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Dyson ZA, Ashton PM, Khanam F, Chunga Chirambo A, Shakya M, Meiring JE, Tonks S, Karkey A, Msefula C, Clemens JD, Dunstan SJ, Baker S, Dougan G, Pitzer VE, Basnyat B, Qadri F, Heyderman RS, Gordon MA, Pollard AJ, Holt KE. Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study. THE LANCET. MICROBE 2024:S2666-5247(24)00047-8. [PMID: 38996496 DOI: 10.1016/s2666-5247(24)00047-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND Enteric fever is a serious public health concern. The causative agents, Salmonella enterica serovars Typhi and Paratyphi A, frequently have antimicrobial resistance (AMR), leading to limited treatment options and poorer clinical outcomes. We investigated the genomic epidemiology, resistance mechanisms, and transmission dynamics of these pathogens at three urban sites in Africa and Asia. METHODS S Typhi and S Paratyphi A bacteria isolated from blood cultures of febrile children and adults at study sites in Dhaka (Bangladesh), Kathmandu (Nepal), and Blantyre (Malawi) during STRATAA surveillance were sequenced. Isolates were charactered in terms of their serotypes, genotypes (according to GenoTyphi and Paratype), molecular determinants of AMR, and population structure. We used phylogenomic analyses incorporating globally representative genomic data from previously published surveillance studies and ancestral state reconstruction to differentiate locally circulating from imported pathogen AMR variants. Clusters of sequences without any single-nucleotide variants in their core genome were identified and used to explore spatiotemporal patterns and transmission dynamics. FINDINGS We sequenced 731 genomes from isolates obtained during surveillance across the three sites between Oct 1, 2016, and Aug 31, 2019 (24 months in Dhaka and Kathmandu and 34 months in Blantyre). S Paratyphi A was present in Dhaka and Kathmandu but not Blantyre. S Typhi genotype 4.3.1 (H58) was common in all sites, but with different dominant variants (4.3.1.1.EA1 in Blantyre, 4.3.1.1 in Dhaka, and 4.3.1.2 in Kathmandu). Multidrug resistance (ie, resistance to chloramphenicol, co-trimoxazole, and ampicillin) was common in Blantyre (138 [98%] of 141 cases) and Dhaka (143 [32%] of 452), but absent from Kathmandu. Quinolone-resistance mutations were common in Dhaka (451 [>99%] of 452) and Kathmandu (123 [89%] of 138), but not in Blantyre (three [2%] of 141). Azithromycin-resistance mutations in acrB were rare, appearing only in Dhaka (five [1%] of 452). Phylogenetic analyses showed that most cases derived from pre-existing, locally established pathogen variants; 702 (98%) of 713 drug-resistant infections resulted from local circulation of AMR variants, not imported variants or recent de novo emergence; and pathogen variants circulated across age groups. 479 (66%) of 731 cases clustered with others that were indistinguishable by point mutations; individual clusters included multiple age groups and persisted for up to 2·3 years, and AMR determinants were invariant within clusters. INTERPRETATION Enteric fever was associated with locally established pathogen variants that circulate across age groups. AMR infections resulted from local transmission of resistant strains. These results form a baseline against which to monitor the impacts of control measures. FUNDING Wellcome Trust, Bill & Melinda Gates Foundation, EU Horizon 2020, and UK National Institute for Health and Care Research.
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Affiliation(s)
- Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Philip M Ashton
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Farhana Khanam
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Angeziwa Chunga Chirambo
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Mila Shakya
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - James E Meiring
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Susan Tonks
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Tropical Medicine and Global Health, Medical Sciences Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - John D Clemens
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh; International Vaccine Institute, Seoul, South Korea
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stephen Baker
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Gordon Dougan
- Department of Medicine, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Tropical Medicine and Global Health, Medical Sciences Division, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK; Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
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Xu P, Liang S, Hahn A, Zhao V, Lo WT‘J, Haller BC, Sobkowiak B, Chitwood MH, Colijn C, Cohen T, Rhee KY, Messer PW, Wells MT, Clark AG, Kim J. e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.29.601123. [PMID: 39005464 PMCID: PMC11244936 DOI: 10.1101/2024.06.29.601123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Infectious disease dynamics are driven by the complex interplay of epidemiological, ecological, and evolutionary processes. Accurately modeling these interactions is crucial for understanding pathogen spread and informing public health strategies. However, existing simulators often fail to capture the dynamic interplay between these processes, resulting in oversimplified models that do not fully reflect real-world complexities in which the pathogen's genetic evolution dynamically influences disease transmission. We introduce the epidemiological-ecological-evolutionary simulator (e3SIM), an open-source framework that concurrently models the transmission dynamics and molecular evolution of pathogens within a host population while integrating environmental factors. Using an agent-based, discrete-generation, forward-in-time approach, e3SIM incorporates compartmental models, host-population contact networks, and quantitative-trait models for pathogens. This integration allows for realistic simulations of disease spread and pathogen evolution. Key features include a modular and scalable design, flexibility in modeling various epidemiological and population-genetic complexities, incorporation of time-varying environmental factors, and a user-friendly graphical interface. We demonstrate e3SIM's capabilities through simulations of realistic outbreak scenarios with SARS-CoV-2 and Mycobacterium tuberculosis, illustrating its flexibility for studying the genomic epidemiology of diverse pathogen types.
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Affiliation(s)
- Peiyu Xu
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Shenni Liang
- Department of Computational Science, Cornell University, Ithaca, NY, USA
| | - Andrew Hahn
- Department of Computational Science, Cornell University, Ithaca, NY, USA
| | - Vivian Zhao
- Department of Computational Science, Cornell University, Ithaca, NY, USA
| | - Wai Tung ‘Jack’ Lo
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Benjamin C. Haller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, USA
| | - Melanie H. Chitwood
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, USA
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, USA
| | - Kyu Y. Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Philipp W. Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Martin T. Wells
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Andrew G. Clark
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Jaehee Kim
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
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Chang T, Cho SI, Yoo DS, Min KD. Trends in Nationally Notifiable Infectious Diseases in Humans and Animals during COVID-19 Pandemic, South Korea. Emerg Infect Dis 2024; 30:1154-1163. [PMID: 38781924 PMCID: PMC11138988 DOI: 10.3201/eid3006.231422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
We investigated trends in notifiable infectious diseases in both humans and animals during the COVID-19 pandemic in South Korea and compared those data against expected trends had nonpharmaceutical interventions (NPIs) not been implemented. We found that human respiratory infectious diseases other than COVID-19 decreased by an average of 54.7% after NPIs were introduced. On the basis of that trend, we estimated that annual medical expenses associated with respiratory infections other than COVID-19 also decreased by 3.8% in 2020 and 18.9% in 2021. However, human gastrointestinal infectious diseases and livestock diseases exhibited similar or even higher incidence rates after NPIs were instituted. Our investigation revealed that the preventive effect of NPIs varied among diseases and that NPIs might have had limited effectiveness in reducing the spread of certain types of infectious diseases. These findings suggest the need for future, novel public health interventions to compensate for such limitations.
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Cuomo-Dannenburg G, McCain K, McCabe R, Unwin HJT, Doohan P, Nash RK, Hicks JT, Charniga K, Geismar C, Lambert B, Nikitin D, Skarp J, Wardle J, Kont M, Bhatia S, Imai N, van Elsland S, Cori A, Morgenstern C. Marburg virus disease outbreaks, mathematical models, and disease parameters: a systematic review. THE LANCET. INFECTIOUS DISEASES 2024; 24:e307-e317. [PMID: 38040006 PMCID: PMC7615873 DOI: 10.1016/s1473-3099(23)00515-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 12/03/2023]
Abstract
The 2023 Marburg virus disease outbreaks in Equatorial Guinea and Tanzania highlighted the importance of better understanding this lethal pathogen. We did a systematic review (PROSPERO CRD42023393345) of peer-reviewed articles reporting historical outbreaks, modelling studies, and epidemiological parameters focused on Marburg virus disease. We searched PubMed and Web of Science from database inception to March 31, 2023. Two reviewers evaluated all titles and abstracts with consensus-based decision making. To ensure agreement, 13 (31%) of 42 studies were double-extracted and a custom-designed quality assessment questionnaire was used for risk of bias assessment. We present detailed information on 478 reported cases and 385 deaths from Marburg virus disease. Analysis of historical outbreaks and seroprevalence estimates suggests the possibility of undetected Marburg virus disease outbreaks, asymptomatic transmission, or cross-reactivity with other pathogens, or a combination of these. Only one study presented a mathematical model of Marburg virus transmission. We estimate an unadjusted, pooled total random effect case fatality ratio of 61·9% (95% CI 38·8-80·6; I2=93%). We identify epidemiological parameters relating to transmission and natural history, for which there are few estimates. This systematic review and the accompanying database provide a comprehensive overview of Marburg virus disease epidemiology and identify key knowledge gaps, contributing crucial information for mathematical models to support future Marburg virus disease epidemic responses.
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Affiliation(s)
- Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Kelly McCain
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Ruth McCabe
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK; Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Patrick Doohan
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Rebecca K Nash
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Joseph T Hicks
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Kelly Charniga
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cyril Geismar
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK
| | - Ben Lambert
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Dariya Nikitin
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Janetta Skarp
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Jack Wardle
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Mara Kont
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK; Modelling and Economics Unit, UK Health Security Agency, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK
| | - Christian Morgenstern
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK.
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da Silva MI, Ott T. Effects of conceptus proteins on endometrium and blood leukocytes of dairy cattle using transcriptome and meta-analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591148. [PMID: 38712302 PMCID: PMC11071483 DOI: 10.1101/2024.04.25.591148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
This study investigates the short and long-term effects of IFNT and PAG on the transcriptome of endometrium and blood leukocytes. Holstein heifers received intrauterine infusions of one of the following treatments: 20 mL of a 200 μg/mL bovine serum albumin solution (BSA; vehicle) from day 14 to 16 of the estrous cycle (BSA), vehicle + 10 μg/mL of IFNT from day 14 to 16 (IFNT3), vehicle + 10 μg/mL of IFNT from day 14 to 19 (IFNT6), and vehicle + 10 μg/mL of IFNT from day 14 to 16 followed by vehicle + 10 μg/mL of IFNT + 5 μg/mL of PAG from day 17 to 19 (IFNT+PAG). RNA-seq analysis was performed in endometrial biopsies and blood leukocytes collected after treatments. Acute IFNT signaling in the endometrium (IFNT3 vs BSA), induced differentially expressed genes (DEG) associated with interferon activation, immune response, inflammation, cell death, and inhibited vesicle transport and extracellular matrix remodeling. Prolonged IFNT signaling (IFNT6 vs IFNT3) altered gene expression related to cell invasion, retinoic acid signaling, and embryo implantation. In contrast, PAG induced numerous DEG in blood leukocytes but only 4 DEG in the endometrium. In blood leukocytes, PAG stimulated genes involved in development and TGFB signaling while inhibiting interferon signaling and cell migration. Overall, IFNT is a primary regulator of endometrial gene expression, while PAG predominantly affected the transcriptome of circulating immune cells during early pregnancy. Further research is essential to fully grasp the roles of identified DEG in both the endometrium and blood leukocytes.
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Affiliation(s)
- Maria Isabel da Silva
- Department of Animal Science, Center for Reproductive Biology and Health, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Troy Ott
- Department of Animal Science, Center for Reproductive Biology and Health, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
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6
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Tran-Kiem C, Bedford T. Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences. Proc Natl Acad Sci U S A 2024; 121:e2305299121. [PMID: 38568971 PMCID: PMC11009662 DOI: 10.1073/pnas.2305299121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Quantifying transmission intensity and heterogeneity is crucial to ascertain the threat posed by infectious diseases and inform the design of interventions. Methods that jointly estimate the reproduction number R and the dispersion parameter k have however mainly remained limited to the analysis of epidemiological clusters or contact tracing data, whose collection often proves difficult. Here, we show that clusters of identical sequences are imprinted by the pathogen offspring distribution, and we derive an analytical formula for the distribution of the size of these clusters. We develop and evaluate an inference framework to jointly estimate the reproduction number and the dispersion parameter from the size distribution of clusters of identical sequences. We then illustrate its application across a range of epidemiological situations. Finally, we develop a hypothesis testing framework relying on clusters of identical sequences to determine whether a given pathogen genetic subpopulation is associated with increased or reduced transmissibility. Our work provides tools to estimate the reproduction number and transmission heterogeneity from pathogen sequences without building a phylogenetic tree, thus making it easily scalable to large pathogen genome datasets.
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Affiliation(s)
- Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- HHMI, Seattle, WA98109
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7
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Dekker JP. Within-Host Evolution of Bacterial Pathogens in Acute and Chronic Infection. ANNUAL REVIEW OF PATHOLOGY 2024; 19:203-226. [PMID: 37832940 DOI: 10.1146/annurev-pathmechdis-051122-111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Bacterial pathogens undergo remarkable adaptive change in response to the selective forces they encounter during host colonization and infection. Studies performed over the past few decades have demonstrated that many general evolutionary processes can be discerned during the course of host adaptation, including genetic diversification of lineages, clonal succession events, convergent evolution, and balanced fitness trade-offs. In some cases, elevated mutation rates resulting from mismatch repair or proofreading deficiencies accelerate evolution, and active mobile genetic elements or phages may facilitate genome plasticity. The host immune response provides another critical component of the fitness landscapes guiding adaptation, and selection operating on pathogens at this level may lead to immune evasion and the establishment of chronic infection. This review summarizes recent advances in this field, with a special focus on different forms of bacterial genome plasticity in the context of infection, and considers clinical consequences of adaptive changes for the host.
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Affiliation(s)
- John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA;
- National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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8
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Shi YT, Harris JD, Martin MA, Koelle K. Transmission Bottleneck Size Estimation from De Novo Viral Genetic Variation. Mol Biol Evol 2024; 41:msad286. [PMID: 38158742 PMCID: PMC10798134 DOI: 10.1093/molbev/msad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
Sequencing of viral infections has become increasingly common over the last decade. Deep sequencing data in particular have proven useful in characterizing the roles that genetic drift and natural selection play in shaping within-host viral populations. They have also been used to estimate transmission bottleneck sizes from identified donor-recipient pairs. These bottleneck sizes quantify the number of viral particles that establish genetic lineages in the recipient host and are important to estimate due to their impact on viral evolution. Current approaches for estimating bottleneck sizes exclusively consider the subset of viral sites that are observed as polymorphic in the donor individual. However, these approaches have the potential to substantially underestimate true transmission bottleneck sizes. Here, we present a new statistical approach for instead estimating bottleneck sizes using patterns of viral genetic variation that arise de novo within a recipient individual. Specifically, our approach makes use of the number of clonal viral variants observed in a transmission pair, defined as the number of viral sites that are monomorphic in both the donor and the recipient but carry different alleles. We first test our approach on a simulated dataset and then apply it to both influenza A virus sequence data and SARS-CoV-2 sequence data from identified transmission pairs. Our results confirm the existence of extremely tight transmission bottlenecks for these 2 respiratory viruses.
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Affiliation(s)
| | | | - Michael A Martin
- Department of Biology, Emory University, Atlanta, GA, USA
- Graduate Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (CEIRR), Atlanta, GA, USA
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Ohlsen EC, Angel K, Maroufi A, Kao A, Victorio MJ, Cua LS, Kimura A, Vanden Esschert K, Logan N, McMichael TM, Beatty ME, Shah S. Shigellosis outbreak among persons experiencing homelessness-San Diego County, California, October-December 2021. Epidemiol Infect 2023; 152:e61. [PMID: 37869979 PMCID: PMC11062786 DOI: 10.1017/s0950268823001681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023] Open
Abstract
During October 2021, the County of San Diego Health and Human Services Agency identified five cases of shigellosis among persons experiencing homelessness (PEH). We conducted an outbreak investigation and developed interventions to respond to shigellosis outbreaks among PEH. Confirmed cases occurred among PEH with stool-cultured Shigella sonnei; probable cases were among PEH with Shigella-positive culture-independent diagnostic testing. Patients were interviewed to determine infectious sources and risk factors. Fifty-three patients were identified (47 confirmed, 6 probable); 34 (64%) were hospitalised. None died. No point source was identified. Patients reported inadequate access to clean water and sanitation facilities, including public restrooms closed because of the COVID-19 pandemic. After implementing interventions, including handwashing stations, more frequent public restroom cleaning, sanitation kit distribution, and isolation housing for ill persons, S. sonnei cases decreased to preoutbreak frequencies. Improving public sanitation access was associated with decreased cases and should be considered to prevent outbreaks among PEH.
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Affiliation(s)
- Elizabeth C Ohlsen
- Epidemic Intelligence Service, San Diego, CA, USA
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kristen Angel
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Azarnoush Maroufi
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Annie Kao
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Maria J Victorio
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Lynnie S Cua
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Akiko Kimura
- California Department of Public Health, Richmond, CA, USA
| | | | - Naeemah Logan
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Temet M McMichael
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Mark E Beatty
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
- University of California San Diego, San Diego, CA, USA
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Torres Ortiz A, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. eLife 2023; 12:e84384. [PMID: 37732733 PMCID: PMC10602588 DOI: 10.7554/elife.84384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 09/20/2023] [Indexed: 09/22/2023] Open
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low-frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is partially maintained among repeated serial samples from the same host, it can transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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Affiliation(s)
- Arturo Torres Ortiz
- Department of Infectious Diseases, Imperial College LondonLondonUnited Kingdom
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | - Michelle Kendall
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Nathaniel Storey
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - James Hatcher
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - Helen Dunn
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | | | | | | | - Xavier Didelot
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Kathryn Harris
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
- Department of Virology, East & South East London Pathology Partnership, Royal London Hospital, Barts Health NHS TrustLondonUnited Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
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11
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Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
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12
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Jin B, Oyama R, Tabe Y, Tsuchiya K, Hando T, Wakita M, Yan Y, Saita M, Takei S, Horiuchi Y, Miida T, Naito T, Takahashi K, Ogawa H. Investigation of the individual genetic evolution of SARS-CoV-2 in a small cluster during the rapid spread of the BF.5 lineage in Tokyo, Japan. Front Microbiol 2023; 14:1229234. [PMID: 37744926 PMCID: PMC10516552 DOI: 10.3389/fmicb.2023.1229234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
There has been a decreasing trend in new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases and fatalities worldwide. The virus has been evolving, indicating the potential emergence of new variants and uncertainties. These challenges necessitate continued efforts in disease control and mitigation strategies. We investigated a small cluster of SARS-CoV-2 Omicron variant infections containing a common set of genomic mutations, which provided a valuable model for investigating the transmission mechanism of genetic alterations. We conducted a study at a medical center in Japan during the Omicron surge (sub-lineage BA.5), sequencing the entire SARS-CoV-2 genomes from infected individuals and evaluating the phylogenetic tree and haplotype network among the variants. We compared the mutations present in each strain within the BA.5 strain, TKYnat2317, which was first identified in Tokyo, Japan. From June 29th to July 4th 2022, nine healthcare workers (HCWs) tested positive for SARS-CoV-2 by real-time PCR. During the same period, five patients also tested positive by real-time PCR. Whole genome sequencing revealed that the infected patients belonged to either the isolated BA.2 or BA.5 sub-lineage, while the healthcare worker infections were classified as BF.5. The phylogenetic tree and haplotype network clearly showed the specificity and similarity of the HCW cluster. We identified 12 common mutations in the cluster, including I110V in nonstructural protein 4 (nsp4), A1020S in the Spike protein, and H47Y in ORF7a, compared to the BA.5 reference. Additionally, one case had the extra nucleotide-deletion mutation I27* in ORF10, and low frequencies of genetic alterations were also found in certain instances. The results of genome sequencing showed that the nine HCWs shared a set of genetic mutations, indicating transmission within the cluster. Minor mutations observed in five HCW individuals suggested the emergence of new virus variants. Five amino acid substitutions occurred in nsp3, which could potentially affect virus replication or immune escape. Intra-host evolution also generated additional mutations. The cluster exhibited a mild disease course, with individuals in this case, recovering without requiring any medical treatments. Further investigation is needed to understand the relationship between the genetic evolution of the virus and the symptoms.
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Affiliation(s)
- Bo Jin
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Rieko Oyama
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoko Tabe
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Koji Tsuchiya
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Tetsuya Hando
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Mitsuru Wakita
- Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
| | - Yan Yan
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mizue Saita
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Satomi Takei
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuki Horiuchi
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toshio Naito
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hideoki Ogawa
- Department of Dermatology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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13
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Kremer C, Torneri A, Libin PJK, Meex C, Hayette MP, Bontems S, Durkin K, Artesi M, Bours V, Lemey P, Darcis G, Hens N, Meuris C. Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data. Epidemics 2023; 44:100701. [PMID: 37379776 PMCID: PMC10273772 DOI: 10.1016/j.epidem.2023.100701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Mathematical modelling studies have shown that repetitive screening can be used to mitigate SARS-CoV-2 transmission in primary schools while keeping schools open. However, not much is known about how transmission progresses within schools and whether there is a risk of importation to households. During the academic year 2020-2021, a prospective surveillance study using repetitive screening was conducted in a primary school and associated households in Liège (Belgium). SARS-CoV-2 screening was performed via throat washing either once or twice a week. We used genomic and epidemiological data to reconstruct the observed school outbreaks using two different models. The outbreaker2 model combines information on the generation time and contact patterns with a model of sequence evolution. For comparison we also used SCOTTI, a phylogenetic model based on the structured coalescent. In addition, we performed a simulation study to investigate how the accuracy of estimated positivity rates in a school depends on the proportion of a school that is sampled in a repetitive screening strategy. We found no difference in SARS-CoV-2 positivity between children and adults and children were not more often asymptomatic compared to adults. Both models for outbreak reconstruction revealed that transmission occurred mainly within the school environment. Uncertainty in outbreak reconstruction was lowest when including genomic as well as epidemiological data. We found that observed weekly positivity rates are a good approximation to the true weekly positivity rate, especially in children, even when only 25% of the school population is sampled. These results indicate that, in addition to reducing infections as shown in modelling studies, repetitive screening in school settings can lead to a better understanding of the extent of transmission in schools during a pandemic and importation risk at the community level.
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Affiliation(s)
- Cécile Kremer
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium.
| | - Andrea Torneri
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Pieter J K Libin
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium; Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium; Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Cécile Meex
- Department of Clinical Microbiology, University of Liège, Liège, Belgium
| | | | - Sébastien Bontems
- Department of Clinical Microbiology, University of Liège, Liège, Belgium
| | - Keith Durkin
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, Liège, Belgium
| | - Maria Artesi
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, Liège, Belgium
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, Liège, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Gilles Darcis
- Department of Infectious Diseases, Liège University Hospital, Liège, Belgium
| | - Niel Hens
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christelle Meuris
- Department of Infectious Diseases, Liège University Hospital, Liège, Belgium
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14
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Sobkowiak B, Haghmaram P, Prystajecky N, Zlosnik JEA, Tyson J, Hoang LMN, Colijn C. The utility of SARS-CoV-2 genomic data for informative clustering under different epidemiological scenarios and sampling. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105484. [PMID: 37531976 DOI: 10.1016/j.meegid.2023.105484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVES Clustering pathogen sequence data is a common practice in epidemiology to gain insights into the genetic diversity and evolutionary relationships among pathogens. We can find groups of cases with a shared transmission history and common origin, as well as identifying transmission hotspots. Motivated by the experience of clustering SARS-CoV-2 cases using whole genome sequence data during the COVID-19 pandemic to aid with public health investigation, we investigated how differences in epidemiology and sampling can influence the composition of clusters that are identified. METHODS We performed genomic clustering on simulated SARS-CoV-2 outbreaks produced with different transmission rates and levels of genomic diversity, along with varying the proportion of cases sampled. RESULTS In single outbreaks with a low transmission rate, decreasing the sampling fraction resulted in multiple, separate clusters being identified where intermediate cases in transmission chains are missed. Outbreaks simulated with a high transmission rate were more robust to changes in the sampling fraction and largely resulted in a single cluster that included all sampled outbreak cases. When considering multiple outbreaks in a sampled jurisdiction seeded by different introductions, low genomic diversity between introduced cases caused outbreaks to be merged into large clusters. If the transmission and sampling fraction, and diversity between introductions was low, a combination of the spurious break-up of outbreaks and the linking of closely related cases in different outbreaks resulted in clusters that may appear informative, but these did not reflect the true underlying population structure. Conversely, genomic clusters matched the true population structure when there was relatively high diversity between introductions and a high transmission rate. CONCLUSION Differences in epidemiology and sampling can impact our ability to identify genomic clusters that describe the underlying population structure. These findings can help to guide recommendations for the use of pathogen clustering in public health investigations.
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Affiliation(s)
| | - Pouya Haghmaram
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | - Natalie Prystajecky
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Canada
| | - James E A Zlosnik
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada
| | - John Tyson
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada
| | - Linda M N Hoang
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
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15
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Wang J, Feng Y, Zong Z. Worldwide transmission of ST11-KL64 carbapenem-resistant Klebsiella pneumoniae: an analysis of publicly available genomes. mSphere 2023; 8:e0017323. [PMID: 37199964 PMCID: PMC10449508 DOI: 10.1128/msphere.00173-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 05/19/2023] Open
Abstract
ST11-KL64 is an internationally distributed lineage of carbapenem-resistant Klebsiella pneumoniae and is the most common type in China. The international and interprovincial (in China) transmission of ST11-KL64 CRKP remains to be elucidated. We used both static clusters defined based on a fixed cutoff of ≤21 pairwise single-nucleotide polymorphisms and dynamic groups defined by modeling the likelihood to be linked by a transmission threshold to investigate the transmission of ST11-KL64 strains based on genome sequences mining. We analyzed all publicly available genomes (n = 730) of ST11-KL64 strains, almost all of which had known carbapenemase genes with KPC-2 being dominant. We identified 4 clusters of international transmission and 14 clusters of interprovincial transmission across China of ST11-KL64 strains. We found that dynamic grouping could provide further resolution for determining clonal relatedness in addition to the widely adopted static clustering and therefore increases the confidence for inferring transmission.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious challenge for clinical management and is prone to spread in and between healthcare settings. ST11-KL64 is the dominant CRKP type in China with a worldwide distribution. Here, we used two different methods, the widely used clustering based on a fixed single-nucleotide polymorphism (SNP) cutoff and the recently developed grouping by modeling transmission likelihood, to mine all 730 publicly available ST11-KL64 genomes. We identified international transmission of several strains and interprovincial transmission in China of a few, which warrants further investigations to uncover the mechanisms for their spread. We found that static clustering based on ≤21 fixed SNPs is sensitive to detect transmission and dynamic grouping has higher resolutions to provide complementary information. We suggest the use of the two methods in combination for analyzing transmission of bacterial strains. Our findings highlight the need of coordinated actions at both international and interprovincial levels for tackling multi-drug resistant organisms.
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Affiliation(s)
- Junna Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Feng
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
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16
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Shi T, Harris JD, Martin MA, Koelle K. Transmission bottleneck size estimation from de novo viral genetic variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553219. [PMID: 37645981 PMCID: PMC10462048 DOI: 10.1101/2023.08.14.553219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Sequencing of viral infections has become increasingly common over the last decade. Deep sequencing data in particular have proven useful in characterizing the roles that genetic drift and natural selection play in shaping within-host viral populations. They have also been used to estimate transmission bottleneck sizes from identified donor-recipient pairs. These bottleneck sizes quantify the number of viral particles that establish genetic lineages in the recipient host and are important to estimate due to their impact on viral evolution. Current approaches for estimating bottleneck sizes exclusively consider the subset of viral sites that are observed as polymorphic in the donor individual. However, allele frequencies can change dramatically over the course of an individual's infection, such that sites that are polymorphic in the donor at the time of transmission may not be polymorphic in the donor at the time of sampling and allele frequencies at donor-polymorphic sites may change dramatically over the course of a recipient's infection. Because of this, transmission bottleneck sizes estimated using allele frequencies observed at a donor's polymorphic sites may be considerable underestimates of true bottleneck sizes. Here, we present a new statistical approach for instead estimating bottleneck sizes using patterns of viral genetic variation that arose de novo within a recipient individual. Specifically, our approach makes use of the number of clonal viral variants observed in a transmission pair, defined as the number of viral sites that are monomorphic in both the donor and the recipient but carry different alleles. We first test our approach on a simulated dataset and then apply it to both influenza A virus sequence data and SARS-CoV-2 sequence data from identified transmission pairs. Our results confirm the existence of extremely tight transmission bottlenecks for these two respiratory viruses, using an approach that does not tend to underestimate transmission bottleneck sizes.
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Affiliation(s)
- Teresa Shi
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jeremy D. Harris
- Department of Biology, Emory University, Atlanta, GA, USA
- Department of Mathematics, Rose-Hulman Institute of Technology, Terre Haute, IN, USA
| | - Michael A. Martin
- Department of Biology, Emory University, Atlanta, GA, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Graduate Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (CEIRR), Atlanta GA, USA
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17
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Stockdale JE, Susvitasari K, Tupper P, Sobkowiak B, Mulberry N, Gonçalves da Silva A, Watt AE, Sherry NL, Minko C, Howden BP, Lane CR, Colijn C. Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19. Nat Commun 2023; 14:4830. [PMID: 37563113 PMCID: PMC10415581 DOI: 10.1038/s41467-023-40544-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Serial intervals - the time between symptom onset in infector and infectee - are a fundamental quantity in infectious disease control. However, their estimation requires knowledge of individuals' exposures, typically obtained through resource-intensive contact tracing efforts. We introduce an alternate framework using virus sequences to inform who infected whom and thereby estimate serial intervals. We apply our technique to SARS-CoV-2 sequences from case clusters in the first two COVID-19 waves in Victoria, Australia. We find that our approach offers high resolution, cluster-specific serial interval estimates that are comparable with those obtained from contact data, despite requiring no knowledge of who infected whom and relying on incompletely-sampled data. Compared to a published serial interval, cluster-specific serial intervals can vary estimates of the effective reproduction number by a factor of 2-3. We find that serial interval estimates in settings such as schools and meat processing/packing plants are shorter than those in healthcare facilities.
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Affiliation(s)
| | | | - Paul Tupper
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | | | - Nicola Mulberry
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Corinna Minko
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
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18
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Permana B, Beatson SA, Forde BM. GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach. BMC Bioinformatics 2023; 24:209. [PMID: 37208588 DOI: 10.1186/s12859-023-05332-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/11/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration. RESULTS GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings. CONCLUSIONS GraphSNP is freely available at https://github.com/nalarbp/graphsnp . An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use at https://graphsnp.fordelab.com .
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Affiliation(s)
- Budi Permana
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
- Herston Infectious Diseases Institute, Metro North Health, Brisbane, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia
| | - Brian M Forde
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.
- Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia.
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19
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Rossi G, Shih BBJ, Egbe NF, Motta P, Duchatel F, Kelly RF, Ndip L, Sander M, Tanya VN, Lycett SJ, Bronsvoort BM, Muwonge A. Unraveling the epidemiology of Mycobacterium bovis using whole-genome sequencing combined with environmental and demographic data. Front Vet Sci 2023; 10:1086001. [PMID: 37266384 PMCID: PMC10230100 DOI: 10.3389/fvets.2023.1086001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/14/2023] [Indexed: 06/03/2023] Open
Abstract
When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-growing and slow-evolving clonal pathogens such as Mycobacterium bovis, the causative agent of bovine (or animal) and zoonotic tuberculosis, it can be challenging to discriminate between these two states. This is a result of the combination of suboptimal detection tests so that the actual extent of the pathogen prevalence is often unknown, as well as of the low genetic diversity, which can hide the temporal signal provided by the accumulation of mutations in the bacterial DNA. In recent years, the increased availability, efficiency, and reliability of genomic reading techniques, such as whole-genome sequencing (WGS), have significantly increased the amount of information we can use to study infectious diseases, and therefore, it has improved the precision of epidemiological inferences for pathogens such as M. bovis. In this study, we use WGS to gain insights into the epidemiology of M. bovis in Cameroon, a developing country where the pathogen has been reported for decades. A total of 91 high-quality sequences were obtained from tissue samples collected in four abattoirs, 64 of which were with complete metadata. We combined these with environmental, demographic, ecological, and cattle movement data to generate inferences using phylodynamic models. Our findings suggest M. bovis in Cameroon is slowly expanding its epidemiological range over time; therefore, endemic stability is unlikely. This suggests that animal movement plays an important role in transmission. The simultaneous prevalence of M. bovis in co-located cattle and humans highlights the risk of such transmission being zoonotic. Therefore, using genomic tools as part of surveillance would vastly improve our understanding of disease ecology and control strategies.
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Affiliation(s)
- Gianluigi Rossi
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barbara Bo-Ju Shih
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Nkongho Franklyn Egbe
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Paolo Motta
- The Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Bangkok, Thailand
| | - Florian Duchatel
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Robert Francis Kelly
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Lucy Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, Cameroon
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | | | | | - Samantha J. Lycett
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barend Mark Bronsvoort
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Adrian Muwonge
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
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20
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Robert A, Tsui Lok Hei J, Watson CH, Gsell PS, Hall Y, Rambaut A, Longini IM, Sakoba K, Kucharski AJ, Touré A, Danmadji Nadlaou S, Saidou Barry M, Fofana TO, Lansana Kaba I, Sylla L, Diaby ML, Soumah O, Diallo A, Niare A, Diallo A, Eggo RM, Caroll MW, Henao-Restrepo AM, Edmunds WJ, Hué S. Quantifying the value of viral genomics when inferring who infected whom in the 2014-16 Ebola virus outbreak in Guinea. Virus Evol 2023; 9:vead007. [PMID: 36926449 PMCID: PMC10013732 DOI: 10.1093/ve/vead007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/17/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
Transmission trees can be established through detailed contact histories, statistical or phylogenetic inference, or a combination of methods. Each approach has its limitations, and the extent to which they succeed in revealing a 'true' transmission history remains unclear. In this study, we compared the transmission trees obtained through contact tracing investigations and various inference methods to identify the contribution and value of each approach. We studied eighty-six sequenced cases reported in Guinea between March and November 2015. Contact tracing investigations classified these cases into eight independent transmission chains. We inferred the transmission history from the genetic sequences of the cases (phylogenetic approach), their onset date (epidemiological approach), and a combination of both (combined approach). The inferred transmission trees were then compared to those from the contact tracing investigations. Inference methods using individual data sources (i.e. the phylogenetic analysis and the epidemiological approach) were insufficiently informative to accurately reconstruct the transmission trees and the direction of transmission. The combined approach was able to identify a reduced pool of infectors for each case and highlight likely connections among chains classified as independent by the contact tracing investigations. Overall, the transmissions identified by the contact tracing investigations agreed with the evolutionary history of the viral genomes, even though some cases appeared to be misclassified. Therefore, collecting genetic sequences during outbreak is key to supplement the information contained in contact tracing investigations. Although none of the methods we used could identify one unique infector per case, the combined approach highlighted the added value of mixing epidemiological and genetic information to reconstruct who infected whom.
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Affiliation(s)
- Alexis Robert
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
| | - Joseph Tsui Lok Hei
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Conall H Watson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Epidemic Diseases Research Group Oxford, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7LG, UK
| | | | - Yper Hall
- UK Health Security Agency, Manor Farm Rd, Porton Down, Salisbury SP4 0JG, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Ira M Longini
- Department of Biostatistics, University of Florida, 2004 Mowry Road, 5th Floor CTRB, Gainesville, FL 32611-7450, USA
| | - Keïta Sakoba
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | - Adam J Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
| | - Alhassane Touré
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | | | | | | | | | - Lansana Sylla
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | | | - Ousmane Soumah
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | - Abdourahime Diallo
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | - Amadou Niare
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | | | - Rosalind M Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
| | - Miles W Caroll
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7BN, UK
| | | | - W John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
| | - Stéphane Hué
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
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21
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Choy HL, Gaylord EA, Doering TL. Ergosterol distribution controls surface structure formation and fungal pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528979. [PMID: 36824733 PMCID: PMC9949117 DOI: 10.1101/2023.02.17.528979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Ergosterol, the major sterol in fungal membranes, is critical for defining membrane fluidity and regulating cellular processes. Although ergosterol synthesis has been well defined in model yeast, little is known about sterol organization in the context of fungal pathogenesis. We identified a retrograde sterol transporter, Ysp2, in the opportunistic fungal pathogen Cryptococcus neoformans . We found that the lack of Ysp2 under host-mimicking conditions leads to abnormal accumulation of ergosterol at the plasma membrane, invagination of the plasma membrane, and malformation of the cell wall, which can be functionally rescued by inhibiting ergosterol synthesis with the antifungal drug fluconazole. We also observed that cells lacking Ysp2 mislocalize the cell surface protein Pma1 and have thinner and more permeable capsules. As a result of perturbed ergosterol distribution and its consequences, ysp2 Î" cells cannot survive in physiologically-rele-vant environments such as host phagocytes and are dramatically attenuated in virulence. These findings expand our knowledge of cryptococcal biology and underscore the importance of sterol homeostasis in fungal pathogenesis. IMPORTANCE Cryptococcus neoformans is an opportunistic fungal pathogen that kills over 100,000 people worldwide each year. Only three drugs are available to treat cryptococcosis, and these are variously limited by toxicity, availability, cost, and resistance. Ergosterol is the most abundant sterol in fungi and a key component in modulating membrane behavior. Two of the drugs used for cryptococcal infection, amphotericin B and fluconazole, target this lipid and its synthesis, highlighting its importance as a therapeutic target. We discovered a cryptococcal ergosterol transporter, Ysp2, and demonstrated its key roles in multiple aspects of cryptococcal biology and pathogenesis. These studies demonstrate the role of ergosterol homeostasis in C. neoformans virulence, deepen our understanding of a pathway with proven therapeutic importance, and open a new area of study.
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Affiliation(s)
- Hau Lam Choy
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elizabeth A. Gaylord
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tamara L. Doering
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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22
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Luterbach CL, Chen L, Komarow L, Ostrowsky B, Kaye KS, Hanson B, Arias CA, Desai S, Gallagher JC, Novick E, Pagkalinawan S, Lautenbach E, Wortmann G, Kalayjian RC, Eilertson B, Farrell JJ, McCarty T, Hill C, Fowler VG, Kreiswirth BN, Bonomo RA, van Duin D. Transmission of Carbapenem-Resistant Klebsiella pneumoniae in US Hospitals. Clin Infect Dis 2023; 76:229-237. [PMID: 36173830 PMCID: PMC10202433 DOI: 10.1093/cid/ciac791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/08/2022] [Accepted: 09/23/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKp) is the most prevalent carbapenem-resistant Enterobacterales in the United States. We evaluated CRKp clustering in patients in US hospitals. METHODS From April 2016 to August 2017, 350 patients with clonal group 258 CRKp were enrolled in the Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae, a prospective, multicenter, cohort study. A maximum likelihood tree was constructed using RAxML. Static clusters shared ≤21 single-nucleotide polymorphisms (SNP) and a most recent common ancestor. Dynamic clusters incorporated SNP distance, culture timing, and rates of SNP accumulation and transmission using the R program TransCluster. RESULTS Most patients were admitted from home (n = 150, 43%) or long-term care facilities (n = 115, 33%). Urine (n = 149, 43%) was the most common isolation site. Overall, 55 static and 47 dynamics clusters were identified involving 210 of 350 (60%) and 194 of 350 (55%) patients, respectively. Approximately half of static clusters were identical to dynamic clusters. Static clusters consisted of 33 (60%) intrasystem and 22 (40%) intersystem clusters. Dynamic clusters consisted of 32 (68%) intrasystem and 15 (32%) intersystem clusters and had fewer SNP differences than static clusters (8 vs 9; P = .045; 95% confidence interval [CI]: -4 to 0). Dynamic intersystem clusters contained more patients than dynamic intrasystem clusters (median [interquartile range], 4 [2, 7] vs 2 [2, 2]; P = .007; 95% CI: -3 to 0). CONCLUSIONS Widespread intrasystem and intersystem transmission of CRKp was identified in hospitalized US patients. Use of different methods for assessing genetic similarity resulted in only minor differences in interpretation.
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Affiliation(s)
- Courtney L Luterbach
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Lauren Komarow
- Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Belinda Ostrowsky
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Blake Hanson
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, USA
- Center for Infectious Diseases, UTHealth School of Public Health, Houston, Texas, USA
| | - Cesar A Arias
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, USA
- Center for Infectious Diseases, UTHealth School of Public Health, Houston, Texas, USA
- Molecular Genetics and Antimicrobial Resistance Unit–International Center for Microbial Genomics, Universidad El Bosque, Bogota, Columbia
| | - Samit Desai
- Division of Infectious Diseases, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Jason C Gallagher
- Temple University School of Pharmacy, Philadelphia, Pennsylvania, USA
| | - Elizabeth Novick
- Temple University School of Pharmacy, Philadelphia, Pennsylvania, USA
| | | | - Ebbing Lautenbach
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Glenn Wortmann
- Section of Infectious Diseases, MedStar Washington Hospital Center, Washington, District of Columbia, USA
| | - Robert C Kalayjian
- Department of Medicine, MetroHealth Medical Center, Cleveland, Ohio, USA
| | - Brandon Eilertson
- Division of Infectious Diseases, Department of Medicine, State University of New York Downstate, Brooklyn, NY, USA
| | - John J Farrell
- Division of Infectious Disease, Department of Internal Medicine, OSF Saint Francis Medical Center, University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - Todd McCarty
- Division of Infectious Disease, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Carol Hill
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Vance G Fowler
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Case Western Reserve University-Cleveland Veterans Affairs Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
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23
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Ashall J, Shah S, Biggs JR, Chang JNR, Jafari Y, Brady OJ, Mai HK, Lien LT, Do Thai H, Nguyen HAT, Anh DD, Iwasaki C, Kitamura N, Van Loock M, Herrera-Taracena G, Rasschaert F, Van Wesenbeeck L, Yoshida LM, Hafalla JCR, Hue S, Hibberd ML. A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains. Virus Evol 2023; 9:vead012. [PMID: 36926448 PMCID: PMC10013730 DOI: 10.1093/ve/vead012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 10/31/2022] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
Dengue virus (DENV) causes repeated outbreaks of disease in endemic areas, with patterns of local transmission strongly influenced by seasonality, importation via human movement, immunity, and vector control efforts. An understanding of how each of these interacts to enable endemic transmission (continual circulation of local virus strains) is largely unknown. There are times of the year when no cases are reported, often for extended periods of time, perhaps wrongly implying the successful eradication of a local strain from that area. Individuals who presented at a clinic or hospital in four communes in Nha Trang, Vietnam, were initially tested for DENV antigen presence. Enrolled positive individuals then had their corresponding household members invited to participate, and those who enrolled were tested for DENV. The presence of viral nucleic acid in all samples was confirmed using quantitative polymerase chain reaction, and positive samples were then whole-genome sequenced using an amplicon and target enrichment library preparation techniques and Illumina MiSeq sequencing technology. Generated consensus genome sequences were then analysed using phylogenetic tree reconstruction to categorise sequences into clades with a common ancestor, enabling investigations of both viral clade persistence and introductions. Hypothetical introduction dates were additionally assessed using a molecular clock model that calculated the time to the most recent common ancestor (TMRCA). We obtained 511 DENV whole-genome sequences covering four serotypes and more than ten distinct viral clades. For five of these clades, we had sufficient data to show that the same viral lineage persisted for at least several months. We noted that some clades persisted longer than others during the sampling time, and by comparison with other published sequences from elsewhere in Vietnam and around the world, we saw that at least two different viral lineages were introduced into the population during the study period (April 2017-2019). Next, by inferring the TMRCA from the construction of molecular clock phylogenies, we predicted that two of the viral lineages had been present in the study population for over a decade. We observed five viral lineages co-circulating in Nha Trang from three DENV serotypes, with two likely to have remained as uninterrupted transmission chains for a decade. This suggests clade cryptic persistence in the area, even during periods of low reported incidence.
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Affiliation(s)
- James Ashall
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Sonal Shah
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Joseph R Biggs
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jui-Ning R Chang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Yalda Jafari
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Oliver J Brady
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Huynh Kim Mai
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Le Thuy Lien
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Hung Do Thai
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Hien Anh Thi Nguyen
- National Institute of Hygiene and Epidemiology, 1 P. Yec Xanh, Phạm Đình Hổ, Hai Bà Trưng, Hà Nội, 100000, Vietnam
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, 1 P. Yec Xanh, Phạm Đình Hổ, Hai Bà Trưng, Hà Nội, 100000, Vietnam
| | - Chihiro Iwasaki
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Noriko Kitamura
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Marnix Van Loock
- Janssen R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Guillermo Herrera-Taracena
- Janssen Global Public Health, Janssen Research & Development, LLC, 800 Ridgeview Drive, Horsham, PA 19044, USA
| | - Freya Rasschaert
- Janssen R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse B-2340, Belgium
| | | | - Lay-Myint Yoshida
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Julius Clemence R Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Stephane Hue
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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24
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Leavitt SV, Jenkins HE, Sebastiani P, Lee RS, Horsburgh CR, Tibbs AM, White LF. Estimation of the generation interval using pairwise relative transmission probabilities. Biostatistics 2022; 23:807-824. [PMID: 33527996 PMCID: PMC9291635 DOI: 10.1093/biostatistics/kxaa059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 11/13/2022] Open
Abstract
The generation interval (the time between infection of primary and secondary cases) and its often used proxy, the serial interval (the time between symptom onset of primary and secondary cases) are critical parameters in understanding infectious disease dynamics. Because it is difficult to determine who infected whom, these important outbreak characteristics are not well understood for many diseases. We present a novel method for estimating transmission intervals using surveillance or outbreak investigation data that, unlike existing methods, does not require a contact tracing data or pathogen whole genome sequence data on all cases. We start with an expectation maximization algorithm and incorporate relative transmission probabilities with noise reduction. We use simulations to show that our method can accurately estimate the generation interval distribution for diseases with different reproductive numbers, generation intervals, and mutation rates. We then apply our method to routinely collected surveillance data from Massachusetts (2010-2016) to estimate the serial interval of tuberculosis in this setting.
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Affiliation(s)
- Sarah V Leavitt
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; Epidemiology Division, University of Toronto Dalla Lana School of Public Health, 155 College St Room 500, Toronto, ON M5T 3M7, Canada; Department of Epidemiology, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; and Massachusetts Department of Public Health, 250 Washington St, Boston, MA 02108
| | - Helen E Jenkins
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; Epidemiology Division, University of Toronto Dalla Lana School of Public Health, 155 College St Room 500, Toronto, ON M5T 3M7, Canada; Department of Epidemiology, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; and Massachusetts Department of Public Health, 250 Washington St, Boston, MA 02108
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; Epidemiology Division, University of Toronto Dalla Lana School of Public Health, 155 College St Room 500, Toronto, ON M5T 3M7, Canada; Department of Epidemiology, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; and Massachusetts Department of Public Health, 250 Washington St, Boston, MA 02108
| | - Robyn S Lee
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; Epidemiology Division, University of Toronto Dalla Lana School of Public Health, 155 College St Room 500, Toronto, ON M5T 3M7, Canada; Department of Epidemiology, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; and Massachusetts Department of Public Health, 250 Washington St, Boston, MA 02108
| | - C Robert Horsburgh
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; Epidemiology Division, University of Toronto Dalla Lana School of Public Health, 155 College St Room 500, Toronto, ON M5T 3M7, Canada; Department of Epidemiology, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; and Massachusetts Department of Public Health, 250 Washington St, Boston, MA 02108
| | - Andrew M Tibbs
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; Epidemiology Division, University of Toronto Dalla Lana School of Public Health, 155 College St Room 500, Toronto, ON M5T 3M7, Canada; Department of Epidemiology, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; and Massachusetts Department of Public Health, 250 Washington St, Boston, MA 02108
| | - Laura F White
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; Epidemiology Division, University of Toronto Dalla Lana School of Public Health, 155 College St Room 500, Toronto, ON M5T 3M7, Canada; Department of Epidemiology, Boston University School of Public Health, 801 Massachusetts Ave, Boston, MA 02118; and Massachusetts Department of Public Health, 250 Washington St, Boston, MA 02108
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25
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Strong R, McCleary S, Grierson S, Choudhury B, Steinbach F, Crooke HR. Molecular Epidemiology Questions Transmission Pathways Identified During the Year 2000 Outbreak of Classical Swine Fever in the UK. Front Microbiol 2022; 13:909396. [PMID: 35836425 PMCID: PMC9274199 DOI: 10.3389/fmicb.2022.909396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
The last outbreak of classical swine fever (CSF) in the UK occurred in 2000. A total of 16 domestic pig holdings in the East Anglia region were confirmed as infected over a 3-month period. Obtaining viral genome sequences has since become easier and more cost-effective and has accordingly been applied to trace viral transmission events for a variety of viruses. The rate of genetic evolution varies for different viruses and is influenced by different transmission events, which will vary according to the epidemiology of an outbreak. To examine if genetic changes over the course of any future CSF outbreak would occur to supplement epidemiological investigations and help to track virus movements, the E2 gene and full genome of the virus present in archived tonsil samples from 14 of these infected premises were sequenced. Insufficient changes occurred in the full E2 gene to discriminate between the viruses from the different premises. In contrast, between 5 and 14 nucleotide changes were detected between the genome sequence of the virus from the presumed index case and the sequences from the other 13 infected premises. Phylogenetic analysis of these full CSFV genome sequences identified clusters of closely related viruses that allowed to corroborate some of the transmission pathways inferred by epidemiological investigations at the time. However, other sequences were more distinct and raised questions about the virus transmission routes previously implicated. We are thus confident that in future outbreaks, real-time monitoring of the outbreak via full genome sequencing will be beneficial.
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26
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Ortiz AT, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.07.495142. [PMID: 35702156 PMCID: PMC9196117 DOI: 10.1101/2022.06.07.495142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches to reconstruct outbreaks exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is stable among repeated serial samples from the same host, is transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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Affiliation(s)
| | - Michelle Kendall
- Department of Statistics, University of Warwick, Coventry, CV4 7AL
| | - Nathaniel Storey
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - James Hatcher
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - Helen Dunn
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
| | - Rachel Williams
- UCL Genomics, Institute of Child Health, UCL, London WC1N 1EH
| | | | | | - Xavier Didelot
- Department of Statistics, University of Warwick, Coventry, CV4 7AL
| | - Kathryn Harris
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
- Department of Virology, East South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London E12ES
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
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27
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Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics. PLoS Comput Biol 2022; 18:e1008800. [PMID: 35604952 PMCID: PMC9166360 DOI: 10.1371/journal.pcbi.1008800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/03/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
The fraction of cases reported, known as 'reporting', is a key performance indicator in an outbreak response, and an essential factor to consider when modelling epidemics and assessing their impact on populations. Unfortunately, its estimation is inherently difficult, as it relates to the part of an epidemic which is, by definition, not observed. We introduce a simple statistical method for estimating reporting, initially developed for the response to Ebola in Eastern Democratic Republic of the Congo (DRC), 2018-2020. This approach uses transmission chain data typically gathered through case investigation and contact tracing, and uses the proportion of investigated cases with a known, reported infector as a proxy for reporting. Using simulated epidemics, we study how this method performs for different outbreak sizes and reporting levels. Results suggest that our method has low bias, reasonable precision, and despite sub-optimal coverage, usually provides estimates within close range (5-10%) of the true value. Being fast and simple, this method could be useful for estimating reporting in real-time in settings where person-to-person transmission is the main driver of the epidemic, and where case investigation is routinely performed as part of surveillance and contact tracing activities.
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28
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Lenggenhager L, Martischang R, Sauser J, Perez M, Vieux L, Graf C, Cordey S, Laubscher F, Nunes TR, Zingg W, Cori A, Harbarth S, Abbas M. Occupational and community risk of SARS-CoV-2 infection among employees of a long-term care facility: an observational study. Antimicrob Resist Infect Control 2022; 11:51. [PMID: 35303939 PMCID: PMC8931578 DOI: 10.1186/s13756-022-01092-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/02/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND We investigated the contribution of both occupational and community exposure for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among employees of a university-affiliated long-term care facility (LTCF), during the 1st pandemic wave in Switzerland (March-June 2020). METHODS We performed a nested analysis of a seroprevalence study among all volunteering LTCF staff to determine community and nosocomial risk factors for SARS-CoV-2 seropositivity using modified Poison regression. We also combined epidemiological and genetic sequencing data from a coronavirus disease 2019 (COVID-19) outbreak investigation in a LTCF ward to infer transmission dynamics and acquisition routes of SARS-CoV-2, and evaluated strain relatedness using a maximum likelihood phylogenetic tree. RESULTS Among 285 LTCF employees, 176 participated in the seroprevalence study, of whom 30 (17%) were seropositive for SARS-CoV-2. Most (141/176, 80%) were healthcare workers (HCWs). Risk factors for seropositivity included exposure to a COVID-19 inpatient (adjusted prevalence ratio [aPR] 2.6; 95% CI 0.9-8.1) and community contact with a COVID-19 case (aPR 1.7; 95% CI 0.8-3.5). Among 18 employees included in the outbreak investigation, the outbreak reconstruction suggests 4 likely importation events by HCWs with secondary transmissions to other HCWs and patients. CONCLUSIONS These two complementary epidemiologic and molecular approaches suggest a substantial contribution of both occupational and community exposures to COVID-19 risk among HCWs in LTCFs. These data may help to better assess the importance of occupational health hazards and related legal implications during the COVID-19 pandemic.
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Affiliation(s)
- Lauriane Lenggenhager
- grid.150338.c0000 0001 0721 9812Infection Control Programme, Geneva University Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland ,grid.8591.50000 0001 2322 4988Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Romain Martischang
- grid.150338.c0000 0001 0721 9812Infection Control Programme, Geneva University Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland
| | - Julien Sauser
- grid.150338.c0000 0001 0721 9812Infection Control Programme, Geneva University Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland
| | - Monica Perez
- grid.150338.c0000 0001 0721 9812Infection Control Programme, Geneva University Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland
| | - Laure Vieux
- grid.150338.c0000 0001 0721 9812Occupational Health Service, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Graf
- grid.150338.c0000 0001 0721 9812Department of Rehabilitation and Geriatrics, Geneva University Hospitals, Geneva, Switzerland
| | - Samuel Cordey
- grid.8591.50000 0001 2322 4988Faculty of Medicine, University of Geneva, Geneva, Switzerland ,grid.150338.c0000 0001 0721 9812Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Florian Laubscher
- grid.150338.c0000 0001 0721 9812Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Tomás Robalo Nunes
- grid.435541.20000 0000 9851 304XInfectious Diseases Service of Hospital Garcia de Orta, EPE, Almada, Portugal
| | - Walter Zingg
- grid.150338.c0000 0001 0721 9812Infection Control Programme, Geneva University Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland
| | - Anne Cori
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Stephan Harbarth
- grid.150338.c0000 0001 0721 9812Infection Control Programme, Geneva University Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland ,grid.8591.50000 0001 2322 4988Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mohamed Abbas
- grid.150338.c0000 0001 0721 9812Infection Control Programme, Geneva University Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland ,grid.8591.50000 0001 2322 4988Faculty of Medicine, University of Geneva, Geneva, Switzerland ,grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
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Huber JH, Hsiang MS, Dlamini N, Murphy M, Vilakati S, Nhlabathi N, Lerch A, Nielsen R, Ntshalintshali N, Greenhouse B, Perkins TA. Inferring person-to-person networks of Plasmodium falciparum transmission: are analyses of routine surveillance data up to the task? Malar J 2022; 21:58. [PMID: 35189905 PMCID: PMC8860266 DOI: 10.1186/s12936-022-04072-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inference of person-to-person transmission networks using surveillance data is increasingly used to estimate spatiotemporal patterns of pathogen transmission. Several data types can be used to inform transmission network inferences, yet the sensitivity of those inferences to different data types is not routinely evaluated. METHODS The influence of different combinations of spatial, temporal, and travel-history data on transmission network inferences for Plasmodium falciparum malaria were evaluated. RESULTS The information content of these data types may be limited for inferring person-to-person transmission networks and may lead to an overestimate of transmission. Only when outbreaks were temporally focal or travel histories were accurate was the algorithm able to accurately estimate the reproduction number under control, Rc. Applying this approach to data from Eswatini indicated that inferences of Rc and spatiotemporal patterns therein depend upon the choice of data types and assumptions about travel-history data. CONCLUSIONS These results suggest that transmission network inferences made with routine malaria surveillance data should be interpreted with caution.
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Affiliation(s)
- John H Huber
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Michelle S Hsiang
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Malaria Elimination Initiative, Global Health Group, University of California, San Francisco, CA, USA.,Department of Pediatrics, University of California, San Francisco,, CA, USA
| | - Nomcebo Dlamini
- National Malaria Elimination Programme, Ministry of Health, Manzini, Eswatini
| | - Maxwell Murphy
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Nomcebo Nhlabathi
- National Malaria Elimination Programme, Ministry of Health, Manzini, Eswatini
| | - Anita Lerch
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Rasmus Nielsen
- Department of Integrative Biology and Statistics, University of California, Berkeley, CA, USA
| | | | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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30
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Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review. Pathogens 2022; 11:pathogens11020252. [PMID: 35215195 PMCID: PMC8875843 DOI: 10.3390/pathogens11020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
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31
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Leavitt SV, Horsburgh CR, Lee RS, Tibbs AM, White LF, Jenkins HE. What Can Genetic Relatedness Tell Us About Risk Factors for Tuberculosis Transmission? Epidemiology 2022; 33:55-64. [PMID: 34847084 PMCID: PMC8638913 DOI: 10.1097/ede.0000000000001414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND To stop tuberculosis (TB), the leading infectious cause of death globally, we need to better understand transmission risk factors. Although many studies have identified associations between individual-level covariates and pathogen genetic relatedness, few have identified characteristics of transmission pairs or explored how closely covariates associated with genetic relatedness mirror those associated with transmission. METHODS We simulated a TB-like outbreak with pathogen genetic data and estimated odds ratios (ORs) to correlate each covariate and genetic relatedness. We used a naive Bayes approach to modify the genetic links and nonlinks to resemble the true links and nonlinks more closely and estimated modified ORs with this approach. We compared these two sets of ORs with the true ORs for transmission. Finally, we applied this method to TB data in Hamburg, Germany, and Massachusetts, USA, to find pair-level covariates associated with transmission. RESULTS Using simulations, we found that associations between covariates and genetic relatedness had the same relative magnitudes and directions as the true associations with transmission, but biased absolute magnitudes. Modifying the genetic links and nonlinks reduced the bias and increased the confidence interval widths, more accurately capturing error. In Hamburg and Massachusetts, pairs were more likely to be probable transmission links if they lived in closer proximity, had a shorter time between observations, or had shared ethnicity, social risk factors, drug resistance, or genotypes. CONCLUSIONS We developed a method to improve the use of genetic relatedness as a proxy for transmission, and aid in understanding TB transmission dynamics in low-burden settings.
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Affiliation(s)
- Sarah V Leavitt
- From the Boston University School of Public Health, Department of Biostatistics, Boston, MA
| | - C Robert Horsburgh
- Boston University School of Public Health, Department of Epidemiology, Boston, MA
| | - Robyn S Lee
- University of Toronto, Dalla Lana School of Public Health, Epidemiology Division, Toronto, ON, Canada
| | | | - Laura F White
- From the Boston University School of Public Health, Department of Biostatistics, Boston, MA
| | - Helen E Jenkins
- From the Boston University School of Public Health, Department of Biostatistics, Boston, MA
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32
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Tonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, Tate N, Pastusiak A, Turner C, Chewapreecha C, Frost SDW, Corander J, Croucher NJ, Turner P, Bentley SD. Pneumococcal within-host diversity during colonization, transmission and treatment. Nat Microbiol 2022; 7:1791-1804. [PMID: 36216891 PMCID: PMC9613479 DOI: 10.1038/s41564-022-01238-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022]
Abstract
Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child's life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.
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Affiliation(s)
- Gerry Tonkin-Hill
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Blindern, Norway
| | - Clare Ling
- grid.10223.320000 0004 1937 0490Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chrispin Chaguza
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.47100.320000000419368710Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT USA
| | - Susannah J. Salter
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Pattaraporn Hinfonthong
- grid.10223.320000 0004 1937 0490Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Elissavet Nikolaou
- grid.48004.380000 0004 1936 9764Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK ,grid.1058.c0000 0000 9442 535XInfection and Immunity, Murdoch Children’s Research Institute, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria Australia
| | - Natalie Tate
- grid.48004.380000 0004 1936 9764Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Claudia Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Claire Chewapreecha
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.10223.320000 0004 1937 0490Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Simon D. W. Frost
- grid.419815.00000 0001 2181 3404Microsoft Research, Redmond, WA USA ,grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Jukka Corander
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Blindern, Norway ,grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Nicholas J. Croucher
- grid.7445.20000 0001 2113 8111MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Paul Turner
- grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK ,grid.459332.a0000 0004 0418 5364Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Stephen D. Bentley
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
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33
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Rossi G, Crispell J, Brough T, Lycett SJ, White PCL, Allen A, Ellis RJ, Gordon SV, Harwood R, Palkopoulou E, Presho EL, Skuce R, Smith GC, Kao RR. Phylodynamic analysis of an emergent
Mycobacterium bovis
outbreak in an area with no previously known wildlife infections. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gianluigi Rossi
- Roslin Institute and R(D)SVS University of Edinburgh Edinburgh UK
| | - Joseph Crispell
- School of Veterinary Medicine University College Dublin Dublin Ireland
| | - Tanis Brough
- Advice Services Team Service Delivery Directorate APHA Penrith UK
| | | | | | - Adrian Allen
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | - Richard J. Ellis
- Surveillance and Laboratory Services Department APHA Addlestone UK
| | - Stephen V. Gordon
- School of Veterinary Medicine University College Dublin Dublin Ireland
- Conway Institute University College Dublin Dublin Ireland
| | | | | | - Eleanor L. Presho
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | - Robin Skuce
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | | | - Rowland R. Kao
- Roslin Institute and R(D)SVS University of Edinburgh Edinburgh UK
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34
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Kahn R, Wang R, Leavitt SV, Hanage WP, Lipsitch M. Leveraging Pathogen Sequence and Contact Tracing Data to Enhance Vaccine Trials in Emerging Epidemics. Epidemiology 2021; 32:698-704. [PMID: 34039898 PMCID: PMC8338748 DOI: 10.1097/ede.0000000000001367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Advance planning of vaccine trials conducted during outbreaks increases our ability to rapidly define the efficacy and potential impact of a vaccine. Vaccine efficacy against infectiousness (VEI) is an important measure for understanding a vaccine's full impact, yet it is currently not identifiable in many trial designs because it requires knowledge of infectors' vaccination status. Recent advances in genomics have improved our ability to reconstruct transmission networks. We aim to assess if augmenting trials with pathogen sequence and contact tracing data can permit them to estimate VEI. METHODS We develop a transmission model with a vaccine trial in an outbreak setting, incorporate pathogen sequence data and contact tracing data, and assign probabilities to likely infectors. We then propose and evaluate the performance of an estimator of VEI. RESULTS We find that under perfect knowledge of infector-infectee pairs, we are able to accurately estimate VEI. Use of sequence data results in imperfect reconstruction of transmission networks, biasing estimates of VEI towards the null, with approaches using deep sequence data performing better than approaches using consensus sequence data. Inclusion of contact tracing data reduces the bias. CONCLUSION Pathogen genomics enhance identifiability of VEI, but imperfect transmission network reconstruction biases estimate toward the null and limits our ability to detect VEI. Given the consistent direction of the bias, estimates obtained from trials using these methods will provide lower bounds on the true VEI. A combination of sequence and epidemiologic data results in the most accurate estimates, underscoring the importance of contact tracing.
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Affiliation(s)
- Rebecca Kahn
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Rui Wang
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Sarah V. Leavitt
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
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35
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Wertheim JO, Steel M, Sanderson MJ. Accuracy in near-perfect virus phylogenies. Syst Biol 2021; 71:426-438. [PMID: 34398231 PMCID: PMC8385947 DOI: 10.1093/sysbio/syab069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022] Open
Abstract
Phylogenetic trees from real-world data often include short edges with very few substitutions per site, which can lead to partially resolved trees and poor accuracy. Theory indicates that the number of sites needed to accurately reconstruct a fully resolved tree grows at a rate proportional to the inverse square of the length of the shortest edge. However, when inferred trees are partially resolved due to short edges, “accuracy” should be defined as the rate of discovering false splits (clades on a rooted tree) relative to the actual number found. Thus, accuracy can be high even if short edges are common. Specifically, in a “near-perfect” parameter space in which trees are large, the tree length ξ (the sum of all edge lengths) is small, and rate variation is minimal, the expected false positive rate is less than ξ∕3; the exact value depends on tree shape and sequence length. This expected false positive rate is far below the false negative rate for small ξ and often well below 5% even when some assumptions are relaxed. We show this result analytically for maximum parsimony and explore its extension to maximum likelihood using theory and simulations. For hypothesis testing, we show that measures of split “support” that rely on bootstrap resampling consistently imply weaker support than that implied by the false positive rates in near-perfect trees. The near-perfect parameter space closely fits several empirical studies of human virus diversification during outbreaks and epidemics, including Ebolavirus, Zika virus, and SARS-CoV-2, reflecting low substitution rates relative to high transmission/sampling rates in these viruses.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Mike Steel
- Biomathematics Research Center, School of Mathematics and Statistics, University of Canterbury, Christchurch, 8041, New Zealand
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA
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36
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Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, Jackson DK, Park N, Lensing SV, Quail MA, Gonçalves S, Ariani C, Spencer Chapman M, Hamilton WL, Meredith LW, Hall G, Jahun AS, Chaudhry Y, Hosmillo M, Pinckert ML, Georgana I, Yakovleva A, Caller LG, Caddy SL, Feltwell T, Khokhar FA, Houldcroft CJ, Curran MD, Parmar S, Alderton A, Nelson R, Harrison EM, Sillitoe J, Bentley SD, Barrett JC, Torok ME, Goodfellow IG, Langford C, Kwiatkowski D. Patterns of within-host genetic diversity in SARS-CoV-2. eLife 2021; 10:e66857. [PMID: 34387545 PMCID: PMC8363274 DOI: 10.7554/elife.66857] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.
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Affiliation(s)
| | | | | | | | | | | | | | - Naomi Park
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | | | | | | | | | | | - Luke W Meredith
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Grant Hall
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Aminu S Jahun
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Myra Hosmillo
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Malte L Pinckert
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Iliana Georgana
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Anna Yakovleva
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Laura G Caller
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Sarah L Caddy
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Theresa Feltwell
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Fahad A Khokhar
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of CambridgeCambridgeUnited Kingdom
| | | | | | | | | | | | | | - Ewan M Harrison
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- European Bioinformatics InstituteHinxtonUnited Kingdom
| | | | | | | | - M Estee Torok
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Ian G Goodfellow
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | - Dominic Kwiatkowski
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
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37
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Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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38
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Wohl S, Giles JR, Lessler J. Sample size calculation for phylogenetic case linkage. PLoS Comput Biol 2021; 17:e1009182. [PMID: 34228722 PMCID: PMC8284614 DOI: 10.1371/journal.pcbi.1009182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/16/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies. Sequencing the genetic material of viral and bacterial pathogens has become an important part of tracking and combating human infectious diseases. Specifically, comparing the pathogen DNA or RNA sequences collected from infected individuals can allow researchers and public health experts to determine who infected whom, or detect when a pathogen entered a specific country or geographic area. However, it is often impossible to collect samples from every single infected person, and these missing sequences can pose problems for this type of analysis, especially if there is some bias behind which samples were selected for sequencing. We have developed a mathematical framework that allows users to determine the probability their conclusions about pathogen transmission are correct given the number and proportion of samples from a pathogen outbreak they have sequenced. This framework is freely available, easy to use, and broadly generalizable to any pathogen, and we hope that it can be used to inform the design and sampling strategies behind future sequencing-based studies.
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Affiliation(s)
- Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
| | - John R Giles
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, Maryland, United States of America
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39
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Winglee K, McDaniel CJ, Linde L, Kammerer S, Cilnis M, Raz KM, Noboa W, Knorr J, Cowan L, Reynolds S, Posey J, Sullivan Meissner J, Poonja S, Shaw T, Talarico S, Silk BJ. Logically Inferred Tuberculosis Transmission (LITT): A Data Integration Algorithm to Rank Potential Source Cases. Front Public Health 2021; 9:667337. [PMID: 34235130 PMCID: PMC8255782 DOI: 10.3389/fpubh.2021.667337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/10/2021] [Indexed: 11/22/2022] Open
Abstract
Understanding tuberculosis (TB) transmission chains can help public health staff target their resources to prevent further transmission, but currently there are few tools to automate this process. We have developed the Logically Inferred Tuberculosis Transmission (LITT) algorithm to systematize the integration and analysis of whole-genome sequencing, clinical, and epidemiological data. Based on the work typically performed by hand during a cluster investigation, LITT identifies and ranks potential source cases for each case in a TB cluster. We evaluated LITT using a diverse dataset of 534 cases in 56 clusters (size range: 2–69 cases), which were investigated locally in three different U.S. jurisdictions. Investigators and LITT agreed on the most likely source case for 145 (80%) of 181 cases. By reviewing discrepancies, we found that many of the remaining differences resulted from errors in the dataset used for the LITT algorithm. In addition, we developed a graphical user interface, user's manual, and training resources to improve LITT accessibility for frontline staff. While LITT cannot replace thorough field investigation, the algorithm can help investigators systematically analyze and interpret complex data over the course of a TB cluster investigation. Code available at:https://github.com/CDCgov/TB_molecular_epidemiology/tree/1.0; https://zenodo.org/badge/latestdoi/166261171.
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Affiliation(s)
- Kathryn Winglee
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Clinton J McDaniel
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lauren Linde
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - Steve Kammerer
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Martin Cilnis
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - Kala M Raz
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Wendy Noboa
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States.,Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Jillian Knorr
- New York City Department of Health and Mental Hygiene, Queens, NY, United States
| | - Lauren Cowan
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sue Reynolds
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - James Posey
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | - Shameer Poonja
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States.,Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Tambi Shaw
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - Sarah Talarico
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Benjamin J Silk
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, GA, United States
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40
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Robert A, Funk S, Kucharski AJ. o2geosocial: Reconstructing who-infected-whom from routinely collected surveillance data. F1000Res 2021; 10:31. [PMID: 36998981 PMCID: PMC10044721.2 DOI: 10.12688/f1000research.28073.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 11/20/2022] Open
Abstract
Reconstructing the history of individual transmission events between cases is key to understanding what factors facilitate the spread of an infectious disease. Since conducting extended contact-tracing investigations can be logistically challenging and costly, statistical inference methods have been developed to reconstruct transmission trees from onset dates and genetic sequences. However, these methods are not as effective if the mutation rate of the virus is very slow, or if sequencing data is sparse. We developed the package o2geosocial to combine variables from routinely collected surveillance data with a simple transmission process model. The model reconstructs transmission trees when full genetic sequences are unavailable, or uninformative. Our model incorporates the reported age-group, onset date, location and genotype of infected cases to infer probabilistic transmission trees. The package also includes functions to summarise and visualise the inferred cluster size distribution. The results generated by o2geosocial can highlight regions where importations repeatedly caused large outbreaks, which may indicate a higher regional susceptibility to infections. It can also be used to generate the individual number of secondary transmissions, and show the features associated with individuals involved in high transmission events. The package is available for download from the Comprehensive R Archive Network (CRAN) and GitHub.
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Affiliation(s)
- Alexis Robert
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Adam J Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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41
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Dawson D, Rasmussen D, Peng X, Lanzas C. Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen. J R Soc Interface 2021; 18:20210041. [PMID: 34102084 DOI: 10.1098/rsif.2021.0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Indirect (environmental) and direct (host-host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. In this study, we used a network-based transmission model that explicitly models pathogen evolution to simulate epidemics with both direct and indirect transmission. Epidemics were simulated according to factorial combinations of direct/indirect transmission proportions, host mutation rates and conditions of environmental pathogen growth. Transmission trees were then reconstructed using the phylodynamic approach SCOTTI (structured coalescent transmission tree inference) and evaluated. We found that although insufficient diversity sets a lower bound on when accurate phylodynamic inferences can be made, transmission routes and assumed pathogen lifestyle affected pathogen population structure and subsequently influenced both reconstruction success and the likelihood of direct versus indirect pathways being reconstructed. We conclude that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.
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Affiliation(s)
- Daniel Dawson
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - David Rasmussen
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Xinxia Peng
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Cristina Lanzas
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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42
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Yadav PD, Nyayanit DA, Majumdar T, Patil S, Kaur H, Gupta N, Shete AM, Pandit P, Kumar A, Aggarwal N, Narayan J, Vijay N, Kalawat U, Sugunan AP, Munivenkatappa A, Sharma T, Devi S, Majumdar T, Jaryal S, Bakshi R, Joshi Y, Sahay R, Shastri J, Singh M, Kumar M, Rawat V, Dutta S, Yadav S, Krishnasamy K, Raut S, Biswas D, Borkakoty B, Verma S, Rani S, Deval H, Patel D, Turuk J, Malhotra B, Fomda B, Nag V, Jain A, Bhargava A, Potdar V, Cherian S, Abraham P, Gopal A, Panda S, Bhargava B. An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Viruses 2021; 13:v13050925. [PMID: 34067745 PMCID: PMC8156686 DOI: 10.3390/v13050925] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022] Open
Abstract
The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the ‘GH’ clade, whereas the southern part reported the ‘GR’, with a few exceptions. These sequences also revealed the presence of single independent mutations—E484Q and N440K—from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January–August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.
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Affiliation(s)
- Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Harmanmeet Kaur
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Nivedita Gupta
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
- Correspondence:
| | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Priyanka Pandit
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Neeraj Aggarwal
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Jitendra Narayan
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Neetu Vijay
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Usha Kalawat
- Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, India;
| | | | | | - Tara Sharma
- VRDL Sikkim Government College of Nursing, Gangtok 737101, India;
| | - Sulochna Devi
- Regional Institute of Medical Sciences IMPHAL, Imphal 795004, India;
| | - Tapan Majumdar
- Government Medical College, Agartala, Tripura 799006, India;
| | - Subhash Jaryal
- Dr. Rajendra Prasad Government Medical College, (H.P.), Kangra 176001, India;
| | | | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Rima Sahay
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Jayanti Shastri
- Kasturba Hospital for Infectious Diseases, Mumbai 400034, India;
| | - Mini Singh
- Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India;
| | - Manoj Kumar
- Rajendra Institute of Medical Sciences, Ranchi 834009, India;
| | - Vinita Rawat
- Government Medical College, Haldwani 263129, India;
| | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases, Kolkata 700010, India;
| | - Sarita Yadav
- Bhagat Phool Singh Government Medical College, Sonipat 131305, India;
| | - Kaveri Krishnasamy
- King Institute of Preventive Medicine & Research, Chennai 600032, India;
| | - Sharmila Raut
- Indira Gandhi Government Medical College & Hospital, Nagpur 440018, India;
| | - Debasis Biswas
- All India Institute of Medical Sciences, Bhopal 462020, India;
| | | | - Santwana Verma
- Indira Gandhi Medical College & Hospital, Shimla 171001, India;
| | - Sudha Rani
- Osmania Medical College, Hyderabad 500095, India;
| | - Hirawati Deval
- Regional Medical Research Center Gorakhpur, Gorakhpur 273013, India;
| | - Disha Patel
- B.J. Medical College, Ahmedabad 380016, India;
| | | | | | - Bashir Fomda
- Sher-I-Kashmir Institute of Medical Sciences, Srinagar 190011, India;
| | | | - Amita Jain
- Department of Microbiology, King George’s Medical University, Lucknow 226003, India;
| | - Anudita Bhargava
- All India Institute of Medical Sciences, Raipur, Raipur 492099, India;
| | - Varsha Potdar
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Sarah Cherian
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Priya Abraham
- Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune 411021, India; (P.D.Y.); (D.A.N.); (T.M.); (S.P.); (A.M.S.); (P.P.); (A.K.); (Y.J.); (R.S.); (V.P.); (S.C.); (P.A.)
| | - Anjani Gopal
- Indian Institute of Science Education and Research, Pune 411008, India;
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
| | - Balram Bhargava
- Indian Council of Medical Research, New Delhi 110029, India; (H.K.); (N.A.); (J.N.); (N.V.); (S.P.); (B.B.)
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43
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Intercontinental transmission and local demographic expansion of SARS-CoV-2. Epidemiol Infect 2021; 149:e94. [PMID: 33845928 PMCID: PMC8060534 DOI: 10.1017/s0950268821000777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The global outbreak of coronavirus disease 2019 (COVID-19) is greatly threatening the public health in the world. We reconstructed global transmissions and potential demographic expansions of severe acute respiratory syndrome coronavirus 2 based on genomic information. We found that intercontinental transmissions were rare in January and early February but drastically increased since late February. After world-wide implements of travel restrictions, the transmission frequencies decreased to a low level in April. We identified a total of 88 potential demographic expansions over the world based on the star-radiative networks and 75 of them were found in Europe and North America. The expansion numbers peaked in March and quickly dropped since April. These findings are highly concordant with epidemic reports and modelling results and highlight the significance of quarantine validity on the global spread of COVID-19. Our analyses indicate that the travel restrictions and social distancing measures are effective in containing the spread of COVID-19.
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44
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Bandoy DJDR, Weimer BC. Analysis of SARS-CoV-2 genomic epidemiology reveals disease transmission coupled to variant emergence and allelic variation. Sci Rep 2021; 11:7380. [PMID: 33795722 PMCID: PMC8016908 DOI: 10.1038/s41598-021-86265-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/12/2021] [Indexed: 01/10/2023] Open
Abstract
The spread of SARS-CoV-2 created a pandemic crisis with > 150,000 cumulative cases in > 65 countries within a few months. The reproductive number (R) is a metric to estimate the transmission of a pathogen during an outbreak. Preliminary published estimates were based on the initial outbreak in China. Whole genome sequences (WGS) analysis found mutational variations in the viral genome; however, previous comparisons failed to show a direct relationship between viral genome diversity, transmission, and the epidemic severity. COVID-19 incidences from different countries were modeled over the epidemic curve. Estimates of the instantaneous R (Wallinga and Teunis method) with a short and standard serial interval were done. WGS were used to determine the populations genomic variation and that underpinned creation of the pathogen genome identity (GENI) score, which was merged with the outbreak curve in four distinct phases. Inference of transmission time was based on a mutation rate of 2 mutations/month. R estimates revealed differences in the transmission and variable infection dynamics between and within outbreak progression for each country examined. Outside China, our R estimates observed propagating dynamics indicating that other countries were poised to move to the takeoff and exponential stages. Population density and local temperatures had no clear relationship to the outbreak progression. Integration of incidence data with the GENI score directly predicted increases in cases as the genome variation increased that led to new variants. Integrating the outbreak curve, dynamic R, and SNP variation found a direct association between increasing cases and transmission genome evolution. By defining the epidemic curve into four stages and integrating the instantaneous country-specific R with the GENI score, we directly connected changes in individual outbreaks based on changes in the virus genome via SNPs. This resulted in the ability to forecast potential increases in cases as well as mutations that may defeat PCR screening and the infection process. By using instantaneous R estimations and WGS, outbreak dynamics were defined to be linked to viral mutations, indicating that WGS, as a surveillance tool, is required to predict shifts in each outbreak that will provide actionable decision making information. Integrating epidemiology with genome sequencing and modeling allows for evidence-based disease outbreak tracking with predictive therapeutically valuable insights in near real time.
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Affiliation(s)
- D J Darwin R Bandoy
- School of Veterinary Medicine, Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA, 95616, USA.,Department of Veterinary Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
| | - Bart C Weimer
- School of Veterinary Medicine, Population Health and Reproduction, 100K Pathogen Genome Project, University of California Davis, Davis, CA, 95616, USA.
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45
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Abbas M, Robalo Nunes T, Martischang R, Zingg W, Iten A, Pittet D, Harbarth S. Nosocomial transmission and outbreaks of coronavirus disease 2019: the need to protect both patients and healthcare workers. Antimicrob Resist Infect Control 2021; 10:7. [PMID: 33407833 PMCID: PMC7787623 DOI: 10.1186/s13756-020-00875-7] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/22/2020] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES To compile current published reports on nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), evaluate the role of healthcare workers (HCWs) in transmission, and evaluate outbreak management practices. METHODS Narrative literature review. SHORT CONCLUSION The coronavirus disease 2019 (COVID-19) pandemic has placed a large burden on hospitals and healthcare providers worldwide, which increases the risk of nosocomial transmission and outbreaks to "non-COVID" patients or residents, who represent the highest-risk population in terms of mortality, as well as HCWs. To date, there are several reports on nosocomial outbreaks of SARS-CoV-2, and although the attack rate is variable, it can be as high as 60%, with high mortality. There is currently little evidence on transmission dynamics, particularly using genomic sequencing, and the role of HCWs in initiating or amplifying nosocomial outbreaks is not elucidated. There has been a paradigm shift in management practices of viral respiratory outbreaks, that includes widespread testing of patients (or residents) and HCWs, including asymptomatic individuals. These expanded testing criteria appear to be crucial in identifying and controlling outbreaks.
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Affiliation(s)
- Mohamed Abbas
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland.
- Health Protection Research Unit, Imperial College London, London, UK.
| | - Tomás Robalo Nunes
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Infectious Diseases Service, Hospital Garcia de Orta, EPE, Almada, Portugal
| | - Romain Martischang
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Walter Zingg
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Infectious Diseases Service, Hospital Garcia de Orta, EPE, Almada, Portugal
- University of Geneva, Geneva, Switzerland
| | - Anne Iten
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Didier Pittet
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Infectious Diseases Service, Hospital Garcia de Orta, EPE, Almada, Portugal
- University of Geneva, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Infectious Diseases Service, Hospital Garcia de Orta, EPE, Almada, Portugal
- University of Geneva, Geneva, Switzerland
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46
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Identifying likely transmissions in Mycobacterium bovis infected populations of cattle and badgers using the Kolmogorov Forward Equations. Sci Rep 2020; 10:21980. [PMID: 33319838 PMCID: PMC7738532 DOI: 10.1038/s41598-020-78900-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022] Open
Abstract
Established methods for whole-genome-sequencing (WGS) technology allow for the detection of single-nucleotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples. The information obtained can be used to track the pathogen’s evolution in time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful methods include ‘phylodynamic approaches’ that integrate evolutionary and epidemiological data. However, they are typically computationally intensive, require extensive data, and are best applied when there is a strong molecular clock signal and substantial pathogen diversity. To determine how much transmission information can be inferred when pathogen genetic diversity is low and metadata limited, we propose an analytical approach that combines pathogen WGS data and sampling times from infected hosts. It accounts for ‘between-scale’ processes, in particular within-host pathogen evolution and between-host transmission. We applied this to a well-characterised population with an endemic Mycobacterium bovis (the causative agent of bovine/zoonotic tuberculosis, bTB) infection. Our results show that, even with such limited data and low diversity, the computation of the transmission probability between host pairs can help discriminate between likely and unlikely infection pathways and therefore help to identify potential transmission networks. However, the method can be sensitive to assumptions about within-host evolution.
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47
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Xu Y, Stockdale JE, Naidu V, Hatherell H, Stimson J, Stagg HR, Abubakar I, Colijn C. Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data. Microb Genom 2020; 6:mgen000450. [PMID: 33174832 PMCID: PMC7725332 DOI: 10.1099/mgen.0.000450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Outbreaks of tuberculosis (TB) - such as the large isoniazid-resistant outbreak centred on London, UK, which originated in 1995 - provide excellent opportunities to model transmission of this devastating disease. Transmission chains for TB are notoriously difficult to ascertain, but mathematical modelling approaches, combined with whole-genome sequencing data, have strong potential to contribute to transmission analyses. Using such data, we aimed to reconstruct transmission histories for the outbreak using a Bayesian approach, and to use machine-learning techniques with patient-level data to identify the key covariates associated with transmission. By using our transmission reconstruction method that accounts for phylogenetic uncertainty, we are able to identify 21 transmission events with reasonable confidence, 9 of which have zero SNP distance, and a maximum distance of 3. Patient age, alcohol abuse and history of homelessness were found to be the most important predictors of being credible TB transmitters.
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Affiliation(s)
- Yuanwei Xu
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, UK
| | | | - Vijay Naidu
- Department of Mathematics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - James Stimson
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, UK
- National Infection Service, Public Health England, London, UK
| | - Helen R. Stagg
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ibrahim Abubakar
- Institute for Global Health, University College London, London, UK
| | - Caroline Colijn
- Centre for Mathematics of Precision Healthcare, Department of Mathematics, Imperial College London, London, UK
- Department of Mathematics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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48
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Salam AP, Raberahona M, Andriantsalama P, Read L, Andrianarintsiferantsoa F, Razafinambinintsoa T, Rakotomalala R, Hasiniatsy RNE, Razafimandimby D, Castle L, Funk A, Mangahasimbola RT, Renaud B, Bertherat E, Lovering A, Heraud JM, Andrianaivoarimanana V, Frédérique R, Razanajatovo N, Baril L, Fontanet A, Rajerison M, Horby P, Randria M, Randremanana R. Factors Influencing Atypical Clinical Presentations during the 2017 Madagascar Pneumonic Plague Outbreak: A Prospective Cohort Study. Am J Trop Med Hyg 2020; 102:1309-1315. [PMID: 32274983 PMCID: PMC7253123 DOI: 10.4269/ajtmh.19-0576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In late 2017, Madagascar experienced a large urban outbreak of pneumonic plague, the largest outbreak to date this century. During the outbreak, there were widespread reports of plague patients presenting with atypical symptoms, such as prolonged duration of illness and upper respiratory tract symptoms. Reported mortality among plague cases was also substantially lower than that reported in the literature (25% versus 50% in treated patients). A prospective multicenter observational study was carried out to investigate potential reasons for these atypical presentations. Few subjects among our cohort had confirmed or probable plague, suggesting that, in part, there was overdiagnosis of plague cases by clinicians. However, 35% subjects reported using an antibiotic with anti-plague activity before hospital admission, whereas 55% had antibiotics with anti-plague activity detected in their serum at admission. Although there may have been overdiagnosis of plague by clinicians during the outbreak, the high frequency of community antibiotic may partly explain the relatively few culture-positive sputum samples during the outbreak. Community antibiotic use may have also altered the clinical presentation of plague patients. These issues make accurate detection of patients and the development of clinical case definitions and triage algorithms in urban pneumonic plague outbreaks difficult.
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Affiliation(s)
- Alex P Salam
- University of Oxford, Oxford, United Kingdom.,United Kingdom Public Health Rapid Support Team, London, United Kingdom
| | | | | | - Liam Read
- North Bristol NHS Trust, Bristol, United Kingdom
| | | | | | | | | | | | | | - Anna Funk
- Institut Pasteur Paris, Paris, France
| | | | | | | | | | | | | | | | | | - Laurence Baril
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Arnaud Fontanet
- Institut Pasteur Paris, Paris, France.,Conservatoire National des Arts et Métiers, Paris, France
| | | | - Peter Horby
- University of Oxford, Oxford, United Kingdom
| | - Mamy Randria
- Centre Hospitalier Befelatanana, Antananarivo, Madagascar
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49
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Walter KS, Colijn C, Cohen T, Mathema B, Liu Q, Bowers J, Engelthaler DM, Narechania A, Lemmer D, Croda J, Andrews JR. Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences. Microb Genom 2020; 6:mgen000418. [PMID: 32735210 PMCID: PMC7641424 DOI: 10.1099/mgen.0.000418] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/15/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet, there is no current consensus on how to measure genomic variation. To test the effect of the variant-identification approach on transmission inferences for Mycobacterium tuberculosis, we conducted an experiment in which five genomic epidemiology groups applied variant-identification pipelines to the same outbreak sequence data. We compared the variants identified by each group in addition to transmission and phylogenetic inferences made with each variant set. To measure the performance of commonly used variant-identification tools, we simulated an outbreak. We compared the performance of three mapping algorithms, five variant callers and two variant filters in recovering true outbreak variants. Finally, we investigated the effect of applying increasingly stringent filters on transmission inferences and phylogenies. We found that variant-calling approaches used by different groups do not recover consistent sets of variants, which can lead to conflicting transmission inferences. Further, performance in recovering true variation varied widely across approaches. While no single variant-identification approach outperforms others in both recovering true genome-wide and outbreak-level variation, variant-identification algorithms calibrated upon real sequence data or that incorporate local reassembly outperform others in recovering true pairwise differences between isolates. The choice of variant filters contributed to extensive differences across pipelines, and applying increasingly stringent filters rapidly eroded the accuracy of transmission inferences and quality of phylogenies reconstructed from outbreak variation. Commonly used approaches to identify M. tuberculosis genomic variation have variable performance, particularly when predicting potential transmission links from pairwise genetic distances. Phylogenetic reconstruction may be improved by less stringent variant filtering. Approaches that improve variant identification in repetitive, hypervariable regions, such as long-read assemblies, may improve transmission inference.
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Affiliation(s)
- Katharine S. Walter
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University Medical Center, New York, New York, USA
| | - Qingyun Liu
- School of Basic Medical Science of Fudan University, Shanghai, PR China
| | - Jolene Bowers
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | | | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Julio Croda
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
- Oswaldo Cruz Foundation, Campo Grande, Brazil
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
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50
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Robert A, Kucharski AJ, Gastañaduy PA, Paul P, Funk S. Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data. J R Soc Interface 2020; 17:20200084. [PMID: 32603651 PMCID: PMC7423430 DOI: 10.1098/rsif.2020.0084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/08/2020] [Indexed: 12/24/2022] Open
Abstract
Pockets of susceptibility resulting from spatial or social heterogeneity in vaccine coverage can drive measles outbreaks, as cases imported into such pockets are likely to cause further transmission and lead to large transmission clusters. Characterizing the dynamics of transmission is essential for identifying which individuals and regions might be most at risk. As data from detailed contact-tracing investigations are not available in many settings, we developed an R package called o2geosocial to reconstruct the transmission clusters and the importation status of the cases from their age, location, genotype and onset date. We compared our inferred cluster size distributions to 737 transmission clusters identified through detailed contact-tracing in the USA between 2001 and 2016. We were able to reconstruct the importation status of the cases and found good agreement between the inferred and reference clusters. The results were improved when the contact-tracing investigations were used to set the importation status before running the model. Spatial heterogeneity in vaccine coverage is difficult to measure directly. Our approach was able to highlight areas with potential for local transmission using a minimal number of variables and could be applied to assess the intensity of ongoing transmission in a region.
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Affiliation(s)
- Alexis Robert
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Centre for the Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - Adam J. Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Centre for the Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - Paul A. Gastañaduy
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Prabasaj Paul
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sebastian Funk
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Centre for the Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London, UK
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