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Stockdale SR, Blanchard AM, Nayak A, Husain A, Nashine R, Dudani H, McClure CP, Tarr AW, Nag A, Meena E, Sinha V, Shrivastava SK, Hill C, Singer AC, Gomes RL, Acheampong E, Chidambaram SB, Bhatnagar T, Vetrivel U, Arora S, Kashyap RS, Monaghan TM. RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance. Lancet Reg Health Southeast Asia 2023; 14:100205. [PMID: 37193348 PMCID: PMC10150210 DOI: 10.1016/j.lansea.2023.100205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/18/2023]
Abstract
Background The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the potential to assess multiple infectious diseases simultaneously and has yet to be explored. Methods A retrospective RNA-Seq epidemiological survey of 140 untreated composite wastewater samples was performed across urban (n = 112) and rural (n = 28) areas of Nagpur, Central India. Composite wastewater samples were prepared by pooling 422 individual grab samples collected prospectively from sewer lines of urban municipality zones and open drains of rural areas from 3rd February to 3rd April 2021, during the second COVID-19 wave in India. Samples were pre-processed and total RNA was extracted prior to genomic sequencing. Findings This is the first study that has utilised culture and/or probe-independent unbiased RNA-Seq to examine Indian wastewater samples. Our findings reveal the detection of zoonotic viruses including chikungunya, Jingmen tick and rabies viruses, which have not previously been reported in wastewater. SARS-CoV-2 was detectable in 83 locations (59%), with stark abundance variations observed between sampling sites. Hepatitis C virus was the most frequently detected infectious virus, identified in 113 locations and co-occurring 77 times with SARS-CoV-2; and both were more abundantly detected in rural areas than urban zones. Concurrent identification of segmented virus genomic fragments of influenza A virus, norovirus, and rotavirus was observed. Geographical differences were also observed for astrovirus, saffold virus, husavirus, and aichi virus that were more prevalent in urban samples, while the zoonotic viruses chikungunya and rabies, were more abundant in rural environments. Interpretation RNA-Seq can effectively detect multiple infectious diseases simultaneously, facilitating geographical and epidemiological surveys of endemic viruses that could help direct healthcare interventions against emergent and pre-existent infectious diseases as well as cost-effectively and qualitatively characterising the health status of the population over time. Funding UK Research and Innovation (UKRI) Global Challenges Research Fund (GCRF) grant number H54810, as supported by Research England.
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Affiliation(s)
| | - Adam M. Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Amit Nayak
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Aliabbas Husain
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Rupam Nashine
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Hemanshi Dudani
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - C. Patrick McClure
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Aditi Nag
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Ekta Meena
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Vikky Sinha
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Sandeep K. Shrivastava
- Centre for Innovation, Research & Development, Dr. B. Lal Clinical Laboratory Pvt. Ltd., Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Andrew C. Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Rachel L. Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, United Kingdom
| | - Edward Acheampong
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, United Kingdom
- Department of Statistics and Actuarial Science, University of Ghana, P.O. Box, LG 115, Legon, Ghana
| | - Saravana B. Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, 570015, KA, India
| | - Tarun Bhatnagar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- National Institute of Traditional Medicine, Indian Council of Medical Research, Belagavi, 590010, India
- Virology and Biotechnology Division, ICMR-National Institute for Research in Tuberculosis, Chennai, 600031, India
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Rajpal Singh Kashyap
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Tanya M. Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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Blanchard AM, Baumbach CM, Michler JK, Pickwell ND, Staley CE, Franklin JM, Wattegedera SR, Entrican G, Tötemeyer S. Natural Mycoplasma Infection Reduces Expression of Pro-Inflammatory Cytokines in Response to Ovine Footrot Pathogens. Animals (Basel) 2022; 12:ani12233235. [PMID: 36496756 PMCID: PMC9737833 DOI: 10.3390/ani12233235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/10/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Ovine footrot is a complex multifactorial infectious disease, causing lameness in sheep with major welfare and economic consequences. Dichelobacter nodosus is the main causative bacterium; however, footrot is a polymicrobial disease with Fusobacterium necrophorum, Mycoplasma fermentans and Porphyromonas asaccharolytica also associated. There is limited understanding of the host response involved. The proinflammatory mediators, interleukin (IL)-1β and C-X-C Motif Chemokine Ligand 8 (CXCL8), have been shown to play a role in the early response to D. nodosus in dermal fibroblasts and interdigital skin explant models. To further understand the response of ovine skin to bacterial stimulation, and to build an understanding of the role of the cytokines and chemokines identified, primary ovine interdigital fibroblasts and keratinocytes were isolated, cultured and stimulated. The expression of mRNA and protein release of CXCL8 and IL-1β were measured after stimulation with LPS, D. nodosus or F. necrophorum, which resulted in increased transcript levels of IL-1β and CXCL8 in the M. fermentans-free cells. However, only an increase in the CXCL8 protein release was observed. No IL-1β protein release was detected, despite increases in IL-1β mRNA, suggesting the signal for intracellular pre-IL-1β processing may be lacking when culturing primary cells in isolation. The keratinocytes and fibroblasts naturally infected with M. fermentans showed little response to the LPS, a range of D. nodosus preparations or heat-inactivated F. necrophorum. Primary single cell culture models complement ex vivo organ culture models to study different aspects of the host response to D. nodosus. The ovine keratinocytes and fibroblasts infected with M. fermentans had a reduced response to the experimental bacterial stimulation. However, in the case of footrot where Mycoplasma spp. are associated with diseased feet, this natural infection gives important insights into the impact of multiple pathogens on the host response.
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Affiliation(s)
- Adam M. Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough LE12 5RD, UK
- Correspondence: (A.M.B.); (S.T.)
| | - Christina-Marie Baumbach
- Institute of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Jule K. Michler
- Institute of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Natalie D. Pickwell
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough LE12 5RD, UK
| | - Ceri E. Staley
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough LE12 5RD, UK
| | - Jemma M. Franklin
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough LE12 5RD, UK
| | - Sean R. Wattegedera
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Gary Entrican
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
- The Roslin Institute, The University of Edinburgh, Easter Bush, Roslin EH25 9RG, UK
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough LE12 5RD, UK
- Correspondence: (A.M.B.); (S.T.)
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Marshall HJ, Blanchard AM, Kelly KR, Goh JN, Williams AD, King L, Lovatt F, Davies PL, Tötemeyer S. The impact of glutaraldehyde based footbaths on Dichelobacter nodosus prevalence and the antimicrobial resistant community of the ovine interdigital skin. Vet Microbiol 2022; 272:109459. [DOI: 10.1016/j.vetmic.2022.109459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 10/18/2022]
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Blanchard AM, Staley CE, Shaw L, Wattegedera SR, Baumbach CM, Michler JK, Rutland C, Back C, Newbold N, Entrican G, Tötemeyer S. A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions. Infect Immun 2021; 89:e0027021. [PMID: 34227837 PMCID: PMC8445190 DOI: 10.1128/iai.00270-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/16/2021] [Indexed: 12/02/2022] Open
Abstract
Footrot is a polymicrobial infectious disease in sheep causing severe lameness, leading to one of the industry's largest welfare problems. The complex etiology of footrot makes in situ or in vitro investigations difficult. Computational methods offer a solution to understanding the bacteria involved and how they may interact with the host, ultimately providing a way to identify targets for future hypothesis-driven investigative work. Here, we present the first combined global analysis of bacterial community transcripts together with the host immune response in healthy and diseased ovine feet during a natural polymicrobial infection state using metatranscriptomics. The intratissue and surface bacterial populations and the most abundant bacterial transcriptomes were analyzed, demonstrating that footrot-affected skin has reduced diversity and increased abundances of not only the causative bacterium Dichelobacter nodosus but also other species such as Mycoplasma fermentans and Porphyromonas asaccharolytica. Host transcriptomics reveals the suppression of biological processes related to skin barrier function, vascular functions, and immunosurveillance in unhealthy interdigital skin, supported by histological findings that type I collagen (associated with scar tissue formation) is significantly increased in footrot-affected interdigital skin compared to outwardly healthy skin. Finally, we provide some interesting indications of host and pathogen interactions associated with virulence genes and the host spliceosome, which could lead to the identification of future therapeutic targets.
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Affiliation(s)
- Adam M. Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Ceri E. Staley
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Laurence Shaw
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Sean R. Wattegedera
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, Scotland
| | - Christina-Marie Baumbach
- Institute of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Jule K. Michler
- Institute of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Catrin Rutland
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Charlotte Back
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Nerissa Newbold
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Gary Entrican
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, Scotland
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
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Archer N, Egan SA, Coffey TJ, Emes RD, Addis MF, Ward PN, Blanchard AM, Leigh JA. A Paradox in Bacterial Pathogenesis: Activation of the Local Macrophage Inflammasome Is Required for Virulence of Streptococcus uberis. Pathogens 2020; 9:pathogens9120997. [PMID: 33260788 PMCID: PMC7768481 DOI: 10.3390/pathogens9120997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/12/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Streptococcus uberis is a common cause of intramammary infection and mastitis in dairy cattle. Unlike other mammary pathogens, S. uberis evades detection by mammary epithelial cells, and the host–pathogen interactions during early colonisation are poorly understood. Intramammary challenge of dairy cows with S. uberis (strain 0140J) or isogenic mutants lacking the surface-anchored serine protease, SUB1154, demonstrated that virulence was dependent on the presence and correct location of this protein. Unlike the wild-type strain, the mutant lacking SUB1154 failed to elicit IL-1β from ex vivo CD14+ cells obtained from milk (bovine mammary macrophages, BMM), but this response was reinstated by complementation with recombinant SUB1154; the protein in isolation elicited no response. Production of IL-1β was ablated in the presence of various inhibitors, indicating dependency on internalisation and activation of NLRP3 and caspase-1, consistent with inflammasome activation. Similar transcriptomic changes were detected in ex vivo BMM in response to the wild-type or the SUB1154 deletion mutant, consistent with S. uberis priming BMM, enabling the SUB1154 protein to activate inflammasome maturation in a transcriptionally independent manner. These data can be reconciled in a novel model of pathogenesis in which, paradoxically, early colonisation is dependent on the innate response to the initial infection.
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Affiliation(s)
- Nathan Archer
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
| | - Sharon A. Egan
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
| | - Tracey J. Coffey
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
| | - Richard D. Emes
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
| | - M. Filippa Addis
- Porto Conte Ricerche, 07041 Alghero, Italy;
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milan, Italy
| | - Philip N. Ward
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK;
| | - Adam M. Blanchard
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
| | - James A. Leigh
- School of Veterinary Medicine and Sciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK; (N.A.); (S.A.E.); (T.J.C.); (R.D.E.); (A.M.B.)
- Correspondence:
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Monaghan TM, Sloan TJ, Stockdale SR, Blanchard AM, Emes RD, Wilcox M, Biswas R, Nashine R, Manke S, Gandhi J, Jain P, Bhotmange S, Ambalkar S, Satav A, Draper LA, Hill C, Kashyap RS. Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. Gut Microbes 2020; 12:1752605. [PMID: 32459982 PMCID: PMC7781581 DOI: 10.1080/19490976.2020.1752605] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The Central Indian gut microbiome remains grossly understudied. Herein, we sought to investigate the burden of antimicrobial resistance and diarrheal diseases, particularly Clostridioides difficile, in rural-agricultural and urban populations in Central India, where there is widespread unregulated antibiotic use. We utilized shotgun metagenomics to comprehensively characterize the bacterial and viral fractions of the gut microbiome and their encoded functions in 105 participants. RESULTS We observed distinct rural-urban differences in bacterial and viral populations, with geography exhibiting a greater influence than diarrheal status. Clostridioides difficile disease was more commonly observed in urban subjects, and their microbiomes were enriched in metabolic pathways relating to the metabolism of industrial compounds and genes encoding resistance to 3rd generation cephalosporins and carbapenems. By linking phages present in the microbiome to their bacterial hosts through CRISPR spacers, phage variation could be directly related to shifts in bacterial populations, with the auxiliary metabolic potential of rural-associated phages enriched for carbon and amino acid energy metabolism. CONCLUSIONS We report distinct differences in antimicrobial resistance gene profiles, enrichment of metabolic pathways and phage composition between rural and urban populations, as well as a higher burden of Clostridioides difficile disease in the urban population. Our results reveal that geography is the key driver of variation in urban and rural Indian microbiomes, with acute diarrheal disease, including C. difficile disease exerting a lesser impact. Future studies will be required to understand the potential role of dietary, cultural, and genetic factors in contributing to microbiome differences between rural and urban populations.
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Affiliation(s)
- Tanya M. Monaghan
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK,Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK,CONTACT Tanya M. Monaghan NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Tim J. Sloan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Adam M. Blanchard
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Richard D. Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Mark Wilcox
- Leeds Teaching Hospitals NHS Trust and University of Leeds, UK
| | - Rima Biswas
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Rupam Nashine
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Sonali Manke
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Jinal Gandhi
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Pratishtha Jain
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrejal Bhotmange
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India
| | - Shrikant Ambalkar
- Department of Clinical Microbiology and Infection, King’s Mill Hospital, Sherwood Forest Hospitals NHS Trust, Sutton in Ashfield, UK
| | | | | | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Rajpal Singh Kashyap
- Biochemistry Research Centre, Central India Institute of Medical Sciences, Nagpur, India,Rajpal Singh Kashyap Biochemistry Research Centre, Central India Institute of Medical Sciences, 88/2 Bajaj Nagar, Nagpur, Maharashtra, India
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7
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Blanchard AM, Billenness R, Warren J, Glanvill A, Roden W, Drinkall E, Maboni G, Robinson RS, Rees CED, Pfarrer C, Tötemeyer S. Characterisation of Listeria monocytogenes isolates from cattle using a bovine caruncular epithelial cell model. Heliyon 2020; 6:e04476. [PMID: 32743095 PMCID: PMC7385464 DOI: 10.1016/j.heliyon.2020.e04476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/22/2020] [Accepted: 07/13/2020] [Indexed: 11/18/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen in human and veterinary health, causing significant morbidity and mortality including abortion. It has a particular tropism for the gravid uterus, however, the route of infection in reproductive tissues of ruminants (i.e. placentome), is much less clear. In this study, we aimed to investigate a bovine caruncular epithelial cell (BCEC) line as a model for L. monocytogenes infection of the bovine reproductive tract. The BCEC infection model was used to assess the ability of 14 different L. monocytogenes isolates to infect these cells. Lysozyme sensitivity and bacterial survival in 580 μg lysozyme/ml correlated with attenuated ability to proliferate in BCEC (p = 0.004 and p = 0.02, respectively). Four isolates were significantly attenuated compared to the control strain 10403S. One of these strains (AR008) showed evidence of compromised cell wall leading to increased sensitivity to ß-lactam antibiotics, and another (7644) had compromised cell membrane integrity leading to increased sensitivity to cationic peptides. Whole genome sequencing followed by Multi Locus Sequence Type analysis identified that five invasive isolates had the same sequence type, ST59, despite originating from three different clinical conditions. Virulence gene analysis showed that the attenuated isolate LM4 was lacking two virulence genes (uhpT, virR) known to be involved in intracellular growth and virulence. In conclusion, the BCEC model was able to differentiate between the infective potential of different isolates. Moreover, resistance to lysozyme correlated with the ability to invade and replicate within BCEC, suggesting co-selection for surviving challenging environments as the abomasum.
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Affiliation(s)
- Adam M Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Rosemarie Billenness
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Jessica Warren
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Amy Glanvill
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - William Roden
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Emma Drinkall
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Grazieli Maboni
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK.,Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Robert S Robinson
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | | | - Christiane Pfarrer
- Department of Anatomy, University of Veterinary Medicine, Hannover, Germany
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
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8
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Davies PL, Blanchard AM, Staley CE, Bollard NJ, Coffey TJ, Tötemeyer S. Genomic heterogeneity of Dichelobacter nodosus within and between UK sheep flocks and between age groups within a flock. BMC Microbiol 2020; 20:107. [PMID: 32357840 PMCID: PMC7193352 DOI: 10.1186/s12866-020-01769-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/29/2020] [Indexed: 12/02/2022] Open
Abstract
Background Footrot and interdigital dermatitis are endemic infectious diseases in all sheep farming regions, impairing welfare and production. The development of efficacious vaccines against the primary causative pathogen has been hampered by the extensive antigenic diversity of Dichelobacter nodosus. Understanding the heterogeneity of the pathogen within and between flocks is essential if the feasibility of bespoke vaccine production is to be assessed for use in the U.K. Results In this study 56 ewe and lamb isolates from 9 flocks were compared by D. nodosus serogroup and Multi Locus Sequence Type which provides significantly enhanced discriminatory power for molecular epidemiology. Serogroup heterogeneity between flocks ranged from two to five unique serogroups per flock. Three flocks contained isolates of two serogroups, two flocks contained isolates of three serogroups and one flock included isolates of five serogroups. Analysis of 25 isolates from one flock with high prevalence of lameness, identified that serogroup and sequence type was significantly correlated with age. Significantly higher proportion of lambs were infected with serogroup B (principally ST85) as opposed to serogroup H (principally ST86), which predominated amongst adult sheep. Conclusions Genomic heterogeneity of the pathogen was significantly lower within flock compared to heterogenicity observed between flocks. Furthermore, this study indicates that within a flock, the host-pathogen dynamics and susceptibility to particular D. nodosus strains may be age dependent.
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Affiliation(s)
- P L Davies
- Department of Epidemiology and Population Health, University of Liverpool, Leahurst Campus, Neston, UK.
| | - A M Blanchard
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington, UK
| | - C E Staley
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington, UK
| | - N J Bollard
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington, UK
| | - T J Coffey
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington, UK
| | - S Tötemeyer
- University of Nottingham, School of Veterinary Medicine and Science, Sutton Bonington, UK
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9
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Blanchard AM, Jolley KA, Maiden MCJ, Coffey TJ, Maboni G, Staley CE, Bollard NJ, Warry A, Emes RD, Davies PL, Tötemeyer S. The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus. Front Microbiol 2018; 9:551. [PMID: 29628922 PMCID: PMC5876313 DOI: 10.3389/fmicb.2018.00551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/12/2018] [Indexed: 11/17/2022] Open
Abstract
Dichelobacter nodosus (D. nodosus) is the causative pathogen of ovine footrot, a disease that has a significant welfare and financial impact on the global sheep industry. Previous studies into the phylogenetics of D. nodosus have focused on Australia and Scandinavia, meaning the current diversity in the United Kingdom (U.K.) population and its relationship globally, is poorly understood. Numerous epidemiological methods are available for bacterial typing; however, few account for whole genome diversity or provide the opportunity for future application of new computational techniques. Multilocus sequence typing (MLST) measures nucleotide variations within several loci with slow accumulation of variation to enable the designation of allele numbers to determine a sequence type. The usage of whole genome sequence data enables the application of MLST, but also core and whole genome MLST for higher levels of strain discrimination with a negligible increase in experimental cost. An MLST database was developed alongside a seven loci scheme using publically available whole genome data from the sequence read archive. Sequence type designation and strain discrimination was compared to previously published data to ensure reproducibility. Multiple D. nodosus isolates from U.K. farms were directly compared to populations from other countries. The U.K. isolates define new clades within the global population of D. nodosus and predominantly consist of serogroups A, B and H, however serogroups C, D, E, and I were also found. The scheme is publically available at https://pubmlst.org/dnodosus/.
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Affiliation(s)
- Adam M Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Tracey J Coffey
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Grazieli Maboni
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Ceri E Staley
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Nicola J Bollard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Andrew Warry
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom.,Advanced Data Analysis Centre, University of Nottingham, Nottingham, United Kingdom
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom.,Advanced Data Analysis Centre, University of Nottingham, Nottingham, United Kingdom
| | - Peers L Davies
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
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Maboni G, Davenport R, Sessford K, Baiker K, Jensen TK, Blanchard AM, Wattegedera S, Entrican G, Tötemeyer S. A Novel 3D Skin Explant Model to Study Anaerobic Bacterial Infection. Front Cell Infect Microbiol 2017; 7:404. [PMID: 28959685 PMCID: PMC5604072 DOI: 10.3389/fcimb.2017.00404] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 06/22/2017] [Accepted: 08/31/2017] [Indexed: 12/11/2022] Open
Abstract
Skin infection studies are often limited by financial and ethical constraints, and alternatives, such as monolayer cell culture, do not reflect many cellular processes limiting their application. For a more functional replacement, 3D skin culture models offer many advantages such as the maintenance of the tissue structure and the cell types present in the host environment. A 3D skin culture model can be set up using tissues acquired from surgical procedures or post slaughter, making it a cost effective and attractive alternative to animal experimentation. The majority of 3D culture models have been established for aerobic pathogens, but currently there are no models for anaerobic skin infections. Footrot is an anaerobic bacterial infection which affects the ovine interdigital skin causing a substantial animal welfare and financial impact worldwide. Dichelobacter nodosus is a Gram-negative anaerobic bacterium and the causative agent of footrot. The mechanism of infection and host immune response to D. nodosus is poorly understood. Here we present a novel 3D skin ex vivo model to study anaerobic bacterial infections using ovine skin explants infected with D. nodosus. Our results demonstrate that D. nodosus can invade the skin explant, and that altered expression of key inflammatory markers could be quantified in the culture media. The viability of explants was assessed by tissue integrity (histopathological features) and cell death (DNA fragmentation) over 76 h showing the model was stable for 28 h. D. nodosus was quantified in all infected skin explants by qPCR and the bacterium was visualized invading the epidermis by Fluorescent in situ Hybridization. Measurement of pro-inflammatory cytokines/chemokines in the culture media revealed that the explants released IL1β in response to bacteria. In contrast, levels of CXCL8 production were no different to mock-infected explants. The 3D skin model realistically simulates the interdigital skin and has demonstrated that D. nodosus invades the skin and triggered an early cellular inflammatory response to this bacterium. This novel model is the first of its kind for investigating an anaerobic bacterial infection.
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Affiliation(s)
- Grazieli Maboni
- School of Veterinary Medicine and Science, University of NottinghamNottingham, United Kingdom
| | - Rebecca Davenport
- School of Veterinary Medicine and Science, University of NottinghamNottingham, United Kingdom
| | - Kate Sessford
- School of Veterinary Medicine and Science, University of NottinghamNottingham, United Kingdom
| | - Kerstin Baiker
- School of Veterinary Medicine and Science, University of NottinghamNottingham, United Kingdom
| | - Tim K Jensen
- National Veterinary Institute, Technical University of DenmarkCopenhagen, Denmark
| | - Adam M Blanchard
- School of Veterinary Medicine and Science, University of NottinghamNottingham, United Kingdom
| | | | | | - Sabine Tötemeyer
- School of Veterinary Medicine and Science, University of NottinghamNottingham, United Kingdom
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11
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Blanchard AM, Egan SA, Emes RD, Warry A, Leigh JA. PIMMS (Pragmatic Insertional Mutation Mapping System) Laboratory Methodology a Readily Accessible Tool for Identification of Essential Genes in Streptococcus. Front Microbiol 2016; 7:1645. [PMID: 27826289 PMCID: PMC5078762 DOI: 10.3389/fmicb.2016.01645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 07/01/2016] [Accepted: 10/03/2016] [Indexed: 12/27/2022] Open
Abstract
The Pragmatic Insertional Mutation Mapping (PIMMS) laboratory protocol was developed alongside various bioinformatics packages (Blanchard et al., 2015) to enable detection of essential and conditionally essential genes in Streptococcus and related bacteria. This extended the methodology commonly used to locate insertional mutations in individual mutants to the analysis of mutations in populations of bacteria. In Streptococcus uberis, a pyogenic Streptococcus associated with intramammary infection and mastitis in ruminants, the mutagen pGhost9:ISS1 was shown to integrate across the entire genome. Analysis of >80,000 mutations revealed 196 coding sequences, which were not be mutated and a further 67 where mutation only occurred beyond the 90th percentile of the coding sequence. These sequences showed good concordance with sequences within the database of essential genes and typically matched sequences known to be associated with basic cellular functions. Due to the broad utility of this mutagen and the simplicity of the methodology it is anticipated that PIMMS will be of value to a wide range of laboratories in functional genomic analysis of a wide range of Gram positive bacteria (Streptococcus, Enterococcus, and Lactococcus) of medical, veterinary, and industrial significance.
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Affiliation(s)
- Adam M Blanchard
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington, UK
| | - Sharon A Egan
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of NottinghamSutton Bonington, UK; Advanced Data Analysis Centre, University of NottinghamSutton Bonington, UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham Sutton Bonington, UK
| | - James A Leigh
- School of Veterinary Medicine and Science, University of Nottingham Sutton Bonington, UK
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Blanchard AM, Leigh JA, Egan SA, Emes RD. Transposon insertion mapping with PIMMS - Pragmatic Insertional Mutation Mapping System. Front Genet 2015; 6:139. [PMID: 25914720 PMCID: PMC4391243 DOI: 10.3389/fgene.2015.00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 03/23/2015] [Indexed: 01/24/2023] Open
Abstract
The PIMMS (Pragmatic Insertional Mutation Mapping System) pipeline has been developed for simple conditionally essential genome discovery experiments in bacteria. Capable of using raw sequence data files alongside a FASTA sequence of the reference genome and GFF file, PIMMS will generate a tabulated output of each coding sequence with corresponding mapped insertions accompanied with normalized results enabling streamlined analysis. This allows for a quick assay of the genome to identify conditionally essential genes on a standard desktop computer prioritizing results for further investigation. Availability: The PIMMS script, manual and accompanying test data is freely available at https://github.com/ADAC-UoN/PIMMS
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Affiliation(s)
- Adam M Blanchard
- School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK
| | - James A Leigh
- School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK
| | - Sharon A Egan
- School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham Loughborough, UK
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