1
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Ndodo N, Ashcroft J, Lewandowski K, Yinka-Ogunleye A, Chukwu C, Ahmad A, King D, Akinpelu A, Maluquer de Motes C, Ribeca P, Sumner RP, Rambaut A, Chester M, Maishman T, Bamidele O, Mba N, Babatunde O, Aruna O, Pullan ST, Gannon B, Brown CS, Ihekweazu C, Adetifa I, Ulaeto DO. Distinct monkeypox virus lineages co-circulating in humans before 2022. Nat Med 2023; 29:2317-2324. [PMID: 37710003 PMCID: PMC10504077 DOI: 10.1038/s41591-023-02456-8] [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: 01/13/2023] [Accepted: 06/12/2023] [Indexed: 09/16/2023]
Abstract
The 2022 global mpox outbreak raises questions about how this zoonotic disease established effective human-to-human transmission and its potential for further adaptation. The 2022 outbreak virus is related to an ongoing outbreak in Nigeria originally reported in 2017, but the evolutionary path linking the two remains unclear due to a lack of genomic data between 2018, when virus exportations from Nigeria were first recorded, and 2022, when the global mpox outbreak began. Here, 18 viral genomes obtained from patients across southern Nigeria in 2019-2020 reveal multiple lineages of monkeypox virus (MPXV) co-circulated in humans for several years before 2022, with progressive accumulation of mutations consistent with APOBEC3 activity over time. We identify Nigerian A.2 lineage isolates, confirming the lineage that has been multiply exported to North America independently of the 2022 outbreak originated in Nigeria, and that it has persisted by human-to-human transmission in Nigeria for more than 2 years before its latest exportation. Finally, we identify a lineage-defining APOBEC3-style mutation in all A.2 isolates that disrupts gene A46R, encoding a viral innate immune modulator. Collectively, our data demonstrate MPXV capacity for sustained diversification within humans, including mutations that may be consistent with established mechanisms of poxvirus adaptation.
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Affiliation(s)
| | - Jonathan Ashcroft
- UK Public Health Rapid Support Team, UK Health Security Agency/London School of Hygiene & Tropical Medicine, London, UK
| | - Kuiama Lewandowski
- UK Health Security Agency, Research & Evaluation Services, Porton Down, UK
| | | | | | - Adama Ahmad
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - David King
- CBR Division, Defence Science and Technology Laboratory, Salisbury, UK
| | | | - Carlos Maluquer de Motes
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Paolo Ribeca
- UK Health Security Agency, London, UK
- Biomathematics and Statistics Scotland, Edinburgh, UK
| | - Rebecca P Sumner
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Michael Chester
- CBR Division, Defence Science and Technology Laboratory, Salisbury, UK
| | - Tom Maishman
- CBR Division, Defence Science and Technology Laboratory, Salisbury, UK
| | | | - Nwando Mba
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | | | - Olusola Aruna
- UK Health Security Agency, International Health Regulations (IHR) Strengthening Project, British High Commission, Abuja, Nigeria
| | - Steven T Pullan
- UK Health Security Agency, Research & Evaluation Services, Porton Down, UK
| | - Benedict Gannon
- UK Public Health Rapid Support Team, UK Health Security Agency/London School of Hygiene & Tropical Medicine, London, UK
| | | | | | | | - David O Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Salisbury, UK.
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2
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Ryan KA, Bewley KR, Watson RJ, Burton C, Carnell O, Cavell BE, Challis A, Coombes NS, Davies ER, Edun-Huges J, Emery K, Fell R, Fotheringham SA, Gooch KE, Gowan K, Handley A, Harris DJ, Hesp R, Hunter L, Humphreys R, Johnson R, Kennard C, Knott D, Lister S, Morley D, Ngabo D, Osman KL, Paterson J, Penn EJ, Pullan ST, Richards KS, Summers S, Thomas SR, Weldon T, Wiblin NR, Rayner EL, Vipond RT, Hallis B, Salguero FJ, Funnell SGP, Hall Y. Syrian hamster convalescence from prototype SARS-CoV-2 confers measurable protection against the attenuated disease caused by the Omicron variant. PLoS Pathog 2023; 19:e1011293. [PMID: 37014911 PMCID: PMC10104347 DOI: 10.1371/journal.ppat.1011293] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 08/23/2022] [Revised: 04/14/2023] [Accepted: 03/11/2023] [Indexed: 04/05/2023] Open
Abstract
The mutation profile of the SARS-CoV-2 Omicron (lineage BA.1) variant posed a concern for naturally acquired and vaccine-induced immunity. We investigated the ability of prior infection with an early SARS-CoV-2 ancestral isolate (Australia/VIC01/2020, VIC01) to protect against disease caused by BA.1. We established that BA.1 infection in naïve Syrian hamsters resulted in a less severe disease than a comparable dose of the ancestral virus, with fewer clinical signs including less weight loss. We present data to show that these clinical observations were almost absent in convalescent hamsters challenged with the same dose of BA.1 50 days after an initial infection with ancestral virus. These data provide evidence that convalescent immunity against ancestral SARS-CoV-2 is protective against BA.1 in the Syrian hamster model of infection. Comparison with published pre-clinical and clinical data supports consistency of the model and its predictive value for the outcome in humans. Further, the ability to detect protection against the less severe disease caused by BA.1 demonstrates continued value of the Syrian hamster model for evaluation of BA.1-specific countermeasures.
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Affiliation(s)
| | | | | | | | | | | | - Amy Challis
- UK Health Security Agency, Salisbury, United Kingdom
| | | | | | | | - Kirsty Emery
- UK Health Security Agency, Salisbury, United Kingdom
| | - Rachel Fell
- UK Health Security Agency, Salisbury, United Kingdom
| | | | - Karen E Gooch
- UK Health Security Agency, Salisbury, United Kingdom
| | - Kathryn Gowan
- UK Health Security Agency, Salisbury, United Kingdom
| | | | | | - Richard Hesp
- UK Health Security Agency, Salisbury, United Kingdom
| | - Laura Hunter
- UK Health Security Agency, Salisbury, United Kingdom
| | | | | | | | - Daniel Knott
- UK Health Security Agency, Salisbury, United Kingdom
| | - Sian Lister
- UK Health Security Agency, Salisbury, United Kingdom
| | - Daniel Morley
- UK Health Security Agency, Salisbury, United Kingdom
| | - Didier Ngabo
- UK Health Security Agency, Salisbury, United Kingdom
| | - Karen L Osman
- UK Health Security Agency, Salisbury, United Kingdom
| | | | | | | | | | - Sian Summers
- UK Health Security Agency, Salisbury, United Kingdom
| | | | - Thomas Weldon
- UK Health Security Agency, Salisbury, United Kingdom
| | | | - Emma L Rayner
- UK Health Security Agency, Salisbury, United Kingdom
| | | | - Bassam Hallis
- UK Health Security Agency, Salisbury, United Kingdom
| | | | | | - Yper Hall
- UK Health Security Agency, Salisbury, United Kingdom
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3
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Medlock JM, Vaux AGC, Gandy S, Cull B, McGinley L, Gillingham E, Catton M, Pullan ST, Hansford KM. Spatial and temporal heterogeneity of the density of Borrelia burgdorferi-infected Ixodes ricinus ticks across a landscape: A 5-year study in southern England. Med Vet Entomol 2022; 36:356-370. [PMID: 35521893 PMCID: PMC9545817 DOI: 10.1111/mve.12574] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
The density of Borrelia burgdorferi-infected Ixodes ricinus nymphs (DIN) was investigated during 2013-2017 across a Lyme disease-endemic landscape in southern England. The density of nymphs (DON), nymph infection prevalence (NIP), and DIN varied across five different natural habitats, with the highest DIN in woodland edge and high biodiversity woodlands. DIN was significantly lower in scrub grassland compared to the woodland edge, with low DON and no evidence of infection in ticks in non-scrub grassland. Over the 5 years, DON, NIP and DIN were comparable within habitats, except in 2014, with NIP varying three-fold and DIN significantly lower compared to 2015-2017. Borrelia garinii was most common, with bird-associated Borrelia (B. garinii/valaisiana) accounting for ~70% of all typed sequences. Borrelia burgdorferi sensu stricto was more common than B. afzelii. Borrelia afzelii was more common in scrub grassland than woodland and absent in some years. The possible impact of scrub on grazed grassland, management of ecotonal woodland margins with public access, and the possible role of birds/gamebirds impacting NIP are discussed. Mean NIP was 7.6%, highlighting the potential risk posed by B. burgdorferi in this endemic area. There is a need for continued research to understand its complex ecology and identify strategies for minimizing risk to public health, through habitat/game management and public awareness.
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Affiliation(s)
- Jolyon M. Medlock
- Medical Entomology & Zoonoses Ecology GroupUK Health Security AgencySalisburyWiltshireUK
| | - Alexander G. C. Vaux
- Medical Entomology & Zoonoses Ecology GroupUK Health Security AgencySalisburyWiltshireUK
| | - Sara Gandy
- Medical Entomology & Zoonoses Ecology GroupUK Health Security AgencySalisburyWiltshireUK
| | - Benjamin Cull
- Medical Entomology & Zoonoses Ecology GroupUK Health Security AgencySalisburyWiltshireUK
| | - Liz McGinley
- Medical Entomology & Zoonoses Ecology GroupUK Health Security AgencySalisburyWiltshireUK
| | - Emma Gillingham
- Medical Entomology & Zoonoses Ecology GroupUK Health Security AgencySalisburyWiltshireUK
| | - Matthew Catton
- Medical Entomology & Zoonoses Ecology GroupUK Health Security AgencySalisburyWiltshireUK
| | - Steven T. Pullan
- Diagnostic & Genomic TechnologiesUK Health Security AgencySalisburyWiltshireUK
| | - Kayleigh M. Hansford
- Medical Entomology & Zoonoses Ecology GroupUK Health Security AgencySalisburyWiltshireUK
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4
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Xu Y, Lewandowski K, Downs LO, Kavanagh J, Hender T, Lumley S, Jeffery K, Foster D, Sanderson ND, Vaughan A, Morgan M, Vipond R, Carroll M, Peto T, Crook D, Walker AS, Matthews PC, Pullan ST. Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. ACTA ACUST UNITED AC 2021; 26. [PMID: 34240696 PMCID: PMC8268652 DOI: 10.2807/1560-7917.es.2021.26.27.2000004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Indexed: 11/20/2022]
Abstract
BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.
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Affiliation(s)
- Yifei Xu
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Kuiama Lewandowski
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Louise O Downs
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.,Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Thomas Hender
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Sheila Lumley
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.,Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Ali Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Marcus Morgan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Richard Vipond
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Miles Carroll
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Timothy Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Philippa C Matthews
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom.,Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Steven T Pullan
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
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5
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Crook JM, Murphy I, Carter DP, Pullan ST, Carroll M, Vipond R, Cunningham AA, Bell D. Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe. Sci Rep 2021; 11:14723. [PMID: 34282196 PMCID: PMC8289822 DOI: 10.1038/s41598-021-94011-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 03/24/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe (rhinolophid) bats. We identified and sequenced a novel sarbecovirus (RhGB01) from a British horseshoe bat, at the western extreme of the rhinolophid range. Our results extend both the geographic and species ranges of sarbecoviruses and suggest their presence throughout the horseshoe bat distribution. Within the spike protein receptor binding domain, but excluding the receptor binding motif, RhGB01 has a 77% (SARS-CoV-2) and 81% (SARS-CoV) amino acid homology. While apparently lacking hACE2 binding ability, and hence unlikely to be zoonotic without mutation, RhGB01 presents opportunity for SARS-CoV-2 and other sarbecovirus homologous recombination. Our findings highlight that the natural distribution of sarbecoviruses and opportunities for recombination through intermediate host co-infection are underestimated. Preventing transmission of SARS-CoV-2 to bats is critical with the current global mass vaccination campaign against this virus.
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Affiliation(s)
- Jack M Crook
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
- NIHR Health Protection Unit in Emerging and Zoonotic Infections, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, L69 7TX, UK
| | - Ivana Murphy
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Daniel P Carter
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Steven T Pullan
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Miles Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - Richard Vipond
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | | | - Diana Bell
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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6
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Holding M, Dowall SD, Medlock JM, Carter DP, McGinley L, Curran-French M, Pullan ST, Chamberlain J, Hansford KM, Baylis M, Vipond R, Hewson R. Detection of new endemic focus of tick-borne encephalitis virus (TBEV), Hampshire/Dorset border, England, September 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 31771701 PMCID: PMC6885748 DOI: 10.2807/1560-7917.es.2019.24.47.1900658] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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] [Indexed: 12/30/2022]
Abstract
The presence of tick-borne encephalitis virus (TBEV) was detected in a questing tick pool in southern England in September 2019. Hitherto, TBEV had only been detected in a limited area in eastern England. This southern English viral genome sequence is distinct from TBEV-UK, being most similar to TBEV-NL. The new location of TBEV presence highlights that the diagnosis of tick-borne encephalitis should be considered in encephalitic patients in areas of the United Kingdom outside eastern England.
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Affiliation(s)
- Maya Holding
- Medical Entomology and Zoonoses Ecology, Emergency Response Department, Public Health England, Porton Down, United Kingdom.,Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Stuart D Dowall
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Jolyon M Medlock
- Medical Entomology and Zoonoses Ecology, Emergency Response Department, Public Health England, Porton Down, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Daniel P Carter
- Genomics, National Infection Service, Public Health England, Porton Down, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Liz McGinley
- Medical Entomology and Zoonoses Ecology, Emergency Response Department, Public Health England, Porton Down, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Mollie Curran-French
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Steven T Pullan
- Genomics, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - John Chamberlain
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Kayleigh M Hansford
- Medical Entomology and Zoonoses Ecology, Emergency Response Department, Public Health England, Porton Down, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Matthew Baylis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Richard Vipond
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Roger Hewson
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
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7
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Neill L, Checkley AM, Benjamin LA, Herdman MT, Carter DP, Pullan ST, Aarons E, Griffiths K, Monaghan B, Karunaratne K, Ciccarelli O, Spillane J, Moore DAJ, Kullmann DM. Rhombencephalitis and Myeloradiculitis Caused by a European Subtype of Tick-Borne Encephalitis Virus. Emerg Infect Dis 2020; 25:2317-2319. [PMID: 31742526 PMCID: PMC6874248 DOI: 10.3201/eid2512.191017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We report a case of a previously healthy man returning to the United Kingdom from Lithuania who developed rhombencephalitis and myeloradiculitis due to tick-borne encephalitis. These findings add to sparse data on tick-borne encephalitis virus phylogeny and associated neurologic syndromes and underscore the importance of vaccinating people traveling to endemic regions.
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8
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van Munster JM, Daly P, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Arvas M, Raulo R, Pullan ST, Delmas S, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose. Biotechnol Biofuels 2020; 13:69. [PMID: 32313551 PMCID: PMC7155255 DOI: 10.1186/s13068-020-01702-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/24/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production. RESULTS We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds. CONCLUSION In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.
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Affiliation(s)
- Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Manchester Institute of Biotechnology (MIB) & School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present Address: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | | | | | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT Espoo, Finland
| | - Roxane Raulo
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Public Health England, National Infection Service, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, 75005 Paris, France
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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9
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Xu Y, Lewandowski K, Jeffery K, Downs LO, Foster D, Sanderson ND, Kavanagh J, Vaughan A, Salvagno C, Vipond R, Carroll M, Danby R, Peto T, Crook D, Walker AS, Matthews PC, Pullan ST. Nanopore metagenomic sequencing to investigate nosocomial transmission of human metapneumovirus from a unique genetic group among haematology patients in the United Kingdom. J Infect 2020; 80:571-577. [PMID: 32092386 DOI: 10.1016/j.jinf.2020.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/05/2020] [Accepted: 02/08/2020] [Indexed: 01/27/2023]
Abstract
BACKGROUND Human metapneumovirus (HMPV) infection causes a spectrum of respiratory tract disease, and may be a significant pathogen in the context of immunocompromise. Here, we report direct-from-sample metagenomic sequencing of HMPV using Oxford Nanopore Technology. METHODS We applied this sequencing approach to 25 respiratory samples that had been submitted to a clinical diagnostic laboratory in a UK teaching hospital. These samples represented 13 patients under the care of a haematology unit over a 20-day period in Spring 2019 (two sampled twice), and ten other patients elsewhere in the hospital between 2017-2019. RESULTS We generated HMPV reads from 20/25 samples (sensitivity 80% compared to routine diagnostic testing) and retrieved complete HMPV genomes from 15/20 of these. Consensus sequences from Nanopore data were identical to those generated by Illumina, and represented HMPV genomes from two distinct sublineages, A2b and B2. Sequences from ten haematology patients formed a unique genetic group in the A2b sublineage, not previously reported in the UK. Among these, eight HMPV genomes formed a cluster (differing by ≤3 SNPs), likely to reflect nosocomial transmission, while two others were more distantly related and may represent independent introductions to the haematology unit. CONCLUSION Nanopore metagenomic sequencing can be used to diagnose HMPV infection, although more work is required to optimise sensitivity. Improvements in the use of metagenomic sequencing, particularly for respiratory viruses, could contribute to antimicrobial stewardship. Generation of full genome sequences can be used to support or rule out nosocomial transmission, and contribute to improving infection prevention and control practices.
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Affiliation(s)
- Yifei Xu
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom.
| | - Kuiama Lewandowski
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Louise O Downs
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom; Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Ali Vaughan
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Claudia Salvagno
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Richard Vipond
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Miles Carroll
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
| | - Robert Danby
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Timothy Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Philippa C Matthews
- NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom; Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom; Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Steven T Pullan
- Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom
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10
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Wise EL, Márquez S, Mellors J, Paz V, Atkinson B, Gutierrez B, Zapata S, Coloma J, Pybus OG, Jackson SK, Trueba G, Fejer G, Logue CH, Pullan ST. Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing. PLoS Negl Trop Dis 2020; 14:e0007897. [PMID: 31961856 PMCID: PMC6994106 DOI: 10.1371/journal.pntd.0007897] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/31/2020] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68–99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens. Oropouche virus (OROV) causes outbreaks of febrile illness in areas of South and Central America and we recently identified it in Ecuador for the first time, using metagenomic sequencing. The genome sequence data revealed that the Ecuadorian strain of the virus was not detected using a published qRT-PCR, as it differed genetically at the binding site of the reverse primer. To address this, we developed a modified qRT-PCR that showed increased sensitivity for the Ecuadorian strain. This test detected OROV infection in 6 out of 196 febrile patients from Esmeraldas, Ecuador in 2016. OROV was isolated from positive patient samples, viral genome sequences were compared to publicly available OROV sequences. This revealed that the Ecuadorian cases are genetically distinct, suggesting that local transmission of the virus should not be ruled out. This work highlights the need for a better understanding of OROV dynamics in Ecuador and surrounding areas, the importance of considering OROV as a cause of fever in Ecuadorian patients and the possibility of selectively using metagenomic sequencing in parallel to traditional molecular techniques in patient testing.
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Affiliation(s)
- Emma L. Wise
- National Infection Service, Public Health England, Salisbury, United Kingdom
- School of Biomedical Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Sully Márquez
- Microbiology Institute, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Jack Mellors
- National Infection Service, Public Health England, Salisbury, United Kingdom
| | - Verónica Paz
- Hospital Delfina Torres de Concha, Esmeraldas, Ecuador
| | - Barry Atkinson
- Arthropod Genetics Group, The Pirbright Institute, Woking, United Kingdom
| | - Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- School of Biological and Environmental Sciences, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sonia Zapata
- Microbiology Institute, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Josefina Coloma
- School of Public Health, University of California Berkeley School of Public Health, Berkeley, California, United States of America
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Simon K. Jackson
- School of Biomedical Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Gabriel Trueba
- Microbiology Institute, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Gyorgy Fejer
- School of Biomedical Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Christopher H. Logue
- National Infection Service, Public Health England, Salisbury, United Kingdom
- School of Biomedical Sciences, University of Plymouth, Plymouth, United Kingdom
- Microbiology Institute, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- * E-mail:
| | - Steven T. Pullan
- National Infection Service, Public Health England, Salisbury, United Kingdom
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11
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Holding M, Dowall SD, Medlock JM, Carter DP, Pullan ST, Lewis J, Vipond R, Rocchi MS, Baylis M, Hewson R. Tick-Borne Encephalitis Virus, United Kingdom. Emerg Infect Dis 2020; 26:90-96. [PMID: 31661056 PMCID: PMC6924911 DOI: 10.3201/eid2601.191085] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During February 2018–January 2019, we conducted large-scale surveillance for the presence and prevalence of tick-borne encephalitis virus (TBEV) and louping ill virus (LIV) in sentinel animals and ticks in the United Kingdom. Serum was collected from 1,309 deer culled across England and Scotland. Overall, 4% of samples were ELISA-positive for the TBEV serocomplex. A focus in the Thetford Forest area had the highest proportion (47.7%) of seropositive samples. Ticks collected from culled deer within seropositive regions were tested for viral RNA; 5 of 2,041 ticks tested positive by LIV/TBEV real-time reverse transcription PCR, all from within the Thetford Forest area. From 1 tick, we identified a full-length genomic sequence of TBEV. Thus, using deer as sentinels revealed a potential TBEV focus in the United Kingdom. This detection of TBEV genomic sequence in UK ticks has important public health implications, especially for undiagnosed encephalitis.
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12
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Lewandowski K, Xu Y, Pullan ST, Lumley SF, Foster D, Sanderson N, Vaughan A, Morgan M, Bright N, Kavanagh J, Vipond R, Carroll M, Marriott AC, Gooch KE, Andersson M, Jeffery K, Peto TEA, Crook DW, Walker AS, Matthews PC. Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples. J Clin Microbiol 2019; 58:e00963-19. [PMID: 31666364 PMCID: PMC6935926 DOI: 10.1128/jcm.00963-19] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [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: 06/18/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023] Open
Abstract
Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 102 to 103 genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (P = 4.7 × 10-5). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [CT ] values, <30) and 6/13 samples with low viral titers (CT values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses.
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Affiliation(s)
- Kuiama Lewandowski
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Yifei Xu
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Steven T Pullan
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Sheila F Lumley
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicholas Sanderson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Marcus Morgan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Nicole Bright
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Richard Vipond
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Miles Carroll
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Anthony C Marriott
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Karen E Gooch
- Public Health England, National infection Service, Porton Down, Salisbury, United Kingdom
| | - Monique Andersson
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
| | - Philippa C Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR BRC, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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13
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Kafetzopoulou LE, Efthymiadis K, Lewandowski K, Crook A, Carter D, Osborne J, Aarons E, Hewson R, Hiscox JA, Carroll MW, Vipond R, Pullan ST. Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples. ACTA ACUST UNITED AC 2019; 23. [PMID: 30563591 PMCID: PMC6299504 DOI: 10.2807/1560-7917.es.2018.23.50.1800228] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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] [Indexed: 12/31/2022]
Abstract
Background The recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. Aim To investigate the feasibility of metagenomic sequencing for recovering whole genome sequences of chikungunya and dengue viruses from clinical samples. Methods We performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION on clinical samples which were real-time reverse transcription-PCR (qRT-PCR) positive for chikungunya (CHIKV) or dengue virus (DENV), two of the most important arboviruses. A total of 26 samples with a range of representative clinical Ct values were included in the study. Results Direct metagenomic sequencing of nucleic acid extracts from serum or plasma without viral enrichment allowed for virus identification, subtype determination and elucidated complete or near-complete genomes adequate for phylogenetic analysis. One PCR-positive CHIKV sample was also found to be coinfected with DENV. Conclusions This work demonstrates that metagenomic whole genome sequencing is feasible for the majority of CHIKV and DENV PCR-positive patient serum or plasma samples. Additionally, it explores the use of Nanopore metagenomic sequencing for DENV and CHIKV, which can likely be applied to other RNA viruses, highlighting the applicability of this approach to front-line public health and potential portable applications using the MinION.
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Affiliation(s)
- Liana E Kafetzopoulou
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Kyriakos Efthymiadis
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kuiama Lewandowski
- Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Ant Crook
- Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Dan Carter
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Jane Osborne
- Rare and Imported Pathogens Laboratory, Public Health England, Porton Down, United Kingdom
| | - Emma Aarons
- Rare and Imported Pathogens Laboratory, Public Health England, Porton Down, United Kingdom
| | - Roger Hewson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Julian A Hiscox
- Institute of Infection and Global Health, University of Liverpool, United Kingdom.,NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
| | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Richard Vipond
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
| | - Steven T Pullan
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.,Public Health England, National Infections Service, Porton Down, United Kingdom
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14
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Kafetzopoulou LE, Pullan ST, Lemey P, Suchard MA, Ehichioya DU, Pahlmann M, Thielebein A, Hinzmann J, Oestereich L, Wozniak DM, Efthymiadis K, Schachten D, Koenig F, Matjeschk J, Lorenzen S, Lumley S, Ighodalo Y, Adomeh DI, Olokor T, Omomoh E, Omiunu R, Agbukor J, Ebo B, Aiyepada J, Ebhodaghe P, Osiemi B, Ehikhametalor S, Akhilomen P, Airende M, Esumeh R, Muoebonam E, Giwa R, Ekanem A, Igenegbale G, Odigie G, Okonofua G, Enigbe R, Oyakhilome J, Yerumoh EO, Odia I, Aire C, Okonofua M, Atafo R, Tobin E, Asogun D, Akpede N, Okokhere PO, Rafiu MO, Iraoyah KO, Iruolagbe CO, Akhideno P, Erameh C, Akpede G, Isibor E, Naidoo D, Hewson R, Hiscox JA, Vipond R, Carroll MW, Ihekweazu C, Formenty P, Okogbenin S, Ogbaini-Emovon E, Günther S, Duraffour S. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 2019; 363:74-77. [PMID: 30606844 DOI: 10.1126/science.aau9343] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022]
Abstract
The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.
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Affiliation(s)
- L E Kafetzopoulou
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S T Pullan
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - P Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - M A Suchard
- Departments of Biomathematics, Biostatistics, and Human Genetics, University of California, Los Angeles, CA, USA
| | - D U Ehichioya
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - M Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - A Thielebein
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - J Hinzmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - L Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - D M Wozniak
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - K Efthymiadis
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - D Schachten
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - F Koenig
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - J Matjeschk
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Lorenzen
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Lumley
- Public Health England, National Infection Service, Porton Down, UK
| | - Y Ighodalo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D I Adomeh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - T Olokor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Omomoh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Omiunu
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Agbukor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - B Ebo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Aiyepada
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - P Ebhodaghe
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - B Osiemi
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - P Akhilomen
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - M Airende
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Esumeh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Muoebonam
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Giwa
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - A Ekanem
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Igenegbale
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Odigie
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Okonofua
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Enigbe
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Oyakhilome
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E O Yerumoh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - I Odia
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - C Aire
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - M Okonofua
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Atafo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Tobin
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D Asogun
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - N Akpede
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - P O Okokhere
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - M O Rafiu
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - K O Iraoyah
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - P Akhideno
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - C Erameh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Akpede
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - E Isibor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D Naidoo
- World Health Organization, Geneva, Switzerland
| | - R Hewson
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK.,Faculty of Clinical Sciences and International Public Health, Liverpool School of Tropical Medicine, Liverpool, UK
| | - J A Hiscox
- National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - R Vipond
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - M W Carroll
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - C Ihekweazu
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - P Formenty
- World Health Organization, Geneva, Switzerland
| | - S Okogbenin
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | | | - S Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany. .,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - S Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
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15
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Bower H, El Karsany M, Alzain M, Gannon B, Mohamed R, Mahmoud I, Eldegail M, Taha R, Osman A, Mohamednour S, Semper A, Atkinson B, Carter D, Dowall S, Furneaux J, Graham V, Mellors J, Osborne J, Pullan ST, Slack GS, Brooks T, Hewson R, Beeching NJ, Whitworth J, Bausch DG, Fletcher TE. Detection of Crimean-Congo Haemorrhagic Fever cases in a severe undifferentiated febrile illness outbreak in the Federal Republic of Sudan: A retrospective epidemiological and diagnostic cohort study. PLoS Negl Trop Dis 2019; 13:e0007571. [PMID: 31291242 PMCID: PMC6645580 DOI: 10.1371/journal.pntd.0007571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/22/2019] [Accepted: 06/22/2019] [Indexed: 01/12/2023] Open
Abstract
Background Undifferentiated febrile illness (UFI) is one of the most common reasons for people seeking healthcare in low-income countries. While illness and death due to specific infections such as malaria are often well-quantified, others are frequently uncounted and their impact underappreciated. A number of high consequence infectious diseases, including Ebola virus, are endemic or epidemic in the Federal Republic of Sudan which has experienced at least 12 UFI outbreaks, frequently associated with haemorrhage and high case fatality rates (CFR), since 2012. One of these occurred in Darfur in 2015/2016 with 594 cases and 108 deaths (CFR 18.2%). The aetiology of these outbreaks remains unknown. Methodology/Principal findings We report a retrospective cohort study of the 2015/2016 Darfur outbreak, using a subset of 65 of 263 outbreak samples received by the National Public Health Laboratory which met selection criteria of sufficient sample volume and epidemiological data. Clinical features included fever (95.8%), bleeding (95.7%), headache (51.6%) and arthralgia (42.2%). No epidemiological patterns indicative of person-to-person transmission or health-worker cases were reported. Samples were tested at the Public Health England Rare and Imported Pathogens Laboratory using a bespoke panel of likely pathogens including haemorrhagic fever viruses, arboviruses and Rickettsia, Leptospira and Borrelia spp. Seven (11%) were positive for Crimean-Congo haemorrhagic fever virus (CCHFV) by real-time reverse transcription PCR. The remaining samples tested negative on all assays. Conclusions/Significance CCHFV is an important cause of fever and haemorrhage in Darfur, but not the sole major source of UFI outbreaks in Sudan. Prospective studies are needed to explore other aetiologies, including novel pathogens. The presence of CCHFV has critical infection, prevention and control as well as clinical implications for future response. Our study reinforces the need to boost surveillance, lab and investigative capacity to underpin effective response, and for local and international health security. The Federal Republic of Sudan has had at least 12 outbreaks of febrile illness of unknown cause associated with symptoms of haemorrhage and high case fatality rates since 2012. Outbreaks without clear diagnosis are concerning, particularly in countries such as Sudan where a range of high consequence diseases, including viral haemorrhagic fevers, are endemic or epidemic, and local laboratory capacity is limited. We transferred historical samples stored in the National Public Health Authority from one of these outbreaks that occurred in Darfur 2015–2016 to the Public Health England Laboratory at Porton, UK, and tested them against a wide range of infectious diseases to try to identify the cause, and to help the Sudanese Federal Ministry of Health to develop and target their limited laboratory capacity. We found that Crimean-Congo Haemorrhagic Fever was an important cause but not the only source of cases in this outbreak. This has implications for prevention and control as well as for treating cases. Our study also highlighted the need for future studies to explore other possible causes, including new pathogens, and reinforced the need to boost surveillance, lab and investigative capacity for more timely and complete outbreak response.
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Affiliation(s)
- Hilary Bower
- UK Public Health Rapid Support Team, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
| | - Mubarak El Karsany
- Department of Medical Microbiology, Karary University, Khartoum, Sudan
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | - Mazza Alzain
- Communicable Disease Surveillance and Event Unit, Federal Ministry of Health, Khartoum, Sudan
| | - Benedict Gannon
- UK Public Health Rapid Support Team, London, United Kingdom
- Global Public Health, Public Health England, London, United Kingdom
| | - Rehab Mohamed
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | - Iman Mahmoud
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | - Mawahib Eldegail
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | - Rihab Taha
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | - Abdalla Osman
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | - Salim Mohamednour
- Communicable Disease Surveillance and Event Unit, Federal Ministry of Health, Khartoum, Sudan
| | - Amanda Semper
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Barry Atkinson
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Daniel Carter
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Stuart Dowall
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Jenna Furneaux
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Victoria Graham
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Jack Mellors
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Jane Osborne
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Steven T. Pullan
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Gillian S. Slack
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Tim Brooks
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Roger Hewson
- National Infection Service, Public Health England, Porton, United Kingdom
| | - Nicholas J. Beeching
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jimmy Whitworth
- UK Public Health Rapid Support Team, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Daniel G. Bausch
- UK Public Health Rapid Support Team, London, United Kingdom
- Global Public Health, Public Health England, London, United Kingdom
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Tom E. Fletcher
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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16
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Wise EL, Pullan ST, Márquez S, Paz V, Mosquera JD, Zapata S, Jackson SK, Fejer G, Trueba G, Logue CH. Isolation of Oropouche Virus from Febrile Patient, Ecuador. Emerg Infect Dis 2019; 24:935-937. [PMID: 29664378 PMCID: PMC5938787 DOI: 10.3201/eid2405.171569] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We report identification of an Oropouche virus strain in a febrile patient from Ecuador by using metagenomic sequencing and real-time reverse transcription PCR. Virus was isolated from patient serum by using Vero cells. Phylogenetic analysis of the whole-genome sequence showed the virus to be similar to a strain from Peru.
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17
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Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, Dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, Dos Santos CC, Dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science 2018; 361:894-899. [PMID: 30139911 PMCID: PMC6874500 DOI: 10.1126/science.aat7115] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [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: 03/31/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022]
Abstract
The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.
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Affiliation(s)
- N R Faria
- Department of Zoology, University of Oxford, Oxford, UK.
| | - M U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - S C Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | - J Goes de Jesus
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R S Aguiar
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - F C M Iani
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - J Xavier
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - J Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - L du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
| | - S Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - J Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - R D O Carvalho
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - G Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - C-H Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - P P Silveira
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M B Arruda
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M A Pereira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - G C Pereira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - J Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
| | - U Obolski
- Department of Zoology, University of Oxford, Oxford, UK
| | - L Abade
- Department of Zoology, University of Oxford, Oxford, UK
- The Global Health Network, University of Oxford, Oxford, UK
| | - T I Vasylyeva
- Department of Zoology, University of Oxford, Oxford, UK
| | - M Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D Yi
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - D J Weiss
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - G R W Wint
- Department of Zoology, University of Oxford, Oxford, UK
| | - F M Shearer
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - S Funk
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - B Nikolay
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Institut Pasteur, Paris, France
- CNRS UMR2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - V Fonseca
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - T E R Adelino
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - M A A Oliveira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - M V F Silva
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - L Sacchetto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - P O Figueiredo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - I M Rezende
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - E M Mello
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - R F C Said
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D A Santos
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M L Ferraz
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M G Brito
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - L F Santana
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M T Menezes
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - R M Brindeiro
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - A Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - F C P Dos Santos
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - M S Cunha
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - J S Nogueira
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - I M Rocco
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - A C da Costa
- Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - S C V Komninakis
- Retrovirology Laboratory, Federal University of São Paulo, São Paulo, Brazil
- School of Medicine of ABC (FMABC), Clinical Immunology Laboratory, Santo André, São Paulo, Brazil
| | - V Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A O Chieppe
- Coordenação de Vigilância Epidemiológica do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - E S M Araujo
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - M C L Mendonça
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - C C Dos Santos
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - C D Dos Santos
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - A M Mares-Guia
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R M R Nogueira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - P C Sequeira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R G Abreu
- Departamento de Vigilância das Doenças Transmissíveis da Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília-DF, Brazil
| | - M H O Garcia
- Departamento de Vigilância das Doenças Transmissíveis da Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília-DF, Brazil
| | - A L Abreu
- Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília-DF, Brazil
| | - O Okumoto
- Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília-DF, Brazil
| | - E G Kroon
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - C F C de Albuquerque
- Organização Pan - Americana da Saúde/Organização Mundial da Saúde - (OPAS/OMS), Brasília-DF, Brazil
| | - K Lewandowski
- Public Health England, National Infections Service, Porton Down, Salisbury, UK
| | - S T Pullan
- Public Health England, National Infections Service, Porton Down, Salisbury, UK
| | - M Carroll
- NIHR HPRU in Emerging and Zoonotic Infections, Public Health England, London, UK
| | - T de Oliveira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - E C Sabino
- Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - R P Souza
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - M A Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - P Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - G S Trindade
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - B P Drumond
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A M B Filippis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - N J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - S Cauchemez
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Institut Pasteur, Paris, France
- CNRS UMR2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - L C J Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - O G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
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18
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Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc 2017; 12:1261-1276. [PMID: 28538739 PMCID: PMC5902022 DOI: 10.1038/nprot.2017.066] [Citation(s) in RCA: 656] [Impact Index Per Article: 93.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved in 1-2 d by starting with clinical samples and following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.
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Affiliation(s)
- Joshua Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Steven T Pullan
- Public Health England, National Infection Service, Porton Down, Salisbury, UK
| | - Ingra M Claro
- Department of Infectious Disease and Institute of Tropical Medicine, University of Saõ Paulo, Saõ Paulo, Brazil
| | - Andrew D Smith
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Glenn Oliveira
- Scripps Translational Science Institute, La Jolla, California, USA
| | | | - Thomas F Rogers
- The Scripps Research Institute, La Jolla, California, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | | | | | - Marta Giovanetti
- Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
- University of Rome, Tor Vergata, Italy
| | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | - Allison Black
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Miles W Carroll
- Public Health England, National Infection Service, Porton Down, Salisbury, UK
- University of Southampton, South General Hospital, Southampton, UK
| | | | | | - Ester C Sabino
- Department of Infectious Disease and Institute of Tropical Medicine, University of Saõ Paulo, Saõ Paulo, Brazil
| | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Kristian G Andersen
- The Scripps Research Institute, La Jolla, California, USA
- Scripps Translational Science Institute, La Jolla, California, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
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19
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Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments. Biotechnol Biofuels 2017; 10:35. [PMID: 28184248 PMCID: PMC5294722 DOI: 10.1186/s13068-017-0700-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/05/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND The capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails. RESULTS We investigated the responses of A. niger to untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics. The ionic liquid pretreatment altered the cellulose crystallinity while retaining more of the hemicellulosic sugars than the hydrothermal pretreatment. Ionic liquid pretreatment of straw led to a dynamic induction and repression of genes, which was correlated with the higher levels of pentose sugars saccharified from the ionic liquid-pretreated straw. Hydrothermal pretreatment of straw led to reduced levels of transcripts of genes encoding carbohydrate-active enzymes as well as the derived proteins and enzyme activities. Both pretreatments abolished the expression of a large set of genes encoding pectinolytic enzymes. These reduced levels could be explained by the removal of parts of the lignocellulose by the hydrothermal pretreatment. The time course also facilitated identification of temporally limited gene induction patterns. CONCLUSIONS The presented transcriptomic and biochemical datasets demonstrate that pretreatments caused modifications of the lignocellulose, to both specific structural features as well as the organisation of the overall lignocellulosic structure, that determined A. niger transcript levels. The experimental setup allowed reliable detection of substrate-specific gene expression patterns as well as hitherto non-expressed genes. Our data suggest beneficial effects of using untreated and IL-pretreated straw, but not HT-pretreated straw, as feedstock for CAZyme production.
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Affiliation(s)
- Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | | | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- TB Programme, Microbiology Services, Public Health England, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- UPMC, Univ. Paris 06, CNRS UMR7238, Sorbonne Universités, 15 rue de l’Ecole de Médecine, 75270 Paris, France
| | - Paul R. Waldron
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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Pullan ST, Allnutt JC, Devine R, Hatch KA, Jeeves RE, Hendon-Dunn CL, Marsh PD, Bacon J. The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity? BMC Infect Dis 2016; 16:205. [PMID: 27184366 PMCID: PMC4869200 DOI: 10.1186/s12879-016-1533-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 12/08/2015] [Accepted: 04/29/2016] [Indexed: 11/24/2022] Open
Abstract
Background Pyrazinamide (PZA) plays an essential part in the shortened six-month tuberculosis (TB) treatment course due to its activity against slow-growing and non-replicating organisms. We tested whether PZA preferentially targets slow growing cells of Mycobacterium tuberculosis that could be representative of bacteria that remain after the initial kill with isoniazid (INH), by observing the response of either slow growing or fast growing bacilli to differing concentrations of PZA. Methods M. tuberculosis H37Rv was grown in continuous culture at either a constant fast growth rate (Mean Generation Time (MGT) of 23.1 h) or slow growth rate (69.3 h MGT) at a controlled dissolved oxygen tension of 10 % and a controlled acidity at pH 6.3 ± 0.1. Cultures were exposed to step-wise increases in the concentration of PZA (25 to 500 μgml−1) every two MGTs, and bacterial survival was measured. PZA-induced global gene expression was explored for each increase in PZA-concentration, using DNA microarray. Results At a constant pH 6.3, actively dividing mycobacteria were susceptible to PZA, with similar responses to increasing concentrations of PZA at both growth rates. Three distinct phases of drug response could be distingished for both slow growing (69.3 h MGT) and fast growing (23.1 h MGT) bacilli. A bacteriostatic phase at a low concentration of PZA was followed by a recovery period in which the culture adapted to the presence of PZA and bacteria were actively dividing in steady-state. In contrast, there was a rapid loss of viability at bactericidal concentrations. There was a notable delay in the onset of the recovery period in quickly dividing cells compared with those dividing more slowly. Fast growers and slow growers adapted to PZA-exposure via very similar mechanisms; through reduced gene expression of tRNA, 50S, and 30S ribosomal proteins. Conclusions PZA had an equivalent level of activity against fast growing and slow growing M. tuberculosis. At both growth rates drug-tolerance to sub-lethal concentrations may have been due to reduced expression of tRNA, 50S, and 30S ribosomal proteins. The findings from this study show that PZA has utility against more than one phenotypic sub-population of bacilli and could be re-assessed for its early bactericidal activity, in combination with other drugs, during TB treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1533-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven T Pullan
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Jon C Allnutt
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Rebecca Devine
- School of Biological Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, UK
| | - Kim A Hatch
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Rose E Jeeves
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Charlotte L Hendon-Dunn
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Philip D Marsh
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Joanna Bacon
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK.
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Pullan ST, Pearson TR, Latham J, Mason J, Atkinson B, Silman NJ, Marston CK, Sahl JW, Birdsell D, Hoffmaster AR, Keim P, Vipond R. Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case. Microb Genom 2015; 1:e000039. [PMID: 28348823 PMCID: PMC5320680 DOI: 10.1099/mgen.0.000039] [Citation(s) in RCA: 6] [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: 07/27/2015] [Accepted: 10/08/2015] [Indexed: 11/18/2022] Open
Abstract
There have been two anthrax cases affecting people that played and/or made animal-skin drums in the UK during the last 10 years, with single fatal occurrences in Scotland in 2006 and London in 2008. Investigations by the Health Protection Agency (now Public Health England) employing multi-locus-variable number tandem repeat analysis had previously linked the clinical cases to spores associated with animal skins and drums the patients had been in contact with. In this study, whole-genome sequencing of 23 Bacillus anthracis isolates harvested during the investigations was performed. High-quality draft assemblies of these genomes provided greater characterization of the B. anthracis strains present and placed them all upon a new branch of the global phylogeny. Although closely related, the clinical isolates from the two events, and another isolated from a drum-skin-associated case in New York in 2006, were distinct from each other. Multiple distinct genotypes were found during both investigations, implying either multiple contamination events or a single heterogeneous contamination. One environmental isolate from the Scottish incident was more closely related to London isolates than to the other Scottish isolates. As B. anthracis of this subgroup was present at both geographically and temporally distinct events, it may be more widespread at the source of contamination. All isolates were distinct from currently characterized West African strains, despite this being the likely origin of the drums and hides, therefore adding to our knowledge of B. anthracis diversity in the region.
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Affiliation(s)
- Steven T Pullan
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Talima R Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Jennie Latham
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Joanne Mason
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Barry Atkinson
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Nigel J Silman
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
| | - Chung K Marston
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jason W Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Dawn Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Alex R Hoffmaster
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Richard Vipond
- Public Health England, Microbiology Services, Porton Down, Salisbury, Wiltshire, UK
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Jeeves RE, Marriott AAN, Pullan ST, Hatch KA, Allnutt JC, Freire-Martin I, Hendon-Dunn CL, Watson R, Witney AA, Tyler RH, Arnold C, Marsh PD, McHugh TD, Bacon J. Mycobacterium tuberculosis Is Resistant to Isoniazid at a Slow Growth Rate by Single Nucleotide Polymorphisms in katG Codon Ser315. PLoS One 2015; 10:e0138253. [PMID: 26382066 PMCID: PMC4575197 DOI: 10.1371/journal.pone.0138253] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/27/2015] [Indexed: 12/21/2022] Open
Abstract
An important aim for improving TB treatment is to shorten the period of antibiotic therapy without increasing relapse rates or encouraging the development of antibiotic-resistant strains. In any M. tuberculosis population there is a proportion of bacteria that are drug-tolerant; this might be because of pre-existing populations of slow growing/non replicating bacteria that are protected from antibiotic action due to the expression of a phenotype that limits drug activity. We addressed this question by observing populations of either slow growing (constant 69.3h mean generation time) or fast growing bacilli (constant 23.1h mean generation time) in their response to the effects of isoniazid exposure, using controlled and defined growth in chemostats. Phenotypic differences were detected between the populations at the two growth rates including expression of efflux mechanisms and the involvement of antisense RNA/small RNA in the regulation of a drug-tolerant phenotype, which has not been explored previously for M. tuberculosis. Genotypic analyses showed that slow growing bacilli develop resistance to isoniazid through mutations specifically in katG codon Ser315 which are present in approximately 50–90% of all isoniazid-resistant clinical isolates. The fast growing bacilli persisted as a mixed population with katG mutations distributed throughout the gene. Mutations in katG codon Ser315 appear to have a fitness cost in vitro and particularly in fast growing cultures. Our results suggest a requirement for functional katG-encoded catalase-peroxide in the slow growers but not the fast-growing bacteria, which may explain why katG codon Ser315 mutations are favoured in the slow growing cultures.
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Affiliation(s)
- Rose E. Jeeves
- Public Health England, Porton Down, Salisbury, United Kingdom
| | | | | | - Kim A. Hatch
- Public Health England, Porton Down, Salisbury, United Kingdom
| | - Jon C. Allnutt
- Public Health England, Porton Down, Salisbury, United Kingdom
| | | | | | - Robert Watson
- Public Health England, Porton Down, Salisbury, United Kingdom
| | - Adam A. Witney
- St George's, University of London, Cranmer Terrace, London, United Kingdom
| | - Richard H. Tyler
- St George's, University of London, Cranmer Terrace, London, United Kingdom
| | - Catherine Arnold
- Public Health England, Colindale, 61 Colindale Avenue, London, United Kingdom
| | - Philip D. Marsh
- Public Health England, Porton Down, Salisbury, United Kingdom
| | - Timothy D. McHugh
- University College London, Centre for Clinical Microbiology, Royal Free Campus, Rowland Hill Street, London, United Kingdom
| | - Joanna Bacon
- Public Health England, Porton Down, Salisbury, United Kingdom
- * E-mail:
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23
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Pullan ST, Daly P, Delmas S, Ibbett R, Kokolski M, Neiteler A, van Munster JM, Wilson R, Blythe MJ, Gaddipati S, Tucker GA, Archer DB. RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger. Fungal Biol Biotechnol 2014. [PMID: 26457194 PMCID: PMC4599204 DOI: 10.1186/s40694-014-0001-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [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] [Indexed: 11/11/2022] Open
Abstract
Background Filamentous fungi are well known for their ability to degrade lignocellulosic biomass and have a natural ability to convert certain products of biomass degradation, for example glucose, into various organic acids. Organic acids are suggested to give a competitive advantage to filamentous fungi over other organisms by decreasing the ambient pH. They also have an impact on the ecosystem by enhancing weathering and metal detoxification. Commercially, organic acids can be used as chemical intermediates or as synthons for the production of biodegradable polymers which could replace petroleum-based or synthetic chemicals. One of the advantages of filamentous fungi as biotechnological production platforms for synthetic biology is their ability to degrade vegetal biomass, which is a promising feedstock for the biotechnological production of organic acids. The Fungal Culture Collection of the International Centre of Microbial Resources (CIRM-CF), curated by our laboratory, contains more than 1600 strains of filamentous fungi, mainly Basidiomycetes and Ascomycetes. The natural biodiversity found in this collection is wide, with strains collected from around the world in different climatic conditions. This collection is mainly studied to unravel the arsenal of secreted lignocellulolytic enzymes available to the fungi in order to enhance biomass degradation. While the fungal biodiversity is a tremendous reservoir for “green” molecules production, its potentiality for organic acids production is not completely known. Results In this study, we screened 40 strains of Ascomycota and 26 strains of Basidiomycota, representing the distribution of fungal diversity of the CIRM-CF collection, in order to evaluate their potential for organic acid and ethanol production, in a glucose liquid medium. We observed that most of the filamentous fungi are able to grow and acidify the medium. We were also able to discriminate two groups of filamentous fungi considering their organic acid production at day 6 of incubation. This first group represented fungi co-producing a wide variety of organic acids and ethanol at concentrations up to 4 g.L−1 and was composed of all the Aspergilli and only 3 other Ascomycota. The second group was composed of the remaining Ascomycota and all the Basidiomycota which produced mainly ethanol. Among the Basidiomycota, two strains produced oxalic acid and one strain produced gluconic and formic acid. Six strains of Aspergillus producing high concentrations of oxalic, citric and gluconic acids, and ethanol were selected for metabolism analysis. Conclusion These results illustrate the versatility in metabolites production among the fungal kingdom. Moreover, we found that some of the studied strains have good predispositions to produce valuable molecules. These strains could be of great interest in the study of metabolism and may represent new models for synthetic biology or consolidated bioprocessing of biomass. Electronic supplementary material The online version of this article (doi:10.1186/s40694-014-0001-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven T Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Almar Neiteler
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Jolanda M van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Raymond Wilson
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Martin J Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Gregory A Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - David B Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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24
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van Munster JM, Daly P, Delmas S, Pullan ST, Blythe MJ, Malla S, Kokolski M, Noltorp ECM, Wennberg K, Fetherston R, Beniston R, Yu X, Dupree P, Archer DB. The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger. Fungal Genet Biol 2014; 72:34-47. [PMID: 24792495 PMCID: PMC4217149 DOI: 10.1016/j.fgb.2014.04.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/21/2014] [Accepted: 04/18/2014] [Indexed: 11/06/2022]
Abstract
Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that the transcriptional response after 6h of exposure to wheat straw was very different from the response at 24h of exposure to the same substrate. For example, less than half of the genes encoding carbohydrate active enzymes that were induced after 24h of exposure to wheat straw, were also induced after 6h exposure. Importantly, over a third of the genes induced after 6h of exposure to wheat straw were also induced during 6h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. We show, using proteomics, that carbon-starved cultures indeed release CAZymes with predicted activity on plant polysaccharides. Analysis of the enzymatic activity and the reaction products, indicates that these proteins are enzymes that can degrade various plant polysaccharides to generate both known, as well as potentially new, inducers of CAZymes.
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Affiliation(s)
- Jolanda M van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Steven T Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Martin J Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Sunir Malla
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Emelie C M Noltorp
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Kristin Wennberg
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Richard Fetherston
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Richard Beniston
- Biological Mass Spectrometry Facility biOMICS, University of Sheffield, Brook Hill Road, Sheffield S3 7HF, UK.
| | - Xiaolan Yu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
| | - David B Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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Ries L, Pullan ST, Delmas S, Malla S, Blythe MJ, Archer DB. Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger. BMC Genomics 2013; 14:541. [PMID: 24060058 PMCID: PMC3750697 DOI: 10.1186/1471-2164-14-541] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [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: 04/05/2013] [Accepted: 08/06/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND A major part of second generation biofuel production is the enzymatic saccharification of lignocellulosic biomass into fermentable sugars. Many fungi produce enzymes that can saccarify lignocellulose and cocktails from several fungi, including well-studied species such as Trichoderma reesei and Aspergillus niger, are available commercially for this process. Such commercially-available enzyme cocktails are not necessarily representative of the array of enzymes used by the fungi themselves when faced with a complex lignocellulosic material. The global induction of genes in response to exposure of T. reesei to wheat straw was explored using RNA-seq and compared to published RNA-seq data and model of how A. niger senses and responds to wheat straw. RESULTS In T. reesei, levels of transcript that encode known and predicted cell-wall degrading enzymes were very high after 24h exposure to straw (approximately 13% of the total mRNA) but were less than recorded in A. niger (approximately 19% of the total mRNA). Closer analysis revealed that enzymes from the same glycoside hydrolase families but different carbohydrate esterase and polysaccharide lyase families were up-regulated in both organisms. Accessory proteins which have been hypothesised to possibly have a role in enhancing carbohydrate deconstruction in A. niger were also uncovered in T. reesei and categories of enzymes induced were in general similar to those in A. niger. Similarly to A. niger, antisense transcripts are present in T. reesei and their expression is regulated by the growth condition. CONCLUSIONS T. reesei uses a similar array of enzymes, for the deconstruction of a solid lignocellulosic substrate, to A. niger. This suggests a conserved strategy towards lignocellulose degradation in both saprobic fungi. This study provides a basis for further analysis and characterisation of genes shown to be highly induced in the presence of a lignocellulosic substrate. The data will help to elucidate the mechanism of solid substrate recognition and subsequent degradation by T. reesei and provide information which could prove useful for efficient production of second generation biofuels.
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Affiliation(s)
- Laure Ries
- School of Biology, University of Nottingham, Nottingham NG7 2RD, UK
| | - Steven T Pullan
- School of Biology, University of Nottingham, Nottingham NG7 2RD, UK
| | - Stéphane Delmas
- School of Biology, University of Nottingham, Nottingham NG7 2RD, UK
- Université Pierre et Marie Curie (UPMC, Université Paris 06), Sorbonne Universités, UMR 7138, Systématique Adapation et Évolution, 75005 Paris, France
| | - Sunir Malla
- Deep Seq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Martin J Blythe
- Deep Seq, Centre for Genetics and Genomics, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - David B Archer
- School of Biology, University of Nottingham, Nottingham NG7 2RD, UK
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Pullan ST, Chandra G, Bibb MJ, Merrick M. Genome-wide analysis of the role of GlnR in Streptomyces venezuelae provides new insights into global nitrogen regulation in actinomycetes. BMC Genomics 2011; 12:175. [PMID: 21463507 PMCID: PMC3087709 DOI: 10.1186/1471-2164-12-175] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [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: 11/29/2010] [Accepted: 04/04/2011] [Indexed: 11/18/2022] Open
Abstract
Background GlnR is an atypical response regulator found in actinomycetes that modulates the transcription of genes in response to changes in nitrogen availability. We applied a global in vivo approach to identify the GlnR regulon of Streptomyces venezuelae, which, unlike many actinomycetes, grows in a diffuse manner that is suitable for physiological studies. Conditions were defined that facilitated analysis of GlnR-dependent induction of gene expression in response to rapid nitrogen starvation. Microarray analysis identified global transcriptional differences between glnR+ and glnR mutant strains under varying nitrogen conditions. To differentiate between direct and indirect regulatory effects of GlnR, chromatin immuno-precipitation (ChIP) using antibodies specific to a FLAG-tagged GlnR protein, coupled with microarray analysis (ChIP-chip), was used to identify GlnR binding sites throughout the S. venezuelae genome. Results GlnR bound to its target sites in both transcriptionally active and apparently inactive forms. Thirty-six GlnR binding sites were identified by ChIP-chip analysis allowing derivation of a consensus GlnR-binding site for S. venezuelae. GlnR-binding regions were associated with genes involved in primary nitrogen metabolism, secondary metabolism, the synthesis of catabolic enzymes and a number of transport-related functions. Conclusions The GlnR regulon of S. venezuelae is extensive and impacts on many facets of the organism's biology. GlnR can apparently bind to its target sites in both transcriptionally active and inactive forms.
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Affiliation(s)
- Steven T Pullan
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
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Abstract
The study of bacterial responses to nitric oxide (NO), nitrosating agents, and other agents of nitrosative stress has a short history but has rapidly produced important insights into the interactions of these agents with model microbial systems as well as pathogenic species. Several methodological problems arise in attempting to define the global responses to these agents, whether in simply measuring growth or performing "omic" experiments in which the objective is to determine the genome-wide (transcriptomic) or proteome-wide responses. The first problem is the relatively long timescale over which the experiments are conducted--minutes, hours, or days in the case of slow-growing cultures. The second problem is not unique to NO and its congeners but concerns the difficulties encountered when sensitive and comprehensive analytical techniques (such as transcriptomics) are applied to cultures whose growth and physiology are perturbed by an inhibitor. In essence, the problem is "seeing the wood for the trees." This chapter reviews briefly the state of knowledge of NO responses and mechanisms in bacteria, particularly Escherichia coli and Campylobacter jejuni. Continuous culture has several advantages for investigating the consequences of NO exposure, and this approach is outlined with examples of recent results and conclusions. The major advantage of the chemostat is establishment of a reproducible quasi-steady state in growth, in which the growth rate can be controlled and maintained. Contrary to common belief, neither the concept nor the apparatus is difficult. Commercially available and homemade systems are described with practical advice. Establishing continuous cultures paves the way for other "omic" approaches, particularly proteomics and metabolomics, which are not covered here, as their application to the field of NO biology is in its infancy. A key to the literature describing methods suitable for assessing toxicity to microbes of NO and reactive nitrogen species is given.
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Affiliation(s)
- Steven T Pullan
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
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Pullan ST, Gidley MD, Jones RA, Barrett J, Stevanin TM, Read RC, Green J, Poole RK. Nitric oxide in chemostat-cultured Escherichia coli is sensed by Fnr and other global regulators: unaltered methionine biosynthesis indicates lack of S nitrosation. J Bacteriol 2006; 189:1845-55. [PMID: 17189370 PMCID: PMC1855760 DOI: 10.1128/jb.01354-06] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We previously elucidated the global transcriptional responses of Escherichia coli to the nitrosating agent S-nitrosoglutathione (GSNO) in both aerobic and anaerobic chemostats, demonstrated the expression of nitric oxide (NO)-protective mechanisms, and obtained evidence of critical thiol nitrosation. The present study was the first to examine the transcriptome of NO-exposed E. coli in a chemostat. Using identical conditions, we compared the GSNO stimulon with the stimulon of NO released from two NO donor compounds {3-[2-hydroxy-1-(1-methyl-ethyl)-2-nitrosohydrazino]-1-propanamine (NOC-5) and 3-(2-hydroxy-1-methyl-2-nitrosohydrazino)-N-methyl-1-propanamine (NOC-7)} simultaneously and demonstrated that there were marked differences in the transcriptional responses to these distinct nitrosative stresses. Exposure to NO did not induce met genes, suggesting that, unlike GSNO, NO does not elicit homocysteine S nitrosation and compensatory increases in methionine biosynthesis. After entry into cells, exogenous methionine provided protection from GSNO-mediated killing but not from NO-mediated killing. Anaerobic exposure to NO led to up-regulation of multiple Fnr-repressed genes and down-regulation of Fnr-activated genes, including nrfA, which encodes cytochrome c nitrite reductase, providing strong evidence that there is NO inactivation of Fnr. Other global regulators apparently affected by NO were IscR, Fur, SoxR, NsrR, and NorR. We tried to identify components of the NorR regulon by performing a microarray comparison of NO-exposed wild-type and norR mutant strains; only norVW, encoding the NO-detoxifying flavorubredoxin and its cognate reductase, were unambiguously identified. Mutation of norV or norR had no effect on E. coli survival in mouse macrophages. Thus, GSNO (a nitrosating agent) and NO have distinct cellular effects; NO more effectively interacts with global regulators that mediate adaptive responses to nitrosative stress but does not affect methionine requirements arising from homocysteine nitrosation.
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Affiliation(s)
- Steven T Pullan
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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Flatley J, Barrett J, Pullan ST, Hughes MN, Green J, Poole RK. Transcriptional responses of Escherichia coli to S-nitrosoglutathione under defined chemostat conditions reveal major changes in methionine biosynthesis. J Biol Chem 2005; 280:10065-72. [PMID: 15647275 DOI: 10.1074/jbc.m410393200] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nitric oxide and nitrosating agents exert powerful antimicrobial effects and are central to host defense and signal transduction. Nitric oxide and S-nitrosothiols can be metabolized by bacteria, but only a few enzymes have been shown to be important in responses to such stresses. Glycerol-limited chemostat cultures in defined medium of Escherichia coli MG1655 were used to provide bacteria in defined physiological states before applying nitrosative stress by addition of S-nitrosoglutathione (GSNO). Exposure to 200 microm GSNO for 5 min was sufficient to elicit an adaptive response as judged by the development of NO-insensitive respiration. Transcriptome profiling experiments were used to investigate the transcriptional basis of the observed adaptation to the presence of GSNO. In aerobic cultures, only 17 genes were significantly up-regulated, including genes known to be involved in NO tolerance, particularly hmp (encoding the NO-consuming flavohemoglobin Hmp) and norV (encoding flavorubredoxin). Significantly, none of the up-regulated genes were members of the Fur regulon. Six genes involved in methionine biosynthesis or regulation were significantly up-regulated; metN, metI, and metR were shown to be important for GSNO tolerance, because mutants in these genes exhibited GSNO growth sensitivity. Furthermore, exogenous methionine abrogated the toxicity of GSNO supporting the hypothesis that GSNO nitrosates homocysteine, thereby withdrawing this intermediate from the methionine biosynthetic pathway. Anaerobically, 10 genes showed significant up-regulation, of which norV, hcp, metR, and metB were also up-regulated aerobically. The data presented here reveal new genes important for nitrosative stress tolerance and demonstrate that methionine biosynthesis is a casualty of nitrosative stress.
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Affiliation(s)
- Janet Flatley
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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Simm AM, Higgins CS, Pullan ST, Avison MB, Niumsup P, Erdozain O, Bennett PM, Walsh TR. A novel metallo-beta-lactamase, Mbl1b, produced by the environmental bacterium Caulobacter crescentus. FEBS Lett 2001; 509:350-4. [PMID: 11749954 DOI: 10.1016/s0014-5793(01)03152-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Caulobacter crescentus 101123 possesses a gene (Mbl1b) encoding a metallo-beta-lactamase with 32% amino acid identity to the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia. The gene was cloned into an expression vector and the enzyme, Mbl1b, was expressed in Escherichia coli. Mbl1b was purified. Catalytic properties for several antibiotics were determined. The enzyme exhibits Michaelis-Menten kinetics for imipenem, meropenem and nitrocefin but substrate inhibition kinetics with cefoxitin, cefaloridine, penicillin G and ampicillin. A homology model predicts Mbl1b has the same structural fold as other metallo-beta-lactamases with a detailed structure very similar to L1 but whereas L1 is a homotetramer, Mbl1b is monomeric. The main differences between Mbl1 and L1 are in the N-terminal region.
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Affiliation(s)
- A M Simm
- Department of Pathology and Microbiology, University of Bristol, University Walk, UK.
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