1
|
Davies ER, Ryan KA, Bewley KR, Coombes NS, Salguero FJ, Carnell OT, Biddlecombe S, Charlton M, Challis A, Cross ES, Handley A, Ngabo D, Weldon TM, Hall Y, Funnell SGP. The Omicron Sub-Variant BA.4 Displays a Remarkable Lack of Clinical Signs in a Golden Syrian Hamster Model of SARS-CoV-2 Infection. Viruses 2023; 15:1133. [PMID: 37243219 PMCID: PMC10224153 DOI: 10.3390/v15051133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The ongoing emergence of SARS-CoV-2 virus variants remains a source of concern because it is accompanied by the potential for increased virulence as well as evasion of immunity. Here we show that, although having an almost identical spike gene sequence as another Omicron variant (BA.5.2.1), a BA.4 isolate lacked all the typical disease characteristics of other isolates seen in the Golden Syrian hamster model despite replicating almost as effectively. Animals infected with BA.4 had similar viral shedding profiles to those seen with BA.5.2.1 (up to day 6 post-infection), but they all failed to lose weight or present with any other significant clinical signs. We hypothesize that this lack of detectable signs of disease during infection with BA.4 was due to a small (nine nucleotide) deletion (∆686-694) in the viral genome (ORF1ab) responsible for the production of non-structural protein 1, which resulted in the loss of three amino acids (aa 141-143).
Collapse
Affiliation(s)
- Elizabeth R. Davies
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Kathryn A. Ryan
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Kevin R. Bewley
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Naomi S. Coombes
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Francisco J. Salguero
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Oliver T. Carnell
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Sarah Biddlecombe
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Michael Charlton
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Amy Challis
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Eleanor S. Cross
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Alastair Handley
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Didier Ngabo
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Thomas M. Weldon
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Yper Hall
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Simon G. P. Funnell
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- World Health Organization, Appia 20, 1211 Geneva, Switzerland
| |
Collapse
|
2
|
Handley A, Ryan KA, Davies ER, Bewley KR, Carnell OT, Challis A, Coombes NS, Fotheringham SA, Gooch KE, Charlton M, Harris DJ, Kennard C, Ngabo D, Weldon TM, Salguero FJ, Funnell SGP, Hall Y. SARS-CoV-2 Disease Severity in the Golden Syrian Hamster Model of Infection Is Related to the Volume of Intranasal Inoculum. Viruses 2023; 15:748. [PMID: 36992457 PMCID: PMC10051760 DOI: 10.3390/v15030748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
The golden Syrian hamster (Mesocricetus auratus) is now commonly used in preclinical research for the study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the assessment of vaccines, drugs and therapeutics. Here, we show that hamsters inoculated via the intranasal route with the same infectious virus dose of prototypical SARS-CoV-2 administered in a different volume present with different clinical signs, weight loss and viral shedding, with a reduced volume resulting in reduced severity of disease similar to that obtained by a 500-fold reduction in the challenge dose. The tissue burden of the virus and the severity of pulmonary pathology were also significantly affected by different challenge inoculum volumes. These findings suggest that a direct comparison between the severity of SARS-CoV-2 variants or studies assessing the efficacy of treatments determined by hamster studies cannot be made unless both the challenge dose and inoculation volume are matched when using the intranasal route. Additionally, analysis of sub-genomic and total genomic RNA PCR data demonstrated no link between sub-genomic and live viral titres and that sub-genomic analyses do not provide any information beyond that provided by more sensitive total genomic PCR.
Collapse
Affiliation(s)
- Alastair Handley
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Kathryn A. Ryan
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Elizabeth R. Davies
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Kevin R. Bewley
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Oliver T. Carnell
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Amy Challis
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Naomi S. Coombes
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Susan A. Fotheringham
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Karen E. Gooch
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Michael Charlton
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Debbie J. Harris
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Chelsea Kennard
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Didier Ngabo
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Thomas M. Weldon
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Francisco J. Salguero
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| | - Simon G. P. Funnell
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- World Health Organization, Appia 20, 1211 Geneva, Switzerland
| | - Yper Hall
- UKHSA Porton, Vaccine Development and Evaluation Centre, UK Health Security Agency, Manor Farm Road, Salisbury SP4 0JG, UK
| |
Collapse
|
3
|
Gibson JF, Pidwill GR, Carnell OT, Surewaard BGJ, Shamarina D, Sutton JAF, Jeffery C, Derré-Bobillot A, Archambaud C, Siggins MK, Pollitt EJG, Johnston SA, Serror P, Sriskandan S, Renshaw SA, Foster SJ. Commensal bacteria augment Staphylococcus aureus infection by inactivation of phagocyte-derived reactive oxygen species. PLoS Pathog 2021; 17:e1009880. [PMID: 34529737 PMCID: PMC8478205 DOI: 10.1371/journal.ppat.1009880] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/28/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Staphylococcus aureus is a human commensal organism and opportunist pathogen, causing potentially fatal disease. The presence of non-pathogenic microflora or their components, at the point of infection, dramatically increases S. aureus pathogenicity, a process termed augmentation. Augmentation is associated with macrophage interaction but by a hitherto unknown mechanism. Here, we demonstrate a breadth of cross-kingdom microorganisms can augment S. aureus disease and that pathogenesis of Enterococcus faecalis can also be augmented. Co-administration of augmenting material also forms an efficacious vaccine model for S. aureus. In vitro, augmenting material protects S. aureus directly from reactive oxygen species (ROS), which correlates with in vivo studies where augmentation restores full virulence to the ROS-susceptible, attenuated mutant katA ahpC. At the cellular level, augmentation increases bacterial survival within macrophages via amelioration of ROS, leading to proliferation and escape. We have defined the molecular basis for augmentation that represents an important aspect of the initiation of infection. S. aureus is a commensal inhabitant of the human skin and nares. However, it can cause serious diseases if it is able to breach our protective barriers such as the skin, often via wounds or surgery. If infection occurs via a wound, this initial inoculum contains both the pathogen, other members of the microflora and also wider environmental microbes. We have previously described “augmentation”, whereby this other non-pathogenic material can enhance the ability of S. aureus to lead to a serious disease outcome. Here we have determined the breadth of augmenting material and elucidated the cellular and molecular basis for its activity. Augmentation occurs via shielding of S. aureus from the direct bactericidal effects of reactive oxygen species produced by macrophages. This initial protection enables the effective establishment of S. aureus infection. Understanding augmentation not only explains an important facet of the interaction of S. aureus with our innate immune system, but also provides a platform for the development of novel prophylaxis approaches.
Collapse
Affiliation(s)
- Josie F. Gibson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
- The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Grace R. Pidwill
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Oliver T. Carnell
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Bas G. J. Surewaard
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Daria Shamarina
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Joshua A. F. Sutton
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Charlotte Jeffery
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | | | - Cristel Archambaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Matthew K. Siggins
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Eric J. G. Pollitt
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
| | - Simon A. Johnston
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
- The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Stephen A. Renshaw
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
- The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
- Department of Infection, Immunity and Cardiovascular disease, Medical School, University of Sheffield, Sheffield, United Kingdom
- * E-mail: (SAR); (SJF)
| | - Simon J. Foster
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
- Florey Institute, University of Sheffield, Sheffield, United Kingdom, Sheffield, United Kingdom
- * E-mail: (SAR); (SJF)
| |
Collapse
|
4
|
Panchal VV, Griffiths C, Mosaei H, Bilyk B, Sutton JAF, Carnell OT, Hornby DP, Green J, Hobbs JK, Kelley WL, Zenkin N, Foster SJ. Evolving MRSA: High-level β-lactam resistance in Staphylococcus aureus is associated with RNA Polymerase alterations and fine tuning of gene expression. PLoS Pathog 2020; 16:e1008672. [PMID: 32706832 PMCID: PMC7380596 DOI: 10.1371/journal.ppat.1008672] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 08/28/2019] [Accepted: 06/02/2020] [Indexed: 12/21/2022] Open
Abstract
Most clinical MRSA (methicillin-resistant S. aureus) isolates exhibit low-level β-lactam resistance (oxacillin MIC 2-4 μg/ml) due to the acquisition of a novel penicillin binding protein (PBP2A), encoded by mecA. However, strains can evolve high-level resistance (oxacillin MIC ≥256 μg/ml) by an unknown mechanism. Here we have developed a robust system to explore the basis of the evolution of high-level resistance by inserting mecA into the chromosome of the methicillin-sensitive S. aureus SH1000. Low-level mecA-dependent oxacillin resistance was associated with increased expression of anaerobic respiratory and fermentative genes. High-level resistant derivatives had acquired mutations in either rpoB (RNA polymerase subunit β) or rpoC (RNA polymerase subunit β') and these mutations were shown to be responsible for the observed resistance phenotype. Analysis of rpoB and rpoC mutants revealed decreased growth rates in the absence of antibiotic, and alterations to, transcription elongation. The rpoB and rpoC mutations resulted in decreased expression to parental levels, of anaerobic respiratory and fermentative genes and specific upregulation of 11 genes including mecA. There was however no direct correlation between resistance and the amount of PBP2A. A mutational analysis of the differentially expressed genes revealed that a member of the S. aureus Type VII secretion system is required for high level resistance. Interestingly, the genomes of two of the high level resistant evolved strains also contained missense mutations in this same locus. Finally, the set of genetically matched strains revealed that high level antibiotic resistance does not incur a significant fitness cost during pathogenesis. Our analysis demonstrates the complex interplay between antibiotic resistance mechanisms and core cell physiology, providing new insight into how such important resistance properties evolve.
Collapse
Affiliation(s)
- Viralkumar V. Panchal
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Caitlin Griffiths
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hamed Mosaei
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bohdan Bilyk
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Joshua A. F. Sutton
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - Oliver T. Carnell
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| | - David P. Hornby
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Jeffrey Green
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Jamie K. Hobbs
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - William L. Kelley
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, Geneva, Switzerland
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simon J. Foster
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, United Kingdom
- The Florey Institute for Host-Pathogen Interactions, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|