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Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N. Author Correction: The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assemblies. Nat Commun 2024; 15:3060. [PMID: 38594277 PMCID: PMC11004113 DOI: 10.1038/s41467-024-47494-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Affiliation(s)
- Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | - William Matlock
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Liam Shaw
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | | | - Gillian Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy Davies
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marcus Morgan
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Susan Hopkins
- National Infection Service, United Kingdom Health Security Agency, Colindale, London, UK
| | - Timothy Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
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Dietz E, Pritchard E, Pouwels K, Ehsaan M, Blake J, Gaughan C, Haduli E, Boothe H, Vihta KD, Peto T, Stoesser N, Matthews P, Taylor N, Diamond I, Studley R, Rourke E, Birrell P, De Angelis D, Fowler T, Watson C, Eyre D, House T, Walker AS. SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort. BMC Med 2024; 22:143. [PMID: 38532381 DOI: 10.1186/s12916-024-03351-w] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Syndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses. METHODS We estimated the positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of the symptoms and influenza vaccination, using adjusted logistic and multinomial models. RESULTS Swabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age groups. Many test positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still, only ~ 25% reported ILI-WHO and ~ 60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio = 0.55 (95% CI 0.32, 0.95)) versus neither season. CONCLUSIONS Symptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity.
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Affiliation(s)
- Elisabeth Dietz
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK.
| | - Emma Pritchard
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
| | - Koen Pouwels
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Joshua Blake
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | | | - Eric Haduli
- Berkshire and Surrey Pathology Services, Camberley, UK
| | - Hugh Boothe
- Berkshire and Surrey Pathology Services, Camberley, UK
| | | | - Tim Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Philippa Matthews
- The Francis Crick Institute, 1 Midland Road, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | | | | | | | | | - Paul Birrell
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- UK Health Security Agency, London, UK
| | | | - Tom Fowler
- UK Health Security Agency, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - David Eyre
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N. The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies. Nat Commun 2024; 15:1612. [PMID: 38383544 PMCID: PMC10881496 DOI: 10.1038/s41467-024-45761-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Plasmids carry genes conferring antimicrobial resistance and other clinically important traits, and contribute to the rapid dissemination of such genes. Previous studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to plasmids carrying antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections in Oxfordshire, UK. The bacteria had been originally isolated in 2009 (194 isolates) and 2018 (368 isolates), plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to a single host species, although there is substantial overlap between species of plasmid gene-repertoire. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative 'backbone' of core genes with those carrying no such genes. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.
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Affiliation(s)
- Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| | - William Matlock
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Liam Shaw
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | | | - Gillian Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy Davies
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marcus Morgan
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Susan Hopkins
- National Infection Service, United Kingdom Health Security Agency, Colindale, London, UK
| | - Timothy Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
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Fyles M, Vihta KD, Sudre CH, Long H, Das R, Jay C, Wingfield T, Cumming F, Green W, Hadjipantelis P, Kirk J, Steves CJ, Ourselin S, Medley GF, Fearon E, House T. Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets. Sci Rep 2023; 13:21705. [PMID: 38065987 PMCID: PMC10709437 DOI: 10.1038/s41598-023-47488-9] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Variability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which infection leads to disease, with different routes requiring potentially different treatment approaches. For public health and control of transmission, symptoms in community cases were the prompt upon which action such as PCR testing and isolation was taken. However, interpreting symptoms presents challenges, for instance, in balancing the sensitivity and specificity of individual symptoms with the need to maximise case finding, whilst managing demand for limited resources such as testing. For both clinical and transmission control reasons, we require an approach that allows for the possibility of distinct symptom phenotypes, rather than assuming variability along a single dimension. Here we address this problem by bringing together four large and diverse datasets deriving from routine testing, a population-representative household survey and participatory smartphone surveillance in the United Kingdom. Through the use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases. We first analyse each dataset in isolation and across age bands, before using methods that allow us to compare multiple datasets. While we observe separation due to the total number of symptoms experienced by cases, we also see a separation of symptoms into gastrointestinal, respiratory and other types, and different symptom co-occurrence patterns at the extremes of age. In this way, we are able to demonstrate the deep structure of symptoms of COVID-19 without usual biases due to study design. This is expected to have implications for the identification and management of community SARS-CoV-2 cases and could be further applied to symptom-based management of other diseases and syndromes.
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Affiliation(s)
- Martyn Fyles
- Department of Mathematics, University of Manchester, Manchester, UK
- The Alan Turing Institute for Data Science and Artificial Intelligence, London, NW1 2DB, UK
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Karina-Doris Vihta
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Engineering, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Carole H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
- MRC Unit for Lifelong Health and Ageing, University College London, London, UK
| | - Harry Long
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Rajenki Das
- Department of Mathematics, University of Manchester, Manchester, UK
| | - Caroline Jay
- The Alan Turing Institute for Data Science and Artificial Intelligence, London, NW1 2DB, UK
- Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Tom Wingfield
- Department of Clinical Sciences and International Public Health, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, L7 8XP, UK
- WHO Collaborating Centre on Tuberculosis and Social Medicine, Department of Global Public Health, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Fergus Cumming
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - William Green
- United Kingdom Health Security Agency (UKHSA), London, UK
| | | | - Joni Kirk
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology King's College London, London, UK
- Department of Ageing and Health Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Graham F Medley
- Centre for the Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Elizabeth Fearon
- Centre for the Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Institute for Global Health, University College London, London, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK.
- The Alan Turing Institute for Data Science and Artificial Intelligence, London, NW1 2DB, UK.
- IBM Research, Hartree Centre, Daresbury, WA4 4AD, UK.
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Harrison RE, Hamada A, Haswell N, Groves A, Vihta KD, Cella K, Garner S, Walker AS, Seale AC. Cycle Threshold Values as Indication of Increasing SARS-CoV-2 New Variants, England, 2020-2022. Emerg Infect Dis 2023; 29:2024-2031. [PMID: 37678158 PMCID: PMC10521603 DOI: 10.3201/eid2910.230030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
Abstract
Early detection of increased infections or new variants of SARS-CoV-2 is critical for public health response. To determine whether cycle threshold (Ct) data from PCR tests for SARS-CoV-2 could serve as an early indicator of epidemic growth, we analyzed daily mean Ct values in England, UK, by gene target and used iterative sequential regression to detect break points in mean Ct values (and positive test counts). To monitor the epidemic in England, we continued those analyses in real time. During September 2020-January 2022, a total of 7,611,153 positive SARS-CoV-2 PCR test results with Ct data were reported. Spike (S) gene target (S+/S-)-specific mean Ct values decreased 6-29 days before positive test counts increased, and S-gene Ct values provided early indication of increasing new variants (Delta and Omicron). Our approach was beneficial in the context of the first waves of the COVID-19 pandemic and can be used to support future infectious disease monitoring.
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Vihta KD, Pouwels KB, Peto TEA, Pritchard E, House T, Studley R, Rourke E, Cook D, Diamond I, Crook D, Clifton DA, Matthews PC, Stoesser N, Eyre DW, Walker AS. Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom. Clin Infect Dis 2022; 76:ciac613. [PMID: 35917440 PMCID: PMC9384604 DOI: 10.1093/cid/ciac613] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The SARS-CoV-2 Delta variant has been replaced by the highly transmissible Omicron BA.1 variant, and subsequently by Omicron BA.2. It is important to understand how these changes in dominant variants affect reported symptoms, while also accounting for symptoms arising from other co-circulating respiratory viruses. METHODS In a nationally representative UK community study, the COVID-19 Infection Survey, we investigated symptoms in PCR-positive infection episodes vs. PCR-negative study visits over calendar time, by age and vaccination status, comparing periods when the Delta, Omicron BA.1 and BA.2 variants were dominant. RESULTS Between October-2020 and April-2022, 120,995 SARS-CoV-2 PCR-positive episodes occurred in 115,886 participants, with 70,683 (58%) reporting symptoms. The comparator comprised 4,766,366 PCR-negative study visits (483,894 participants); 203,422 (4%) reporting symptoms. Symptom reporting in PCR-positives varied over time, with a marked reduction in loss of taste/smell as Omicron BA.1 dominated, maintained with BA.2 (44%/45% 17 October 2021, 16%/13% 2 January 2022, 15%/12% 27 March 2022). Cough, fever, shortness of breath, myalgia, fatigue/weakness and headache also decreased after Omicron BA.1 dominated, but sore throat increased, the latter to a greater degree than concurrent increases in PCR-negatives. Fatigue/weakness increased again after BA.2 dominated, although to a similar degree to concurrent increases in PCR-negatives. Symptoms were consistently more common in adults aged 18-65 years than in children or older adults. CONCLUSIONS Increases in sore throat (also common in the general community), and a marked reduction in loss of taste/smell, make Omicron harder to detect with symptom-based testing algorithms, with implications for institutional and national testing policies.
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Affiliation(s)
- Karina-Doris Vihta
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, United Kingdom
- Department of Engineering, University of Oxford, Oxford, United Kingdom
| | - Koen B Pouwels
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, United Kingdom
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Emma Pritchard
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, United Kingdom
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
- IBM Research, Hartree Centre, Sci-Tech Daresbury, Daresbury, United Kingdom
| | - Ruth Studley
- Office for National Statistics, Newport, United Kingdom
| | - Emma Rourke
- Office for National Statistics, Newport, United Kingdom
| | - Duncan Cook
- Office for National Statistics, Newport, United Kingdom
| | - Ian Diamond
- Office for National Statistics, Newport, United Kingdom
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - David A Clifton
- Department of Engineering, University of Oxford, Oxford, United Kingdom
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Francis Crick Institute, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Infection, University College London Hospitals, London, United Kingdom
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, Oxford, United Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
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Chau KK, Barker L, Budgell EP, Vihta KD, Sims N, Kasprzyk-Hordern B, Harriss E, Crook DW, Read DS, Walker AS, Stoesser N. Systematic review of wastewater surveillance of antimicrobial resistance in human populations. Environ Int 2022; 162:107171. [PMID: 35290866 PMCID: PMC8960996 DOI: 10.1016/j.envint.2022.107171] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/23/2022] [Accepted: 02/28/2022] [Indexed: 05/05/2023]
Abstract
OBJECTIVES We systematically reviewed studies using wastewater for AMR surveillance in human populations, to determine: (i) evidence of concordance between wastewater-human AMR prevalence estimates, and (ii) methodological approaches which optimised identifying such an association, and which could be recommended as standard. We used Lin's concordance correlation coefficient (CCC) to quantify concordance between AMR prevalence estimates in wastewater and human compartments (where CCC = 1 reflects perfect concordance), and logistic regression to identify study features (e.g. sampling methods) associated with high agreement studies (defined as >70% of within-study wastewater-human AMR prevalence comparisons within ±10%). RESULTS Of 8,867 records and 441 full-text methods reviewed, 33 studies were included. AMR prevalence data was extractable from 24 studies conducting phenotypic-only (n = 7), genotypic-only (n = 1) or combined (n = 16) AMR detection. Overall concordance of wastewater-human AMR prevalence estimates was reasonably high for both phenotypic (CCC = 0.85 [95% CI 0.8-0.89]) and genotypic approaches (CCC = 0.88 (95% CI 0.84-0.9)) despite diverse study designs, bacterial species investigated and phenotypic/genotypic targets. No significant relationships between methodological approaches and high agreement studies were identified using logistic regression; however, this was limited by inconsistent reporting of study features, significant heterogeneity in approaches and limited sample size. Based on a secondary, descriptive synthesis, studies conducting composite sampling of wastewater influent, longitudinal sampling >12 months, and time-/location-matched sampling of wastewater and human compartments generally had higher agreement. CONCLUSION Wastewater-based surveillance of AMR appears promising, with high overall concordance between wastewater and human AMR prevalence estimates in studies irrespective of heterogenous approaches. However, our review suggests future work would benefit from: time-/location-matched sampling of wastewater and human populations, composite sampling of influent, and sampling >12 months for longitudinal studies. Further research and clear and consistent reporting of study methods is required to identify optimal practice.
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Affiliation(s)
- K K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - L Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - E P Budgell
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - K D Vihta
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - N Sims
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - B Kasprzyk-Hordern
- Department of Chemistry, Faculty of Science, University of Bath, Bath BA2 7AY, United Kingdom.
| | - E Harriss
- Bodleian Healthcare Libraries, University of Oxford, Oxford OX3 9DU, United Kingdom.
| | - D W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - D S Read
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, United Kingdom.
| | - A S Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, United Kingdom.
| | - N Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
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8
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Pritchard E, Jones J, Vihta KD, Stoesser N, Matthews PPC, Eyre DW, House T, Bell JI, Newton PJN, Farrar J, Crook PD, Hopkins S, Cook D, Rourke E, Studley R, Diamond PI, Peto PT, Pouwels KB, Walker PAS. Monitoring populations at increased risk for SARS-CoV-2 infection in the community using population-level demographic and behavioural surveillance. Lancet Reg Health Eur 2022; 13:100282. [PMID: 34927119 PMCID: PMC8665900 DOI: 10.1016/j.lanepe.2021.100282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND The COVID-19 pandemic is rapidly evolving, with emerging variants and fluctuating control policies. Real-time population screening and identification of groups in whom positivity is highest could help monitor spread and inform public health messaging and strategy. METHODS To develop a real-time screening process, we included results from nose and throat swabs and questionnaires taken 19 July 2020-17 July 2021 in the UK's national COVID-19 Infection Survey. Fortnightly, associations between SARS-CoV-2 positivity and 60 demographic and behavioural characteristics were estimated using logistic regression models adjusted for potential confounders, considering multiple testing, collinearity, and reverse causality. FINDINGS Of 4,091,537 RT-PCR results from 482,677 individuals, 29,903 (0·73%) were positive. As positivity rose September-November 2020, rates were independently higher in younger ages, and those living in Northern England, major urban conurbations, more deprived areas, and larger households. Rates were also higher in those returning from abroad, and working in healthcare or outside of home. When positivity peaked December 2020-January 2021 (Alpha), high positivity shifted to southern geographical regions. With national vaccine roll-out from December 2020, positivity reduced in vaccinated individuals. Associations attenuated as rates decreased between February-May 2021. Rising positivity rates in June-July 2021 (Delta) were independently higher in younger, male, and unvaccinated groups. Few factors were consistently associated with positivity. 25/45 (56%) confirmed associations would have been detected later using 28-day rather than 14-day periods. INTERPRETATION Population-level demographic and behavioural surveillance can be a valuable tool in identifying the varying characteristics driving current SARS-CoV-2 positivity, allowing monitoring to inform public health policy. FUNDING Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.
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Affiliation(s)
- Emma Pritchard
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joel Jones
- Office for National Statistics, Newport, UK
| | - Karina-Doris Vihta
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Department of Engineering, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Prof Philippa C. Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - David W. Eyre
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Department of Engineering, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK
- IBM Research, Hartree Centre, Sci-Tech Daresbury, UK
| | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | | | | | - Prof Derrick Crook
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Susan Hopkins
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Healthcare-Associated Infection and Antimicrobial Resistance Division, Public Health England, London, UK
- National Institute for Health Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | | | | | | | | | - Prof Tim Peto
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Koen B. Pouwels
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Prof A. Sarah Walker
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
| | - COVID-19 Infection Survey Team
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Office for National Statistics, Newport, UK
- Department of Engineering, University of Oxford, Oxford, UK
- The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Mathematics, University of Manchester, Manchester, UK
- IBM Research, Hartree Centre, Sci-Tech Daresbury, UK
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
- Health Improvement Directorate, Public Health England, London, UK
- Wellcome Trust, London, UK
- Healthcare-Associated Infection and Antimicrobial Resistance Division, Public Health England, London, UK
- National Institute for Health Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Clinical Trials Unit at UCL, UCL, London, UK
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9
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Lipworth S, Vihta KD, Davies T, Wright S, Tabirao M, Chau K, Vaughan A, Kavanagh J, Barker L, George S, Segal S, Paulus S, Barrett L, Oakley S, Jeffery K, Butcher L, Peto T, Crook D, Walker S, Kadambari S, Stoesser N. Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by Gram-negative bacteria. Commun Med (Lond) 2022; 2:101. [PMID: 35968045 PMCID: PMC9372158 DOI: 10.1038/s43856-022-00161-0] [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: 11/11/2021] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
Background Gram-negative organisms are common causes of bloodstream infection (BSI) during the neonatal period and early childhood. Whilst several large studies have characterised these isolates in adults, equivalent data (particularly incorporating whole genome sequencing) is lacking in the paediatric population. Methods We perform an epidemiological and sequencing based analysis of Gram-negative bloodstream infections (327 isolates (296 successfully sequenced) from 287 patients) in children <18 years old between 2008 and 2018 in Oxfordshire, UK. Results Here we show that the burden of infection lies predominantly in neonates and that most infections are caused by Escherichia coli, Klebsiella spp. and Enterobacter hormaechei. There is no evidence in our setting that the proportion of antimicrobial resistant isolates is increasing in the paediatric population although we identify some evidence of sub-breakpoint increases in gentamicin resistance. The population structure of E. coli BSI isolates in neonates and children mirrors that in adults with a predominance of STs 131/95/73/69 and the same proportions of O-antigen serotypes. In most cases in our setting there is no evidence of transmission/point-source acquisition and we demonstrate the utility of whole genome sequencing to refute a previously suspected outbreak. Conclusions Our findings support continued use of current empirical treatment guidelines and suggest that O-antigen targeted vaccines may have a role in reducing the incidence of neonatal sepsis.
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Affiliation(s)
- Sam Lipworth
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Karina-Doris Vihta
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.4991.50000 0004 1936 8948Department of Engineering, University of Oxford, Oxford, UK
| | - Tim Davies
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Wright
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Merline Tabirao
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kevin Chau
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alison Vaughan
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie George
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Shelley Segal
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephane Paulus
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucinda Barrett
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Katie Jeffery
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lisa Butcher
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tim Peto
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- grid.4991.50000 0004 1936 8948NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom
- grid.454382.c0000 0004 7871 7212NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Derrick Crook
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- grid.4991.50000 0004 1936 8948NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom
- grid.454382.c0000 0004 7871 7212NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Sarah Walker
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.4991.50000 0004 1936 8948NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom
- grid.454382.c0000 0004 7871 7212NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Seilesh Kadambari
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- grid.4991.50000 0004 1936 8948Department of Paediatrics, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, University of Oxford, Oxford, UK
- grid.410556.30000 0001 0440 1440Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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10
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Walker AS, Vihta KD, Gethings O, Pritchard E, Jones J, House T, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Studley R, Rourke E, Hay J, Hopkins S, Crook D, Peto T, Matthews PC, Eyre DW, Stoesser N, Pouwels KB. Tracking the Emergence of SARS-CoV-2 Alpha Variant in the United Kingdom. N Engl J Med 2021; 385:2582-2585. [PMID: 34879193 PMCID: PMC8693687 DOI: 10.1056/nejmc2103227] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | - Owen Gethings
- Office for National Statistics, Newport, United Kingdom
| | | | - Joel Jones
- Office for National Statistics, Newport, United Kingdom
| | - Thomas House
- University of Manchester, Manchester, United Kingdom
| | - Iain Bell
- Office for National Statistics, Newport, United Kingdom
| | - John I Bell
- University of Oxford, Oxford, United Kingdom
| | - John N Newton
- Office for Health Improvement and Disparities, London, United Kingdom
| | | | - Ian Diamond
- Office for National Statistics, Newport, United Kingdom
| | - Ruth Studley
- Office for National Statistics, Newport, United Kingdom
| | - Emma Rourke
- Office for National Statistics, Newport, United Kingdom
| | - Jodie Hay
- University of Glasgow, Glasgow, United Kingdom
| | | | | | - Tim Peto
- University of Oxford, Oxford, United Kingdom
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11
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Aliabadi S, Jauneikaite E, Müller-Pebody B, Hope R, Vihta KD, Horner C, Costelloe CE. Exploring temporal trends and risk factors for resistance in Escherichia coli-causing bacteraemia in England between 2013 and 2018: an ecological study. J Antimicrob Chemother 2021; 77:782-792. [PMID: 34921311 DOI: 10.1093/jac/dkab440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/27/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Escherichia coli are Gram-negative bacteria associated with an increasing burden of antimicrobial resistance (AMR) in England. OBJECTIVES To create a comprehensive epidemiological picture of E. coli bacteraemia resistance trends and risk factors in England by linking national microbiology data sources and performing a longitudinal analysis of rates. METHODS A retrospective observational study was conducted on all national records for antimicrobial susceptibility testing on E. coli bacteraemia in England from 1 January 2013 to 31 December 2018 from the UK Health Security Agency (UKHSA) and the BSAC Resistance Surveillance Programme (BSAC-RSP). Trends in AMR and MDR were estimated using iterative sequential regression. Logistic regression analyses were performed on UKHSA data to estimate the relationship between risk factors and AMR or MDR in E. coli bacteraemia isolates. RESULTS An increase in resistance rates was observed in community- and hospital-onset bacteraemia for third-generation cephalosporins, co-amoxiclav, gentamicin and ciprofloxacin. Among community-acquired cases, and after adjustment for other factors, patients aged >65 years were more likely to be infected by E. coli isolates resistant to at least one of 11 antibiotics than those aged 18-64 years (OR: 1.21, 95% CI: 1.18-1.25; P < 0.05). In hospital-onset cases, E. coli isolates from those aged 1-17 years were more likely to be resistant than those aged 18-64 years (OR: 1.33, 95% CI: 1.02-1.73; P < 0.05). CONCLUSIONS Antibiotic resistance rates in E. coli-causing bacteraemia increased between 2013 and 2018 in England for key antimicrobial agents. Findings of this study have implications for guiding future policies on a prescribing of antimicrobial agents, for specific patient populations in particular.
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Affiliation(s)
- Shirin Aliabadi
- Global Digital Health Unit, Department of Primary Care and Public Health, Imperial College London, London, UK
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Berit Müller-Pebody
- Division of Healthcare Associated Infections and Antimicrobial Resistance, National Infection Service, UK Health Security Agency, London, UK
| | - Russell Hope
- Division of Healthcare Associated Infections and Antimicrobial Resistance, National Infection Service, UK Health Security Agency, London, UK
| | - Karina-Doris Vihta
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Carolyne Horner
- British Society for Antimicrobial Chemotherapy, Birmingham, UK
| | - Céire E Costelloe
- Global Digital Health Unit, Department of Primary Care and Public Health, Imperial College London, London, UK.,Division of Clinical studies, Institute of Cancer Research, London, UK
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12
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Vihta KD, Gordon NC, Stoesser N, Quan TP, Tyrrell CSB, Vongsouvath M, Ashley EA, Chansamouth V, Turner P, Ling CL, Eyre DW, White NJ, Crook D, Peto TEA, Walker AS. Antimicrobial resistance in commensal opportunistic pathogens isolated from non-sterile sites can be an effective proxy for surveillance in bloodstream infections. Sci Rep 2021; 11:23359. [PMID: 34862445 PMCID: PMC8642463 DOI: 10.1038/s41598-021-02755-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/12/2021] [Accepted: 11/23/2021] [Indexed: 11/10/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance in bloodstream infections (BSIs) is challenging in low/middle-income countries (LMICs) given limited laboratory capacity. Other specimens are easier to collect and process and are more likely to be culture-positive. In 8102 E. coli BSIs, 322,087 E. coli urinary tract infections, 6952 S. aureus BSIs and 112,074 S. aureus non-sterile site cultures from Oxfordshire (1998-2018), and other (55,296 isolates) rarer commensal opportunistic pathogens, antibiotic resistance trends over time in blood were strongly associated with those in other specimens (maximum cross-correlation per drug 0.51-0.99). Resistance prevalence was congruent across drug-years for each species (276/312 (88%) species-drug-years with prevalence within ± 10% between blood/other isolates). Results were similar across multiple countries in high/middle/low income-settings in the independent ATLAS dataset (103,559 isolates, 2004-2017) and three further LMIC hospitals/programmes (6154 isolates, 2008-2019). AMR in commensal opportunistic pathogens cultured from BSIs is strongly associated with AMR in commensal opportunistic pathogens cultured from non-sterile sites over calendar time, suggesting the latter could be used as an effective proxy for AMR surveillance in BSIs.
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Affiliation(s)
- Karina-Doris Vihta
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
- National Institute for Health Research Health Protection Research Unit, Oxford, UK.
- Microbiology Research Level 7, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
| | | | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
| | | | | | - Elizabeth A Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Vilada Chansamouth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Turner
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - David W Eyre
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Nicholas J White
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Derrick Crook
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- National Institute for Health Research Health Protection Research Unit, Oxford, UK
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13
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Pouwels KB, Pritchard E, Matthews PC, Stoesser N, Eyre DW, Vihta KD, House T, Hay J, Bell JI, Newton JN, Farrar J, Crook D, Cook D, Rourke E, Studley R, Peto TEA, Diamond I, Walker AS. Effect of Delta variant on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK. Nat Med 2021; 27:2127-2135. [PMID: 34650248 PMCID: PMC8674129 DOI: 10.1038/s41591-021-01548-7] [Citation(s) in RCA: 319] [Impact Index Per Article: 106.3] [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: 08/18/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022]
Abstract
The effectiveness of the BNT162b2 and ChAdOx1 vaccines against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections requires continuous re-evaluation, given the increasingly dominant B.1.617.2 (Delta) variant. In this study, we investigated the effectiveness of these vaccines in a large, community-based survey of randomly selected households across the United Kingdom. We found that the effectiveness of BNT162b2 and ChAdOx1 against infections (new polymerase chain reaction (PCR)-positive cases) with symptoms or high viral burden is reduced with the B.1.617.2 variant (absolute difference of 10-13% for BNT162b2 and 16% for ChAdOx1) compared to the B.1.1.7 (Alpha) variant. The effectiveness of two doses remains at least as great as protection afforded by prior natural infection. The dynamics of immunity after second doses differed significantly between BNT162b2 and ChAdOx1, with greater initial effectiveness against new PCR-positive cases but faster declines in protection against high viral burden and symptomatic infection with BNT162b2. There was no evidence that effectiveness varied by dosing interval, but protection was higher in vaccinated individuals after a prior infection and in younger adults. With B.1.617.2, infections occurring after two vaccinations had similar peak viral burden as those in unvaccinated individuals. SARS-CoV-2 vaccination still reduces new infections, but effectiveness and attenuation of peak viral burden are reduced with B.1.617.2.
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Affiliation(s)
- Koen B Pouwels
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
| | - Emma Pritchard
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - David W Eyre
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Karina-Doris Vihta
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Department of Engineering, University of Oxford, Oxford, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK
- IBM Research, Hartree Centre, Sci-Tech Daresbury, UK
| | - Jodie Hay
- Glasgow Lighthouse Laboratory, Glasgow, UK
- University of Glasgow, Glasgow, UK
| | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | - John N Newton
- Health Improvement Directorate, Public Health England, London, UK
| | | | - Derrick Crook
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | | | | | - Tim E A Peto
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | | | - A Sarah Walker
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- MRC Clinical Trials Unit at UCL, University College London, London, UK
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14
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Lipworth S, Vihta KD, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto TEA, Crook DW, Walker AS, Stoesser N. Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK. Genome Med 2021; 13:144. [PMID: 34479643 PMCID: PMC8414751 DOI: 10.1186/s13073-021-00947-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 01/22/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
Background The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interventions are therefore hard to design. Methods In this study, we sequenced 3468 unselected isolates over a decade in Oxfordshire (UK) and linked this data to routinely collected electronic healthcare records and mandatory surveillance reports. We annotated genomes for clinically relevant genes, contrasting the distribution of these within and between species, and compared incidence trends over time using stacked negative binomial regression. Results We demonstrate that the observed increases in E. coli incidence were not driven by the success of one or more sequence types (STs); instead, four STs continue to dominate a stable population structure, with no evidence of adaptation to hospital/community settings. Conversely in Klebsiella spp., most infections are caused by sporadic STs with the exception of a local drug-resistant outbreak strain (ST490). Virulence elements are highly structured by ST in E. coli but not Klebsiella spp. where they occur in a diverse spectrum of STs and equally across healthcare and community settings. Most clinically hypervirulent (i.e. community-onset) Klebsiella BSIs have no known acquired virulence loci. Finally, we demonstrate a diverse but largely genus-restricted mobilome with close associations between antimicrobial resistance (AMR) genes and insertion sequences but not typically specific plasmid replicon types, consistent with the dissemination of AMR genes being highly contingent on smaller mobile genetic elements (MGEs). Conclusions Our large genomic study highlights distinct differences in the molecular epidemiology of E. coli and Klebsiella BSIs and suggests that no single specific pathogen genetic factors (e.g. AMR/virulence genes/sequence type) are likely contributing to the increasing incidence of BSI overall, that association with AMR genes in E. coli is a contributor to the increasing number of E. coli BSIs, and that more attention should be given to AMR gene associations with non-plasmid MGEs to try and understand horizontal gene transfer networks. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00947-2.
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Affiliation(s)
- Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,Oxford University Hospitals NHS Foundation Trust, Oxford, UK. .,John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | | | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy Davies
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marcus Morgan
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Susan Hopkins
- National Infection Service, Public Health England, Colindale, London, UK
| | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,John Radcliffe Hospital, Oxford, OX3 9DU, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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15
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Walker AS, Pritchard E, House T, Robotham JV, Birrell PJ, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Studley R, Hay J, Vihta KD, Peto TEA, Stoesser N, Matthews PC, Eyre DW, Pouwels KB. Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time. eLife 2021; 10:e64683. [PMID: 34250907 PMCID: PMC8282332 DOI: 10.7554/elife.64683] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [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: 11/06/2020] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Background Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load). Methods We included all positive nose and throat swabs 26 April 2020 to 13 March 2021 from the UK's national COVID-19 Infection Survey, tested by RT-PCR for the N, S, and ORF1ab genes. We investigated predictors of median Ct value using quantile regression. Results Of 3,312,159 nose and throat swabs, 27,902 (0.83%) were RT-PCR-positive, 10,317 (37%), 11,012 (40%), and 6550 (23%) for 3, 2, or 1 of the N, S, and ORF1ab genes, respectively, with median Ct = 29.2 (~215 copies/ml; IQR Ct = 21.9-32.8, 14-56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity, and age. Single-gene positives almost invariably had Ct > 30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity. Of 6189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4808 (78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody negative. Conclusions Marked variation in community SARS-CoV-2 Ct values suggests that they could be a useful epidemiological early-warning indicator. Funding Department of Health and Social Care, National Institutes of Health Research, Huo Family Foundation, Medical Research Council UK; Wellcome Trust.
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Affiliation(s)
- A Sarah Walker
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- MRC Clinical Trials Unit at UCL, UCLLondonUnited Kingdom
| | - Emma Pritchard
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
| | - Thomas House
- Department of Mathematics, University of ManchesterManchesterUnited Kingdom
- IBM Research, Hartree CentreSci-Tech DaresburyUnited Kingdom
| | - Julie V Robotham
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- National Infection Service, Public Health EnglandLondonUnited Kingdom
| | - Paul J Birrell
- National Infection Service, Public Health EnglandLondonUnited Kingdom
- MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public HealthCambridgeUnited Kingdom
| | - Iain Bell
- Office for National StatisticsNewportUnited Kingdom
| | - John I Bell
- Office of the Regius Professor of Medicine, University of OxfordOxfordUnited Kingdom
| | - John N Newton
- Health Improvement Directorate, Public Health EnglandLondonUnited Kingdom
| | | | - Ian Diamond
- Office for National StatisticsNewportUnited Kingdom
| | - Ruth Studley
- Office for National StatisticsNewportUnited Kingdom
| | - Jodie Hay
- University of GlasgowGlasgowUnited Kingdom
- Lighthouse Laboratory in Glasgow, Queen Elizabeth University HospitalGlasgowUnited Kingdom
| | - Karina-Doris Vihta
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
| | - Timothy EA Peto
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Oxford Biomedical Research Centre, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe HospitalOxfordUnited Kingdom
| | - David W Eyre
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- Lighthouse Laboratory in Glasgow, Queen Elizabeth University HospitalGlasgowUnited Kingdom
- Big Data Institute, Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
| | - Koen B Pouwels
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of OxfordOxfordUnited Kingdom
- Health Economics Research Centre, Nuffield Department of Population Health, University of OxfordOxfordUnited Kingdom
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16
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Pritchard E, Matthews PC, Stoesser N, Eyre DW, Gethings O, Vihta KD, Jones J, House T, VanSteenHouse H, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Rourke E, Studley R, Crook D, Peto TEA, Walker AS, Pouwels KB. Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom. Nat Med 2021; 27:1370-1378. [PMID: 34108716 PMCID: PMC8363500 DOI: 10.1038/s41591-021-01410-w] [Citation(s) in RCA: 183] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
The effectiveness of COVID-19 vaccination in preventing new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in the general community is still unclear. Here, we used the Office for National Statistics COVID-19 Infection Survey—a large community-based survey of individuals living in randomly selected private households across the United Kingdom—to assess the effectiveness of the BNT162b2 (Pfizer–BioNTech) and ChAdOx1 nCoV-19 (Oxford–AstraZeneca; ChAdOx1) vaccines against any new SARS-CoV-2 PCR-positive tests, split according to self-reported symptoms, cycle threshold value (<30 versus ≥30; as a surrogate for viral load) and gene positivity pattern (compatible with B.1.1.7 or not). Using 1,945,071 real-time PCR results from nose and throat swabs taken from 383,812 participants between 1 December 2020 and 8 May 2021, we found that vaccination with the ChAdOx1 or BNT162b2 vaccines already reduced SARS-CoV-2 infections ≥21 d after the first dose (61% (95% confidence interval (CI) = 54–68%) versus 66% (95% CI = 60–71%), respectively), with greater reductions observed after a second dose (79% (95% CI = 65–88%) versus 80% (95% CI = 73–85%), respectively). The largest reductions were observed for symptomatic infections and/or infections with a higher viral burden. Overall, COVID-19 vaccination reduced the number of new SARS-CoV-2 infections, with the largest benefit received after two vaccinations and against symptomatic and high viral burden infections, and with no evidence of a difference between the BNT162b2 and ChAdOx1 vaccines. Results from the Office of National Statistics COVID-19 Infection Survey in the United Kingdom demonstrate that the ChAdOx1 nCoV-19 and BNT162b2 vaccines reduce the incidence of new SARS-CoV-2 infections by up to 65% with a single dose and up to 80% after two doses, with no significant differences in efficacy observed between the two vaccines.
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Affiliation(s)
- Emma Pritchard
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,Department of Infectious Diseases and Microbiology, Oxford, University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,Department of Infectious Diseases and Microbiology, Oxford, University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - David W Eyre
- National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,Department of Infectious Diseases and Microbiology, Oxford, University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Karina-Doris Vihta
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Joel Jones
- Office for National Statistics, Newport, UK
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK.,IBM Research, Hartree Centre, Daresbury, UK
| | | | - Iain Bell
- Office for National Statistics, Newport, UK
| | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | - John N Newton
- Health Improvement Directorate, Public Health England, London, UK
| | | | | | | | | | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,Department of Infectious Diseases and Microbiology, Oxford, University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,Department of Infectious Diseases and Microbiology, Oxford, University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,MRC Clinical Trials Unit at UCL, University College London, London, UK
| | - Koen B Pouwels
- National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK. .,Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK. .,Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
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17
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Lipworth S, Vihta KD, Chau KK, Kavanagh J, Davies T, George S, Barker L, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Peto TEA, Crook DW, Walker AS, Stoesser N. Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections. Clin Infect Dis 2021; 73:2276-2282. [PMID: 33411882 PMCID: PMC8677521 DOI: 10.1093/cid/ciab006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/21/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The incidence of bloodstream infections (BSIs) caused by Escherichia coli and Klebsiella pneumoniae is increasing, with substantial associated morbidity, mortality and antimicrobial resistance. Unbiased serotyping studies to guide vaccine target selection are limited. METHODS We conducted unselected, population-level genomic surveillance of bloodstream E. coli and Klebsiella pneumoniae isolates from 2008-2018 in Oxfordshire, UK. We supplemented this with an analysis of publicly available global sequencing data (n=3678). RESULTS We sequenced 3478 E. coli isolates (3278 passed quality control) and 556 K. pneumoniae isolates (535 (K-antigen) and 549 (O-antigen) passed quality control). The four most common E. coli O-antigens (O1/O2/O6/O25) were identified in 1499/3278 isolates; the incidence of these O-types increased over time (IRRy=1.14, 95% CI:1.11-1.16). These O-types accounted for 616/1434 multidrug resistant (MDR) and 173/256 extended-spectrum beta-lactamase(ESBL)-resistant isolates in Oxfordshire, but only 19/90 carbapenem-resistant isolates across all studies. For Klebsiella pneumoniae, the most common O-antigens (O2v2/O1v1/O3b/O1v2) accounted for 410/549 isolates; the incidence of BSIs caused by these also increased annually (IRRy=1.09; 95% CI:1.05-1.12). These O-types accounted for 122/148 MDR and 106/123 ESBL isolates in Oxfordshire and 557/734 carbapenem-resistant isolates across all studies. Conversely we observed substantial capsular antigen diversity. Analysis of 3678 isolates from global studies demonstrated the generalisability of these findings. For E. coli, based on serotyping, the ExPEC4V and ExPEC10V vaccines under investigation would cover 46% and 72% of Oxfordshire isolates respectively, and 47% and 71% of MDR isolates. CONCLUSIONS O-antigen targeted vaccines may be useful in reducing the morbidity, mortality and antimicrobial resistance associated with E. coli and K. pneumoniae BSIs.
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Affiliation(s)
- Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy Davies
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ali Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marcus Morgan
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Timothy E A Peto
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom.,NIHR Biomedical Research Centre, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom.,NIHR Biomedical Research Centre, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, United Kingdom.,NIHR Biomedical Research Centre, Oxford, United Kingdom
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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18
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Pouwels KB, House T, Pritchard E, Robotham JV, Birrell PJ, Gelman A, Vihta KD, Bowers N, Boreham I, Thomas H, Lewis J, Bell I, Bell JI, Newton JN, Farrar J, Diamond I, Benton P, Walker AS. Community prevalence of SARS-CoV-2 in England from April to November, 2020: results from the ONS Coronavirus Infection Survey. Lancet Public Health 2021; 6:e30-e38. [PMID: 33308423 PMCID: PMC7786000 DOI: 10.1016/s2468-2667(20)30282-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [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: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Decisions about the continued need for control measures to contain the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on accurate and up-to-date information about the number of people testing positive for SARS-CoV-2 and risk factors for testing positive. Existing surveillance systems are generally not based on population samples and are not longitudinal in design. METHODS Samples were collected from individuals aged 2 years and older living in private households in England that were randomly selected from address lists and previous Office for National Statistics surveys in repeated cross-sectional household surveys with additional serial sampling and longitudinal follow-up. Participants completed a questionnaire and did nose and throat self-swabs. The percentage of individuals testing positive for SARS-CoV-2 RNA was estimated over time by use of dynamic multilevel regression and poststratification, to account for potential residual non-representativeness. Potential changes in risk factors for testing positive over time were also assessed. The study is registered with the ISRCTN Registry, ISRCTN21086382. FINDINGS Between April 26 and Nov 1, 2020, results were available from 1 191 170 samples from 280 327 individuals; 5231 samples were positive overall, from 3923 individuals. The percentage of people testing positive for SARS-CoV-2 changed substantially over time, with an initial decrease between April 26 and June 28, 2020, from 0·40% (95% credible interval 0·29-0·54) to 0·06% (0·04-0·07), followed by low levels during July and August, 2020, before substantial increases at the end of August, 2020, with percentages testing positive above 1% from the end of October, 2020. Having a patient-facing role and working outside your home were important risk factors for testing positive for SARS-CoV-2 at the end of the first wave (April 26 to June 28, 2020), but not in the second wave (from the end of August to Nov 1, 2020). Age (young adults, particularly those aged 17-24 years) was an important initial driver of increased positivity rates in the second wave. For example, the estimated percentage of individuals testing positive was more than six times higher in those aged 17-24 years than in those aged 70 years or older at the end of September, 2020. A substantial proportion of infections were in individuals not reporting symptoms around their positive test (45-68%, dependent on calendar time. INTERPRETATION Important risk factors for testing positive for SARS-CoV-2 varied substantially between the part of the first wave that was captured by the study (April to June, 2020) and the first part of the second wave of increased positivity rates (end of August to Nov 1, 2020), and a substantial proportion of infections were in individuals not reporting symptoms, indicating that continued monitoring for SARS-CoV-2 in the community will be important for managing the COVID-19 pandemic moving forwards. FUNDING Department of Health and Social Care.
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Affiliation(s)
- Koen B Pouwels
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK; The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, University of Oxford, Oxford, UK.
| | - Thomas House
- Department of Mathematics, University of Manchester, Manchester, UK; IBM Research, Hartree Centre, Sci-Tech, Daresbury, UK
| | - Emma Pritchard
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Paul J Birrell
- National Infection Service, Public Health England, London, UK; Medical Research Council (MRC) Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Cambridge, UK
| | - Andrew Gelman
- Department of Statistics, Columbia University, New York, NY, USA
| | - Karina-Doris Vihta
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | - Iain Bell
- Office for National Statistics, Newport, UK
| | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | - John N Newton
- Health Improvement Directorate, Public Health England, London, UK
| | | | | | | | - Ann Sarah Walker
- The National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; The National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK; MRC Clinical Trials Unit at University College London, London, UK
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19
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Zhong LL, Phan HTT, Shen C, Vihta KD, Sheppard AE, Huang X, Zeng KJ, Li HY, Zhang XF, Patil S, Crook DW, Walker AS, Xing Y, Lin JL, Feng LQ, Doi Y, Xia Y, Stoesser N, Tian GB. High Rates of Human Fecal Carriage of mcr-1-Positive Multidrug-Resistant Enterobacteriaceae Emerge in China in Association With Successful Plasmid Families. Clin Infect Dis 2019; 66:676-685. [PMID: 29040419 DOI: 10.1093/cid/cix885] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/07/2017] [Indexed: 12/21/2022] Open
Abstract
Background mcr-1-mediated colistin resistance in Enterobacteriaceae is concerning, as colistin is used in treating multidrug-resistant Enterobacteriaceae infections. We identified trends in human fecal mcr-1-positivity rates and colonization with mcr-1-positive, third-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae in Guangzhou, China, and investigated the genetic contexts of mcr-1 in mcr-1-positive 3GC-R strains. Methods Fecal samples were collected from in-/out-patients submitting specimens to 3 hospitals (2011-2016). mcr-1 carriage trends were assessed using iterative sequential regression. A subset of mcr-1-positive isolates was sequenced (whole-genome sequencing [WGS], Illumina), and genetic contexts (flanking regions, plasmids) of mcr-1 were characterized. Results Of 8022 fecal samples collected, 497 (6.2%) were mcr-1 positive, and 182 (2.3%) harbored mcr-1-positive 3GC-R Enterobacteriaceae. We observed marked increases in mcr-1 (0% [April 2011] to 31% [March 2016]) and more recent (since January 2014; 0% [April 2011] to 15% [March 2016]) increases in human colonization with mcr-1-positive 3GC-R Enterobacteriaceae (P < .001). mcr-1-positive 3GC-R isolates were commonly multidrug resistant. WGS of mcr-1-positive 3GC-R isolates (70 Escherichia coli, 3 Klebsiella pneumoniae) demonstrated bacterial strain diversity; mcr-1 in association with common plasmid backbones (IncI, IncHI2/HI2A, IncX4) and sometimes in multiple plasmids; frequent mcr-1 chromosomal integration; and high mobility of the mcr-1-associated insertion sequence ISApl1. Sequence data were consistent with plasmid spread among animal/human reservoirs. Conclusions The high prevalence of mcr-1 in multidrug-resistant E. coli colonizing humans is a clinical threat; diverse genetic mechanisms (strains/plasmids/insertion sequences) have contributed to the dissemination of mcr-1, and will facilitate its persistence.
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Affiliation(s)
- Lan-Lan Zhong
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Hang T T Phan
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Cong Shen
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Karina-Doris Vihta
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Anna E Sheppard
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Xi Huang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Program of Immunology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Guangzhou, China
| | - Kun-Jiao Zeng
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Hong-Yu Li
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xue-Fei Zhang
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Sandip Patil
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Derrick W Crook
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - A Sarah Walker
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Yong Xing
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Jia-Lin Lin
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Lian-Qiang Feng
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Yohei Doi
- University of Pittsburgh Medical Center, Pennsylvania
| | - Yong Xia
- Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Nicole Stoesser
- Modernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Guo-Bao Tian
- Program in Pathobiology, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
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Vihta KD, Stoesser N, Llewelyn MJ, Quan TP, Davies T, Fawcett NJ, Dunn L, Jeffery K, Butler CC, Hayward G, Andersson M, Morgan M, Oakley S, Mason A, Hopkins S, Wyllie DH, Crook DW, Wilcox MH, Johnson AP, Peto TEA, Walker AS. Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998-2016: a study of electronic health records. Lancet Infect Dis 2018; 18:1138-1149. [PMID: 30126643 DOI: 10.1016/s1473-3099(18)30353-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 05/21/2018] [Accepted: 05/24/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Escherichia coli bloodstream infections are increasing in the UK and internationally. The evidence base to guide interventions against this major public health concern is small. We aimed to investigate possible drivers of changes in the incidence of E coli bloodstream infection and antibiotic susceptibilities in Oxfordshire, UK, over the past two decades, while stratifying for time since hospital exposure. METHODS In this observational study, we used all available data on E coli bloodstream infections and E coli urinary tract infections (UTIs) from one UK region (Oxfordshire) using anonymised linked microbiological data and hospital electronic health records from the Infections in Oxfordshire Research Database (IORD). We estimated the incidence of infections across a two decade period and the annual incidence rate ratio (aIRR) in 2016. We modelled the data using negative binomial regression on the basis of microbiological, clinical, and health-care-exposure risk factors. We investigated infection severity, 30-day all-cause mortality, and community and hospital amoxicillin plus clavulanic acid (co-amoxiclav) use to estimate changes in bacterial virulence and the effect of antimicrobial resistance on incidence. FINDINGS From Jan 1, 1998, to Dec 31, 2016, 5706 E coli bloodstream infections occurred in 5215 patients, and 228 376 E coli UTIs occurred in 137 075 patients. 1365 (24%) E coli bloodstream infections were nosocomial (onset >48 h after hospital admission), 1132 (20%) were quasi-nosocomial (≤30 days after discharge), 1346 (24%) were quasi-community (31-365 days after discharge), and 1863 (33%) were community (>365 days after hospital discharge). The overall incidence increased year on year (aIRR 1·06, 95% CI 1·05-1·06). In 2016, 212 (41%) of 515 E coli bloodstream infections and 3921 (28%) of 13 792 E coli UTIs were co-amoxiclav resistant. Increases in E coli bloodstream infections were driven by increases in community (aIRR 1·10, 95% CI 1·07-1·13; p<0·0001) and quasi-community (aIRR 1·08, 1·07-1·10; p<0·0001) cases. 30-day mortality associated with E coli bloodstream infection decreased over time in the nosocomial (adjusted rate ratio [RR] 0·98, 95% CI 0·96-1·00; p=0·03) group, and remained stable in the quasi-nosocomial (adjusted RR 0·98, 0·95-1·00; p=0·06), quasi-community (adjusted RR 0·99, 0·96-1·01; p=0·32), and community (adjusted RR 0·99, 0·96-1·01; p=0·21) groups. Mortality was, however, substantial at 14-25% across all hospital-exposure groups. Co-amoxiclav-resistant E coli bloodstream infections increased in all groups across the study period (by 11-18% per year, significantly faster than co-amoxiclav-susceptible E coli bloodstream infections; pheterogeneity<0·0001), as did co-amoxiclav-resistant E coli UTIs (by 14-29% per year; pheterogeneity<0·0001). Previous year co-amoxiclav use in primary-care facilities was associated with increased subsequent year community co-amoxiclav-resistant E coli UTIs (p=0·003). INTERPRETATION Increases in E coli bloodstream infections in Oxfordshire are primarily community associated, with substantial co-amoxiclav resistance; nevertheless, we found little or no change in mortality. Focusing interventions on primary care facilities, particularly those with high co-amoxiclav use, could be effective in reducing the incidence of co-amoxiclav-resistant E coli bloodstream infections, in this region and more generally. FUNDING National Institute for Health Research.
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Affiliation(s)
- Karina-Doris Vihta
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK.
| | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Martin J Llewelyn
- Brighton and Sussex Medical School, University of Sussex, Falmer, UK
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Tim Davies
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Nicola J Fawcett
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Laura Dunn
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Chris C Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Gail Hayward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Marcus Morgan
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Amy Mason
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susan Hopkins
- National Infection Service, Public Health England, Colindale, UK
| | - David H Wyllie
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK; National Infection Service, Public Health England, Colindale, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Alan P Johnson
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK; National Infection Service, Public Health England, Colindale, UK
| | - Tim E A Peto
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK
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