
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Miles Carroll
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Senthil K. Chinnakannan
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Elizabeth Clutterbuck
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Richard J. Cornall
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Derrick W. Crook
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Thushan de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2RX, UK
| | - Wanwisa Dejnirattisai
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Kate E. Dingle
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Alexis Espinosa
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - David W. Eyre
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Helen Farmer
- Department of Health and Social Care, UK Government, London, UK
| | | | | | - Sarah J. Hoosdally
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Alastair Hunter
- NHS Blood and Transplant Basildon, Burnt Mills Industrial Estate, Basildon, SS13 1FH, UK
| | - Katie Jefferey
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dominic F. Kelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Julian Knight
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Clarice Knowles
- Department of Health and Social Care, UK Government, London, UK
| | - Andrew J. Kwok
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Ullrich Leuschner
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Chang Liu
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - César López-Camacho
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Jose Martinez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Philippa C. Matthews
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah McGivern
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Alexander J. Mentzer
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Jonathan Milton
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Juthathip Mongkolsapaya
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Shona C. Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Marta S. Oliveira
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Elena Perez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Timothy Peto
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Rutger J. Ploeg
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Andrew Pollard
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Tessa Prince
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - David J. Roberts
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | - Justine K. Rudkin
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Veronica Sanchez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Gavin R. Screaton
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Alder Hey Children's Hospital, Liverpool, UK
| | - Jose Slon-Campos
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Donal T. Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | | | - Julie Staves
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - David I. Stuart
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 ODE, UK
| | - Piyada Supasa
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Tomas Surik
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah Thraves
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Pat Tsang
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Tropical & Infectious Disease Unit, Royal Liverpool University Hospital (member of Liverpool Health Partners), Liverpool, L7 8XP, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Beibei Wang
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Nicholas Watkins
- NHS Blood and Transplant Cambridge, Long Road, Cambridge, CB2 0PT, UK
| | | | - National COVID Testing Scientific Advisory Panel
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- NHS Blood and Transplant Birmingham, Vincent Drive, Birmingham, B15 2SG, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RJ, UK
- Department of Health and Social Care, UK Government, London, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
- Public Health England, Porton Down, Salisbury, SP4 0JG, UK
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2RX, UK
- NHS Blood and Transplant Basildon, Burnt Mills Industrial Estate, Basildon, SS13 1FH, UK
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
- Worthing Hospital, Worthing, BN11 2DH, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Imperial College London, London, SW7 2AZ, UK
- Alder Hey Children's Hospital, Liverpool, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 ODE, UK
- Tropical & Infectious Disease Unit, Royal Liverpool University Hospital (member of Liverpool Health Partners), Liverpool, L7 8XP, UK
- NHS Blood and Transplant Cambridge, Long Road, Cambridge, CB2 0PT, UK
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6
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Adams ER, Ainsworth M, Anand R, Andersson MI, Auckland K, Baillie JK, Barnes E, Beer S, Bell JI, Berry T, Bibi S, Carroll M, Chinnakannan SK, Clutterbuck E, Cornall RJ, Crook DW, de Silva T, Dejnirattisai W, Dingle KE, Dold C, Espinosa A, Eyre DW, Farmer H, Fernandez Mendoza M, Georgiou D, Hoosdally SJ, Hunter A, Jefferey K, Kelly DF, Klenerman P, Knight J, Knowles C, Kwok AJ, Leuschner U, Levin R, Liu C, López-Camacho C, Martinez J, Matthews PC, McGivern H, Mentzer AJ, Milton J, Mongkolsapaya J, Moore SC, Oliveira MS, Pereira F, Perez E, Peto T, Ploeg RJ, Pollard A, Prince T, Roberts DJ, Rudkin JK, Sanchez V, Screaton GR, Semple MG, Slon-Campos J, Skelly DT, Smith EN, Sobrinodiaz A, Staves J, Stuart DI, Supasa P, Surik T, Thraves H, Tsang P, Turtle L, Walker AS, Wang B, Washington C, Watkins N, Whitehouse J. Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel. Wellcome Open Res 2020. [PMID: 33748431 DOI: 10.12688/wellcomeopenres10.12688/wellcomeopenres.15927.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023] Open
Abstract
Background: The COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices. Methods: We tested plasma for COVID (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142). Results: ELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested ≥10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar. Conclusions: Currently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.
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Affiliation(s)
- Emily R Adams
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Mark Ainsworth
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Rekha Anand
- NHS Blood and Transplant Birmingham, Vincent Drive, Birmingham, B15 2SG, UK
| | | | - Kathryn Auckland
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Sally Beer
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - John I Bell
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Tamsin Berry
- Department of Health and Social Care, UK Government, London, UK
| | - Sagida Bibi
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Miles Carroll
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Public Health England, Porton Down, Salisbury, SP4 0JG, UK
| | - Senthil K Chinnakannan
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Elizabeth Clutterbuck
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Richard J Cornall
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Derrick W Crook
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Thushan de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, S10 2RX, UK
| | - Wanwisa Dejnirattisai
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Kate E Dingle
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Christina Dold
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Alexis Espinosa
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - David W Eyre
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Helen Farmer
- Department of Health and Social Care, UK Government, London, UK
| | | | | | - Sarah J Hoosdally
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Alastair Hunter
- NHS Blood and Transplant Basildon, Burnt Mills Industrial Estate, Basildon, SS13 1FH, UK
| | - Katie Jefferey
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dominic F Kelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Julian Knight
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Clarice Knowles
- Department of Health and Social Care, UK Government, London, UK
| | - Andrew J Kwok
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Ullrich Leuschner
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - Chang Liu
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - César López-Camacho
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Jose Martinez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Philippa C Matthews
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah McGivern
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Alexander J Mentzer
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Jonathan Milton
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Juthathip Mongkolsapaya
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Marta S Oliveira
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Elena Perez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Timothy Peto
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Rutger J Ploeg
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Andrew Pollard
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, OX3 7LE, UK
| | - Tessa Prince
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - David J Roberts
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | - Justine K Rudkin
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Veronica Sanchez
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Gavin R Screaton
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Alder Hey Children's Hospital, Liverpool, UK
| | - Jose Slon-Campos
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Donal T Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | | | | | - Julie Staves
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - David I Stuart
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 ODE, UK
| | - Piyada Supasa
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Tomas Surik
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hannah Thraves
- Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Pat Tsang
- NHS Blood and Transplant Oxford, John Radcliffe Hospital, Oxford, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Tropical & Infectious Disease Unit, Royal Liverpool University Hospital (member of Liverpool Health Partners), Liverpool, L7 8XP, UK
| | - A Sarah Walker
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | - Beibei Wang
- Nuffield Department of Medicine and NIHR Oxford Biomedical Research Centre,, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Nicholas Watkins
- NHS Blood and Transplant Cambridge, Long Road, Cambridge, CB2 0PT, UK
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7
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Eyre DW, Davies KA, Davis G, Fawley WN, Dingle KE, De Maio N, Karas A, Crook DW, Peto TEA, Walker AS, Wilcox MH. Two Distinct Patterns of Clostridium difficile Diversity Across Europe Indicating Contrasting Routes of Spread. Clin Infect Dis 2019; 67:1035-1044. [PMID: 29659747 PMCID: PMC6137122 DOI: 10.1093/cid/ciy252] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 04/05/2018] [Indexed: 01/05/2023] Open
Abstract
Background Rates of Clostridium difficile infection vary widely across Europe, as do prevalent ribotypes. The extent of Europe-wide diversity within each ribotype, however, is unknown. Methods Inpatient diarrheal fecal samples submitted on a single day in summer and winter (2012–2013) to laboratories in 482 European hospitals were cultured for C. difficile, and isolates the 10 most prevalent ribotypes were whole-genome sequenced. Within each ribotype, country-based sequence clustering was assessed using the ratio of the median number of single-nucleotide polymorphisms between isolates within versus across different countries, using permutation tests. Time-scaled Bayesian phylogenies were used to reconstruct the historical location of each lineage. Results Sequenced isolates (n = 624) were from 19 countries. Five ribotypes had within-country clustering: ribotype 356, only in Italy; ribotype 018, predominantly in Italy; ribotype 176, with distinct Czech and German clades; ribotype 001/072, including distinct German, Slovakian, and Spanish clades; and ribotype 027, with multiple predominantly country-specific clades including in Hungary, Italy, Germany, Romania, and Poland. By contrast, we found no within-country clustering for ribotypes 078, 015, 002, 014, and 020, consistent with a Europe-wide distribution. Fluoroquinolone resistance was significantly more common in within-country clustered ribotypes (P = .009). Fluoroquinolone-resistant isolates were also more tightly clustered geographically with a median (interquartile range) of 43 (0–213) miles between each isolate and the most closely genetically related isolate, versus 421 (204–680) miles in nonresistant pairs (P < .001). Conclusions Two distinct patterns of C. difficile ribotype spread were observed, consistent with either predominantly healthcare-associated acquisition or Europe-wide dissemination via other routes/sources, for example, the food chain.
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Affiliation(s)
- David W Eyre
- Nuffield Department of Medicine, University of Oxford
| | - Kerrie A Davies
- Healthcare Associated Infections Research Group, University of Leeds
| | - Georgina Davis
- Healthcare Associated Infections Research Group, University of Leeds
| | - Warren N Fawley
- Healthcare Associated Infections Research Group, University of Leeds.,Public Health England, Leeds
| | - Kate E Dingle
- Nuffield Department of Medicine, University of Oxford
| | | | | | | | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford
| | | | - Mark H Wilcox
- Healthcare Associated Infections Research Group, University of Leeds
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8
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Eyre DW, Didelot X, Buckley AM, Freeman J, Moura IB, Crook DW, Peto TEA, Walker AS, Wilcox MH, Dingle KE. Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage. EBioMedicine 2019; 43:347-355. [PMID: 31036529 PMCID: PMC6558026 DOI: 10.1016/j.ebiom.2019.04.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
Background Clostridium difficile ribotype-027, ribotype-078, and ribotype-017 are virulent and epidemic lineages. Trehalose metabolism variants in these ribotypes, combined with increased human trehalose consumption, have been hypothesised to have contributed to their emergence and virulence. Methods 5232 previously whole-genome sequenced C. difficile isolates were analysed. Clinical isolates were used to investigate the impact of trehalose metabolism variants on mortality. Import data were used to estimate changes in dietary trehalose. Ribotype-027 virulence was investigated in a clinically reflective gut model. Findings Trehalose metabolism variants found in ribotype-027 and ribotype-017 were widely distributed throughout C. difficile clade-2 and clade-4 in 24/29 (83%) and 10/11 (91%) of sequence types (STs), respectively. The four-gene trehalose metabolism cluster described in ribotype-078 was common in genomes from all five clinically-important C. difficile clades (40/167 [24%] STs). The four-gene cluster was variably present in 208 ribotype-015 infections (98 [47%]); 27/208 (13%) of these patients died within 30-days of diagnosis. Adjusting for age, sex, and infecting ST, there was no association between 30-day all-cause mortality and the four-gene cluster (OR 0.36 [95%CI 0.09–1.34, p = 0.13]). Synthetic trehalose imports in the USA, UK, Germany and the EU were < 1 g/capita/year during 2000–2006, and < 9 g/capita/year 2007–2012, compared with dietary trehalose from natural sources of ~100 g/capita/year. Trehalose supplementation did not increase ribotype-027 virulence in a clinically-validated gut model. Interpretation Trehalose metabolism variants are common in C. difficile. Increases in total dietary trehalose during the early-mid 2000s C. difficile epidemic were likely relatively minimal. Alternative explanations are required to explain why ribotype-027, ribotype-078 and ribotype-017 have been successful. Funding National Institute for Health Research. Gut model experiments only: Hayashibara Co. Ltd.
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Affiliation(s)
- David W Eyre
- Big Data Institute, University of Oxford, UK; Nuffield Department of Medicine, University of Oxford, UK.
| | - Xavier Didelot
- School of Life Sciences, Department of Statistics, University of Warwick, UK
| | - Anthony M Buckley
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Jane Freeman
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Ines B Moura
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Kate E Dingle
- Nuffield Department of Medicine, University of Oxford, UK
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9
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Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Marwick CA, Coia J, Brown D, Buchanan S, Ijaz UZ, Goswami C, Douce G, Fawley WN, Wilcox MH, Peto TEA, Walker AS, Crook DW. A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078. mBio 2019; 10:e02790-18. [PMID: 30862754 PMCID: PMC6414706 DOI: 10.1128/mbio.02790-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/31/2019] [Indexed: 02/04/2023] Open
Abstract
The increasing clinical importance of human infections (frequently severe) caused by Clostridium difficile PCR ribotype 078 (RT078) was first reported in 2008. The severity of symptoms (mortality of ≤30%) and the higher proportion of infections among community and younger patients raised concerns. Farm animals, especially pigs, have been identified as RT078 reservoirs. We aimed to understand the recent changes in RT078 epidemiology by investigating a possible role for antimicrobial selection in its recent evolutionary history. Phylogenetic analysis of international RT078 genomes (isolates from 2006 to 2014, n = 400), using time-scaled, recombination-corrected, maximum likelihood phylogenies, revealed several recent clonal expansions. A common ancestor of each expansion had independently acquired a different allele of the tetracycline resistance gene tetM Consequently, an unusually high proportion (76.5%) of RT078 genomes were tetM positive. Multiple additional tetracycline resistance determinants were also identified (including efflux pump tet40), frequently sharing a high level of nucleotide sequence identity (up to 100%) with sequences found in the pig pathogen Streptococcus suis and in other zoonotic pathogens such as Campylobacter jejuni and Campylobacter coli Each RT078 tetM clonal expansion lacked geographic structure, indicating rapid, recent international spread. Resistance determinants for C. difficile infection-triggering antimicrobials, including fluoroquinolones and clindamycin, were comparatively rare in RT078. Tetracyclines are used intensively in agriculture; this selective pressure, plus rapid, international spread via the food chain, may explain the increased RT078 prevalence in humans. Our work indicates that the use of antimicrobials outside the health care environment has selected for resistant organisms, and in the case of RT078, has contributed to the emergence of a human pathogen.IMPORTANCEClostridium difficile PCR ribotype 078 (RT078) has multiple reservoirs; many are agricultural. Since 2005, this genotype has been increasingly associated with human infections in both clinical settings and the community. Investigations of RT078 whole-genome sequences revealed that tetracycline resistance had been acquired on multiple independent occasions. Phylogenetic analysis revealed a rapid, recent increase in numbers of closely related tetracycline-resistant RT078 (clonal expansions), suggesting that tetracycline selection has strongly influenced its recent evolutionary history. We demonstrate recent international spread of emergent, tetracycline-resistant RT078. A similar tetracycline-positive clonal expansion was also identified in unrelated nontoxigenic C. difficile, suggesting that this process may be widespread and may be independent of disease-causing ability. Resistance to typical C. difficile infection-associated antimicrobials (e.g., fluoroquinolones, clindamycin) occurred only sporadically within RT078. Selective pressure from tetracycline appears to be a key factor in the emergence of this human pathogen and the rapid international dissemination that followed, plausibly via the food chain.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - David W Eyre
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Charis A Marwick
- Population Health Sciences, School of Medicine, University of Dundee, Scotland, United Kingdom
| | - John Coia
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Derek Brown
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | | | - Umer Z Ijaz
- University of Glasgow, Scotland, United Kingdom
| | | | - Gill Douce
- University of Glasgow, Scotland, United Kingdom
| | - Warren N Fawley
- Department of Microbiology, Leeds General Infirmary, Leeds Teaching Hospitals, University of Leeds, Leeds, United Kingdom
| | - Mark H Wilcox
- Department of Microbiology, Leeds General Infirmary, Leeds Teaching Hospitals, University of Leeds, Leeds, United Kingdom
| | - Timothy E A Peto
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
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10
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Stoesser N, Eyre DW, Quan TP, Godwin H, Pill G, Mbuvi E, Vaughan A, Griffiths D, Martin J, Fawley W, Dingle KE, Oakley S, Wanelik K, Finney JM, Kachrimanidou M, Moore CE, Gorbach S, Riley TV, Crook DW, Peto TEA, Wilcox MH, Walker AS. Epidemiology of Clostridium difficile in infants in Oxfordshire, UK: Risk factors for colonization and carriage, and genetic overlap with regional C. difficile infection strains. PLoS One 2017; 12:e0182307. [PMID: 28813461 PMCID: PMC5559064 DOI: 10.1371/journal.pone.0182307] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/16/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Approximately 30-40% of children <1 year of age are Clostridium difficile colonized, and may represent a reservoir for adult C. difficile infections (CDI). Risk factors for colonization with toxigenic versus non-toxigenic C. difficile strains and longitudinal acquisition dynamics in infants remain incompletely characterized. METHODS Predominantly healthy infants (≤2 years) were recruited in Oxfordshire, UK, and provided ≥1 fecal samples. Independent risk factors for toxigenic/non-toxigenic C. difficile colonization and acquisition were identified using multivariable regression. Infant C. difficile isolates were whole-genome sequenced to assay genetic diversity and prevalence of toxin-associated genes, and compared with sequenced strains from Oxfordshire CDI cases. RESULTS 338/365 enrolled infants provided 1332 fecal samples, representing 158 C. difficile colonization or carriage episodes (107[68%] toxigenic). Initial colonization was associated with age, and reduced with breastfeeding but increased with pet dogs. Acquisition was associated with older age, Caesarean delivery, and diarrhea. Breastfeeding and pre-existing C. difficile colonization reduced acquisition risk. Overall 13% of CDI C. difficile strains were genetically related to infant strains. 29(18%) infant C. difficile sequences were consistent with recent direct/indirect transmission to/from Oxfordshire CDI cases (≤2 single nucleotide variants [SNVs]); 79(50%) shared a common origin with an Oxfordshire CDI case within the last ~5 years (0-10 SNVs). The hypervirulent, epidemic ST1/ribotype 027 remained notably absent in infants in this large study, as did other lineages such as STs 10/44 (ribotype 015); the most common strain in infants was ST2 (ribotype 020/014)(22%). CONCLUSIONS In predominantly healthy infants without significant healthcare exposure C. difficile colonization and acquisition reflect environmental exposures, with pet dogs identified as a novel risk factor. Genetic overlap between some infant strains and those isolated from CDI cases suggest common community reservoirs of these C. difficile lineages, contrasting with those lineages found only in CDI cases, and therefore more consistent with healthcare-associated spread.
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Affiliation(s)
- Nicole Stoesser
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - David W. Eyre
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - T. Phuong Quan
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - Heather Godwin
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
| | - Gemma Pill
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
| | - Emily Mbuvi
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
| | - Alison Vaughan
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - David Griffiths
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - Jessica Martin
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Old Medical School, Leeds General Infirmary, Leeds, United Kingdom
| | - Warren Fawley
- Public Health England (Leeds laboratory), Old Medical School, Leeds General Infirmary, Leeds, United Kingdom
| | - Kate E. Dingle
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - Sarah Oakley
- Microbiology Laboratory, John Radcliffe Hospital, Headington, United Kingdom
| | - Kazimierz Wanelik
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
| | - John M. Finney
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - Melina Kachrimanidou
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, University Campus, Thessaloniki, Greece
| | - Catrin E. Moore
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
| | - Sherwood Gorbach
- Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Thomas V. Riley
- Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Derrick W. Crook
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - Tim E. A. Peto
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
| | - Mark H. Wilcox
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Old Medical School, Leeds General Infirmary, Leeds, United Kingdom
| | - A. Sarah Walker
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Headington, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Headington, United Kingdom
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11
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Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Golubchik T, Harding RM, Wilson DJ, Griffiths D, Vaughan A, Finney JM, Wyllie DH, Oakley SJ, Fawley WN, Freeman J, Morris K, Martin J, Howard P, Gorbach S, Goldstein EJC, Citron DM, Hopkins S, Hope R, Johnson AP, Wilcox MH, Peto TEA, Walker AS, Crook DW. Effects of control interventions on Clostridium difficile infection in England: an observational study. Lancet Infect Dis 2017; 17:411-421. [PMID: 28130063 PMCID: PMC5368411 DOI: 10.1016/s1473-3099(16)30514-x] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/02/2023]
Abstract
BACKGROUND The control of Clostridium difficile infections is an international clinical challenge. The incidence of C difficile in England declined by roughly 80% after 2006, following the implementation of national control policies; we tested two hypotheses to investigate their role in this decline. First, if C difficile infection declines in England were driven by reductions in use of particular antibiotics, then incidence of C difficile infections caused by resistant isolates should decline faster than that caused by susceptible isolates across multiple genotypes. Second, if C difficile infection declines were driven by improvements in hospital infection control, then transmitted (secondary) cases should decline regardless of susceptibility. METHODS Regional (Oxfordshire and Leeds, UK) and national data for the incidence of C difficile infections and antimicrobial prescribing data (1998-2014) were combined with whole genome sequences from 4045 national and international C difficile isolates. Genotype (multilocus sequence type) and fluoroquinolone susceptibility were determined from whole genome sequences. The incidence of C difficile infections caused by fluoroquinolone-resistant and fluoroquinolone-susceptible isolates was estimated with negative-binomial regression, overall and per genotype. Selection and transmission were investigated with phylogenetic analyses. FINDINGS National fluoroquinolone and cephalosporin prescribing correlated highly with incidence of C difficile infections (cross-correlations >0·88), by contrast with total antibiotic prescribing (cross-correlations <0·59). Regionally, C difficile decline was driven by elimination of fluoroquinolone-resistant isolates (approximately 67% of Oxfordshire infections in September, 2006, falling to approximately 3% in February, 2013; annual incidence rate ratio 0·52, 95% CI 0·48-0·56 vs fluoroquinolone-susceptible isolates: 1·02, 0·97-1·08). C difficile infections caused by fluoroquinolone-resistant isolates declined in four distinct genotypes (p<0·01). The regions of phylogenies containing fluoroquinolone-resistant isolates were short-branched and geographically structured, consistent with selection and rapid transmission. The importance of fluoroquinolone restriction over infection control was shown by significant declines in inferred secondary (transmitted) cases caused by fluoroquinolone-resistant isolates with or without hospital contact (p<0·0001) versus no change in either group of cases caused by fluoroquinolone-susceptible isolates (p>0·2). INTERPRETATION Restricting fluoroquinolone prescribing appears to explain the decline in incidence of C difficile infections, above other measures, in Oxfordshire and Leeds, England. Antimicrobial stewardship should be a central component of C difficile infection control programmes. FUNDING UK Clinical Research Collaboration (Medical Research Council, Wellcome Trust, National Institute for Health Research); NIHR Oxford Biomedical Research Centre; NIHR Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance (Oxford University in partnership with Public Health England [PHE]), and on Modelling Methodology (Imperial College, London in partnership with PHE); and the Health Innovation Challenge Fund.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, and NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London in partnership with Public Health England, Imperial College, London, London, UK
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - David W Eyre
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Tanya Golubchik
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Rosalind M Harding
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Department of Zoology, Oxford University, Oxford, UK
| | - Daniel J Wilson
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Griffiths
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Alison Vaughan
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - John M Finney
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - David H Wyllie
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Public Health England Academic Collaborating Centre, Oxford, UK
| | - Sarah J Oakley
- Microbiology Department, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Warren N Fawley
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Jane Freeman
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Kirsti Morris
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Jessica Martin
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | | | - Sherwood Gorbach
- Cubist Pharmaceuticals, Lexington, MA, USA; Tufts University School of Medicine, Boston, MA, USA
| | | | | | - Susan Hopkins
- NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK; Healthcare-Associated Infection, Antimicrobial Resistance and Stewardship and Healthcare-Associated Infections Programme, Public Health England, London, UK; Royal Free London NHS Foundation Trust and Public Health England, London, UK
| | - Russell Hope
- Department of Healthcare-Associated Infections and Antimicrobial Resistance, Centre for Infectious Disease Surveillance and Control, National Infection Service, Public Health England, London, UK
| | - Alan P Johnson
- NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK; Department of Infectious Disease Epidemiology, and NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London in partnership with Public Health England, Imperial College, London, London, UK; Department of Healthcare-Associated Infections and Antimicrobial Resistance, Centre for Infectious Disease Surveillance and Control, National Infection Service, Public Health England, London, UK
| | - Mark H Wilcox
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Timothy E A Peto
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
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12
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Cody AJ, McCarthy ND, Bray JE, Wimalarathna HML, Colles FM, Jansen van Rensburg MJ, Dingle KE, Waldenström J, Maiden MCJ. Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom. Environ Microbiol Rep 2015; 7:782-8. [PMID: 26109474 PMCID: PMC4755149 DOI: 10.1111/1758-2229.12314] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/18/2015] [Indexed: 05/27/2023]
Abstract
The contribution of wild birds as a source of human campylobacteriosis was investigated in Oxfordshire, United Kingdom (UK) over a 10 year period. The probable origin of human Campylobacter jejuni genotypes, as described by multilocus sequence typing, was estimated by comparison with reference populations of isolates from farm animals and five wild bird families, using the STRUCTURE algorithm. Wild bird-attributed isolates accounted for between 476 (2.1%) and 543 (3.5%) cases annually. This proportion did not vary significantly by study year (P = 0.934) but varied seasonally, with wild bird-attributed genotypes comprising a greater proportion of isolates during warmer compared with cooler months (P = 0.003). The highest proportion of wild bird-attributed illness occurred in August (P < 0.001), with a significantly lower proportion in November (P = 0.018). Among genotypes attributed to specific groups of wild birds, seasonality was most apparent for Turdidae-attributed isolates, which were absent during cooler, winter months. This study is consistent with some wild bird species representing a persistent source of campylobacteriosis, and contributing a distinctive seasonal pattern to disease burden. If Oxfordshire is representative of the UK as a whole in this respect, these data suggest that the national burden of wild bird-attributed isolates could be in the order of 10,000 annually.
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Affiliation(s)
- Alison J Cody
- Department of Zoology, University of Oxford, Oxford, UK
| | - Noel D McCarthy
- Department of Zoology, University of Oxford, Oxford, UK
- Health Protection Agency, London, UK
- Warwick Medical School, University of Warwick, Coventry, UK
- NIHR Health Protections Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, UK
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford, UK
| | | | | | | | - Kate E Dingle
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Oxford, UK
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, Oxford, UK
- NIHR Health Protections Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, UK
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13
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Pankhurst L, Macfarlane-Smith L, Buchanan J, Anson L, Davies K, O'Connor L, Ashwin H, Pike G, Dingle KE, Peto TE, Wordsworth S, Walker AS, Wilcox MH, Crook DW. Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study. Health Technol Assess 2015; 18:1-167. [PMID: 25146932 DOI: 10.3310/hta18530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Every year approximately 5000-9000 patients are admitted to a hospital with diarrhoea, which in up to 90% of cases has a non-infectious cause. As a result, single rooms are 'blocked' by patients with non-infectious diarrhoea, while patients with infectious diarrhoea are still in open bays because of a lack of free side rooms. A rapid test for differentiating infectious from non-infectious diarrhoea could be very beneficial for patients. OBJECTIVE To evaluate MassCode multiplex polymerase chain reaction (PCR) for the simultaneous diagnosis of multiple enteropathogens directly from stool, in terms of sensitivity/specificity to detect four common important enteropathogens: Clostridium difficile, Campylobacter spp., Salmonella spp. and norovirus. DESIGN A retrospective study of fixed numbers of samples positive for C. difficile (n = 200), Campylobacter spp. (n = 200), Salmonella spp. (n = 100) and norovirus (n = 200) plus samples negative for all these pathogens (n = 300). Samples were sourced from NHS microbiology laboratories in Oxford and Leeds where initial diagnostic testing was performed according to Public Health England methodology. Researchers carrying out MassCode assays were blind to this information. A questionnaire survey, examining current practice for infection control teams and microbiology laboratories managing infectious diarrhoea, was also carried out. SETTING MassCode assays were carried out at Oxford University Hospitals NHS Trust. Further multiplex assays, carried out using Luminex, were run on the same set of samples at Leeds Teaching Hospitals NHS Trust. The questionnaire was completed by various NHS trusts. MAIN OUTCOME MEASURES Sensitivity and specificity to detect C. difficile, Campylobacter spp., Salmonella spp., and norovirus. RESULTS Nucleic acids were extracted from 948 clinical samples using an optimised protocol (200 Campylobacter spp., 199 C. difficile, 60 S. enterica, 199 norovirus and 295 negative samples; some samples contained more than one pathogen). Using the MassCode assay, sensitivities for each organism compared with standard microbiological testing ranged from 43% to 94% and specificities from 95% to 98%, with particularly poor performance for S. enterica. Relatively large numbers of unexpected positives not confirmed with quantitative PCR were also observed, particularly for S. enterica, Giardia lamblia and Cryptosporidium spp. As the results indicated that S. enterica detection might provide generic challenges to other multiplex assays for gastrointestinal pathogens, the Luminex xTag(®) gastrointestinal assay was also run blinded on the same extracts (937/948 remaining) and on re-extracted samples (839/948 with sufficient material). For Campylobacter spp., C. difficile and norovirus, high sensitivities (> 92%) and specificities (> 96%) were observed. For S. enterica, on the original MassCode/Oxford extracts, Luminex sensitivity compared with standard microbiological testing was 84% [95% confidence interval (CI) 73% to 93%], but this dropped to 46% on a fresh extract, very similar to MassCode, with a corresponding increase in specificity from 92% to 99%. Overall agreement on the per-sample diagnosis compared with combined microbiology plus PCR for the main four/all pathogens was 85.6%/64.7%, 87.0%/82.9% and 89.8%/86.8% for the MassCode assay, Luminex assay/MassCode extract and Luminex assay/fresh extract, respectively. Luminex assay results from fresh extracts implied that 5% of samples did not represent infectious diarrhoea, even though enteropathogens were genuinely present. Managing infectious diarrhoea was a significant burden for infection control teams (taking 21% of their time) and better diagnostics were identified as having major potential benefits for patients. CONCLUSIONS Overall, the Luminex xTag gastrointestinal panel showed similar or superior sensitivity and specificity to the MassCode assay. However, on fresh extracts, this test had low sensitivity to detect a key enteric pathogen, S. enterica; making it an unrealistic option for most microbiology laboratories. Extraction efficiency appears to be a major obstacle for nucleic acid-based tests for this organism, and possibly the whole Enterobacteriaceae family. To improve workflows in service microbiology laboratories, to reduce workload for infection control practitioners, and to improve outcomes for NHS patients, further research on deoxyribonucleic acid-based multiplex gastrointestinal diagnostics is urgently needed. FUNDING The Health Technology Assessment programme of the National Institute for Health Research.
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Affiliation(s)
- Louise Pankhurst
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Luke Anson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Lily O'Connor
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Helen Ashwin
- University of Leeds, Microbiology, Leeds General Infirmary Old Medical School, Leeds, UK
| | - Graham Pike
- Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Timothy Ea Peto
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Mark H Wilcox
- Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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14
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Eyre DW, Tracey L, Elliott B, Slimings C, Huntington PG, Stuart RL, Korman TM, Kotsiou G, McCann R, Griffiths D, Fawley WN, Armstrong P, Dingle KE, Walker AS, Peto TE, Crook DW, Wilcox MH, Riley TV. Emergence and spread of predominantly community-onset Clostridium difficile PCR ribotype 244 infection in Australia, 2010 to 2012. ACTA ACUST UNITED AC 2015; 20:21059. [PMID: 25788254 DOI: 10.2807/1560-7917.es2015.20.10.21059] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe an Australia-wide Clostridium difficile outbreak in 2011 and 2012 involving the previously uncommon ribotype 244. In Western Australia, 14 of 25 cases were community-associated, 11 were detected in patients younger than 65 years, 14 presented to emergency/outpatient departments, and 14 to non-tertiary/community hospitals. Using whole genome sequencing, we confirm ribotype 244 is from the same C. difficile clade as the epidemic ribotype 027. Like ribotype 027, it produces toxins A, B, and binary toxin, however it is fluoroquinolone-susceptible and thousands of single nucleotide variants distinct from ribotype 027. Fifteen outbreak isolates from across Australia were sequenced. Despite their geographic separation, all were genetically highly related without evidence of geographic clustering, consistent with a point source, for example affecting the national food chain. Comparison with reference laboratory strains revealed the outbreak clone shared a common ancestor with isolates from the United States and United Kingdom (UK). A strain obtained in the UK was phylogenetically related to our outbreak. Follow-up of that case revealed the patient had recently returned from Australia. Our data demonstrate new C. difficile strains are an on-going threat, with potential for rapid spread. Active surveillance is needed to identify and control emerging lineages.
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Affiliation(s)
- D W Eyre
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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15
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Abstract
The symptoms of Clostridium difficile infection are caused by two closely related toxins, TcdA and TcdB, which are encoded by the 19.6 kb Pathogenicity Locus (PaLoc). The PaLoc is variably present among strains, and in this respect it resembles a mobile genetic element. The C. difficile population structure consists mainly of five phylogenetic clades designated 1–5. Certain genotypes of clade 5 are associated with recently emergent highly pathogenic strains causing human disease and animal infections. The aim of this study was to explore the evolutionary history of the PaLoc in C. difficile clade 5. Phylogenetic analyses and annotation of clade 5 PaLoc variants and adjoining genomic regions were undertaken using a representative collection of toxigenic and nontoxigenic strains. Comparison of the core genome and PaLoc phylogenies obtained for clade 5 and representatives of the other clades identified two distinct PaLoc acquisition events, one involving a toxin A+B+ PaLoc variant and the other an A−B+ variant. Although the exact mechanism of each PaLoc acquisition is unclear, evidence of possible homologous recombination with other clades and between clade 5 lineages was found within the PaLoc and adjacent regions. The generation of nontoxigenic variants by PaLoc loss via homologous recombination with PaLoc-negative members of other clades was suggested by analysis of cdu2, although none is likely to have occurred recently. A variant of the putative holin gene present in the clade 5 A−B+ PaLoc was likely acquired via allelic exchange with an unknown element. Fine-scale phylogenetic analysis of C. difficile clade 5 revealed the extent of its genetic diversity, consistent with ancient evolutionary origins and a complex evolutionary history for the PaLoc.
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Affiliation(s)
- Briony Elliott
- Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, United Kingdom National Institute for Health Research, Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, United Kingdom National Institute for Health Research, Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Thomas V Riley
- Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
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Dingle KE, Elliott B, Robinson E, Griffiths D, Eyre DW, Stoesser N, Vaughan A, Golubchik T, Fawley WN, Wilcox MH, Peto TE, Walker AS, Riley TV, Crook DW, Didelot X. Evolutionary history of the Clostridium difficile pathogenicity locus. Genome Biol Evol 2014; 6:36-52. [PMID: 24336451 PMCID: PMC3914685 DOI: 10.1093/gbe/evt204] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The symptoms of Clostridium difficile infection are caused by toxins expressed from its 19 kb pathogenicity locus (PaLoc). Stable integration of the PaLoc is suggested by its single chromosomal location and the clade specificity of its different genetic variants. However, the PaLoc is variably present, even among closely related strains, and thus resembles a mobile genetic element. Our aim was to explain these apparently conflicting observations by reconstructing the evolutionary history of the PaLoc. Phylogenetic analyses and annotation of the regions spanning the PaLoc were performed using C. difficile population-representative genomes chosen from a collection of 1,693 toxigenic (PaLoc present) and nontoxigenic (PaLoc absent) isolates. Comparison of the core genome and PaLoc phylogenies demonstrated an eventful evolutionary history, with distinct PaLoc variants acquired clade specifically after divergence. In particular, our data suggest a relatively recent PaLoc acquisition in clade 4. Exchanges and losses of the PaLoc DNA have also occurred, via long homologous recombination events involving flanking chromosomal sequences. The most recent loss event occurred ∼30 years ago within a clade 1 genotype. The genetic organization of the clade 3 PaLoc was unique in containing a stably integrated novel transposon (designated Tn6218), variants of which were found at multiple chromosomal locations. Tn6218 elements were Tn916-related but nonconjugative and occasionally contained genes conferring resistance to clinically relevant antibiotics. The evolutionary histories of two contrasting but clinically important genetic elements were thus characterized: the PaLoc, mobilized rarely via homologous recombination, and Tn6218, mobilized frequently through transposition.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, United Kingdom
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Wong THN, Dearlove BL, Hedge J, Giess AP, Piazza P, Trebes A, Paul J, Smit E, Smith EG, Sutton JK, Wilcox MH, Dingle KE, Peto TEA, Crook DW, Wilson DJ, Wyllie DH. Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England. Virol J 2013; 10:335. [PMID: 24220146 PMCID: PMC3874643 DOI: 10.1186/1743-422x-10-335] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/11/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Norovirus is the commonest cause of epidemic gastroenteritis among people of all ages. Outbreaks frequently occur in hospitals and the community, costing the UK an estimated £110 m per annum. An evolutionary explanation for periodic increases in norovirus cases, despite some host-specific post immunity is currently limited to the identification of obvious recombinants. Our understanding could be significantly enhanced by full length genome sequences for large numbers of intensively sampled viruses, which would also assist control and vaccine design. Our objective is to develop rapid, high-throughput, end-to-end methods yielding complete norovirus genome sequences. We apply these methods to recent English outbreaks, placing them in the wider context of the international norovirus epidemic of winter 2012. METHOD Norovirus sequences were generated from 28 unique clinical samples by Illumina RNA sequencing (RNA-Seq) of total faecal RNA. A range of de novo sequence assemblers were attempted. The best assembler was identified by validation against three replicate samples and two norovirus qPCR negative samples, together with an additional 20 sequences determined by PCR and fractional capillary sequencing. Phylogenetic methods were used to reconstruct evolutionary relationships from the whole genome sequences. RESULTS Full length norovirus genomes were generated from 23/28 samples. 5/28 partial norovirus genomes were associated with low viral copy numbers. The de novo assembled sequences differed from sequences determined by capillary sequencing by <0.003%. Intra-host nucleotide sequence diversity was rare, but detectable by mapping short sequence reads onto its de novo assembled consensus. Genomes similar to the Sydney 2012 strain caused 78% (18/23) of cases, consistent with its previously documented association with the winter 2012 global outbreak. Interestingly, phylogenetic analysis and recombination detection analysis of the consensus sequences identified two related viruses as recombinants, containing sequences in prior circulation to Sydney 2012 in open reading frame (ORF) 2. CONCLUSION Our approach facilitates the rapid determination of complete norovirus genomes. This method provides high resolution of full norovirus genomes which, when coupled with detailed epidemiology, may improve the understanding of evolution and control of this important healthcare-associated pathogen.
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Affiliation(s)
- T H Nicholas Wong
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Public Health England Collaborating Centre, Oxford; John Radcliffe Hospital, Oxford, UK
| | - Bethany L Dearlove
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jessica Hedge
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Adam P Giess
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - John Paul
- Public Health Laboratory, Royal Sussex County Hospital, Brighton, UK
| | - Erasmus Smit
- Public Health Laboratory, Heart of England NHS Foundation Trust, Birmingham, UK
| | - E Grace Smith
- Public Health Laboratory, Heart of England NHS Foundation Trust, Birmingham, UK
| | - Julian K Sutton
- Public Health Laboratory, Southampton General Hospital, Southampton, UK
| | - Mark H Wilcox
- Public Health Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kate E Dingle
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Public Health England Collaborating Centre, Oxford; John Radcliffe Hospital, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Public Health England Collaborating Centre, Oxford; John Radcliffe Hospital, Oxford, UK
| | - Daniel J Wilson
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - David H Wyllie
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Public Health England Collaborating Centre, Oxford; John Radcliffe Hospital, Oxford, UK
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18
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Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O'Connor L, Ip CLC, Golubchik T, Batty EM, Finney JM, Wyllie DH, Didelot X, Piazza P, Bowden R, Dingle KE, Harding RM, Crook DW, Wilcox MH, Peto TEA, Walker AS. Diverse sources of C. difficile infection identified on whole-genome sequencing. N Engl J Med 2013; 369:1195-205. [PMID: 24066741 PMCID: PMC3868928 DOI: 10.1056/nejmoa1216064] [Citation(s) in RCA: 484] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND It has been thought that Clostridium difficile infection is transmitted predominantly within health care settings. However, endemic spread has hampered identification of precise sources of infection and the assessment of the efficacy of interventions. METHODS From September 2007 through March 2011, we performed whole-genome sequencing on isolates obtained from all symptomatic patients with C. difficile infection identified in health care settings or in the community in Oxfordshire, United Kingdom. We compared single-nucleotide variants (SNVs) between the isolates, using C. difficile evolution rates estimated on the basis of the first and last samples obtained from each of 145 patients, with 0 to 2 SNVs expected between transmitted isolates obtained less than 124 days apart, on the basis of a 95% prediction interval. We then identified plausible epidemiologic links among genetically related cases from data on hospital admissions and community location. RESULTS Of 1250 C. difficile cases that were evaluated, 1223 (98%) were successfully sequenced. In a comparison of 957 samples obtained from April 2008 through March 2011 with those obtained from September 2007 onward, a total of 333 isolates (35%) had no more than 2 SNVs from at least 1 earlier case, and 428 isolates (45%) had more than 10 SNVs from all previous cases. Reductions in incidence over time were similar in the two groups, a finding that suggests an effect of interventions targeting the transition from exposure to disease. Of the 333 patients with no more than 2 SNVs (consistent with transmission), 126 patients (38%) had close hospital contact with another patient, and 120 patients (36%) had no hospital or community contact with another patient. Distinct subtypes of infection continued to be identified throughout the study, which suggests a considerable reservoir of C. difficile. CONCLUSIONS Over a 3-year period, 45% of C. difficile cases in Oxfordshire were genetically distinct from all previous cases. Genetically diverse sources, in addition to symptomatic patients, play a major part in C. difficile transmission. (Funded by the U.K. Clinical Research Collaboration Translational Infection Research Initiative and others.).
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Affiliation(s)
- David W Eyre
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Madeleine L Cule
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Daniel J Wilson
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - David Griffiths
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Alison Vaughan
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Lily O'Connor
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Camilla L C Ip
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Tanya Golubchik
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Elizabeth M Batty
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - John M Finney
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - David H Wyllie
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Xavier Didelot
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Paolo Piazza
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Rory Bowden
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Rosalind M Harding
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Mark H Wilcox
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - Tim E A Peto
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine (D.W.E., D.J.W., D.G., A.V., L.O., J.M.F., D.H.W., K.E.D., D.W.C., T.E.A.P., A.S.W.), and the Departments of Statistics (M.L.C., C.L.C.I., T.G., X.D., R.B.) and Zoology (R.M.H.), University of Oxford, the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital (D.W.E., M.L.C., D.G., A.V., C.L.C.I., T.G., E.M.B., J.M.F., D.H.W., X.D., R.B., K.E.D., R.M.H., D.W.C., T.E.A.P., A.S.W.), Wellcome Trust Centre for Human Genetics (D.J.W., E.M.B., P.P., R.B.), and Oxford University Hospitals National Health Service Trust (L.O., D.W.C., T.E.A.P.), Oxford, the Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds (M.H.W.), and the Medical Research Council, Clinical Trials Unit, London (A.S.W.) - all in the United Kingdom
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Batty EM, Wong THN, Trebes A, Argoud K, Attar M, Buck D, Ip CLC, Golubchik T, Cule M, Bowden R, Manganis C, Klenerman P, Barnes E, Walker AS, Wyllie DH, Wilson DJ, Dingle KE, Peto TEA, Crook DW, Piazza P. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One 2013; 8:e66129. [PMID: 23762474 PMCID: PMC3677912 DOI: 10.1371/journal.pone.0066129] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/02/2013] [Indexed: 12/12/2022] Open
Abstract
To date, very large scale sequencing of many clinically important RNA viruses has been complicated by their high population molecular variation, which creates challenges for polymerase chain reaction and sequencing primer design. Many RNA viruses are also difficult or currently not possible to culture, severely limiting the amount and purity of available starting material. Here, we describe a simple, novel, high-throughput approach to Norovirus and Hepatitis C virus whole genome sequence determination based on RNA shotgun sequencing (also known as RNA-Seq). We demonstrate the effectiveness of this method by sequencing three Norovirus samples from faeces and two Hepatitis C virus samples from blood, on an Illumina MiSeq benchtop sequencer. More than 97% of reference genomes were recovered. Compared with Sanger sequencing, our method had no nucleotide differences in 14,019 nucleotides (nt) for Noroviruses (from a total of 2 Norovirus genomes obtained with Sanger sequencing), and 8 variants in 9,542 nt for Hepatitis C virus (1 variant per 1,193 nt). The three Norovirus samples had 2, 3, and 2 distinct positions called as heterozygous, while the two Hepatitis C virus samples had 117 and 131 positions called as heterozygous. To confirm that our sample and library preparation could be scaled to true high-throughput, we prepared and sequenced an additional 77 Norovirus samples in a single batch on an Illumina HiSeq 2000 sequencer, recovering >90% of the reference genome in all but one sample. No discrepancies were observed across 118,757 nt compared between Sanger and our custom RNA-Seq method in 16 samples. By generating viral genomic sequences that are not biased by primer-specific amplification or enrichment, this method offers the prospect of large-scale, affordable studies of RNA viruses which could be adapted to routine diagnostic laboratory workflows in the near future, with the potential to directly characterize within-host viral diversity.
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Affiliation(s)
| | - T. H. Nicholas Wong
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Karène Argoud
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Moustafa Attar
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - David Buck
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Camilla L. C. Ip
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Tanya Golubchik
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Madeleine Cule
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Charis Manganis
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - A. Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David H. Wyllie
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Daniel J. Wilson
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Kate E. Dingle
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, Headley Way, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tim E. A. Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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20
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Walker AS, Eyre DW, Wyllie DH, Dingle KE, Griffiths D, Shine B, Oakley S, O'Connor L, Finney J, Vaughan A, Crook DW, Wilcox MH, Peto TEA. Relationship between bacterial strain type, host biomarkers, and mortality in Clostridium difficile infection. Clin Infect Dis 2013; 56:1589-600. [PMID: 23463640 PMCID: PMC3641870 DOI: 10.1093/cid/cit127] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Clostridium difficile genotype predicts 14-day mortality in 1893 enzyme immunoassay–positive/culture-positive adults. Excess mortality correlates with genotype-specific changes in biomarkers, strongly implicating inflammatory pathways as a major influence on poor outcome. Polymerase chain reaction ribotype 078/ST 11(clade 5) is associated with high mortality; ongoing surveillance remains essential. Background. Despite substantial interest in biomarkers, their impact on clinical outcomes and variation with bacterial strain has rarely been explored using integrated databases. Methods. From September 2006 to May 2011, strains isolated from Clostridium difficile toxin enzyme immunoassay (EIA)–positive fecal samples from Oxfordshire, United Kingdom (approximately 600 000 people) underwent multilocus sequence typing. Fourteen-day mortality and levels of 15 baseline biomarkers were compared between consecutive C. difficile infections (CDIs) from different clades/sequence types (STs) and EIA-negative controls using Cox and normal regression adjusted for demographic/clinical factors. Results. Fourteen-day mortality was 13% in 2222 adults with 2745 EIA-positive samples (median, 78 years) vs 5% in 20 722 adults with 27 550 EIA-negative samples (median, 74 years) (absolute attributable mortality, 7.7%; 95% CI, 6.4%–9.0%). Mortality was highest in clade 5 CDIs (25% [16 of 63]; polymerase chain reaction (PCR) ribotype 078/ST 11), then clade 2 (20% [111 of 560]; 99% PCR ribotype 027/ST 1) versus clade 1 (12% [137 of 1168]; adjusted P < .0001). Within clade 1, 14-day mortality was only 4% (3 of 84) in ST 44 (PCR ribotype 015) (adjusted P = .05 vs other clade 1). Mean baseline neutrophil counts also varied significantly by genotype: 12.4, 11.6, and 9.5 × 109 neutrophils/L for clades 5, 2 and 1, respectively, vs 7.0 × 109 neutrophils/L in EIA-negative controls (P < .0001) and 7.9 × 109 neutrophils/L in ST 44 (P = .08). There were strong associations between C. difficile-type-specific effects on mortality and neutrophil/white cell counts (rho = 0.48), C-reactive-protein (rho = 0.43), eosinophil counts (rho = −0.45), and serum albumin (rho = −0.47). Biomarkers predicted 30%–40% of clade-specific mortality differences. Conclusions. C. difficile genotype predicts mortality, and excess mortality correlates with genotype-specific changes in biomarkers, strongly implicating inflammatory pathways as a major influence on poor outcome after CDI. PCR ribotype 078/ST 11 (clade 5) leads to severe CDI; thus ongoing surveillance remains essential.
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Didelot X, Eyre DW, Cule M, Ip CLC, Ansari MA, Griffiths D, Vaughan A, O'Connor L, Golubchik T, Batty EM, Piazza P, Wilson DJ, Bowden R, Donnelly PJ, Dingle KE, Wilcox M, Walker AS, Crook DW, A Peto TE, Harding RM. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol 2012; 13:R118. [PMID: 23259504 PMCID: PMC4056369 DOI: 10.1186/gb-2012-13-12-r118] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 11/08/2012] [Accepted: 12/21/2012] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The control of Clostridium difficile infection is a major international healthcare priority, hindered by a limited understanding of transmission epidemiology for these bacteria. However, transmission studies of bacterial pathogens are rapidly being transformed by the advent of next generation sequencing. RESULTS Here we sequence whole C. difficile genomes from 486 cases arising over four years in Oxfordshire. We show that we can estimate the times back to common ancestors of bacterial lineages with sufficient resolution to distinguish whether direct transmission is plausible or not. Time depths were inferred using a within-host evolutionary rate that we estimated at 1.4 mutations per genome per year based on serially isolated genomes. The subset of plausible transmissions was found to be highly associated with pairs of patients sharing time and space in hospital. Conversely, the large majority of pairs of genomes matched by conventional typing and isolated from patients within a month of each other were too distantly related to be direct transmissions. CONCLUSIONS Our results confirm that nosocomial transmission between symptomatic C. difficile cases contributes far less to current rates of infection than has been widely assumed, which clarifies the importance of future research into other transmission routes, such as from asymptomatic carriers. With the costs of DNA sequencing rapidly falling and its use becoming more and more widespread, genomics will revolutionize our understanding of the transmission of bacterial pathogens.
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Affiliation(s)
- Xavier Didelot
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - David W Eyre
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Madeleine Cule
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Camilla LC Ip
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - M Azim Ansari
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - David Griffiths
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Alison Vaughan
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Lily O'Connor
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Tanya Golubchik
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Elizabeth M Batty
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniel J Wilson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Rory Bowden
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Peter J Donnelly
- Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kate E Dingle
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- Nuffield Department of Clinical Laboratory Sciences, Headley Way, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Mark Wilcox
- Department of Microbiology, The General Infirmary, Old Medical School, Great George Street, Leeds LS1 3EX, UK
- Leeds Institute of Molecular Medicine, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- MRC Clinical Trials Unit, 125 Kingsway, London, WC2B 6NH, UK
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Tim E A Peto
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
- Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Rosalind M Harding
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Dingle KE, Didelot X, Ansari MA, Eyre DW, Vaughan A, Griffiths D, Ip CLC, Batty EM, Golubchik T, Bowden R, Jolley KA, Hood DW, Fawley WN, Walker AS, Peto TE, Wilcox MH, Crook DW. Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing. J Infect Dis 2012. [PMID: 23204167 DOI: 10.1093/infdis/jis734] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Clostridium difficile is a major cause of nosocomial diarrhea, with 30-day mortality reaching 30%. The cell surface comprises a paracrystalline proteinaceous S-layer encoded by the slpA gene within the cell wall protein (cwp) gene cluster. Our purpose was to understand the diversity and evolution of slpA and nearby genes also encoding immunodominant cell surface antigens. METHODS Whole-genome sequences were determined for 57 C. difficile isolates representative of the population structure and different clinical phenotypes. Phylogenetic analyses were performed on their genomic region (>63 kb) spanning the cwp cluster. RESULTS Genetic diversity across the cwp cluster peaked within slpA, cwp66 (adhesin), and secA2 (secretory translocase). These genes formed a 10-kb cassette, of which 12 divergent variants were found. Homologous recombination involving this cassette caused it to associate randomly with genotype. One cassette contained a novel insertion (length, approximately 24 kb) that resembled S-layer glycosylation gene clusters. CONCLUSIONS Genetic exchange of S-layer cassettes parallels polysaccharide capsular switching in other species. Both cause major antigenic shifts, while the remainder of the genome is unchanged. C. difficile genotype is therefore not predictive of antigenic type. S-layer switching and immune escape could help explain temporal and geographic variation in C. difficile epidemiology and may inform genotyping and vaccination strategies.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, Oxford Biomedical Research Centre, John Radcliffe Hospital, UK.
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Eyre DW, Walker AS, Wyllie D, Dingle KE, Griffiths D, Finney J, O'Connor L, Vaughan A, Crook DW, Wilcox MH, Peto TEA. Predictors of first recurrence of Clostridium difficile infection: implications for initial management. Clin Infect Dis 2012; 55 Suppl 2:S77-87. [PMID: 22752869 PMCID: PMC3388024 DOI: 10.1093/cid/cis356] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Symptomatic recurrence of Clostridium difficile infection (CDI) occurs in approximately 20% of patients and is challenging to treat. Identifying those at high risk could allow targeted initial management and improve outcomes. Adult toxin enzyme immunoassay–positive CDI cases in a population of approximately 600 000 persons from September 2006 through December 2010 were combined with epidemiological/clinical data. The cumulative incidence of recurrence ≥14 days after the diagnosis and/or onset of first-ever CDI was estimated, treating death without recurrence as a competing risk, and predictors were identified from cause-specific proportional hazards regression models. A total of 1678 adults alive 14 days after their first CDI were included; median age was 77 years, and 1191 (78%) were inpatients. Of these, 363 (22%) experienced a recurrence ≥14 days after their first CDI, and 594 (35%) died without recurrence through March 2011. Recurrence risk was independently and significantly higher among patients admitted as emergencies, with previous gastrointestinal ward admission(s), last discharged 4–12 weeks before first diagnosis, and with CDI diagnosed at admission. Recurrence risk also increased with increasing age, previous total hours admitted, and C-reactive protein level at first CDI (all P < .05). The 4-month recurrence risk increased by approximately 5% (absolute) for every 1-point increase in a risk score based on these factors. Risk factors, including increasing age, initial disease severity, and hospital exposure, predict CDI recurrence and identify patients likely to benefit from enhanced initial CDI treatment.
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Affiliation(s)
- David W Eyre
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
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Stabler RA, Dawson LF, Valiente E, Cairns MD, Martin MJ, Donahue EH, Riley TV, Songer JG, Kuijper EJ, Dingle KE, Wren BW. Macro and micro diversity of Clostridium difficile isolates from diverse sources and geographical locations. PLoS One 2012; 7:e31559. [PMID: 22396735 PMCID: PMC3292544 DOI: 10.1371/journal.pone.0031559] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 01/13/2012] [Indexed: 12/29/2022] Open
Abstract
Clostridium difficile has emerged rapidly as the leading cause of antibiotic-associated diarrheal disease, with the temporal and geographical appearance of dominant PCR ribotypes such as 017, 027 and 078. Despite this continued threat, we have a poor understanding of how or why particular variants emerge and the sources of strains that dominate different human populations. We have undertaken a breadth genotyping study using multilocus sequence typing (MLST) analysis of 385 C. difficile strains from diverse sources by host (human, animal and food), geographical locations (North America, Europe and Australia) and PCR ribotypes. Results identified 18 novel sequence types (STs) and 3 new allele sequences and confirmed the presence of five distinct clonal lineages generally associated with outbreaks of C. difficile infection in humans. Strains of animal and food origin were found of both ST-1 and ST-11 that are frequently associated with human disease. An in depth MLST analysis of the evolutionary distant ST-11/PCR ribotype 078 clonal lineage revealed that ST-11 can be found in alternative but closely related PCR ribotypes and PCR ribotype 078 alleles contain mutations generating novel STs. PCR ribotype 027 and 017 lineages may consist of two divergent subclades. Furthermore evidence of microdiversity was present within the heterogeneous clade 1. This study helps to define the evolutionary origin of dominant C. difficile lineages and demonstrates that C. difficile is continuing to evolve in concert with human activity.
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Affiliation(s)
- Richard A. Stabler
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lisa F. Dawson
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Esmeralda Valiente
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michelle D. Cairns
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Public Health Laboratory London, Health Protection Agency, Division of Infection, The Royal London Hospital, London, United Kingdom
- UCL Centre for Clinical Microbiology, University College London, Royal Free Campus, London, United Kingdom
| | - Melissa J. Martin
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Elizabeth H. Donahue
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Thomas V. Riley
- Microbiology and Immunology, University of Western Australia, Perth, Western Australia, Australia
| | - J. Glenn Songer
- College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Ed J. Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef, Leiden, Netherlands
| | - Kate E. Dingle
- Nuffield Department of Clinical Laboratory Sciences, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom
| | - Brendan W. Wren
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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Walker AS, Eyre DW, Wyllie DH, Dingle KE, Harding RM, O'Connor L, Griffiths D, Vaughan A, Finney J, Wilcox MH, Crook DW, Peto TEA. Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing. PLoS Med 2012; 9:e1001172. [PMID: 22346738 PMCID: PMC3274560 DOI: 10.1371/journal.pmed.1001172] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/28/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Clostridium difficile infection (CDI) is a leading cause of antibiotic-associated diarrhoea and is endemic in hospitals, hindering the identification of sources and routes of transmission based on shared time and space alone. This may compromise rational control despite costly prevention strategies. This study aimed to investigate ward-based transmission of C. difficile, by subdividing outbreaks into distinct lineages defined by multi-locus sequence typing (MLST). METHODS AND FINDINGS All C. difficile toxin enzyme-immunoassay-positive and culture-positive samples over 2.5 y from a geographically defined population of ~600,000 persons underwent MLST. Sequence types (STs) were combined with admission and ward movement data from an integrated comprehensive healthcare system incorporating three hospitals (1,700 beds) providing all acute care for the defined geographical population. Networks of cases and potential transmission events were constructed for each ST. Potential infection sources for each case and transmission timescales were defined by prior ward-based contact with other cases sharing the same ST. From 1 September 2007 to 31 March 2010, there were means of 102 tests and 9.4 CDIs per 10,000 overnight stays in inpatients, and 238 tests and 15.7 CDIs per month in outpatients/primary care. In total, 1,276 C. difficile isolates of 69 STs were studied. From MLST, no more than 25% of cases could be linked to a potential ward-based inpatient source, ranging from 37% in renal/transplant, 29% in haematology/oncology, and 28% in acute/elderly medicine to 6% in specialist surgery. Most of the putative transmissions identified occurred shortly (≤ 1 wk) after the onset of symptoms (141/218, 65%), with few >8 wk (21/218, 10%). Most incubation periods were ≤ 4 wk (132/218, 61%), with few >12 wk (28/218, 13%). Allowing for persistent ward contamination following ward discharge of a CDI case did not increase the proportion of linked cases after allowing for random meeting of matched controls. CONCLUSIONS In an endemic setting with well-implemented infection control measures, ward-based contact with symptomatic enzyme-immunoassay-positive patients cannot account for most new CDI cases.
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Affiliation(s)
- A Sarah Walker
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom.
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Cody AJ, Maiden MJC, Dingle KE. Genetic diversity and stability of the porA allele as a genetic marker in human Campylobacter infection. Microbiology (Reading) 2009; 155:4145-4154. [PMID: 19744989 PMCID: PMC2885669 DOI: 10.1099/mic.0.031047-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The major outer-membrane protein (MOMP) of Campylobacter jejuni and Campylobacter coli, encoded by the porA gene, is extremely genetically diverse. Conformational MOMP epitopes are important in host immunity, and variation in surface-exposed regions probably occurs as a result of positive immune selection during infection. porA diversity has been exploited in genotyping studies using highly discriminatory nucleotide sequences to identify potentially epidemiologically linked cases of human campylobacteriosis. To understand the overall nature and extent of porA diversity and stability in C. jejuni and C. coli we investigated sequences in isolates (n=584) obtained from a defined human population (approx. 600 000) over a defined time period (1 year). A total of 196 distinct porA variants were identified. Regions encoding putative extracellular loops were the most variable in both nucleotide sequence and length. Phylogenetic analysis identified three porA allele clusters that originated in (i) predominantly C. jejuni and a few C. coli, (ii) solely C. jejuni or (iii) predominantly C. coli and a few C. jejuni. The stability of porA within an individual human host was investigated using isolates cultured longitudinally from 64 sporadic cases, 27 of which had prolonged infection lasting between 5 and 98 days (the remainder having illness of normal duration, 0–4 days), and 20 cases from family outbreaks. Evidence of mutation was detected in two patients with prolonged illness. Despite demonstrable positive immune selection in these two unusual cases, the persistence of numerous variants within the population indicated that the porA allele is a valuable tool for use in extended typing schemes.
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Affiliation(s)
- A J Cody
- The Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
| | - M J C Maiden
- The Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
| | - K E Dingle
- National Institute for Health Research, Oxford Biomedical Research Centre Programme, John Radcliffe Hospital, Oxford OX3 9DU, UK.,Nuffield Department of Clinical Laboratory Sciences, Oxford University, John Radcliffe Hospital, Oxford OX3 9DU, UK
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Abstract
Supplementing Campylobacter spp. multilocus sequence typing with nucleotide sequence typing of 3 antigen genes increased the discriminatory index achieved from 0.975 to 0.992 among 620 clinical isolates from Oxfordshire, United Kingdom. This enhanced typing scheme enabled identification of clusters and retained data required for long-range epidemiologic comparisons of isolates.
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Colles FM, Jones TA, McCarthy ND, Sheppard SK, Cody AJ, Dingle KE, Dawkins MS, Maiden MCJ. Campylobacter infection of broiler chickens in a free-range environment. Environ Microbiol 2008; 10:2042-50. [PMID: 18412548 PMCID: PMC2702501 DOI: 10.1111/j.1462-2920.2008.01623.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Campylobacter jejuni is the most common cause of bacterial gastroenteritis worldwide, with contaminated chicken meat considered to represent a major source of human infection. Biosecurity measures can reduce C. jejuni shedding rates of housed chickens, but the increasing popularity of free-range and organic meat raises the question of whether the welfare benefits of extensive production are compatible with food safety. The widespread assumption that the free-range environment contaminates extensively reared chickens has not been rigorously tested. A year-long survey of 64 free-range broiler flocks reared on two sites in Oxfordshire, UK, combining high-resolution genotyping with behavioural and environmental observations revealed: (i) no evidence of colonization of succeeding flocks by the C. jejuni genotypes shed by preceding flocks, (ii) a high degree of similarity between C. jejuni genotypes from both farm sites, (iii) no association of ranging behaviour with likelihood of Campylobacter shedding, and (iv) higher genetic differentiation between C. jejuni populations from chickens and wild birds on the same farm than between the chicken samples, human disease isolates from the same region and national samples of C. jejuni from chicken meat.
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Affiliation(s)
- Frances M Colles
- The Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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Mickan L, Doyle R, Valcanis M, Dingle KE, Unicomb L, Lanser J. Multilocus sequence typing of Campylobacter jejuni isolates from New South Wales, Australia. J Appl Microbiol 2007; 102:144-52. [PMID: 17184329 DOI: 10.1111/j.1365-2672.2006.03049.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Multilocus sequence typing (MLST) was used to examine the diversity and population structure of Campylobacter jejuni isolates associated with sporadic cases of gastroenteritis in Australia, and to compare these isolates with those from elsewhere. METHODS AND RESULTS A total of 153 Camp. jejuni isolates were genotyped. Forty sequence types (STs) were found, 19 of which were previously undescribed and 21 identified in other countries. The 19 newly described STs accounted for 43% of isolates, 16 of which were assigned to known clonal complexes. Eighty-eight percent of isolates were assigned to a total of 15 clonal complexes. Of these, four clonal complexes accounted for 60% of isolates. Three STs accounted for nearly 40% of all isolates and appeared to be endemic, while 21 STs were represented by more than one isolate. Seven infections were acquired during international travel, and the associated isolates all had different STs, three of which were exclusive to the travel-acquired cases. Comparison of serotypes among isolates from clonal complexes revealed further diversity. Eight serotypes were identified among isolates from more than one clonal complex, while isolates from six clonal complexes displayed serotypes not previously associated with those clonal complexes. CONCLUSIONS Multilocus sequence typing is a useful tool for the discrimination of subtypes and examination of the population structure of Camp. jejuni associated with sporadic infections. SIGNIFICANCE AND IMPACT OF THE STUDY This study highlights the genotypic diversity of Camp. jejuni in Australia, demonstrating that STs causing disease have both a global and a local distribution evident from the typing of domestically and internationally acquired Camp. jejuni isolates.
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Affiliation(s)
- L Mickan
- Infectious Diseases Laboratories, Institute of Medical and Veterinary Science, Adelaide, SA, Australia.
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Ogden ID, MacRae M, Johnston M, Strachan NJC, Cody AJ, Dingle KE, Newell DG. Use of multilocus sequence typing to investigate the association between the presence of Campylobacter spp. in broiler drinking water and Campylobacter colonization in broilers. Appl Environ Microbiol 2007; 73:5125-9. [PMID: 17586665 PMCID: PMC1950966 DOI: 10.1128/aem.00884-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The presence of campylobacters in broiler chickens and throughout the broiler water delivery systems of 12 farms in northeastern Scotland was investigated by sensitive enrichment methods and large-volume filtration. Campylobacter presence was independent of the water source and whether the water was treated. The genotypes of Campylobacter jejuni isolates recovered from chickens and various locations within the water delivery systems were compared by multilocus sequence typing. Matching strains in shed header tanks and birds were found at 1 of the 12 farms investigated. However, the sequence of contamination or whether the source was within or outside the shed was not determined. Nevertheless, these data provide evidence that drinking water could be associated with broiler infection by campylobacters.
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Affiliation(s)
- I D Ogden
- Department of Medical Microbiology, School of Medicine, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom.
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Abstract
C. jejuni genomes have a host signature that enables attribution of isolates to animal sources. Establishing sources of human infection supports effective disease control measures. Host association with Campylobacter jejuni was analyzed by using multilocus sequence typing data for 713 isolates from chickens and bovids (cattle and sheep). Commonly used summary measures of genotypes (sequence type and clonal complex) showed poor accuracy, but a method using the full allelic profile showed 80% accuracy in distinguishing isolates from these 2 host groups. We explored the biologic basis of more accurate results with allelic profiles. Strains isolated from specific hosts have imported a substantial number of alleles while circulating in those host species. These results imply that 1) although Campylobacter moves frequently between hosts, most transmission is within species, and 2) lineages can acquire a host signature and potentially adapt to the host through recombination. Assignment using this signature enables improved prediction of source for pathogens that undergo frequent genetic recombination.
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Affiliation(s)
- Noel D McCarthy
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
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van Bergen MAP, Dingle KE, Maiden MCJ, Newell DG, van der Graaf-Van Bloois L, van Putten JPM, Wagenaar JA. Clonal nature of Campylobacter fetus as defined by multilocus sequence typing. J Clin Microbiol 2006; 43:5888-98. [PMID: 16333072 PMCID: PMC1317208 DOI: 10.1128/jcm.43.12.5888-5898.2005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter fetus can be divided into the subspecies C. fetus subsp. fetus and C. fetus subsp. venerealis. C. fetus subsp. fetus causes sporadic infections in humans and abortion in cattle and sheep and has been isolated from a variety of sites in different hosts. C. fetus subsp. venerealis is host restricted, being isolated mainly from the genital tracts of cattle, and is the causative agent of bovine genital campylobacteriosis. Despite differences in niche preference, microbiological subspecies differentiation has proven difficult. Different typing methods divided C. fetus isolates into different subgroups, depending on the methods used. The relative value of these methods can be assessed by the evolutionary relationship of isolates belonging to the genus; therefore, we developed a multilocus sequence typing (MLST) scheme for C. fetus. This scheme was applied to 140 C. fetus isolates previously typed by amplified fragment length polymorphism (AFLP) analysis. A total of 14 different sequence types (STs) were identified, and these exhibited low levels of inter-ST genetic diversity, with only 22 variable sites in 3,312 nucleotides. These MLST data indicate that C. fetus is genetically homogeneous compared to the homogeneity of other Campylobacter species. The two C. fetus subspecies were extremely closely related genetically, but ST-4 was associated only with C. fetus subsp. venerealis, which represents a "bovine" clone. The C. fetus subsp. fetus isolates studied were more diverse in terms of their STs, and the STs correlated with epidemiological relationships. Congruence was observed among C. fetus subspecies, sap type, and ST; therefore, MLST confirms that mammalian C. fetus is genetically stable, probably as result of the introduction of a single ancestral clone into a mammalian niche.
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Affiliation(s)
- Marcel A P van Bergen
- Animal Sciences Group, Division of Infectious Diseases, P.O. Box 65, 8200 AB Lelystad, The Netherlands
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Dingle KE, Clarke L, Bowler ICJW. Ciprofloxacin resistance among human Campylobacter isolates 1991–2004: an update. J Antimicrob Chemother 2005; 56:435-7. [PMID: 15956098 DOI: 10.1093/jac/dki192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Dingle KE, Colles FM, Falush D, Maiden MCJ. Sequence typing and comparison of population biology of Campylobacter coli and Campylobacter jejuni. J Clin Microbiol 2005; 43:340-7. [PMID: 15634992 PMCID: PMC540151 DOI: 10.1128/jcm.43.1.340-347.2005] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multilocus sequence typing (MLST) scheme that uses the same loci as a previously described system for Campylobacter jejuni was developed for Campylobacter coli. The C. coli-specific primers were validated with 53 isolates from humans, chickens, and pigs, together with 15 Penner serotype reference isolates. The nucleotide sequence of the flaA short variable region (SVR) was determined for each isolate. These sequence data were compared to equivalent information for 17 C. jejuni isolates representing the known genetic diversity of this species. C. coli and C. jejuni share approximately 86.5% identity at the nucleotide sequence level within the MLST loci. There is evidence of genetic exchange of the housekeeping genes between the two species, but at a very low rate; only one sequence type from each species showed evidence of imported DNA. The flaA gene was more variable and has been exchanged many times between the two species, making it an unreliable marker for species identification but useful for distinguishing closely related strains. All but 3 of 21 human C. coli clinical isolates were distinct, according to the combined MLST and SVR sequences. The use of a common MLST scheme allows direct comparisons of the population biology and molecular epidemiology of these two closely related human pathogens.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Sciences, Oxford University, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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Abstract
An increase in norovirus outbreaks was reported internationally during 2002 and 2003 and was also observed in Oxfordshire (United Kingdom) hospitals. To understand their epidemiological relationships, viruses from 22 outbreaks (15 from one hospital) were subjected to nucleotide sequencing. The 3'-terminal 3,255 nt or complete genomes were determined for 49 viruses. All outbreaks were caused by a genogroup II norovirus related to the Lordsdale virus (GII 4), common in healthcare settings. The norovirus mutation rate was sufficiently high that the 3,255-nucleotide sequences allowed separate and potentially connected outbreaks to be identified, since all outbreaks with identical sequences were temporally or geographically linked. The high mutation rate was further indicated by four mutations and three microheterogeneities in 3,255 nucleotides during 17 days of norovirus shedding by an immunocompromised patient. The data suggested that multiple virus introductions from the community, occasional transmission among wards, and one instance of ongoing environmental contamination had occurred. The accumulation, or lack, of mutations within an outbreak was also used to indicate the predominant transmission route. In an outbreak where person-to-person spread was thought to predominate, six mutations were detected throughout the genome, whereas one mutation was detected when point source infection was suspected. This norovirus epidemic strain differed from its closest previously described relative by 11.4 to 13.6% in the outer P2 domain of the capsid, which also had a single-amino-acid insertion. Alterations to the capsid structure compared to previous noroviruses may explain the increased number of outbreaks during 2002 and 2003.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Sciences, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom, OX3 9DU.
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Abstract
Clinical diagnostic tests based on nucleic acid amplification assist with the prompt diagnosis of microbial infections because of their speeds and extremely low limits of detection. However, the design of appropriate internal controls for such assays has proven difficult. We describe a reaction-specific RNA internal control for diagnostic reverse transcription (RT)-PCR which allows extraction, RT, amplification, and detection to be monitored. The control consists of a G+C-rich (60%) RNA molecule with an extensive secondary structure, based on a modified hepatitis delta virus genome. The rod-like structure of this RNA, with 70% intramolecular base pairing, provides a difficult template for RT-PCR. This ensures that the more favorable target virus amplicon is generated in preference to the control, with the control being detected only if the target virus is absent. The unusual structure of hepatitis delta virus RNA has previously been shown to enhance its stability and resistance to nucleases, an advantage for routine use as an internal control. The control was implemented in three nested multiplex RT-PCRs to detect nine clinically important respiratory viruses: (i) influenza A and B viruses, (ii) respiratory syncytial viruses A and B and human metapneumovirus, and (iii) parainfluenza virus types 1 to 4. The detection limits of these assays were not detectably compromised by the presence of the RNA control. During routine testing of 324 consecutive unselected respiratory samples, the presence of the internal control ensured that genuine and false-negative results were distinguishable, thus increasing the diagnostic confidence in the assay.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Sciences, Oxford University, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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Duim B, Godschalk PCR, van den Braak N, Dingle KE, Dijkstra JR, Leyde E, van der Plas J, Colles FM, Endtz HP, Wagenaar JA, Maiden MCJ, van Belkum A. Molecular evidence for dissemination of unique Campylobacter jejuni clones in Curaçao, Netherlands Antilles. J Clin Microbiol 2004; 41:5593-7. [PMID: 14662946 PMCID: PMC309031 DOI: 10.1128/jcm.41.12.5593-5597.2003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter jejuni isolates (n = 234) associated with gastroenteritis and the Guillain-Barré syndrome (GBS) in the island of Curaçao, Netherlands Antilles, and collected from March 1999 to March 2000 were investigated by a range of molecular typing techniques. Data obtained by pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), automated ribotyping, and sequence analysis of the short variable region of the flagellin gene (flaA) were analyzed separately and in combination. Similar groupings were obtained by all methods, with the data obtained by MLST and AFLP analysis exhibiting the highest degree of congruency. MLST identified 29 sequence types, which were assigned to 10 major clonal complexes. PFGE, AFLP analysis, and ribotyping identified 10, 9, and 8 of these clonal groups, respectively; however, these three techniques permitted subdivision of the clonal groups into more different types. Members of seven clonal groups comprising 107 isolates were obtained from November 1999 to February 2000, and no distinguishing characteristics were identified for two GBS-associated strains. The sequence type 41 (ST-41), ST-508, and ST-657 clonal complexes and their corresponding AFLP types have been rare or absent in the Campylobacter data sets described to date. We conclude that several clonal complexes of C. jejuni are associated with human disease in Curaçao, and some of these have not been reported elsewhere. Furthermore, given the observation that C. jejuni-associated diseases appear to be more severe from November to February, it can be speculated that this may be due to the presence of virulent clones with a limited span of circulation.
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Affiliation(s)
- Birgitta Duim
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands.
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Abstract
AIMS To identify and make available through the National Collection of Type Cultures (NCTC) a set of reference isolates for the clonal complexes of Campylobacter jejuni. METHODS AND RESULTS The development of a multilocus sequence typing scheme for C. jejuni enabled the genetic characterization of a large number of isolates (n = 814) from cases of human disease, animals, birds and their food products. The nucleotide sequence data were used to assign each isolate an allelic profile or sequence type (ST) and examine the C. jejuni population structure in terms of clonal complexes. The clonal complexes consisted of an abundant central or founder genotype (ST), after which the complex was named, together with very closely related, generally less abundant genotypes differing from the founder at one, two or three loci. The clonal complex is an informative unit for the study C. jejuni epidemiology. It provides data which enabled the choice of 13 C. jejuni founder isolates for submission to the NCTC as a representative cross-section of the C. jejuni population. CONCLUSIONS These 13 isolates provide a defined resource for further research into aspects of C. jejuni biology such as genomic diversity, virulence and adaptation to particular hosts or environmental survival. SIGNIFICANCE AND IMPACT OF STUDY This isolate collection is available through the NCTC and provides a resource for further research.
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Affiliation(s)
- D R A Wareing
- The Public Health Laboratory, Royal Preston Hospital, P.O. Box 202, Preston PR2 9HG, UK.
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40
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Schouls LM, Reulen S, Duim B, Wagenaar JA, Willems RJL, Dingle KE, Colles FM, Van Embden JDA. Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination. J Clin Microbiol 2003; 41:15-26. [PMID: 12517820 PMCID: PMC149617 DOI: 10.1128/jcm.41.1.15-26.2003] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic region with short tandem repeats designated clustered regularly interspaced short palindromic repeats (CRISPRs). MLST and AFLP analysis yielded more than 100 different profiles and patterns, respectively. These multiple-locus typing methods resulted in similar genetic clustering, indicating that both are useful in disclosing genetic relationships between Campylobacter jejuni isolates. Group separation analysis of the AFLP analysis and MLST data revealed an unexpected association between cattle and human strains, suggesting a common source of infection. Analysis of the polymorphic CRISPR region carrying short repeats allowed about two-thirds of the typeable strains to be distinguished, similar to AFLP analysis and MLST. The three methods proved to be equally powerful in identifying strains from outbreaks of human campylobacteriosis. Analysis of the MLST data showed that intra- and interspecies recombination occurs frequently and that the role of recombination in sequence variation is 50 times greater than that of mutation. Examination of strains cultured from cecum swabs revealed that individual chickens harbored multiple Campylobacter strain types and that some genotypes were found in more than one chicken. We conclude that typing of Campylobacter strains is useful for identification of outbreaks but is probably not useful for source tracing and global epidemiology because of carriage of strains of multiple types and an extremely high diversity of strains in animals.
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Affiliation(s)
- Leo M Schouls
- Research Laboratory for Infectious Diseases, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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Dingle KE, Colles FM, Ure R, Wagenaar JA, Duim B, Bolton FJ, Fox AJ, Wareing DRA, Maiden MCJ. Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation. Emerg Infect Dis 2002. [PMID: 12194772 PMCID: PMC2732546 DOI: 10.3201/eid0809.02-0122] [Citation(s) in RCA: 172] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A total of 814 isolates of the foodborne pathogen Campylobacter jejuni were characterized by multilocus sequence typing (MLST) and analysis of the variation of two cell-surface components: the heat-stable (HS) serotyping antigen and the flagella protein FlaA short variable region (SVR). We identified 379 combinations of the MLST loci (sequence types) and 215 combinations of the cell-surface components among these isolates, which had been obtained from human disease, animals, food, and the environment. Despite this diversity, 748 (92%) of the isolates belonged to one of 17 clonal complexes, 6 of which contained many (318, 63%) of the human disease isolates. Several clonal complexes exhibited associations with isolation source or particular cell-surface components; however, the latter were poorly predictive of clonal complex. These data demonstrate that the clonal complex, as defined by MLST, is an epidemiologically relevant unit for both long and short-term investigations of C. jejuni epidemiology.
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Affiliation(s)
- Kate E Dingle
- Department of Zoology, University of Oxford, United Kingdom
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42
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Dingle KE, Colles FM, Ure R, Wagenaar JA, Duim B, Bolton FJ, Fox AJ, Wareing DR, Maiden MC. Molecular characterization of Campylobacter jejuni clones: a basis for epidemiologic investigation. Emerg Infect Dis 2002; 8:949-55. [PMID: 12194772 PMCID: PMC2732546 DOI: 10.3201/eid0809.020122] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A total of 814 isolates of the foodborne pathogen Campylobacter jejuni were characterized by multilocus sequence typing (MLST) and analysis of the variation of two cell-surface components: the heat-stable (HS) serotyping antigen and the flagella protein FlaA short variable region. We identified 379 combinations of the MLST loci (sequence types) and 215 combinations of the cell-surface components among these isolates, which had been obtained from human disease, animals, food, and the environment. Despite this diversity, 748 (92%) of the isolates belonged to one of 17 clonal complexes, 6 of which contained many (318, 63%) of the human disease isolates. Several clonal complexes exhibited associations with isolation source or particular cell-surface components; however, the latter were poorly predictive of clonal complex. These data demonstrate that the clonal complex, as defined by MLST, is an epidemiologically relevant unit for both long and short-term investigations of C. jejuni epidemiology.
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Affiliation(s)
- Kate E. Dingle
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
| | - Frances M. Colles
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
| | - Roisin Ure
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
- Institute for Animal Science and Health, Lelystad, the Netherlands
- Public Health Laboratory, Withington Hospital, Manchester, United Kingdom
| | - Jaap A. Wagenaar
- Institute for Animal Science and Health, Lelystad, the Netherlands
| | - Birgitta Duim
- Institute for Animal Science and Health, Lelystad, the Netherlands
| | - Frederick J. Bolton
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
- Institute for Animal Science and Health, Lelystad, the Netherlands
- Public Health Laboratory, Withington Hospital, Manchester, United Kingdom
| | - Andrew J. Fox
- Public Health Laboratory, Withington Hospital, Manchester, United Kingdom
| | - David R.A. Wareing
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
- Institute for Animal Science and Health, Lelystad, the Netherlands
- Public Health Laboratory, Withington Hospital, Manchester, United Kingdom
| | - Martin C.J. Maiden
- University of Oxford, Oxford, United Kingdom; †Public Health Laboratory, Royal Preston Hospital, Preston, United Kingdom
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Dingle KE, Van den Braak N, Colles FM, Price LJ, Woodward DL, Rodgers FG, Endtz HP, Van Belkum A, Maiden MCJ. SEQUENCE TYPING CONFIRMS THAT CAMPYLOBACTER JEJUNI STRAINS ASSOCIATED WITH GUILLAIN-BARRE AND MILLER-FISHER SYNDROMES ARE OF DIVERSE GENETIC LINEAGE, SEROTYPE, AND FLAGELLA TYPE. J Peripher Nerv Syst 2002. [DOI: 10.1046/j.1529-8027.2002.2008_16.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Dingle KE, Van Den Braak N, Colles FM, Price LJ, Woodward DL, Rodgers FG, Endtz HP, Van Belkum A, Maiden MC. Sequence typing confirms that Campylobacter jejuni strains associated with Guillain-Barré and Miller-Fisher syndromes are of diverse genetic lineage, serotype, and flagella type. J Clin Microbiol 2001; 39:3346-9. [PMID: 11526174 PMCID: PMC88342 DOI: 10.1128/jcm.39.9.3346-3349.2001] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2001] [Accepted: 06/28/2001] [Indexed: 11/20/2022] Open
Abstract
Guillain-Barré syndrome (GBS) and Miller-Fisher syndrome (MFS) are correlated with prior infection by Campylobacter jejuni in up to 40% of cases. Nucleotide sequence-based typing of 25 C. jejuni isolates associated with neuropathy permitted robust comparisons with equivalent data from approximately 800 C. jejuni isolates not associated with neuropathy. A total of 13 genetic lineages and 20 flaA short variable region nucleotide sequences were present among the 25 isolates. A minority of isolates (4 of 25) had the flaA short variable region nucleotide sequences that were previously proposed as a marker for GBS-associated isolates. These 4 isolates probably represented the Penner serotype 19 lineage, which has been proposed to have an association with GBS.
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Affiliation(s)
- K E Dingle
- Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford, OX1 3FY, United Kingdom
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Dingle KE, Colles FM, Wareing DR, Ure R, Fox AJ, Bolton FE, Bootsma HJ, Willems RJ, Urwin R, Maiden MC. Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol 2001; 39:14-23. [PMID: 11136741 PMCID: PMC87672 DOI: 10.1128/jcm.39.1.14-23.2001] [Citation(s) in RCA: 632] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gram-negative bacterium Campylobacter jejuni has extensive reservoirs in livestock and the environment and is a frequent cause of gastroenteritis in humans. To date, the lack of (i) methods suitable for population genetic analysis and (ii) a universally accepted nomenclature has hindered studies of the epidemiology and population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in seven housekeeping loci to determine the genetic relationships among isolates. The MLST system was established using 194 C. jejuni isolates of diverse origins, from humans, animals, and the environment. The allelic profiles, or sequence types (STs), of these isolates were deposited on the Internet (http://mlst.zoo.ox.ac.uk), forming a virtual isolate collection which could be continually expanded. These data indicated that C. jejuni is genetically diverse, with a weakly clonal population structure, and that intra- and interspecies horizontal genetic exchange was common. Of the 155 STs observed, 51 (26% of the isolate collection) were unique, with the remainder of the collection being categorized into 11 lineages or clonal complexes of related STs with between 2 and 56 members. In some cases membership in a given lineage or ST correlated with the possession of a particular Penner HS serotype. Application of this approach to further isolate collections will enable an integrated global picture of C. jejuni epidemiology to be established and will permit more detailed studies of the population genetics of this organism.
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Affiliation(s)
- K E Dingle
- Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, Oxford OX1 3FY, United Kingdom
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Noel JS, Ando T, Leite JP, Green KY, Dingle KE, Estes MK, Seto Y, Monroe SS, Glass RI. Correlation of patient immune responses with genetically characterized small round-structured viruses involved in outbreaks of nonbacterial acute gastroenteritis in the United States, 1990 to 1995. J Med Virol 1997; 53:372-83. [PMID: 9407386 DOI: 10.1002/(sici)1096-9071(199712)53:4<372::aid-jmv10>3.0.co;2-h] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Small round-structured viruses (SRSVs) are a genetically and antigenically diverse group of caliciviruses that are the most common cause of outbreaks of acute nonbacterial gastroenteritis. We have applied both molecular techniques to characterize SRSVs in fecal specimens and serologic assays using four different expressed SRSV antigens to examine the distribution of outbreak strains in the United States and determine if the immune responses of patients were strain specific. Strains from 23 outbreaks of SRSV gastroenteritis were characterized by reverse transcription-PCR and nucleotide sequencing of a 277-base region of the capsid gene. These strains segregated into two distinct genogroups, I and II, comprising four and six clusters of strains respectively, each representing a distinct phylogenetic lineage. Serum IgG responses in patients were measured by enzyme immunoassay using expressed capsid antigens of Norwalk virus (NV), Toronto virus (TV), Hawaii virus (HV), and Lordsdale virus (LV), representing four of the 10 clusters. While strains in genogroups I and II were antigenically distinct, within genogroups, the specificity of the immune response varied greatly. Patients infected with genogroup I strains which had as much as 38.5% aa divergence from NV demonstrated relatively homologous seroresponses to the single NV antigen. In contrast, in genogroup II, homologous seroresponses to TV and HV were only present when the infecting strains showed less than 6.5% aa divergence from these antigens. These results suggest that TV and HV represent not only separate genetic clusters in genogroup II but also separate antigenic groups, each of which is related but distinguishable. In addition, two genetically distinct SRSV strains were identified for which we have no homologous antigen. This study suggests that while current molecular diagnostics are capable of detecting the full range of SRSVs, additional expressed antigens will be required to detect an immune response to SRSV infection caused by all the antigenically diverse strains.
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Affiliation(s)
- J S Noel
- Viral Gastroenteritis Section, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Dingle KE, Lambden PR, Caul EO, Clarke IN. Human enteric Caliciviridae: the complete genome sequence and expression of virus-like particles from a genetic group II small round structured virus. J Gen Virol 1995; 76 ( Pt 9):2349-55. [PMID: 7561776 DOI: 10.1099/0022-1317-76-9-2349] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Comparisons of the RNA polymerase and capsid sequences of small round structured viruses (SRSVs) have recently shown these are genetically diverse viruses which fall into two distinct groups. The genomes of two group I viruses, Southampton and Norwalk viruses have been characterized; however, similar data for the genetic group II SRSVs have not been available until now. We report here the complete genome sequence of a recent group II SRSV, Lordsdale virus. The Lordsdale virus genome is 7555 nt in length and has a similar organization to the group I SRSVs. The large ORF in the 5' half of the genome (5100 nt) is shorter than the group I SRSV ORF1 (5367 nt), but has the characteristic 2C helicase, 3C protease and 3D RNA polymerase enzyme motifs. ORF2, encoding the structural protein is of a similar size to the group I viruses but the small 3'-terminal ORF is significantly larger in group II. A highly conserved sequence of 28 nt was identified at the start of Lordsdale virus ORF1 and repeated at the start of ORF2. These conserved motifs are typical of the animal caliciviruses. Comparison of the 150 N-terminal amino acids in the ORF1 protein revealed little identity between the two SRSV genetic groups, reflecting the shorter ORF1 in the group II virus. Recombinant baculoviruses containing ORF2 and ORF3 sequences were constructed and used to express large quantities of the group II Lordsdale virus structural protein. The capsid protein formed virus-like particles by self assembly which resembled 'empty' SRSVs.
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Affiliation(s)
- K E Dingle
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, UK
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Green SM, Dingle KE, Lambden PR, Caul EO, Ashley CR, Clarke IN. Human enteric Caliciviridae: a new prevalent small round-structured virus group defined by RNA-dependent RNA polymerase and capsid diversity. J Gen Virol 1994; 75 ( Pt 8):1883-8. [PMID: 8046390 DOI: 10.1099/0022-1317-75-8-1883] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Sequence comparison of the RNA-dependent RNA polymerases of small round-structured viruses (SRSVs) from 10 recent U.K. outbreaks of gastroenteritis revealed significant genetic variation. Computer analyses indicated that these viruses can be divided into two discrete groups. SRSV group I contains the previously characterized antigenic type 1 Norwalk and type 3 Southampton viruses. The amino acid sequences of the RNA polymerase, capsid and ORF3 of these two viruses are relatively similar (about 92%, 69% and 72% amino acid identity, respectively). A representative member of group II SRSVs, Bristol virus, was subjected to a detailed genetic analysis. Bristol virus is a recent antigenic type 2 isolate from a U.K. hospital outbreak of gastroenteritis. Using a single clinical sample the 3'-terminal 3881 nucleotide cDNA sequence [excluding the poly(A) tail] of this virus was determined. Analysis of the sequence revealed significant differences from those of group I viruses with the RNA polymerase region, capsid and ORF3 showing only about 62%, 43% and 30% amino acid identity respectively with the equivalent proteins of the Norwalk and Southampton viruses. These data suggest that the morphologically identical SRSVs belong to at least two genetically distinct groups.
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Affiliation(s)
- S M Green
- Department of Molecular Microbiology, University Medical School, Southampton General Hospital, U.K
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