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Lam T, Saso A, Torres Ortiz A, Hatcher J, Woodman M, Chandran S, Thistlethwayte R, Best T, Johnson M, Wagstaffe H, Mai A, Buckland M, Gilmour K, Goldblatt D, Grandjean L. Socioeconomic and Demographic Risk Factors for SARS-CoV-2 Seropositivity Among Healthcare Workers in a UK Hospital: A Prospective Cohort Study. Clin Infect Dis 2024; 78:594-602. [PMID: 37647517 PMCID: PMC10954340 DOI: 10.1093/cid/ciad522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND To protect healthcare workers (HCWs) from the consequences of disease due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is necessary to understand the risk factors that drive exposure and infection within hospitals. Insufficient consideration of key socioeconomic variables is a limitation of existing studies that can lead to bias and residual confounding of proposed risk factors for infection. METHODS The Co-STARs study prospectively enrolled 3679 HCWs between April 2020 and September 2020. We used multivariate logistic regression to comprehensively characterize the demographic, occupational, socioeconomic, and environmental risk factors for SARS-CoV-2 seropositivity. RESULTS After adjusting for key confounders, relative household overcrowding (odds ratio [OR], 1.4 [95% confidence interval {CI}, 1.1-1.9]; P = .006), Black, Black British, Caribbean, or African ethnicity (OR, 1.7 [95% CI, 1.2-2.3]; P = .003), increasing age (ages 50-60 years: OR, 1.8 [95% CI, 1.3-2.4]; P < .001), lack of access to sick pay (OR, 1.8 [95% CI, 1.3-2.4]; P < .001). CONCLUSIONS Socioeconomic and demographic factors outside the hospital were the main drivers of infection and exposure to SARS-CoV-2 during the first wave of the pandemic in an urban pediatric referral hospital. Overcrowding and out-of-hospital SARS-CoV-2 contact are less amenable to intervention. However, lack of access to sick pay among externally contracted staff is more easily rectifiable. Our findings suggest that providing easier access to sick pay would lead to a decrease in SARS-CoV-2 transmission and potentially that of other infectious diseases in hospital settings. CLINICAL TRIALS REGISTRATION NCT04380896.
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Affiliation(s)
- Tanya Lam
- Department of Infectious Diseases, Great Ormond Street Hospital, London, United Kingdom
| | - Anja Saso
- Department of Infectious Diseases, Great Ormond Street Hospital, London, United Kingdom
- Department of Tropical and Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Medical Research Council Gambia at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Arturo Torres Ortiz
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, United Kingdom
| | - James Hatcher
- Department of Microbiology, Great Ormond Street Hospital, London, United Kingdom
| | - Marc Woodman
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, United Kingdom
| | - Shruthi Chandran
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, United Kingdom
| | | | - Timothy Best
- Department of Microbiology, Great Ormond Street Hospital, London, United Kingdom
| | - Marina Johnson
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, United Kingdom
| | - Helen Wagstaffe
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, United Kingdom
| | - Annabelle Mai
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, London, United Kingdom
| | - Matthew Buckland
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, London, United Kingdom
| | - Kimberly Gilmour
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, London, United Kingdom
| | - David Goldblatt
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, United Kingdom
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, United Kingdom
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2
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Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024; 16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.
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Affiliation(s)
- Camus Nimmo
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
- Division of Infection and Immunity, University College London, London, UK.
- Africa Health Research Institute, Durban, South Africa.
| | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Department of Medicine, Imperial College, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - Juanita Pang
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
- Department of Medicine & Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Pym
- Africa Health Research Institute, Durban, South Africa
| | - Ola B Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis Grandjean
- Division of Infection and Immunity, University College London, London, UK
- Laboratorio de Investigacion y Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - François Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
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3
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Ellis S, Way R, Nel M, Burleigh A, Doykov I, Kembou-Ringert J, Woodall M, Masonou T, Case KM, Ortez AT, McHugh TD, Casal A, McCoy LE, Murdan S, Hynds RE, Gilmour KC, Grandjean L, Cortina-Borja M, Heywood WE, Mills K, Smith CM. Salivary IgA and vimentin differentiate in vitro SARS-CoV-2 infection: A study of 290 convalescent COVID-19 patients. Mucosal Immunol 2024; 17:124-136. [PMID: 38007005 DOI: 10.1016/j.mucimm.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
SARS-CoV-2 initially infects cells in the nasopharynx and oral cavity. The immune system at these mucosal sites plays a crucial role in minimizing viral transmission and infection. To develop new strategies for preventing SARS-CoV-2 infection, this study aimed to identify proteins that protect against viral infection in saliva. We collected 551 saliva samples from 290 healthcare workers who had tested positive for COVID-19, before vaccination, between June and December 2020. The samples were categorized based on their ability to block or enhance infection using in vitro assays. Mass spectrometry and enzyme-linked immunosorbent assay experiments were used to identify and measure the abundance of proteins that specifically bind to SARS-CoV-2 antigens. Immunoglobulin (Ig)A specific to SARS-CoV-2 antigens was detectable in over 83% of the convalescent saliva samples. We found that concentrations of anti-receptor-binding domain IgA >500 pg/µg total protein in saliva correlate with reduced viral infectivity in vitro. However, there is a dissociation between the salivary IgA response to SARS-CoV-2, and systemic IgG titers in convalescent COVID-19 patients. Then, using an innovative technique known as spike-baited mass spectrometry, we identified novel spike-binding proteins in saliva, most notably vimentin, which correlated with increased viral infectivity in vitro and could serve as a therapeutic target against COVID-19.
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Affiliation(s)
- Samuel Ellis
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Rosie Way
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Miranda Nel
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Alice Burleigh
- UCL Great Ormond Street Institute of Child Health, London, UK; Centre for Adolescent Rheumatology, University College London, London, UK
| | - Ivan Doykov
- UCL Great Ormond Street Institute of Child Health, London, UK
| | | | | | - Tereza Masonou
- UCL Great Ormond Street Institute of Child Health, London, UK
| | | | | | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Royal Free Hospital, London, UK
| | - Antonio Casal
- Department of Pharmaceutics, UCL School of Pharmacy, London, UK
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | | | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Kimberly C Gilmour
- UCL Great Ormond Street Institute of Child Health, London, UK; Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Louis Grandjean
- UCL Great Ormond Street Institute of Child Health, London, UK; Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | | | - Wendy E Heywood
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Kevin Mills
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire M Smith
- UCL Great Ormond Street Institute of Child Health, London, UK.
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4
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Barilar I, Battaglia S, Borroni E, Brandao AP, Brankin A, Cabibbe AM, Carter J, Chetty D, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Earle SG, Escuyer V, Ferrazoli L, Fowler PW, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Gibertoni Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SJ, Hunt M, Iqbal Z, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SG, Laurenson IF, Letcher B, Lin WH, Liu C, Liu D, Malone KM, Mandal A, Mansjö M, Calisto Matias DVL, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung HN, Niemann S, Nilgiriwala KS, Nimmo C, O’Donnell M, Okozi N, Oliveira RS, Omar SV, Paton N, Peto TEA, Pinhata JMW, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PMV, Rathod P, Robinson ER, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Smith G, Kohl TA, Solano W, Spitaleri A, Steyn AJC, Supply P, Surve U, Tahseen S, Thuong NTT, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker AS, Walker TM, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wilson DJ, Wintringer P, Xiao YX, Yang Y, Yanlin Z, Yao SY, Zhu B. Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. Nat Commun 2024; 15:488. [PMID: 38216576 PMCID: PMC10786857 DOI: 10.1038/s41467-023-44325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024] Open
Abstract
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary manner (classifying strains as either susceptible or resistant). Here, we used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration (MIC) in 15,211 Mycobacterium tuberculosis clinical isolates from 23 countries across five continents. We identified 492 unique MIC-elevating variants across 13 drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.
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5
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Du DH, Geskus RB, Zhao Y, Codecasa LR, Cirillo DM, van Crevel R, Pascapurnama DN, Chaidir L, Niemann S, Diel R, Omar SV, Grandjean L, Rokadiya S, Ortitz AT, Lân NH, Hà ĐTM, Smith EG, Robinson E, Dedicoat M, Nhat LTH, Thwaites GE, Van LH, Thuong NTT, Walker TM. The effect of M. tuberculosis lineage on clinical phenotype. PLOS Glob Public Health 2023; 3:e0001788. [PMID: 38117783 PMCID: PMC10732390 DOI: 10.1371/journal.pgph.0001788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Six lineages of Mycobacterium tuberculosis sensu stricto (which excludes M. africanum) are described. Single-country or small observational data suggest differences in clinical phenotype between lineages. We present strain lineage and clinical phenotype data from 12,246 patients from 3 low-incidence and 5 high-incidence countries. We used multivariable logistic regression to explore the effect of lineage on site of disease and on cavities on chest radiography, given pulmonary TB; multivariable multinomial logistic regression to investigate types of extra-pulmonary TB, given lineage; and accelerated failure time and Cox proportional-hazards models to explore the effect of lineage on time to smear and culture-conversion. Mediation analyses quantified the direct effects of lineage on outcomes. Pulmonary disease was more likely among patients with lineage(L) 2, L3 or L4, than L1 (adjusted odds ratio (aOR) 1.79, (95% confidence interval 1.49-2.15), p<0.001; aOR = 1.40(1.09-1.79), p = 0.007; aOR = 2.04(1.65-2.53), p<0.001, respectively). Among patients with pulmonary TB, those with L1 had greater risk of cavities on chest radiography versus those with L2 (aOR = 0.69(0.57-0.83), p<0.001) and L4 strains (aOR = 0.73(0.59-0.90), p = 0.002). L1 strains were more likely to cause osteomyelitis among patients with extra-pulmonary TB, versus L2-4 (p = 0.033, p = 0.008 and p = 0.049 respectively). Patients with L1 strains showed shorter time-to-sputum smear conversion than for L2. Causal mediation analysis showed the effect of lineage in each case was largely direct. The pattern of clinical phenotypes seen with L1 strains differed from modern lineages (L2-4). This has implications for clinical management and could influence clinical trial selection strategies.
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Affiliation(s)
- Duc Hong Du
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ronald B. Geskus
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Luigi Ruffo Codecasa
- Regional TB Reference Centre/ Istituto Villa Marelli- ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | | | - Reinout van Crevel
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Lidya Chaidir
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, Indonesia
| | - Stefan Niemann
- Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Roland Diel
- University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- Lung Clinic Grosshansdorf, Airway Disease Center North (ARCN), German Center for Lung Research (DZL), Grosshansdorf, Germany
| | | | | | - Sakib Rokadiya
- University College London Hospital, London, United Kingdom
| | | | | | | | - E. Grace Smith
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, Birmingham, United Kingdom
| | - Esther Robinson
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, Birmingham, United Kingdom
| | - Martin Dedicoat
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | | | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Le Hong Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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6
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Narayan A, Salindri AD, Keshavjee S, Muyoyeta M, Velen K, Rueda ZV, Croda J, Charalambous S, García-Basteiro AL, Shenoi SV, Gonçalves CCM, Ferreira da Silva L, Possuelo LG, Aguirre S, Estigarribia G, Sequera G, Grandjean L, Telisinghe L, Herce ME, Dockhorn F, Altice FL, Andrews JR. Prioritizing persons deprived of liberty in global guidelines for tuberculosis preventive treatment. PLoS Med 2023; 20:e1004288. [PMID: 37788448 PMCID: PMC10547494 DOI: 10.1371/journal.pmed.1004288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
In this Policy Forum piece, Aditya Narayan and colleagues discuss the challenges and opportunities for tuberculosis preventive treatment in carceral settings.
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Affiliation(s)
- Aditya Narayan
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Argita D. Salindri
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Salmaan Keshavjee
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Global Health Equity, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Monde Muyoyeta
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka, Zambia
| | - Kavindhran Velen
- Implementation Division, The Aurum Institute, Johannesburg, South Africa
| | - Zulma V. Rueda
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Research Department, School of Medicine, Universidad Pontificia Bolivariana, Medellin, Colombia
| | - Julio Croda
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
- Oswaldo Cruz Foundation, Campo Grande, Brazil
| | - Salome Charalambous
- Implementation Division, The Aurum Institute, Johannesburg, South Africa
- Wits School of Public Health, Johannesburg, South Africa
| | - Alberto L. García-Basteiro
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
- Manhiça Health Research Center, Maputo, Mozambique
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Sheela V. Shenoi
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | | | | | - Lia G. Possuelo
- Department of Life Sciences, Santa Cruz do Sul University, Santa Cruz do Sul, Brazil
| | - Sarita Aguirre
- National Tuberculosis Control Program, Ministry of Public Health and Social Welfare (MSPyBS), Asunción, Paraguay
| | | | - Guillermo Sequera
- Department of Public Health, Facultad de Ciencias Médicas, Universidad Nacional de Asunción, Asunción, Paraguay
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, United Kingdom
| | - Lily Telisinghe
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael E. Herce
- Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka, Zambia
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Fernanda Dockhorn
- Ministry of Health, Health and Environmental Surveillance Secretariat, General Coordination for Tuberculosis, Endemic Mycoses and Non-Tuberculous Mycobacteria Surveillance, Brasília, (DF) Brazil
| | - Frederick L. Altice
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, United States of America
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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8
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Leclerc Q, Clements A, Dunn H, Hatcher J, Lindsay JA, Grandjean L, Knight GM. Quantifying patient- and hospital-level antimicrobial resistance dynamics in Staphylococcus aureus from routinely collected data. J Med Microbiol 2023; 72. [PMID: 37431889 DOI: 10.1099/jmm.0.001724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023] Open
Abstract
Introduction. Antimicrobial resistance (AMR) to all antibiotic classes has been found in the pathogen Staphylococcus aureus. The reported prevalence of these resistances varies, driven by within-host AMR evolution at the patient level, and between-host transmission at the hospital level. Without dense longitudinal sampling, pragmatic analysis of AMR dynamics at multiple levels using routine surveillance data is essential to inform control measures.Gap Statement. The value and limitations of routinely collected hospital data to gain insight into AMR dynamics at the hospital and individual levels simultaneously are unclear.Methodology. We explored S. aureus AMR diversity in 70 000 isolates from a UK paediatric hospital between 2000-2021, using electronic datasets containing multiple routinely collected isolates per patient with phenotypic antibiograms and information on hospitalization and antibiotic consumption.Results. At the hospital level, the proportion of isolates that were meticillin-resistant (MRSA) increased between 2014-2020 from 25-50 %, before sharply decreasing to 30%, likely due to a change in inpatient demographics. Temporal trends in the proportion of isolates resistant to different antibiotics were often correlated in MRSA, but independent in meticillin-susceptible S. aureus. Ciprofloxacin resistance in MRSA decreased from 70-40 % of tested isolates between 2007-2020, likely linked to a national policy to reduce fluoroquinolone usage in 2007. At the patient level, we identified frequent AMR diversity, with 4 % of patients ever positive for S. aureus simultaneously carrying, at some point, multiple isolates with different resistances. We detected changes over time in AMR diversity in 3 % of patients ever positive for S. aureus. These changes equally represented gain and loss of resistance.Conclusion. Within this routinely collected dataset, we found that 65 % of changes in resistance within a patient's S. aureus population could not be explained by antibiotic exposure or between-patient transmission of bacteria, suggesting that within-host evolution via frequent gain and loss of AMR genes may be responsible for these changing AMR profiles. Our study highlights the value of exploring existing routine surveillance data to determine underlying mechanisms of AMR. These insights may substantially improve our understanding of the importance of antibiotic exposure variation, and the success of single S. aureus clones.
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Affiliation(s)
- Quentin Leclerc
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, UK
- Institute for Infection and Immunity, St George's University of London, London, UK
- Present address: Epidemiology and Modelling of Bacterial Escape to Antimicrobials, Institut Pasteur, Paris, France
| | - Alastair Clements
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Helen Dunn
- Great Ormond Street Hospital, London, UK
| | | | - Jodi A Lindsay
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Gwenan M Knight
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, UK
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9
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Charalambous S, Velen K, Rueda Z, Croda J, Herce ME, Shenoi SV, Altice FL, Muyoyeta M, Telisinghe L, Grandjean L, Keshavjee S, Andrews JR. Scaling up evidence-based approaches to tuberculosis screening in prisons. Lancet Public Health 2023; 8:e305-e310. [PMID: 36780916 DOI: 10.1016/s2468-2667(23)00002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/09/2022] [Accepted: 12/20/2022] [Indexed: 02/12/2023]
Abstract
People deprived of liberty have among the highest rates of tuberculosis globally. The incidence of tuberculosis is ten times greater than the incidence of tuberculosis in the general population. In 2021, WHO updated its guidance to strongly recommend systematic screening for tuberculosis in prisons and penitentiary systems. Which case-finding strategies should be adopted, and how to effectively implement these strategies in these settings, will be crucial questions facing ministries of health and justice. In this Viewpoint, we review the evidence base for tuberculosis screening and diagnostic strategies in prisons, highlighting promising approaches and knowledge gaps. Drawing upon past experiences of implementing active case-finding and care programmes in settings with a high tuberculosis burden, we discuss challenges and opportunities for improving the tuberculosis diagnosis and treatment cascade in these settings. We argue that improved transparency in reporting of tuberculosis notifications and outcomes in prisons and renewed focus and resourcing from WHO and other stakeholders will be crucial for building the commitment and investments needed from countries to address the continued crisis of tuberculosis in prisons.
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Affiliation(s)
- Salome Charalambous
- The Aurum Institute, Johannesburg, South Africa; School of Public Health, Wits University, Johannesburg, South Africa; Division of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA.
| | | | - Zulma Rueda
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MT, Canada; School of Medicine, Universidad Pontificia Bolivariana, Medellin, Colombia
| | - Julio Croda
- Division of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA; Departamento de Clínica Médica, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil; Fiocruz Mato Grosso do Sul, Campo Grade, Brazil
| | - Michael E Herce
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Sheela V Shenoi
- Division of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA; Section of Infectious Diseases, School of Medicine, Yale University, New Haven, CT, USA; University of Malaya, Centre of Excellence on Research in AIDS, Kuala Lumpur, Malaysia
| | - Frederick L Altice
- Division of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA; Section of Infectious Diseases, School of Medicine, Yale University, New Haven, CT, USA; University of Malaya, Centre of Excellence on Research in AIDS, Kuala Lumpur, Malaysia
| | - Monde Muyoyeta
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Lily Telisinghe
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, UK
| | - Salmaan Keshavjee
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA; Division of Global Health Equity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
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10
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Wingrove J, Makaronidis J, Prados F, Kanber B, Yiannakas MC, Magee C, Castellazzi G, Grandjean L, Golay X, Tur C, Ciccarelli O, D'Angelo E, Gandini Wheeler-Kingshott CA, Batterham RL. Aberrant olfactory network functional connectivity in people with olfactory dysfunction following COVID-19 infection: an exploratory, observational study. EClinicalMedicine 2023; 58:101883. [PMID: 36883140 PMCID: PMC9980836 DOI: 10.1016/j.eclinm.2023.101883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Olfactory impairments and anosmia from COVID-19 infection typically resolve within 2-4 weeks, although in some cases, symptoms persist longer. COVID-19-related anosmia is associated with olfactory bulb atrophy, however, the impact on cortical structures is relatively unknown, particularly in those with long-term symptoms. METHODS In this exploratory, observational study, we studied individuals who experienced COVID-19-related anosmia, with or without recovered sense of smell, and compared against individuals with no prior COVID-19 infection (confirmed by antibody testing, all vaccine naïve). MRI Imaging was carried out between the 15th July and 17th November 2020 at the Queen Square House Clinical Scanning Facility, UCL, United Kingdom. Using functional magnetic resonance imaging (fMRI) and structural imaging, we assessed differences in functional connectivity (FC) between olfactory regions, whole brain grey matter (GM) cerebral blood flow (CBF) and GM density. FINDINGS Individuals with anosmia showed increased FC between the left orbitofrontal cortex (OFC), visual association cortex and cerebellum and FC reductions between the right OFC and dorsal anterior cingulate cortex compared to those with no prior COVID-19 infection (p < 0.05, from whole brain statistical parametric map analysis). Individuals with anosmia also showed greater CBF in the left insula, hippocampus and ventral posterior cingulate when compared to those with resolved anosmia (p < 0.05, from whole brain statistical parametric map analysis). INTERPRETATION This work describes, for the first time to our knowledge, functional differences within olfactory areas and regions involved in sensory processing and cognitive functioning. This work identifies key areas for further research and potential target sites for therapeutic strategies. FUNDING This study was funded by the National Institute for Health and Care Research and supported by the Queen Square Scanner business case.
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Affiliation(s)
- Jed Wingrove
- Centre for Obesity Research, Department of Medicine, University College London, London, UK
- National Institute for Health and Care Research, Biomedical Research Centre at UCLH and UCL, London, UK
| | - Janine Makaronidis
- Centre for Obesity Research, Department of Medicine, University College London, London, UK
- National Institute for Health and Care Research, Biomedical Research Centre at UCLH and UCL, London, UK
| | - Ferran Prados
- National Institute for Health and Care Research, Biomedical Research Centre at UCLH and UCL, London, UK
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, University College London, London, UK
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Baris Kanber
- National Institute for Health and Care Research, Biomedical Research Centre at UCLH and UCL, London, UK
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, University College London, London, UK
- Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Marios C. Yiannakas
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Cormac Magee
- Centre for Obesity Research, Department of Medicine, University College London, London, UK
- National Institute for Health and Care Research, Biomedical Research Centre at UCLH and UCL, London, UK
| | - Gloria Castellazzi
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, University College London, London, UK
- Brain Connectivity Research Centre, IRCCS Mondino Foundation, Pavia, Italy
| | - Louis Grandjean
- Department of Infection, Immunity & Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Xavier Golay
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, University College London, London, UK
- Department of Brain Repair and Rehabilitation, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Carmen Tur
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Olga Ciccarelli
- National Institute for Health and Care Research, Biomedical Research Centre at UCLH and UCL, London, UK
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Egidio D'Angelo
- Brain Connectivity Research Centre, IRCCS Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Claudia A.M. Gandini Wheeler-Kingshott
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Queen Square Institute of Neurology, University College London, London, UK
- Brain Connectivity Research Centre, IRCCS Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Rachel L. Batterham
- Centre for Obesity Research, Department of Medicine, University College London, London, UK
- National Institute for Health and Care Research, Biomedical Research Centre at UCLH and UCL, London, UK
- Corresponding author. Division of Medicine, University College London, Rayne Building, 5 University Street, London, WC1E 6JF, UK.
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11
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Du DH, Geskus RB, Zhao Y, Codecasa LR, Cirillo DM, van Crevel R, Pascapurnama DN, Chaidir L, Niemann S, Diel R, Omar SV, Grandjean L, Rokadiya S, Ortitz AT, Lân NH, Hà ÐTM, Smith EG, Robinson E, Dedicoat M, Nhat LTH, Thwaites GE, Van LH, Thuong NTT, Walker TM. The effect of M. tuberculosis lineage on clinical phenotype. medRxiv 2023:2023.03.14.23287284. [PMID: 36993190 PMCID: PMC10055556 DOI: 10.1101/2023.03.14.23287284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Eight lineages of Mycobacterium tuberculosis sensu stricto are described. Single-country or small observational data suggest differences in clinical phenotype between lineages. We present strain lineage and clinical phenotype data from 12,246 patients from 3 low-incidence and 5 high-incidence countries. We used multivariable logistic regression to explore the effect of lineage on site of disease and on cavities on chest radiography, given pulmonary TB; multivariable multinomial logistic regression to investigate types of extra-pulmonary TB, given lineage; and accelerated failure time and Cox proportional-hazards models to explore the effect of lineage on time to smear and culture-conversion. Mediation analyses quantified the direct effects of lineage on outcomes. Pulmonary disease was more likely among patients with lineage(L) 2, L3 or L4, than L1 (adjusted odds ratio (aOR) 1.79, (95% confidence interval 1.49-2.15), p<0.001; aOR=1.40(1.09-1.79), p=0.007; aOR=2.04(1.65-2.53), p<0.001, respectively). Among patients with pulmonary TB, those with L1 had greater risk of cavities on chest radiography versus those with L2 (aOR=0.69(0.57-0.83), p<0.001) and L4 strains (aOR=0.73(0.59-0.90), p=0.002). L1 strains were more likely to cause osteomyelitis among patients with extra-pulmonary TB, versus L2-4 (p=0.033, p=0.008 and p=0.049 respectively). Patients with L1 strains showed shorter time-to-sputum smear conversion than for L2. Causal mediation analysis showed the effect of lineage in each case was largely direct. The pattern of clinical phenotypes seen with L1 strains differed from modern lineages (L2-4). This has implications for clinical management and could influence clinical trial selection strategies.
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Affiliation(s)
- Duc Hong Du
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ronald B Geskus
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Luigi Ruffo Codecasa
- Regional TB Reference Centre/Istituto Villa Marelli- ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | | | - Reinout van Crevel
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Lidya Chaidir
- Division of Microbiology, Department of Biomedical Science, Faculty of Medicine, Padjadjaran University, Bandung, West Java, Indonesia
| | - Stefan Niemann
- Research Center Borstel, Germany
- German Center for Infection Research, partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Roland Diel
- University Hospital Schleswig-Holstein, Campus Kiel, Germany
- Lung Clinic Grosshansdorf, Germany, Airway Disease Center North (ARCN), German Center for Lung Research (DZL)
| | | | | | | | | | | | | | - E Grace Smith
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Esther Robinson
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Martin Dedicoat
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
- University Hospitals Birmingham NHS Foundation Trust, UK
| | | | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Le Hong Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy M Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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12
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Leclerc Q, Clements A, Dunn H, Hatcher J, Lindsay JA, Grandjean L, Knight GM. Quantifying patient- and hospital-level antimicrobial resistance dynamics in Staphylococcus aureus from routinely collected data. medRxiv 2023:2023.02.15.23285946. [PMID: 36824943 PMCID: PMC9949191 DOI: 10.1101/2023.02.15.23285946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Antimicrobial resistance (AMR) to all antibiotic classes has been found in the pathogen Staphylococcus aureus . The reported prevalence of these resistances vary, driven by within-host AMR evolution at the patient level, and between-host transmission at the hospital level. Without dense longitudinal sampling, pragmatic analysis of AMR dynamics at multiple levels using routine surveillance data is essential to inform control measures. We explored S. aureus AMR diversity in 70,000 isolates from a UK paediatric hospital between 2000-2020, using electronic datasets containing multiple routinely collected isolates per patient with phenotypic antibiograms, hospitalisation information, and antibiotic consumption. At the hospital-level, the proportion of isolates that were meticillin-resistant (MRSA) increased between 2014-2020 from 25 to 50%, before sharply decreasing to 30%, likely due to a change in inpatient demographics. Temporal trends in the proportion of isolates resistant to different antibiotics were often correlated in MRSA, but independent in meticillin-susceptible S. aureus . Ciprofloxacin resistance in MRSA decreased from 70% to 40% of tested isolates between 2007-2020, likely linked to a national policy to reduce fluoroquinolone usage in 2007. At the patient level, we identified frequent AMR diversity, with 4% of patients ever positive for S. aureus simultaneously carrying, at some point, multiple isolates with different resistances. We detected changes over time in AMR diversity in 3% of patients ever positive for S. aureus . These changes equally represented gain and loss of resistance. Within this routinely collected dataset, we found that 65% of changes in resistance within a patient’s S. aureus population could not be explained by antibiotic exposure or between-patient transmission of bacteria, suggesting that within-host evolution via frequent gain and loss of AMR genes may be responsible for these changing AMR profiles. Our study highlights the value of exploring existing routine surveillance data to determine underlying mechanisms of AMR. These insights may substantially improve our understanding of the importance of antibiotic exposure variation, and the success of single S. aureus clones.
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13
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Wang S, Ge S, Sobkowiak B, Wang L, Grandjean L, Colijn C, Elliott LT. Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix. J Comput Biol 2023; 30:189-203. [PMID: 36374242 DOI: 10.1089/cmb.2022.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Genome-wide association studies (GWASs) are often confounded by population stratification and structure. Linear mixed models (LMMs) are a powerful class of methods for uncovering genetic effects, while controlling for such confounding. LMMs include random effects for a genetic similarity matrix, and they assume that a true genetic similarity matrix is known. However, uncertainty about the phylogenetic structure of a study population may degrade the quality of LMM results. This may happen in bacterial studies in which the number of samples or loci is small, or in studies with low-quality genotyping. In this study, we develop methods for linear mixed models in which the genetic similarity matrix is unknown and is derived from Markov chain Monte Carlo estimates of the phylogeny. We apply our model to a GWAS of multidrug resistance in tuberculosis, and illustrate our methods on simulated data.
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Affiliation(s)
- Shijia Wang
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China
| | - Shufei Ge
- Institute of Mathematical Sciences, ShanghaiTech University, Shanghai, China
| | | | - Liangliang Wang
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, Canada
| | - Louis Grandjean
- Department of Infectious Diseases, University College London, London, United Kingdom
| | - Caroline Colijn
- Department of Mathematics and Simon Fraser University, Burnaby, Canada
| | - Lloyd T Elliott
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, Canada
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14
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Rodriguez J, Alcántara R, Rodríguez J, Vargas J, Roncal E, Antiparra R, Gilman RH, Grandjean L, Moore D, Zimic M, Sheen P. Evaluation of three alternatives cost-effective culture media for Mycobacterium tuberculosis detection and drug susceptibility determination using the microscopic observation drug susceptibility (MODS) assay. Tuberculosis (Edinb) 2022; 137:102273. [PMID: 36403561 PMCID: PMC10022417 DOI: 10.1016/j.tube.2022.102273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/28/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
Tuberculosis phenotypic detection assays are commonly used in low-resource countries. Therefore, reliable detection methods are crucial for early diagnosis and treatment. The microscopic observation drug susceptibility (MODS) assay is a culture-based test to detect Mycobacterium tuberculosis and characterize drug resistance in 7-10 days directly from sputum. The use of MODS is limited by the availability of supplies necessary for preparing the enriched culture. In this study, we evaluated three dry culture media that are easier to produce and cheaper than the standard one used in MODS [1]: an unsterilized powder-based mixed (Boldú et al., 2007) [2], a sterile-lyophilized medium, and (Sengstake et al., 2017) [3] an irradiated powder-based mixed. Mycobacterial growth and drug susceptibility were evaluated for rifampin, isoniazid, and pyrazinamide (PZA). The alternative cultures were evaluated using 282 sputum samples with positive acid-fast smears. No significant differences were observed in the positivity test rates. The positivity time showed high correlations (Rho) of 0.925, 0.889, and 0.866 between each of the three alternative media and the standard. Susceptibility testing for MDR and PZA showed an excellent concordance of 1 compared to the reference test. These results demonstrate that dry culture media are appropriate and advantageous for use in MODS in low-resource settings.
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Affiliation(s)
- Jhojailith Rodriguez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Roberto Alcántara
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, 15023, Peru
| | - Joseline Rodríguez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Johnny Vargas
- Instituto Peruano de Energía Nuclear (IPEN), Lima, 15076, Peru
| | - Elisa Roncal
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Robert H Gilman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, United States
| | - Louis Grandjean
- Department of Infection, Immunity, and Inflammation, Institute of Child Health, London, WC1N 1EH, UK
| | - David Moore
- TB Centre, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru.
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15
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Malik A, Tóth EN, Teng MS, Hurst J, Watt E, Wise L, Kent N, Bartram J, Grandjean L, Dominguez-Villar M, Adams S, Cooper N. Distorted TCR repertoires define multisystem inflammatory syndrome in children. PLoS One 2022; 17:e0274289. [PMID: 36301874 PMCID: PMC9612519 DOI: 10.1371/journal.pone.0274289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/24/2022] [Indexed: 11/08/2022] Open
Abstract
While the majority of children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) display mild or no symptoms, rare individuals develop severe disease presenting with multisystem inflammatory syndrome (MIS-C). The reason for variable clinical manifestations is not understood. Here, we carried out TCR sequencing and conducted comparative analyses of TCR repertoires between children with MIS-C (n = 12) and mild (n = 8) COVID-19. We compared these repertoires with unexposed individuals (samples collected pre-COVID-19 pandemic: n = 8) and with the Adaptive Biotechnologies MIRA dataset, which includes over 135,000 high-confidence SARS-CoV-2-specific TCRs. We show that the repertoires of children with MIS-C are characterised by the expansion of TRBV11-2 chains with high junctional and CDR3 diversity. Moreover, the CDR3 sequences of TRBV11-2 clones shift away from SARS-CoV-2 specific T cell clones, resulting in distorted TCR repertoires. In conclusion, our study reports that CDR3-independent expansion of TRBV11-2+ cells, lacking SARS-CoV-2 specificity, defines MIS-C in children.
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Affiliation(s)
- Amna Malik
- Department of Immunology and Inflammation, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Eszter N. Tóth
- Etcembly Ltd, Magdalen Centre, Robert Robinson Way, Oxford, United Kingdom
| | - Michelle S. Teng
- Etcembly Ltd, Magdalen Centre, Robert Robinson Way, Oxford, United Kingdom
| | - Jacob Hurst
- Etcembly Ltd, Magdalen Centre, Robert Robinson Way, Oxford, United Kingdom
| | - Eleanor Watt
- Molecular and Cellular Immunology Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Lauren Wise
- SIHMDS-Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Natalie Kent
- SIHMDS-Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Jack Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Louis Grandjean
- Paediatric Infectious Diseases, Great Ormond Street Hospital for Children, London, United Kingdom
| | | | - Stuart Adams
- SIHMDS-Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Nichola Cooper
- Department of Immunology and Inflammation, Centre for Haematology, Imperial College London, London, United Kingdom
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Martinez L, Cords O, Liu Q, Acuna-Villaorduna C, Bonnet M, Fox GJ, Carvalho ACC, Chan PC, Croda J, Hill PC, Lopez-Varela E, Donkor S, Fielding K, Graham SM, Espinal MA, Kampmann B, Reingold A, Huerga H, Villalba JA, Grandjean L, Sotgiu G, Egere U, Singh S, Zhu L, Lienhardt C, Denholm JT, Seddon JA, Whalen CC, García-Basteiro AL, Triasih R, Chen C, Singh J, Huang LM, Sharma S, Hannoun D, Del Corral H, Mandalakas AM, Malone LL, Ling DL, Kritski A, Stein CM, Vashishtha R, Boulahbal F, Fang CT, Boom WH, Netto EM, Lemos AC, Hesseling AC, Kay A, Jones-López EC, Horsburgh CR, Lange C, Andrews JR. Infant BCG vaccination and risk of pulmonary and extrapulmonary tuberculosis throughout the life course: a systematic review and individual participant data meta-analysis. Lancet Glob Health 2022; 10:e1307-e1316. [PMID: 35961354 PMCID: PMC10406427 DOI: 10.1016/s2214-109x(22)00283-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND BCG vaccines are given to more than 100 million children every year, but there is considerable debate regarding the effectiveness of BCG vaccination in preventing tuberculosis and death, particularly among older children and adults. We therefore aimed to investigate the age-specific impact of infant BCG vaccination on tuberculosis (pulmonary and extrapulmonary) development and mortality. METHODS In this systematic review and individual participant data meta-analysis, we searched MEDLINE, Web of Science, BIOSIS, and Embase without language restrictions for case-contact cohort studies of tuberculosis contacts published between Jan 1, 1998, and April 7, 2018. Search terms included "mycobacterium tuberculosis", "TB", "tuberculosis", and "contact". We excluded cohort studies that did not provide information on BCG vaccination or were done in countries that did not recommend BCG vaccination at birth. Individual-level participant data for a prespecified list of variables, including the characteristics of the exposed participant (contact), the index case, and the environment, were requested from authors of all eligible studies. Our primary outcome was a composite of prevalent (diagnosed at or within 90 days of baseline) and incident (diagnosed more than 90 days after baseline) tuberculosis in contacts exposed to tuberculosis. Secondary outcomes were pulmonary tuberculosis, extrapulmonary tuberculosis, and mortality. We derived adjusted odds ratios (aORs) using mixed-effects, binary, multivariable logistic regression analyses with study-level random effects, adjusting for the variable of interest, baseline age, sex, previous tuberculosis, and whether data were collected prospectively or retrospectively. We stratified our results by contact age and Mycobacterium tuberculosis infection status. This study is registered with PROSPERO, CRD42020180512. FINDINGS We identified 14 927 original records from our database searches. We included participant-level data from 26 cohort studies done in 17 countries in our meta-analysis. Among 68 552 participants, 1782 (2·6%) developed tuberculosis (1309 [2·6%] of 49 686 BCG-vaccinated participants vs 473 [2·5%] of 18 866 unvaccinated participants). The overall effectiveness of BCG vaccination against all tuberculosis was 18% (aOR 0·82, 95% CI 0·74-0·91). When stratified by age, BCG vaccination only significantly protected against all tuberculosis in children younger than 5 years (aOR 0·63, 95% CI 0·49-0·81). Among contacts with a positive tuberculin skin test or IFNγ release assay, BCG vaccination significantly protected against tuberculosis among all participants (aOR 0·81, 95% CI 0·69-0·96), participants younger than 5 years (0·68, 0·47-0·97), and participants aged 5-9 years (0·62, 0·38-0·99). There was no protective effect among those with negative tests, unless they were younger than 5 years (0·54, 0·32-0·90). 14 cohorts reported on whether tuberculosis was pulmonary or extrapulmonary (n=57 421). BCG vaccination significantly protected against pulmonary tuberculosis among all participants (916 [2·2%] in 41 119 vaccinated participants vs 334 [2·1%] in 16 161 unvaccinated participants; aOR 0·81, 0·70-0·94) but not against extrapulmonary tuberculosis (106 [0·3%] in 40 318 vaccinated participants vs 38 [0·2%] in 15 865 unvaccinated participants; 0·96, 0·65-1·41). In the four studies with mortality data, BCG vaccination was significantly protective against death (0·25, 0·13-0·49). INTERPRETATION Our results suggest that BCG vaccination at birth is effective at preventing tuberculosis in young children but is ineffective in adolescents and adults. Immunoprotection therefore needs to be boosted in older populations. FUNDING National Institutes of Health.
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Affiliation(s)
- Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA, USA.
| | - Olivia Cords
- Center for Animal Disease Modeling and Surveillance, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Qiao Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Carlos Acuna-Villaorduna
- Section of Infectious Diseases, Department of Medicine, Boston University Medical Center, Boston, MA, USA
| | - Maryline Bonnet
- Université de Montpellier, IRD, INSERM, TransVIHMI, Montpellier, France
| | - Greg J Fox
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia; Woolcock Institute of Medical Research, Glebe, NSW, Australia
| | - Anna Cristina C Carvalho
- Laboratory of Innovations in Therapies, Education and Bioproducts, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Pei-Chun Chan
- Division of Chronic Infectious Disease, Taiwan Centers for Disease Control, Taipei, Taiwan; Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Julio Croda
- Oswaldo Cruz Foundation Mato Grosso do Sul, Campo Grande, Brazil; Federal University of Mato Grosso do Sul, Campo Grande, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Philip C Hill
- Centre for International Health, Division of Health Sciences, University of Otago, Dunedin, New Zealand
| | - Elisa Lopez-Varela
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Simon Donkor
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Katherine Fielding
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Stephen M Graham
- Centre for International Health, University of Melbourne Department of Paediatrics and Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Marcos A Espinal
- Communicable Diseases and Environmental Determinants of Health, Pan American Health Organization, Washington, DC, USA
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Banjul, The Gambia
| | - Arthur Reingold
- Division of Epidemiology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Julian A Villalba
- Laboratorio de Tuberculosis, Instituto de Biomedicina, Universidad Central de Venezuela, Caracas, Venezuela; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Louis Grandjean
- Department of Infection, Inflammation and Immunity, Institute of Child Health, University College London, London, UK
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Uzochukwu Egere
- Department of International Public Health, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sarman Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India; Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India; Medical Science and Engineering Research Centre, Indian Institute of Science Education and Research, Bhopal, India
| | - Limei Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Christian Lienhardt
- Université de Montpellier, IRD, INSERM, TransVIHMI, Montpellier, France; Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, VIC, Australia; Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - James A Seddon
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Cape Town, South Africa; Department of Infectious Disease, Imperial College London, London, UK
| | - Christopher C Whalen
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA; Global Health Institute, University of Georgia, Athens, GA, USA
| | - Alberto L García-Basteiro
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Barcelona, Spain
| | - Rina Triasih
- Department of Pediatrics, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada and Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Cheng Chen
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Jitendra Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India; Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India; Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Surendra Sharma
- Department of Molecular Medicine, Jamia Hamdard Institute of Molecular Medicine, New Delhi, India; Department of General Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Medical Sciences, Wardha, India; Department of Respiratory Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Medical Sciences, Wardha, India
| | - Djohar Hannoun
- Department of Information, National Institute of Public Health, Algiers, Algeria
| | - Helena Del Corral
- Grupo de Inmunología Celulare Inmunogenética, Facultad de Medicina, Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia; Grupo de Epidemiologıa, Universidad de Antioquia, Medellin, Colombia
| | - Anna M Mandalakas
- The Global TB Program, Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Division of Clinical Infectious Diseases, Medical Clinic, Research Center Borstel, Borstel, Germany; Tuberculosis Unit, German Center for Infection Research, Borstel, Germany
| | - LaShaunda L Malone
- Uganda-CWRU Research Collaboration, Kampala, Uganda; Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Du-Lin Ling
- Taichung Regional Center, Taiwan Centers for Disease Control, Taipei, Taiwan
| | - Afrânio Kritski
- Tuberculosis Academic Program, Medical School, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Catherine M Stein
- Uganda-CWRU Research Collaboration, Kampala, Uganda; Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH, USA; Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Richa Vashishtha
- Department of Internal Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Fadila Boulahbal
- Groupe de recherche sur la tuberculose latente, Laboratoire National de Référence pour la Tuberculose, Institut Pasteur d'Algérie, Algiers, Algeria
| | - Chi-Tai Fang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - W Henry Boom
- Uganda-CWRU Research Collaboration, Kampala, Uganda; Tuberculosis Research Unit, Case Western Reserve University, Cleveland, OH, USA; Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Eduardo Martins Netto
- Medicine Department, University Hospital Professor Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | - Antonio Carlos Lemos
- Medicine Department, University Hospital Professor Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Cape Town, South Africa
| | - Alexander Kay
- The Global TB Program, Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Edward C Jones-López
- Division of Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - C Robert Horsburgh
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA, USA
| | - Christoph Lange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Division of Clinical Infectious Diseases, Medical Clinic, Research Center Borstel, Borstel, Germany; Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany; Tuberculosis Unit, German Center for Infection Research, Borstel, Germany
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
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Sheen P, Rodriguez J, Alcántara R, Vargas J, Grandjean L, Moore DAJ, Gilman RH, Zimic M. Alternative cost-effective media to facilitate MODS culture for diagnostics of tuberculosis. Tuberculosis (Edinb) 2022; 135:102225. [PMID: 35728429 DOI: 10.1016/j.tube.2022.102225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/08/2022] [Accepted: 06/12/2022] [Indexed: 12/30/2022]
Abstract
Most culture-based methods for tuberculosis diagnosis remain low-cost options for low- and mid-income countries. The MODS culture is a rapid and low-cost assay to diagnose tuberculosis and determine drug susceptibility. However, its implementation is limited due to the low accessibility to supplies required for the enriched medium. In this study, we evaluate two alternative culture media: A powder-based mixed (PM) and a lyophilized media (LM). Catalase, PANTA, and gamma irradiation were evaluated as additions to PM and LM. The culture performance of the alternative media was compared with the standard MODS medium (MM) using Mycobacterium tuberculosis isolates and positive acid-fast smear sputum samples. Overall, no significant difference was observed in the bacterial growth between PM and LM with MM. However, PANTA and gamma irradiation combined reduced bacterial growth significantly in all media variants. A median positivity day of 6 ± 5 days was observed for sputum samples, regardless of the culture medium. The preliminary results show that the two variants culture media have a similar performance to the standard MODS medium. The powder-based media with PANTA (PM_P) showed a time-to-positivity and sensitivity similar to the standard MODS medium. It is the simplest to prepare and does not require any sterilization process.
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Affiliation(s)
- Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, 15102, Peru.
| | - Joseline Rodriguez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Roberto Alcántara
- Biomolecules Laboratory, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, 15023, Peru
| | - Johnny Vargas
- Instituto Peruano de Energía Nuclear (IPEN), Lima, 15076, Peru
| | - Louis Grandjean
- Department of Infection, Immunity, and Inflammation, Institute of Child Health, WC1N 1EH, London, UK
| | - David A J Moore
- TB Centre, London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK
| | - Robert H Gilman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, United States
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
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18
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Torres Ortiz A, Fenn Torrente F, Twigg A, Hatcher J, Saso A, Lam T, Johnson M, Wagstaffe H, Dhillon R, Mai AL, Goldblatt D, Still R, Buckland M, Gilmour K, Grandjean L. The influence of time on the sensitivity of SARS-CoV-2 serological testing. Sci Rep 2022; 12:10517. [PMID: 35732870 PMCID: PMC9214469 DOI: 10.1038/s41598-022-14351-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/06/2022] [Indexed: 11/11/2022] Open
Abstract
Sensitive serological testing is essential to estimate the proportion of the population exposed or infected with SARS-CoV-2, to guide booster vaccination and to select patients for treatment with anti-SARS-CoV-2 antibodies. The performance of serological tests is usually evaluated at 14–21 days post infection. This approach fails to take account of the important effect of time on test performance after infection or exposure has occurred. We performed parallel serological testing using 4 widely used assays (a multiplexed SARS-CoV-2 Nucleoprotein (N), Spike (S) and Receptor Binding Domain assay from Meso Scale Discovery (MSD), the Roche Elecsys-Nucleoprotein (Roche-N) and Spike (Roche-S) assays and the Abbott Nucleoprotein assay (Abbott-N) on serial positive monthly samples collected as part of the Co-STARs study (www.clinicaltrials.gov, NCT04380896) up to 200 days following infection. Our findings demonstrate the considerable effect of time since symptom onset on the diagnostic sensitivity of different assays. Using a time-to-event analysis, we demonstrated that 50% of the Abbott nucleoprotein assays will give a negative result after 175 days (median survival time 95% CI 168–185 days), compared to the better performance over time of the Roche Elecsys nucleoprotein assay (93% survival probability at 200 days, 95% CI 88–97%). Assays targeting the spike protein showed a lower decline over the follow-up period, both for the MSD spike assay (97% survival probability at 200 days, 95% CI 95–99%) and the Roche Elecsys spike assay (95% survival probability at 200 days, 95% CI 93–97%). The best performing quantitative Roche Elecsys Spike assay showed no evidence of waning Spike antibody titers over the 200-day time course of the study. We have shown that compared to other assays evaluated, the Abbott-N assay fails to detect SARS-CoV-2 antibodies as time passes since infection. In contrast the Roche Elecsys Spike Assay and the MSD assay maintained a high sensitivity for the 200-day duration of the study. These limitations of the Abbott assay should be considered when quantifying the immune correlates of protection or the need for SARS-CoV-2 antibody therapy. The high levels of maintained detectable neutralizing spike antibody titers identified by the quantitative Roche Elecsys assay is encouraging and provides further evidence in support of long-lasting SARS-CoV-2 protection following natural infection.
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Affiliation(s)
- Arturo Torres Ortiz
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK.,Department of Infectious Diseases, Imperial College London, Paddington, London, W2 1NY, UK
| | - Fernanda Fenn Torrente
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK.,UCL Medical School, University College London, 74 Huntley Street, London, WC1E 6DE, UK
| | - Adam Twigg
- Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK.,School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 111, Cambridge, CB2 0SP, UK
| | - James Hatcher
- Department of Microbiology, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - Anja Saso
- Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK.,Department of Tropical and Infectious Diseases, LSHTM, Keppel St, Bloomsbury, London, WC1E 7HT, UK.,MRC Gambia at LSHTM, PO Box 273, Fajara, The Gambia
| | - Tanya Lam
- Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - Marina Johnson
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Helen Wagstaffe
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Rishi Dhillon
- Public Health Wales Microbiology, University Hospital of Wales, Heath Park Way, Cardiff, CF14 4XW, UK
| | - Anabelle Lea Mai
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - David Goldblatt
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Rachel Still
- Laboratory Medicine Service Swansea, Bay University Health Board Morriston Hospital, Swansea, SA6 6NL, UK
| | - Matthew Buckland
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - Kimberly Gilmour
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - Louis Grandjean
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK. .,Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK.
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19
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Ellis S, Burleigh A, Way R, Kembou-Ringert J, Masonou T, Gilmour K, Grandjean L, Smith C. Longevity and neutralisation activity of secretory IgA following SARS-CoV-2 infection. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mucosal barrier is a primary defence against inhaled pathogens, comprising secretory antibodies which have the potential to block viral entry and neutralise infection. There is an ongoing need for greater understanding of the mucosal immunity to SARS-CoV-2 infection. In this study, we investigated mucosal IgA through non-invasive saliva sampling of healthcare workers.
A total of 551 saliva samples were collected from staff at Great Ormond Street Children’s Hospital who previously tested positive for COVID-19. Participant metadata included age, gender, ethnicity and symptoms. IgA titres were measured by ELISA against viral antigens spike protein, nucleocapsid protein, and spike receptor-binding domain. SARS-CoV-2 neutralisation was measured using a VERO E6 cell culture infection assay.
We found that approximately 30% of saliva samples contained detectable IgA specific for at least one of the SARS-CoV-2 antigens. IgA levels in saliva decreased with the time post-infection, and were largely undetectable after six months. IgA titres specific to SARS-CoV-2 were lowest in participants over 60 years old. Specific saliva samples were identified which effectively neutralised SARS-CoV-2 virus infection of epithelial cells.
Our results suggest secretory IgA specific to SARS-CoV-2 can be detected in saliva following infection, an accessible sample type for testing, although titres decreased over time. Some saliva samples were able to neutralise SARS-CoV-2 infectivity against cultured epithelial cells. This data could be used to assess the risk of re-infection with SARS-CoV-2, as well as accelerate efforts to develop effective mucosal vaccination with longer lasting protection.
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Affiliation(s)
| | | | - Rosie Way
- University College London, United Kingdom
| | | | | | | | - Louis Grandjean
- Great Ormond Street Hospital, United Kingdom
- University College London, United Kingdom
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21
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Ortiz AT, Torrente FF, Twigg A, Hatcher J, Saso A, Lam T, Johnson M, Wagstaffe H, Dhillon R, Mai AL, Goldblatt D, Still R, Buckland M, Gilmour K, Grandjean L. The Influence of Time on the Sensitivity of SARS-CoV-2 Serological Testing. Res Sq 2022:rs.3.rs-1286644. [PMID: 35194596 PMCID: PMC8863153 DOI: 10.21203/rs.3.rs-1286644/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Background: Serological testing is used to quantify SARS-CoV-2 seroprevalence, guide booster vaccination and select patients for anti-SARS-CoV-2 antibodies therapy. However, our understanding of how serological tests perform as time passes after infection is limited. Methods: Four assays were compared in parallel: 1) the multiplexed spike, nucleoprotein and receptor binding domain Meso Scale Discovery (MSD) assay 2) the Roche Elecsys-Nucleoprotein assay (Roche-N) 3) the Roche Spike assay (Roche-S) and 4) the Abbott Nucleoprotein assay (Abbott-N) on serial positive monthly samples from hospital staff up to 200 days following infection as part of the Co-Stars study. Results: We demonstrate that 50% of the Abbott-N assays give a negative result after 175 days (median survival time 95% CI 168-185 days) while the Roche-N assay (93% survival probability at 200 days, 95% CI 88-97%) maintained seropositivity. The MSD spike (97% survival probability at 200 days, 95% CI 95-99%) and the Roche-S assay (95% survival probability at 200 days, 95% CI 93-97%) also remained seropositive. The best performing quantitative Roche-S assay showed no evidence of waning Spike antibody titres over 200-days. Conclusions: The Abbott-N assay fails to detect SARS-CoV-2 antibodies as time passes since infection. In contrast the Roche and the MSD assays maintained high sensitivity. The limitations of the Abbott assay must be considered in clinical decision making. The long duration of detectable neutralizing spike antibody titres by the quantitative Roche-S assay provides further evidence in support of long-lasting SARS-CoV-2 protection to pre-existing strains of SARS-CoV-2 following natural infection. Trial registration : Co-STARs study was registered with ClinicalTrials.gov on May 8th, 2020, with trial number NCT04380896 (www.clinicaltrials.gov, NCT04380896).
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Affiliation(s)
| | | | | | | | - Anja Saso
- London School of Hygiene & Tropical Medicine
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22
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Awuah A, Zamani A, Tahami F, Davis M, Grandjean L, Buckland M, Gilmour K. T cell responses to SARS-CoV-2 in healthy controls and primary immunodeficiency patients. Clin Exp Immunol 2022; 207:uxac001. [PMID: 35020892 PMCID: PMC8807284 DOI: 10.1093/cei/uxac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/03/2021] [Accepted: 01/05/2022] [Indexed: 01/03/2023] Open
Abstract
Understanding the T cell response to SARS-CoV-2 is key in patients who lack antibody production. We demonstrate the applicability of a functional assay to measure the T cell response in a cohort of patients with immunodeficiency.
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Affiliation(s)
- Arnold Awuah
- Department of Immunology, Great Ormond Street Hospital (GOSH), London, UK
| | - Ava Zamani
- Affiliate of Department of Immunology, Great Ormond Street Hospital (GOSH), London, UK
| | - Fariba Tahami
- Department of Immunology, Great Ormond Street Hospital (GOSH), London, UK
| | - Mark Davis
- Department of Immunology, Great Ormond Street Hospital (GOSH), London, UK
| | - Louis Grandjean
- Department of Infectious Diseases, Great Ormond Street Hospital (GOSH), London, UK
| | - Matthew Buckland
- Department of Immunology, Great Ormond Street Hospital (GOSH), London, UK
| | - Kimberly Gilmour
- Department of Immunology, Great Ormond Street Hospital (GOSH), London, UK
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23
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Boshier FAT, Pang J, Penner J, Parker M, Alders N, Bamford A, Grandjean L, Grunewald S, Hatcher J, Best T, Dalton C, Bynoe PD, Frauenfelder C, Köeglmeier J, Myerson P, Roy S, Williams R, de Silva TI, Goldstein RA, Breuer J. Evolution of viral variants in remdesivir-treated and untreated SARS-CoV-2-infected pediatrics patients. J Med Virol 2022; 94:161-172. [PMID: 34415583 PMCID: PMC8426849 DOI: 10.1002/jmv.27285] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/04/2021] [Accepted: 08/18/2021] [Indexed: 11/07/2022]
Abstract
Detailed information on intrahost viral evolution in SARS-CoV-2 with and without treatment is limited. Sequential viral loads and deep sequencing of SARS-CoV-2 from the upper respiratory tract of nine hospitalized children, three of whom were treated with remdesivir, revealed that remdesivir treatment suppressed viral load in one patient but not in a second infected with an identical strain without any evidence of drug resistance found. Reduced levels of subgenomic RNA during treatment of the second patient, suggest an additional effect of remdesivir on viral replication. Haplotype reconstruction uncovered persistent SARS-CoV-2 variant genotypes in four patients. These likely arose from within-host evolution, although superinfection cannot be excluded in one case. Although our dataset is small, observed sample-to-sample heterogeneity in variant frequencies across four of nine patients suggests the presence of discrete viral populations in the lung with incomplete population sampling in diagnostic swabs. Such compartmentalization could compromise the penetration of remdesivir into the lung, limiting the drugs in vivo efficacy, as has been observed in other lung infections.
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Affiliation(s)
- Florencia A. T. Boshier
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Juanita Pang
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Justin Penner
- Department of Infectious DiseaseGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Matthew Parker
- Department of Infection, Immunity and Cardiovascular Diseases, The Florey InstituteUniversity of SheffieldSheffieldUK
| | - Nele Alders
- Department of Infectious DiseaseGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Alasdair Bamford
- Department of Infectious DiseaseGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Stephanie Grunewald
- Department of Metabolic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - James Hatcher
- Department of MicrobiologyGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Timothy Best
- Department of MicrobiologyGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Caroline Dalton
- Department of PharmacyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Patricia Dyal Bynoe
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Claire Frauenfelder
- Department of EarsNose and Throat, Great Ormond Street Hospital for Children NHS Foundation TrustLondonUK
- Division of SurgeryUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Jutta Köeglmeier
- Department of GastroenterologyGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - Phoebe Myerson
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Rachel Williams
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Thushan I. de Silva
- Department of Infection, Immunity and Cardiovascular Diseases, The Florey InstituteUniversity of SheffieldSheffieldUK
| | | | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- Department of MicrobiologyGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
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24
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Shrestha A, Picoy J, Torres A, Moore DA, Gilman RH, Coronel J, Grandjean L. A case report of transmission and disease caused by Mycobacterium caprae and Mycobacterium bovis in Lima, Peru. BMC Infect Dis 2021; 21:1265. [PMID: 34930187 PMCID: PMC8686613 DOI: 10.1186/s12879-021-06944-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/03/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The Tuberculosis (TB) burden in Peru is significant with respect to both disease morbidity and mortality. Furthermore the recent diversification of farming enterprise to include a wide range of animal species has necessitated the consideration of members of the Mycobacterium Tuberculosis Complex (MTBC) with the potential for zoonotic transmission. M. bovis and M. caprae, a lesser known member of the MTBC exhibit an exceptionally wide host spectrum in animals and are capable of causing disease in humans. M. bovis has a predictable resistance profile which includes resistance to pyrazinamide. Thus, failure to identify M. bovis as the causative agent in reported TB cases leads to higher levels of treatment failure and contributes to the transmission of drug-resistant TB. CASE PRESENTATION Reported here are the clinical presentations, investigations and treatment histories of two patients identified from a population level genotyping study in Lima, Peru that were at the time of treatment thought to be M. tuberculosis patients but in retrospect were spectated using whole genome sequencing as M. caprae and M. Bovis. CONCLUSIONS The cases reported here constitute convincing evidence that M. caprae and M. bovis are causative agents of TB infection in humans in Peru and underscore the importance of species-level MTBC member identification to effectively control and treat zoonotic TB. Furthermore these cases highlight the challenges of using clinical risk factors to identify cases of zoonotic TB in humans as their clinical presentation and transmission history is often difficult to distinguish from anthroponotic TB.
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Affiliation(s)
- Amber Shrestha
- grid.420468.cDepartment of Infectious Disease, Great Ormond Street Hospital for Children, London, WC1N 3JH UK
| | - Janeth Picoy
- Department of Infectious Disease, Diresa Callao Jr, Colina #879, Bellavista, 07016 Lima, Peru
| | - Arturo Torres
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, South Kensington, London, SW7 2AZ UK
| | - David A. Moore
- grid.8991.90000 0004 0425 469XTB Centre, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Robert H. Gilman
- grid.11100.310000 0001 0673 9488Laboratorio de Tuberculosis, Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru ,grid.21107.350000 0001 2171 9311Department of International Health, School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Jorge Coronel
- grid.11100.310000 0001 0673 9488Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia: Lima, Lima, Peru
| | - Louis Grandjean
- Department of Infectious Disease, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK. .,University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK.
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25
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Torres Ortiz A, Coronel J, Vidal JR, Bonilla C, Moore DAJ, Gilman RH, Balloux F, Kon OM, Didelot X, Grandjean L. Genomic signatures of pre-resistance in Mycobacterium tuberculosis. Nat Commun 2021; 12:7312. [PMID: 34911948 PMCID: PMC8674244 DOI: 10.1038/s41467-021-27616-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022] Open
Abstract
Recent advances in bacterial whole-genome sequencing have resulted in a comprehensive catalog of antibiotic resistance genomic signatures in Mycobacterium tuberculosis. With a view to pre-empt the emergence of resistance, we hypothesized that pre-existing polymorphisms in susceptible genotypes (pre-resistance mutations) could increase the risk of becoming resistant in the future. We sequenced whole genomes from 3135 isolates sampled over a 17-year period. After reconstructing ancestral genomes on time-calibrated phylogenetic trees, we developed and applied a genome-wide survival analysis to determine the hazard of resistance acquisition. We demonstrate that M. tuberculosis lineage 2 has a higher risk of acquiring resistance than lineage 4, and estimate a higher hazard of rifampicin resistance evolution following isoniazid mono-resistance. Furthermore, we describe loci and genomic polymorphisms associated with a higher risk of resistance acquisition. Identifying markers of future antibiotic resistance could enable targeted therapy to prevent resistance emergence in M. tuberculosis and other pathogens.
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Affiliation(s)
- Arturo Torres Ortiz
- grid.7445.20000 0001 2113 8111Imperial College London, Department of Infectious Diseases, London, UK
| | - Jorge Coronel
- grid.11100.310000 0001 0673 9488Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Julia Rios Vidal
- grid.419858.90000 0004 0371 3700Unidad Técnica de Tuberculosis MDR, Ministerio de Salud, Lima, Perú
| | - Cesar Bonilla
- grid.419858.90000 0004 0371 3700Unidad Técnica de Tuberculosis MDR, Ministerio de Salud, Lima, Perú ,grid.441740.20000 0004 0542 2122Universidad Privada San Juan Bautista, Lima, Perú
| | - David A. J. Moore
- grid.8991.90000 0004 0425 469XLondon School of Hygiene and Tropical Medicine, London, UK
| | - Robert H. Gilman
- grid.21107.350000 0001 2171 9311Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | | | - Onn Min Kon
- grid.7445.20000 0001 2113 8111Respiratory Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Xavier Didelot
- grid.7372.10000 0000 8809 1613University of Warwick, School of Life Sciences and Department of Statistics, Warwick, UK
| | - Louis Grandjean
- Imperial College London, Department of Infectious Diseases, London, UK. .,UCL Department of Infection, Institute of Child Health, London, UK.
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26
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Grandjean L, Saso A, Ortiz AT, Lam T, Hatcher J, Thistlethwayte R, Harris M, Best T, Johnson M, Wagstaffe H, Ralph E, Mai A, Colijn C, Breuer J, Buckland M, Gilmour K, Goldblatt D. Long-Term Persistence of Spike Antibody and Predictive Modeling of Antibody Dynamics Following Infection with SARS-CoV-2. Clin Infect Dis 2021; 74:1220-1229. [PMID: 34218284 PMCID: PMC8994590 DOI: 10.1093/cid/ciab607] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 01/08/2023] Open
Abstract
Background Antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to neutralize the virus in vitro and prevent disease in animal challenge models on reexposure. However, the current understanding of SARS-CoV-2 humoral dynamics and longevity is conflicting. Methods The COVID-19 Staff Testing of Antibody Responses Study (Co-Stars) prospectively enrolled 3679 healthcare workers to comprehensively characterize the kinetics of SARS-CoV-2 spike protein (S), receptor-binding domain, and nucleoprotein (N) antibodies in parallel. Participants screening seropositive had serial monthly serological testing for a maximum of 7 months with the Meso Scale Discovery Assay. Survival analysis determined the proportion of seroreversion, while 2 hierarchical gamma models predicted the upper and lower bounds of long-term antibody trajectory. Results A total of 1163 monthly samples were provided from 349 seropositive participants. At 200 days after symptoms, >95% of participants had detectable S antibodies, compared with 75% with detectable N antibodies. S antibody was predicted to remain detectable in 95% of participants until 465 days (95% confidence interval, 370–575 days) using a “continuous-decay” model and indefinitely using a “decay-to-plateau” model to account for antibody secretion by long-lived plasma cells. S-antibody titers were correlated strongly with surrogate neutralization in vitro (R2 = 0.72). N antibodies, however, decayed rapidly with a half-life of 60 days (95% confidence interval, 52–68 days). Conclusions The Co-Stars data presented here provide evidence for long-term persistence of neutralizing S antibodies. This has important implications for the duration of functional immunity after SARS-CoV-2 infection. In contrast, the rapid decay of N antibodies must be considered in future seroprevalence studies and public health decision-making. This is the first study to establish a mathematical framework capable of predicting long-term humoral dynamics after SARS-CoV-2 infection. Clinical Trials Registration NCT04380896.
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Affiliation(s)
- Louis Grandjean
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, UK.,Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London
| | - Anja Saso
- Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London.,Department of Tropical and Infectious diseases; LSHTM, Keppel St, Bloomsbury, London.,MRC Gambia at LSHTM, PO Box 273, Fajara, The Gambia
| | - Arturo Torres Ortiz
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, UK.,Department of Medicine, Imperial College, Paddington, London
| | - Tanya Lam
- Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London
| | - James Hatcher
- Department of Microbiology, Great Ormond Street Hospital, Great Ormond Street, London
| | | | - Mark Harris
- Quality Improvement, Great Ormond Street Hospital, Great Ormond Street, London
| | - Timothy Best
- Department of Medicine, Imperial College, Paddington, London
| | - Marina Johnson
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, UK
| | - Helen Wagstaffe
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, UK
| | - Elizabeth Ralph
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London
| | - Annabelle Mai
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Vancouver, British Colombia, Canada
| | - Judith Breuer
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, UK
| | - Matthew Buckland
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London
| | - Kimberly Gilmour
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London
| | - David Goldblatt
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, UK
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27
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Bui DP, Chandran SS, Oren E, Brown HE, Harris RB, Knight GM, Grandjean L. Community transmission of multidrug-resistant tuberculosis is associated with activity space overlap in Lima, Peru. BMC Infect Dis 2021; 21:275. [PMID: 33736597 PMCID: PMC7977184 DOI: 10.1186/s12879-021-05953-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background Transmission of multidrug-resistant tuberculosis (MDRTB) requires spatial proximity between infectious cases and susceptible persons. We assess activity space overlap among MDRTB cases and community controls to identify potential areas of transmission. Methods We enrolled 35 MDRTB cases and 64 TB-free community controls in Lima, Peru. Cases were whole genome sequenced and strain clustering was used as a proxy for transmission. GPS data were gathered from participants over seven days. Kernel density estimation methods were used to construct activity spaces from GPS locations and the utilization distribution overlap index (UDOI) was used to quantify activity space overlap. Results Activity spaces of controls (median = 35.6 km2, IQR = 25.1–54) were larger than cases (median = 21.3 km2, IQR = 17.9–48.6) (P = 0.02). Activity space overlap was greatest among genetically clustered cases (mean UDOI = 0.63, sd = 0.67) and lowest between cases and controls (mean UDOI = 0.13, sd = 0.28). UDOI was positively associated with genetic similarity of MDRTB strains between case pairs (P < 0.001). The odds of two cases being genetically clustered increased by 22% per 0.10 increase in UDOI (OR = 1.22, CI = 1.09–1.36, P < 0.001). Conclusions Activity space overlap is associated with MDRTB clustering. MDRTB transmission may be occurring in small, overlapping activity spaces in community settings. GPS studies may be useful in identifying new areas of MDRTB transmission. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05953-8.
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Affiliation(s)
- David P Bui
- Department of Epidemiology and Biostatistics, The University of Arizona, Mel and Enid Zuckerman College of Public Health, 1295 N Martin Ave., Tucson, AZ, 85724, USA
| | - Shruthi S Chandran
- The London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Eyal Oren
- San Diego State University, School of Public Health, 5500 Campanile Drive, San Diego, California, 92182, USA
| | - Heidi E Brown
- Department of Epidemiology and Biostatistics, The University of Arizona, Mel and Enid Zuckerman College of Public Health, 1295 N Martin Ave., Tucson, AZ, 85724, USA
| | - Robin B Harris
- Department of Epidemiology and Biostatistics, The University of Arizona, Mel and Enid Zuckerman College of Public Health, 1295 N Martin Ave., Tucson, AZ, 85724, USA
| | - Gwenan M Knight
- The London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Louis Grandjean
- Universidad Peruana Cayetano Heredia, Lima, Peru. .,Institute of Child Health, University College London, 30 Guilford Street, London, UK.
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28
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Woodman M, Grandjean L. Detecting Tuberculosis in Prisons: Switching Off the Disease at Its Source. Clin Infect Dis 2021; 72:778-779. [PMID: 32064517 PMCID: PMC7935381 DOI: 10.1093/cid/ciaa139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marc Woodman
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
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29
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Abstract
Many studies have demonstrated that prisons are hotspots of tuberculosis disease and transmission. Despite this, it remains unclear which interventions are most effective at controlling tuberculosis in prisons. The objective was to determine the study designs used to investigate tuberculosis control in prisons, and the efficacy of interventions undertaken. This systematic review included published studies which had the aim of reducing TB incidence or prevalence, or increasing the number of people screened for active pulmonary tuberculosis in incarcerated populations. 2,429 records were identified, 178 full-text articles were screened, and 17 studies included. The majority of reports were before/after or prospective non-comparative studies. The median study duration was 23 months (range 5-144). The most common intervention was the introduction of active case finding (10/17 studies) but the timing and methods varied. Comparable pre- and post intervention outcome values were infrequently reported; therefore, it was not possible to quantify the efficacy of interventions. Data from studies of tuberculosis control in prisons is limited by a lack of: controlled interventions, reporting of pre-intervention methods, and comparable pre- and post-intervention outcomes. Prospective comparative trials of adequate duration to determine trends in incidence are necessary to understand which interventions are effective in prisons.
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Affiliation(s)
- Ilsa Louisa Haeusler
- University College London Great Ormond Street Institute of Child Health, London, UK
| | - Arturo Torres-Ortiz
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
| | - Louis Grandjean
- University College London Great Ormond Street Institute of Child Health, London, UK.,Imperial College London, Department of Infectious Disease Epidemiology, London, UK.,Laboratorio de Bioinformatica y Biologia Molecular, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
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30
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Doykov I, Hällqvist J, Gilmour KC, Grandjean L, Mills K, Heywood WE. 'The long tail of Covid-19' - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients. F1000Res 2021; 9:1349. [PMID: 33391730 PMCID: PMC7745182 DOI: 10.12688/f1000research.27287.2] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
'Long Covid', or medical complications associated with post SARS-CoV-2 infection, is a significant post-viral complication that is being more and more commonly reported in patients. Therefore, there is an increasing need to understand the disease mechanisms, identify drug targets and inflammatory processes associated with a SARS-CoV-2 infection. To address this need, we created a targeted mass spectrometry based multiplexed panel of 96 immune response associated proteins. We applied the multiplex assay to a cohort of serum samples from asymptomatic and moderately affected patients. All patients had tested positive for a SARS-CoV-2 infection by PCR and were determined to be subsequently positive for antibodies. Even 40-60 days post-viral infection, we observed a significant remaining inflammatory response in all patients. Proteins that were still affected were associated with the anti-inflammatory response and mitochondrial stress. This indicates that biochemical and inflammatory pathways within the body can remain perturbed long after SARS-CoV-2 infections have subsided even in asymptomatic and moderately affected patients.
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Affiliation(s)
- Ivan Doykov
- Translational Mass Spectrometry Research Group, University College London Institute of Child Health, London, UK
| | - Jenny Hällqvist
- Translational Mass Spectrometry Research Group, University College London Institute of Child Health, London, UK,Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| | - Kimberly C. Gilmour
- Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Louis Grandjean
- Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Kevin Mills
- Translational Mass Spectrometry Research Group, University College London Institute of Child Health, London, UK
| | - Wendy E. Heywood
- Translational Mass Spectrometry Research Group, University College London Institute of Child Health, London, UK,
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31
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Doykov I, Hällqvist J, Gilmour KC, Grandjean L, Mills K, Heywood WE. 'The long tail of Covid-19' - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients. F1000Res 2021; 9:1349. [PMID: 33391730 PMCID: PMC7745182 DOI: 10.12688/f1000research.27287.1] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 12/14/2022] Open
Abstract
'Long Covid', or medical complications associated with post SARS-CoV-2 infection, is a significant post-viral complication that is being more and more commonly reported in patients. Therefore, there is an increasing need to understand the disease mechanisms, identify drug targets and inflammatory processes associated with a SARS-CoV-2 infection. To address this need, we created a targeted mass spectrometry based multiplexed panel of 96 immune response associated proteins. We applied the multiplex assay to a cohort of serum samples from asymptomatic and moderately affected patients. All patients had tested positive for a SARS-CoV-2 infection by PCR and were determined to be subsequently positive for antibodies. Even 40-60 days post-viral infection, we observed a significant remaining inflammatory response in all patients. Proteins that were still affected were associated with the anti-inflammatory response and mitochondrial stress. This indicates that biochemical and inflammatory pathways within the body can remain perturbed long after SARS-CoV-2 infections have subsided even in asymptomatic and moderately affected patients.
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Affiliation(s)
- Ivan Doykov
- Translational Mass Spectrometry Research Group, University College London Institute of Child Health, London, UK
| | - Jenny Hällqvist
- Translational Mass Spectrometry Research Group, University College London Institute of Child Health, London, UK,Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| | - Kimberly C. Gilmour
- Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Louis Grandjean
- Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Kevin Mills
- Translational Mass Spectrometry Research Group, University College London Institute of Child Health, London, UK
| | - Wendy E. Heywood
- Translational Mass Spectrometry Research Group, University College London Institute of Child Health, London, UK,
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Goldblatt D, Johnson M, Falup-Pecurariu O, Ivaskeviciene I, Spoulou V, Tamm E, Wagner M, Zar HJ, Bleotu L, Ivaskevicius R, Papadatou I, Jõgi P, Lischka J, Franckling-Smith Z, Isarova D, Grandjean L, Zavadska D. Cross-sectional prevalence of SARS-CoV-2 antibodies in healthcare workers in paediatric facilities in eight countries. J Hosp Infect 2021; 110:60-66. [PMID: 33422589 PMCID: PMC7836791 DOI: 10.1016/j.jhin.2020.12.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 12/11/2022]
Abstract
Background Healthcare workers (HCWs) have been disproportionately affected by coronavirus disease 2019 (COVID-19), which may be driven, in part, by nosocomial exposure. If HCW exposure is predominantly nosocomial, HCWs in paediatric facilities, where few patients are admitted with COVID-19, may lack antibodies to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and be at increased risk during the current resurgence. Aim To compare the seroprevalence of SARS-CoV-2 amongst HCWs in paediatric facilities in seven European countries and South Africa (N=8). Methods All categories of paediatric HCWs were invited to participate in the study, irrespective of previous symptoms. A single blood sample was taken and data about previous symptoms were documented. Serum was shipped to a central laboratory in London where SARS-CoV-2 immunoglobulin G was measured. Findings In total, 4114 HCWs were recruited between 1st May and mid-July 2020. The range of seroprevalence was 0–16.93%. The highest seroprevalence was found in London (16.93%), followed by Cape Town, South Africa (10.36%). There were no positive HCWs in the Austrian, Estonian and Latvian cohorts; 2/300 [0.66%, 95% confidence interval (CI) 0.18–2.4] HCWs tested positive in Lithuania; 1/124 (0.81%, 95% CI 0.14–4.3) HCWs tested positive in Romania; and 1/76 (1.3%, 95% CI 0.23–7.0) HCWs tested positive in Greece. Conclusion Overall seroprevalence amongst paediatric HCWs is similar to their national populations and linked to the national COVID-19 burden. Staff working in paediatric facilities in low-burden countries have very low seroprevalence rates and thus are likely to be susceptible to COVID-19. Their susceptibility to infection may affect their ability to provide care in the face of increasing cases of COVID-19, and this highlights the need for appropriate preventative strategies in paediatric healthcare settings.
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Affiliation(s)
- D Goldblatt
- Great Ormond Street Institute of Child Health, University College London, London, UK; Great Ormond Street Children's Hospital NHS Foundation Trust, London, UK.
| | - M Johnson
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - O Falup-Pecurariu
- Children's Clinic Hospital, Faculty of Medicine, Transilvania University, Brasov, Romania
| | - I Ivaskeviciene
- Paediatric Centre, Institute of Clinical Medicine, Vilnius University, Vilnius, Lithuania
| | - V Spoulou
- 'Agia Sophia' Children's Hospital of Athens, Athens, Greece
| | - E Tamm
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
| | - M Wagner
- Division of Neonatology, Paediatric Intensive Care and Neuropaediatrics, Department of Paediatrics, Comprehensive Centre for Paediatrics, Medical University of Vienna, Vienna, Austria
| | - H J Zar
- Department of Paediatrics and Child Health, Red Cross Children's Hospital, and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - L Bleotu
- Children's Clinic Hospital, Faculty of Medicine, Transilvania University, Brasov, Romania
| | - R Ivaskevicius
- Paediatric Centre, Institute of Clinical Medicine, Vilnius University, Vilnius, Lithuania
| | - I Papadatou
- Immunobiology and Vaccinology Research Laboratory, National and Kapodistrian University of Athens, Athens, Greece
| | - P Jõgi
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
| | - J Lischka
- Clinical Division of Paediatric Pulmonology, Allergology and Endocrinology, Department of Paediatrics and Adolescent Medicine, Comprehensive Centre for Paediatrics, Medical University of Vienna, Vienna, Austria
| | - Z Franckling-Smith
- Department of Paediatrics and Child Health, Red Cross Children's Hospital, and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - D Isarova
- Children's Clinical University Hospital, Riga, Latvia
| | - L Grandjean
- Great Ormond Street Institute of Child Health, University College London, London, UK; Great Ormond Street Children's Hospital NHS Foundation Trust, London, UK
| | - D Zavadska
- Children's Clinical University Hospital, Riga, Latvia
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33
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Huang CC, Becerra MC, Calderon R, Contreras C, Galea J, Grandjean L, Lecca L, Yataco R, Zhang Z, Murray M. Isoniazid Preventive Therapy in Contacts of Multidrug-Resistant Tuberculosis. Am J Respir Crit Care Med 2020; 202:1159-1168. [PMID: 32551948 DOI: 10.1164/rccm.201908-1576oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rationale: The World Health Organization recommends the use of isoniazid (INH) alone or in combination with rifapentine to treat latent tuberculosis infections. The recent rise of drug-resistant tuberculosis has complicated the choice of treatment regimen for latent tuberculosis infection.Objectives: To evaluate the effects of INH preventive therapy on the contacts of patients with multidrug-resistant tuberculosis.Methods: In a prospective cohort study conducted between September 2009 and August 2012, we identified 4,500 index patients with tuberculosis and 14,044 tuberculosis-exposed household contacts who we followed for 1 year for the occurrence of incident tuberculosis disease. Although Peruvian national guidelines specify that INH preventive therapy should be provided to contacts aged 19 years old or younger, only half this group received INH preventive therapy.Measurements and Main Results: Among 4,216 contacts under 19 years of age, 2,106 contacts (50%) initiated INH preventive therapy at enrollment. The protective effect of INH was more extreme in contacts exposed to drug-sensitive tuberculosis (adjusted hazard ratio, 0.30; 95% confidence interval, 0.18-0.48) and to multidrug-resistant tuberculosis (adjusted hazard ratio, 0.19; 95% confidence interval, 0.05-0.66) compared with those exposed to mono-INH-resistant tuberculosis (adjusted hazard ratio, 0.80; 95% confidence interval, 0.23-2.80). In the second independent study, tuberculosis occurred in none of the 76 household contacts who received INH preventive therapy compared with 3% (8 of 273) of those who did not.Conclusions: Household contacts who received INH preventive therapy had a lower incidence of tuberculosis disease even when they had been exposed to an index patient with multidrug-resistant tuberculosis. INH may have a role in the management of latent multidrug-resistant tuberculosis infection.
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Affiliation(s)
- Chuan-Chin Huang
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | - Mercedes C Becerra
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | - Jerome Galea
- School of Social Work, University of South Florida, Tampa, Florida
| | - Louis Grandjean
- Wellcome Centre for Clinical Tropical Medicine, Imperial College London, London, United Kingdom.,Universidad Peruana Cayetano Heredia, Lima, Peru; and.,TB Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Leonid Lecca
- Partners in Health-Socios En Salud Sucursal, Lima, Peru
| | - Rosa Yataco
- Partners in Health-Socios En Salud Sucursal, Lima, Peru
| | - Zibiao Zhang
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | - Megan Murray
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
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Johnson M, Wagstaffe HR, Gilmour KC, Mai AL, Lewis J, Hunt A, Sirr J, Bengt C, Grandjean L, Goldblatt D. Evaluation of a novel multiplexed assay for determining IgG levels and functional activity to SARS-CoV-2. J Clin Virol 2020; 130:104572. [PMID: 32769024 PMCID: PMC7396134 DOI: 10.1016/j.jcv.2020.104572] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND The emergence of SARS-CoV-2 has led to the development of serological assays that could aid in an understanding of the burden of COVID-19 disease. Many available tests lack rigorous evaluation and therefore results may be misleading. OBJECTIVES The aim of this study was to assess the performance of a novel multiplexed immunoassay for the simultaneous detection of antibodies against SARS-CoV-2 trimeric spike (S), spike receptor binding domain (RBD), spike N terminal domain and nucleocapsid antigen and a novel pseudo-neutralisation assay. METHODS A multiplexed solid-phase chemiluminescence assay (Meso Scale Discovery) was evaluated for the simultaneous detection of IgG binding to four SARS-CoV-2 antigens and the quantification of antibody-induced ACE-2 binding inhibition (pseudo-neutralisation assay). Sensitivity was evaluated with a total of 196 COVID-19 serum samples (169 confirmed PCR positive and 27 anti-nucleocapsid IgG positive) from individuals with mild symptomatic or asymptomatic disease. Specificity was evaluated with 194 control serum samples collected from adults prior to December 2019. RESULTS The specificity and sensitivity of the binding IgG assay was highest for S protein with a specificity of 97.4 % and sensitivity of 96.2 % for samples taken 14 days and 97.9 % for samples taken 21 days following the onset of symptoms. IgG concentration to S and RBD correlated strongly with percentage inhibition measured by the pseudo-neutralisation assay. CONCLUSION Excellent sensitivity for IgG detection was obtained over 14 days since onset of symptoms for three SARS-CoV-2 antigens (S, RBD and N) in this multiplexed assay which can also measure antibody functionality.
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Affiliation(s)
- Marina Johnson
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Helen R Wagstaffe
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Kimberly C Gilmour
- Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Annabelle Lea Mai
- Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Joanna Lewis
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Adam Hunt
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Jake Sirr
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Christopher Bengt
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK
| | - Louis Grandjean
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK; Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1 EH, UK; Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK.
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35
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Orf K, Rogosic S, Dexter D, Ancliff P, Badle S, Brierley J, Cheng D, Dalton C, Dixon G, Du Pré P, Grandjean L, Ghorashian S, Mittal P, O'Connor D, Pavasovic V, Rao A, Samarasinghe S, Vora A, Bamford A, Bartram J. Remdesivir during induction chemotherapy for newly diagnosed paediatric acute lymphoblastic leukaemia with concomitant SARS-CoV-2 infection. Br J Haematol 2020; 190:e274-e276. [PMID: 32652563 PMCID: PMC7404383 DOI: 10.1111/bjh.17014] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 07/08/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Katharine Orf
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Srdan Rogosic
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Daniel Dexter
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Phil Ancliff
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Saket Badle
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Joe Brierley
- Paediatric Bioethics CentreGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Danny Cheng
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Caroline Dalton
- Department of PharmacyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Garth Dixon
- Department of MicrobiologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Pascale Du Pré
- Department of Paediatric Intensive CareGreat Ormond Street Hospital for Children NHS TrustvLondonUK
| | - Louis Grandjean
- Department of Infectious DiseasesGreat Ormond Street Hospital for Children NHS TrustLondonUK
- UCL Great Ormond Street Institute of Child HealthLondonUK
| | - Sara Ghorashian
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Prabal Mittal
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - David O'Connor
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
- UCL Cancer InstituteLondonUK
| | - Vesna Pavasovic
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Anupama Rao
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Sujith Samarasinghe
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Ajay Vora
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
| | - Alasdair Bamford
- Department of Infectious DiseasesGreat Ormond Street Hospital for Children NHS TrustLondonUK
- UCL Great Ormond Street Institute of Child HealthLondonUK
| | - Jack Bartram
- Department of HaematologyGreat Ormond Street Hospital for Children NHS TrustLondonUK
- UCL Great Ormond Street Institute of Child HealthLondonUK
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36
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Grandjean L, Monteserin J, Gilman R, Pauschardt J, Rokadiya S, Bonilla C, Ritacco V, Vidal JR, Parkhill J, Peacock S, Moore DA, Balloux F. Association between bacterial homoplastic variants and radiological pathology in tuberculosis. Thorax 2020; 75:584-591. [PMID: 32546574 PMCID: PMC7361023 DOI: 10.1136/thoraxjnl-2019-213281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Understanding how pathogen genetic factors contribute to pathology in TB could enable tailored treatments to the most pathogenic and infectious strains. New strategies are needed to control drug-resistant TB, which requires longer and costlier treatment. We hypothesised that the severity of radiological pathology on the chest radiograph in TB disease was associated with variants arising independently, multiple times (homoplasies) in the Mycobacterium tuberculosis genome. METHODS We performed whole genome sequencing (Illumina HiSeq2000 platform) on M. tuberculosis isolates from 103 patients with drug-resistant TB in Lima between 2010 and 2013. Variables including age, sex, HIV status, previous TB disease and the percentage of lung involvement on the pretreatment chest radiograph were collected from health posts of the national TB programme. Genomic variants were identified using standard pipelines. RESULTS Two mutations were significantly associated with more widespread radiological pathology in a multivariable regression model controlling for confounding variables (Rv2828c.141, RR 1.3, 95% CI 1.21 to 1.39, p<0.01; rpoC.1040 95% CI 1.77 to 2.16, RR 1.9, p<0.01). The rpoB.450 mutation was associated with less extensive radiological pathology (RR 0.81, 95% CI 0.69 to 0.94, p=0.03), suggestive of a bacterial fitness cost for this mutation in vivo. Patients with a previous episode of TB disease and those between 10 and 30 years of age also had significantly increased radiological pathology. CONCLUSIONS This study is the first to compare the M. tuberculosis genome to radiological pathology on the chest radiograph. We identified two variants significantly positively associated with more widespread radiological pathology and one with reduced pathology. Prospective studies are warranted to determine whether mutations associated with increased pathology also predict the spread of drug-resistant TB.
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Affiliation(s)
- Louis Grandjean
- Department of Medicine, Imperial College London, London, UK .,Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru.,Institute of Child Health, UCL Division of Infection and Immunity, London, UK
| | - Joha Monteserin
- Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS, Administración Nacional de Laboratorios e Institutos de Salud Dr Carlos G Malbrán, Buenos Aires, Argentina
| | - Robert Gilman
- Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru.,Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Julia Pauschardt
- Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru
| | - Sakib Rokadiya
- Faculty of Medicine, Imperial College London, London, UK
| | - Cesar Bonilla
- Unidad Tecnica de Tuberculosis MDR, Ministerio de Salud, Lima, Peru
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS, Administración Nacional de Laboratorios e Institutos de Salud Dr Carlos G Malbrán, Buenos Aires, Argentina
| | - Julia Rios Vidal
- Unidad Tecnica de Tuberculosis MDR, Ministerio de Salud, Lima, Peru
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sharon Peacock
- Faculty of Medicine, University of Cambridge, Cambridge, UK
| | - David Aj Moore
- TB Centre, London School of Hygiene and Tropical Medicine, London, UK
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Handel A, Martinez L, Sekandi JN, Bellan SE, Zhu L, Chen C, Liu Q, Donkor S, Sutherland J, Hill PC, Gilman RH, Grandjean L, Whalen CC. Evidence for supercoughers in an analysis of six tuberculosis cohorts from China, Peru, The Gambia and Uganda. Int J Tuberc Lung Dis 2020; 23:1286-1292. [PMID: 31931913 DOI: 10.5588/ijtld.18.0819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: It is very difficult to observe tuberculosis (TB) transmission chains and thus, identify superspreaders. We investigate cough duration as a proxy measure of transmission to assess the presence of potential TB superspreaders.DESIGN: We analyzed six studies from China, Peru, The Gambia and Uganda, and determined the distribution of cough duration and compared it with several theoretical distributions. To determine factors associated with cough duration, we used linear regression and boosted regression trees to examine the predictive power of patient, clinical and environmental characteristics.RESULTS: We found within-study heterogeneity in cough duration and strong similarities across studies. Approximately 20% of patients contributed 50% of total cough days, and around 50% of patients contributed 80% of total cough days. The cough duration distribution suggested an initially increasing, and subsequently, decreasing hazard of diagnosis. While some of the exposure variables showed statistically significant associations with cough duration, none of them had a strong effect. Multivariate analyses of different model types did not produce a model that had good predictive power.CONCLUSION: We found consistent evidence for the presence of supercoughers, but no characteristics predictive of such individuals.
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Affiliation(s)
- A Handel
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - L Martinez
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - J N Sekandi
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - S E Bellan
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - L Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, People's Republic of China
| | - C Chen
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, People's Republic of China
| | - Q Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, People's Republic of China
| | - S Donkor
- Vaccines and Immunity, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - J Sutherland
- Vaccines and Immunity, Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - P C Hill
- Centre for International Health, School of Medicine, University of Otago, Dunedin, New Zealand
| | - R H Gilman
- Universidad Peruana Cayetano Heredia, Lima, Peru, Johns Hopkins Bloomberg School of Public Health, Department of International Health, Baltimore, MD, USA
| | - L Grandjean
- Universidad Peruana Cayetano Heredia, Lima, Peru, Wellcome Centre for Clinical Tropical Medicine, Imperial College London, London, Institute of Child Health, University College London, London, UK
| | - C C Whalen
- Department of Epidemiology and Biostatistics, and Health Informatics Institute and Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
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Vargas AP, Rios AA, Grandjean L, Kirwan DE, Gilman RH, Sheen P, Zimic MJ. Determination of potentially novel compensatory mutations in rpoc associated with rifampin resistance and rpob mutations in Mycobacterium tuberculosis Clinical isolates from peru. Int J Mycobacteriol 2020; 9:121-137. [PMID: 32474533 PMCID: PMC10022416 DOI: 10.4103/ijmy.ijmy_27_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Rifampicin (RIF) resistance in Mycobacterium tuberculosis is frequently caused by mutations in the rpoB gene. These mutations are associated with a fitness cost, which can be overcome by compensatory mutations in other genes, among which rpoC may be the most important. We analyzed 469 Peruvian M. tuberculosis clinical isolates to identify compensatory mutations in rpoC/rpoA associated with RIF resistance. Methods The M. tuberculosis isolates were collected and tested for RIF susceptibility and spoligotyping. Samples were sequenced and aligned to the reference genome to identify mutations. By analyzing the sequences and the metadata, we identified a list of rpoC mutations exclusively associated with RIF resistance and mutations in rpoB. We then evaluated the distribution of these mutations along the protein sequence and tridimensional structure. Results One hundred and twenty-five strains were RIF susceptible and 346 were resistant. We identified 35 potential new compensatory mutations, some of which were distributed on the interface surface between rpoB and rpoC, arising in clusters and suggesting the presence of hotspots for compensatory mutations. Conclusion This study identifies 35 putative novel compensatory mutations in the β' subunit of M. tuberculosis RNApol. Six of these (S428T, L507V, A734V, I997V, and V1252LM) are considered most likely to have a compensatory role, as they fall in the interaction zone of the two subunits and the mutation did not lead to any change in the protein's physical-chemical properties.
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Affiliation(s)
- Ana Paula Vargas
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Angela A. Rios
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Louis Grandjean
- Department of Paediatric Infectious Diseases, Imperial College, University of London, London, England
| | - Daniela E. Kirwan
- Infection and Immunity Research Institute, St. George’s, University of London, London, England
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Patricia Sheen
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko J. Zimic
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
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39
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Knight GM, Zimic M, Funk S, Gilman RH, Friedland JS, Grandjean L. The relative fitness of drug-resistant Mycobacterium tuberculosis: a modelling study of household transmission in Peru. J R Soc Interface 2019; 15:rsif.2018.0025. [PMID: 29950511 PMCID: PMC6030636 DOI: 10.1098/rsif.2018.0025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
The relative fitness of drug-resistant versus susceptible bacteria in an environment dictates resistance prevalence. Estimates for the relative fitness of resistant Mycobacterium tuberculosis (Mtb) strains are highly heterogeneous and mostly derived from in vitro experiments. Measuring fitness in the field allows us to determine how the environment influences the spread of resistance. We designed a household structured, stochastic mathematical model to estimate the fitness costs associated with multidrug resistance (MDR) carriage in Mtb in Lima, Peru during 2010–2013. By fitting the model to data from a large prospective cohort study of TB disease in household contacts, we estimated the fitness, relative to susceptible strains with a fitness of 1, of MDR-Mtb to be 0.32 (95% credible interval: 0.15–0.62) or 0.38 (0.24–0.61), if only transmission or progression to disease, respectively, was affected. The relative fitness of MDR-Mtb increased to 0.56 (0.42–0.72) when the fitness cost influenced both transmission and progression to disease equally. We found the average relative fitness of MDR-Mtb circulating within households in Lima, Peru during 2010–2013 to be significantly lower than concurrent susceptible Mtb. If these fitness levels do not change, then existing TB control programmes are likely to keep MDR-TB prevalence at current levels in Lima, Peru.
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Affiliation(s)
- Gwenan M Knight
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Commonwealth Building, Hammersmith Campus, Du Cane Road, London W12 0NN, UK .,Infectious Diseases and Immunity, Imperial College London, Commonwealth Building, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Centre for the Mathematical Modelling of Infectious Diseases, Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,TB Centre, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, 31 Avenue Honorio Delgado 430, Distrito de Lima, Peru
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Robert H Gilman
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, 31 Avenue Honorio Delgado 430, Distrito de Lima, Peru.,Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA
| | - Jon S Friedland
- Infectious Diseases and Immunity, Imperial College London, Commonwealth Building, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Wellcome Trust Imperial College Centre for Global Health, St Mary's Hospital Campus, Imperial College London, Praed Street, London, W2 1NY, UK
| | - Louis Grandjean
- TB Centre, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, 31 Avenue Honorio Delgado 430, Distrito de Lima, Peru.,Wellcome Trust Imperial College Centre for Global Health, St Mary's Hospital Campus, Imperial College London, Praed Street, London, W2 1NY, UK
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Bui DP, Oren E, Roe DJ, Brown HE, Harris RB, Knight GM, Gilman RH, Grandjean L. A Case-Control Study to Identify Community Venues Associated with Genetically-clustered, Multidrug-resistant Tuberculosis Disease in Lima, Peru. Clin Infect Dis 2019; 68:1547-1555. [PMID: 30239609 PMCID: PMC7181380 DOI: 10.1093/cid/ciy746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/24/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The majority of tuberculosis transmission occurs in community settings. Our primary aim in this study was to assess the association between exposure to community venues and multidrug-resistant (MDR) tuberculosis. Our secondary aim was to describe the social networks of MDR tuberculosis cases and controls. METHODS We recruited laboratory-confirmed MDR tuberculosis cases and community controls that were matched on age and sex. Whole-genome sequencing was used to identify genetically clustered cases. Venue tracing interviews (nonblinded) were conducted to enumerate community venues frequented by participants. Logistic regression was used to assess the association between MDR tuberculosis and person-time spent in community venues. A location-based social network was constructed, with respondents connected if they reported frequenting the same venue, and an exponential random graph model (ERGM) was fitted to model the network. RESULTS We enrolled 59 cases and 65 controls. Participants reported 729 unique venues. The mean number of venues reported was similar in both groups (P = .92). Person-time in healthcare venues (adjusted odds ratio [aOR] = 1.67, P = .01), schools (aOR = 1.53, P < .01), and transportation venues (aOR = 1.25, P = .03) was associated with MDR tuberculosis. Healthcare venues, markets, cinemas, and transportation venues were commonly shared among clustered cases. The ERGM indicated significant community segregation between cases and controls. Case networks were more densely connected. CONCLUSIONS Exposure to healthcare venues, schools, and transportation venues was associated with MDR tuberculosis. Intervention across the segregated network of case venues may be necessary to effectively stem transmission.
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Affiliation(s)
- David P Bui
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson
| | - Eyal Oren
- School of Public Health, San Diego State University, California
| | - Denise J Roe
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson
| | - Heidi E Brown
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson
| | - Robin B Harris
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson
| | - Gwenan M Knight
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Robert H Gilman
- Universidad Peruana Cayetano Heredia, Lima, Peru
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Louis Grandjean
- London School of Hygiene and Tropical Medicine, United Kingdom
- Universidad Peruana Cayetano Heredia, Lima, Peru
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41
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Lamande M, Grandjean L, Gonne E, Van Daele D, Collignon J, Polus M, Loly C, Vanderick J, Coucke P, Martinive P. PO-0801 Esophageal Cancer: One Organ, Two Histologies, One Treatment Strategy: Why? Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)31221-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Grandjean L, Lamande M, Gonne E, Van Daele D, Collignon J, Polus M, Loly C, Seydel L, Vanderick J, Coucke P, Martinive P. EP-1450 How smoking status impacts patients undergoing radiochemotherapy for anal canal carcinoma? Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)31870-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Woodman M, Haeusler IL, Grandjean L. Tuberculosis Genetic Epidemiology: A Latin American Perspective. Genes (Basel) 2019; 10:genes10010053. [PMID: 30654542 PMCID: PMC6356704 DOI: 10.3390/genes10010053] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 11/16/2022] Open
Abstract
There are an estimated 10 million new cases of tuberculosis worldwide annually, with 282,000 new or relapsed cases each year reported from the Americas. With improvements in genome sequencing technology, it is now possible to study the genetic diversity of tuberculosis with much greater resolution. Although tuberculosis bacteria do not engage in horizontal gene transfer, the genome is far more variable than previously thought. The study of genome-wide variation in tuberculosis has improved our understanding of the evolutionary origins of tuberculosis, the arrival of tuberculosis in Latin America, the genetic determinants of drug resistance, and lineage-specific associations with important clinical phenotypes. This article reviews what is known about the arrival of tuberculosis in Latin America, the genetic diversity of tuberculosis in Latin America, and the genotypic determinants of clinical phenotypes.
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Affiliation(s)
- Marc Woodman
- Institute of Child Health, University College London, London WC1N 3JH, UK.
| | - Ilsa L Haeusler
- Institute of Child Health, University College London, London WC1N 3JH, UK.
| | - Louis Grandjean
- Institute of Child Health, University College London, London WC1N 3JH, UK.
- Department of Medicine, Imperial College London, London W2 1NY, UK.
- Great Ormond Street Hospital, Institute of Child Health, University College London, London WC1N 3JH, UK.
- Laboratorio de Investigacion y Desarollo, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martin de Porres 15102, Lima, Peru.
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Abstract
A 6-year-old girl presented acutely with worsening frontal headaches. She had a 3-month history of lethargy, reduced appetite, weight loss, cough and intermittent fevers. A chest X-ray showed a left upper lobe consolidation, and a CT head showed multiple enhancing lesions with significant surrounding oedema in both cerebral hemispheres. Due to the strong suspicion of tuberculosis (TB), she was admitted and treated with anti-TB therapy and steroids. Following this, pulmonary infection with Mycobacterium tuberculosis was confirmed by a positive PCR from induced sputum. Cerebral spinal fluid (CSF) analysis was normal and tested negative for M. tuberculosis on PCR. During her first week of treatment, she developed polyuria, nocturia and polydipsia and was diagnosed with central diabetes insipidus. She was started on desmopressin which rapidly improved her symptoms, and she was continued on desmopressin for 3 months. Currently, she remains well and has shown a good response to TB treatment.
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Affiliation(s)
- Shavindra Chellen
- Paediatric Speciality Trainee, Imperial College Healthcare NHS Trust, London, London, UK
| | - Elizabeth Whittaker
- Consultant Paediatric Infectious Diseases and Immunology, Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK.,Department of Academic Paediatrics, Imperial College, London, UK
| | - Michael Eisenhut
- Consultant Paediatrician, Luton and Dunstable University Hospital NHS Foundation Trust, Luton, UK
| | - Louis Grandjean
- Consultant Paediatric Infectious Diseases and Immunology, Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
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45
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Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RTH, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N Engl J Med 2018; 379:1403-1415. [PMID: 30280646 PMCID: PMC6121966 DOI: 10.1056/nejmoa1800474] [Citation(s) in RCA: 300] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted. CONCLUSIONS Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).
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46
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Williams B, Pickard L, Grandjean L, Pope S, Anderson SR, Morgan G, Williams A. The need to implement effective new entrant tuberculosis screening in children: evidence from school 'outbreak'. J Public Health (Oxf) 2018; 38:e511-e515. [PMID: 28158852 DOI: 10.1093/pubmed/fdv186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Bhanu Williams
- Department of Paediatrics, LNWH NHS Trust, Watford Road, Harrow, HA1 3UJ, Ealing, UK
| | - Lucy Pickard
- Department of Paediatrics, LNWH NHS Trust, Watford Road, Harrow, HA1 3UJ, Ealing, UK
| | - Louis Grandjean
- Department of Paediatrics, LNWH NHS Trust, Watford Road, Harrow, HA1 3UJ, Ealing, UK
| | - Sue Pope
- Department of Paediatrics, LNWH NHS Trust, Watford Road, Harrow, HA1 3UJ, Ealing, UK
| | - Sarah R Anderson
- NW London Health Protection Team, Public Health England, London, UK
| | - Gail Morgan
- NW London Health Protection Team, Public Health England, London, UK
| | - Amanda Williams
- Department of Paediatrics, LNWH NHS Trust, Watford Road, Harrow, HA1 3UJ, Ealing, UK
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47
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Brynildsrud OB, Pepperell CS, Suffys P, Grandjean L, Monteserin J, Debech N, Bohlin J, Alfsnes K, Pettersson JOH, Kirkeleite I, Fandinho F, da Silva MA, Perdigao J, Portugal I, Viveiros M, Clark T, Caws M, Dunstan S, Thai PVK, Lopez B, Ritacco V, Kitchen A, Brown TS, van Soolingen D, O’Neill MB, Holt KE, Feil EJ, Mathema B, Balloux F, Eldholm V. Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation. Sci Adv 2018; 4:eaat5869. [PMID: 30345355 PMCID: PMC6192687 DOI: 10.1126/sciadv.aat5869] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/11/2018] [Indexed: 05/23/2023]
Abstract
On the basis of population genomic and phylogeographic analyses of 1669 Mycobacterium tuberculosis lineage 4 (L4) genomes, we find that dispersal of L4 has been completely dominated by historical migrations out of Europe. We demonstrate an intimate temporal relationship between European colonial expansion into Africa and the Americas and the spread of L4 tuberculosis (TB). Markedly, in the age of antibiotics, mutations conferring antimicrobial resistance overwhelmingly emerged locally (at the level of nations), with minimal cross-border transmission of resistance. The latter finding was found to reflect the relatively recent emergence of these mutations, as a similar degree of local restriction was observed for susceptible variants emerging on comparable time scales. The restricted international transmission of drug-resistant TB suggests that containment efforts at the level of individual countries could be successful.
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Affiliation(s)
- Ola B. Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Caitlin S. Pepperell
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Philip Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Avenida Brasil 4365, C.P. 926, Manguinhos 21040-360, Rio de Janeiro, Brazil
| | - Louis Grandjean
- Department of Paediatric Infectious Diseases, Imperial College London, W2 1NY, London, UK
| | - Johana Monteserin
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Nadia Debech
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Jon Bohlin
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Kristian Alfsnes
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - John O.-H. Pettersson
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
- Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
| | - Ingerid Kirkeleite
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
| | - Fatima Fandinho
- Laboratorio de Bacteriologia da Tuberculose, Centro de Referłncia Professor Helio Fraga-Jacarepagu, Estrada de Curicica 2000, Brazil
| | - Marcia Aparecida da Silva
- Laboratorio de Bacteriologia da Tuberculose, Centro de Referłncia Professor Helio Fraga-Jacarepagu, Estrada de Curicica 2000, Brazil
| | - Joao Perdigao
- Instituto de Investigao do Medicamento, Faculdade de Farmcia, Universidade de Lisboa, Lisboa, Portugal
| | - Isabel Portugal
- Instituto de Investigao do Medicamento, Faculdade de Farmcia, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Medica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Taane Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Maxine Caws
- Liverpool School of Tropical medicine, Department of Clinical Sciences, Liverpool, UK
- Birat-Nepal Medical Trust, Lazimpat, Kathmandu, Nepal
| | - Sarah Dunstan
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Beatriz Lopez
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas, ANLIS Carlos Malbran, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, IA 52242, USA
| | - Tyler S. Brown
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dick van Soolingen
- Center for Infectious Disease Research, Diagnostics and Perinatal Screening, National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven, Netherlands
| | - Mary B. O’Neill
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53726, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kathryn E. Holt
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Department of Biochemistry and Molecular Biology and Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Edward J. Feil
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, USA
| | - Francois Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, 0456 Oslo, Norway
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Warren JL, Grandjean L, Moore DAJ, Lithgow A, Coronel J, Sheen P, Zelner JL, Andrews JR, Cohen T. Investigating spillover of multidrug-resistant tuberculosis from a prison: a spatial and molecular epidemiological analysis. BMC Med 2018; 16:122. [PMID: 30071850 PMCID: PMC6091024 DOI: 10.1186/s12916-018-1111-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Congregate settings may serve as institutional amplifiers of tuberculosis (TB) and multidrug-resistant tuberculosis (MDR-TB). We analyze spatial, epidemiological, and pathogen genetic data prospectively collected from neighborhoods surrounding a prison in Lima, Peru, where inmates experience a high risk of MDR-TB, to investigate the risk of spillover into the surrounding community. METHODS Using hierarchical Bayesian statistical modeling, we address three questions regarding the MDR-TB risk: (i) Does the excess risk observed among prisoners also extend outside the prison? (ii) If so, what is the magnitude, shape, and spatial range of this spillover effect? (iii) Is there evidence of additional transmission across the region? RESULTS The region of spillover risk extends for 5.47 km outside of the prison (95% credible interval: 1.38, 9.63 km). Within this spillover region, we find that nine of the 467 non-inmate patients (35 with MDR-TB) have MDR-TB strains that are genetic matches to strains collected from current inmates with MDR-TB, compared to seven out of 1080 patients (89 with MDR-TB) outside the spillover region (p values: 0.022 and 0.008). We also identify eight spatially aggregated genetic clusters of MDR-TB, four within the spillover region, consistent with local transmission among individuals living close to the prison. CONCLUSIONS We demonstrate a clear prison spillover effect in this population, which suggests that interventions in the prison may have benefits that extend to the surrounding community.
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Affiliation(s)
- Joshua L Warren
- Department of Biostatistics, Yale University, New Haven, CT, 06510, USA.
| | - Louis Grandjean
- Paediatric Infectious Diseases, Section of Paediatrics, Department of Medicine, Imperial College, London, W2 1NY, UK.,Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - David A J Moore
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru.,TB Centre and Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Anna Lithgow
- TB Centre and Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Jorge Coronel
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - Patricia Sheen
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - Jonathan L Zelner
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason R Andrews
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, 06510, USA
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Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Ha DM, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Sousa EO, Streicher EM, Van Helden P, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG. Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet 2018; 50:764. [PMID: 29674744 DOI: 10.1038/s41588-018-0074-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, the URL listed for TubercuList was incorrect. The correct URL is https://mycobrowser.epfl.ch/. The error has been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Grant A Hill-Cawthorne
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mridul B Nair
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Shahjahan Ali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah M Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mona Alsomali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah O Ahmed
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Stephanie Portelli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Yaa Oppong
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Alves
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, UK.,Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | | | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Keertan Dheda
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Nicholas Furnham
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.,Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Louis Grandjean
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dang Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | | | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - David J Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nora Mocillo
- Reference Laboratory of Tuberculosis Control, Buenos Aires, Argentina
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Carlos Penha
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - João Perdigão
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Zineb Rchiad
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jaime Robledo
- Corporación para Investigaciones Biológicas, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Patricia Sheen
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | | | - Frik A Sirgel
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Christophe Sola
- Institute for Integrative Cell Biology, CEA, CNRS, Université Paris-Saclay, Orsay, France
| | - Erivelton Oliveira Sousa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.,Laboratorio Central de Saúde Pública Professor Gonçalo Moniz, Salvador, Brazil
| | - Elizabeth M Streicher
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Paul Van Helden
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Robert M Warren
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. .,Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa.
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. .,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. .,Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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50
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Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K, Ali S, Abdallah AM, Alghamdi S, Alsomali M, Ahmed AO, Portelli S, Oppong Y, Alves A, Bessa TB, Campino S, Caws M, Chatterjee A, Crampin AC, Dheda K, Furnham N, Glynn JR, Grandjean L, Minh Ha D, Hasan R, Hasan Z, Hibberd ML, Joloba M, Jones-López EC, Matsumoto T, Miranda A, Moore DJ, Mocillo N, Panaiotov S, Parkhill J, Penha C, Perdigão J, Portugal I, Rchiad Z, Robledo J, Sheen P, Shesha NT, Sirgel FA, Sola C, Oliveira Sousa E, Streicher EM, Helden PV, Viveiros M, Warren RM, McNerney R, Pain A, Clark TG. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet 2018; 50:307-316. [PMID: 29358649 DOI: 10.1038/s41588-017-0029-0] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022]
Abstract
To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Grant A Hill-Cawthorne
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mridul B Nair
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Shahjahan Ali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah M Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mona Alsomali
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdallah O Ahmed
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Stephanie Portelli
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Yaa Oppong
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Adriana Alves
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | | | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, UK
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | | | - Amelia C Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Keertan Dheda
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Nicholas Furnham
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Karonga, Malawi
| | - Louis Grandjean
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dang Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Diseases, Ho Chi Minh City, Vietnam
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | | | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - David J Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Laboratorio de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nora Mocillo
- Reference Laboratory of Tuberculosis Control, Buenos Aires, Argentina
| | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Carlos Penha
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - João Perdigão
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- iMed.ULisboa-Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Zineb Rchiad
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jaime Robledo
- Corporación para Investigaciones Biológicas, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Patricia Sheen
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | | | - Frik A Sirgel
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Christophe Sola
- Institute for Integrative Cell Biology, CEA, CNRS, Université Paris-Saclay, Orsay, France
| | - Erivelton Oliveira Sousa
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Laboratorio Central de Saúde Pública Professor Gonçalo Moniz, Salvador, Brazil
| | - Elizabeth M Streicher
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Paul Van Helden
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (UNL), Lisbon, Portugal
| | - Robert M Warren
- Division of Molecular Biology and Human Genetics, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Lung Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa.
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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