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Hailu E, Cantillon D, Madrazo C, Rose G, Wheeler PR, Golby P, Adnew B, Gagneux S, Aseffa A, Gordon SV, Comas I, Young DB, Waddell SJ, Larrouy-Maumus G, Berg S. Corrigendum: Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex. Microb Genom 2024; 10:001226. [PMID: 38546336 PMCID: PMC11000246 DOI: 10.1099/mgen.0.001226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Indexed: 04/10/2024] Open
Affiliation(s)
- Elena Hailu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Daire Cantillon
- Brighton and Sussex Centre for Global Health Research, Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, UK
| | - Carlos Madrazo
- Biomedicine Institute of Valencia, Spanish Research Council (IBV-CSIC), Valencia, Spain
| | | | | | - Paul Golby
- Animal and Plant Health Agency, Weybridge, UK
| | | | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Iñaki Comas
- Biomedicine Institute of Valencia, Spanish Research Council (IBV-CSIC), Valencia, Spain
| | - Douglas B. Young
- Francis Crick Institute, London, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Simon J. Waddell
- Brighton and Sussex Centre for Global Health Research, Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Stefan Berg
- Animal and Plant Health Agency, Weybridge, UK
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Kapalamula TF, Chizimu JY, Akapelwa ML, Barnes DA, Toyting J, Bwalya P, Basikolo L, Squarre D, Chambaro HM, Gordon SV, Thapa J, Nakajima C, Suzuki Y. Insight into the genetic diversity of Mycobacterium bovis isolated from cattle in Malawi. Res Vet Sci 2023; 164:105030. [PMID: 37788548 DOI: 10.1016/j.rvsc.2023.105030] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
We describe the genetic diversity and phylogenetic relationships of Mycobacterium bovis, isolated from cattle in Malawi. Deletion analysis, spoligotyping, and MIRU-VNTR typing were used to genotype the isolates. Combined with a larger dataset from neighboring countries, the overall M. bovis diversity in Southern Africa was contextualized. From the southern and northern regions of Malawi, 24 isolates were confirmed as M. bovis. We pooled data for the central region (60 isolates) from our recent publication to conceptualize the genetic and phylogenetic relationships of M. bovis in Malawi. European 1 was the dominant M. bovis clonal complex, with 10 unique spoligotype patterns, and SB0131 was ubiquitous. High genetic diversity, a low clustering rate, and many singletons, coupled with a low mutation transmission index, infer a low level of recent transmission, and suggest an endemic status of bovine tuberculosis (bTB) in Malawi. M. bovis isolates from Zambia, Mozambique, and South Africa were genetically related to Malawian isolates, whereas Tanzanian isolates were distantly related. The diversity and phylogenetic analysis suggest earlier introductions and maintenance of M. bovis by constant reinfection from reservoir animals. These findings are fundamental to understanding the source and route of infection in order to establish alternative management strategies for bTB.
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Affiliation(s)
- Thoko Flav Kapalamula
- Faculty of Veterinary Medicine, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi; Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Joseph Yamweka Chizimu
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia
| | - Mwangala Lonah Akapelwa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - David Atomanyi Barnes
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Jirachaya Toyting
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Precious Bwalya
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Linda Basikolo
- Department of Animal Health and Livestock Development, Ministry of Agriculture, Lilongwe, Malawi
| | - David Squarre
- Department of National Parks and Wildlife, Wildlife Veterinary Unit, Chilanga, Zambia
| | - Herman M Chambaro
- Division of Molecular Pathobiology, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; Department of National Parks and Wildlife, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan; Hokkaido University Institute for Vaccine Research and Development, Sapporo, Hokkaido, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan; Hokkaido University Institute for Vaccine Research and Development, Sapporo, Hokkaido, Japan.
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3
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Mitermite M, Elizari JMU, Ma R, Farrell D, Gordon SV. Exploring virulence in Mycobacterium bovis: clues from comparative genomics and perspectives for the future. Ir Vet J 2023; 76:26. [PMID: 37770951 PMCID: PMC10540498 DOI: 10.1186/s13620-023-00257-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Here we provide a summary of a plenary lecture delivered on Mycobacterium bovis, the bovine TB bacillus, at the M. bovis 2022 meeting held in Galway, Ireland, in June 2022. We focus on the analysis of genetic differences between M. bovis and the human pathogen Mycobacterium tuberculosis as a route to gain knowledge on what makes M. bovis function as an animal pathogen. We provide a brief historical background around M. bovis and comparative virulence experiments with M. tuberculosis, before moving to what we have learned from the studies of the M. bovis genome sequence. We discuss the need to translate knowledge on the molecular basis of virulence in M. bovis into improved control of bovine tuberculosis.
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Affiliation(s)
- Morgane Mitermite
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Jose Maria Urtasun Elizari
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland.
- UCD School of Medicine, University College Dublin, Dublin, Ireland.
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
- UCD Conway Institute, University College Dublin, Dublin, Ireland.
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4
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Thapa J, Chizimu JY, Kitamura S, Akapelwa ML, Suwanthada P, Miura N, Toyting J, Nishimura T, Hasegawa N, Nishiuchi Y, Gordon SV, Nakajima C, Suzuki Y. Characterization of DNA Gyrase Activity and Elucidation of the Impact of Amino Acid Substitution in GyrA on Fluoroquinolone Resistance in Mycobacterium avium. Microbiol Spectr 2023; 11:e0508822. [PMID: 37067420 PMCID: PMC10269562 DOI: 10.1128/spectrum.05088-22] [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: 12/12/2022] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
Mycobacterium avium, a member of the M. avium complex (MAC), is the major pathogen contributing to nontuberculous mycobacteria (NTM) infections worldwide. Fluoroquinolones (FQs) are recommended for the treatment of macrolide-resistant MACs. The association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA of M. avium is not yet clearly understood, as many FQ-resistant clinical M. avium isolates do not have such mutations. This study aimed to elucidate the role of amino acid substitution in the QRDR of M. avium GyrA in the development of FQ resistance. We found four clinical M. avium subsp. hominissuis isolates with Asp-to-Gly change at position 95 (Asp95Gly) and Asp95Tyr mutations in gyrA that were highly resistant to FQs and had 2- to 32-fold-higher MICs than the wild-type (WT) isolates. To clarify the contribution of amino acid substitutions to FQ resistance, we produced recombinant WT GyrA, GyrB, and four GyrA mutant proteins (Ala91Val, Asp95Ala, Asp95Gly, and Asp95Tyr) to elucidate their potential role in FQ resistance, using them to perform FQ-inhibited DNA supercoiling assays. While all the mutant GyrAs contributed to the higher (1.3- to 35.6-fold) FQ 50% inhibitory concentration (IC50) than the WT, Asp95Tyr was the most resistant mutant, with an IC50 15- to 35.6-higher than that of the WT, followed by the Asp95Gly mutant, with an IC50 12.5- to 17.6-fold higher than that of the WT, indicating that these amino acid substitutions significantly reduced the inhibitory activity of FQs. Our results showed that amino acid substitutions in the gyrA of M. avium contribute to FQ resistance. IMPORTANCE The emergence of fluoroquinolone (FQ) resistance has further compounded the control of emerging Mycobacterium avium-associated nontuberculous mycobacteria infections worldwide. For M. avium, the association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA is not yet clearly understood. Here, we report that four clinical M. avium isolates with a mutation in the QRDR of gyrA were highly resistant to FQs. We further clarified the impact of mutations in the QRDR of GyrA proteins by performing in vitro FQ-inhibited DNA supercoiling assays. These results confirmed that, like in Mycobacterium tuberculosis, mutations in the QRDR of gyrA also strongly contribute to FQ resistance in M. avium. Since many FQ-resistant M. avium isolates do have these mutations, the detailed molecular mechanism of FQ resistance in M. avium needs further exploration.
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Affiliation(s)
- Jeewan Thapa
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Joseph Yamweka Chizimu
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Zambian National Public Health Institute, Ministry of Health, Lusaka, Zambia
| | - Soyoka Kitamura
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Mwangala Lonah Akapelwa
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Pondpan Suwanthada
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Nami Miura
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Jirachaya Toyting
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
- Office of Academic Research and Industry-Government Collaboration, Section of Microbial Genomics and Ecology, Hiroshima University, Higashi-Hiroshima, Japan
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
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Matthews C, Walsh AM, Gordon SV, Markey B, Cotter PD, O' Mahony J. Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP). Animals (Basel) 2023; 13:ani13101652. [PMID: 37238082 DOI: 10.3390/ani13101652] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, a chronic enteritis which results in emaciation and eventual loss of the animal. Recent advances in metagenomics have allowed a more in-depth study of complex microbiomes, including that of gastrointestinal tracts, and have the potential to provide insights into consequences of the exposure of an animal to MAP or other pathogens. This study aimed to investigate taxonomic diversity and compositional changes of the faecal microbiome of cattle experimentally challenged with MAP compared to an unexposed control group. Faecal swab samples were collected from a total of 55 animals [exposed group (n = 35) and a control group (n = 20)], across three time points (months 3, 6 and 9 post-inoculation). The composition and functional potential of the faecal microbiota differed across time and between the groups (p < 0.05), with the primary differences, from both a taxonomic and functional perspective, occurring at 3 months post inoculation. These included significant differences in the relative abundance of the genera Methanobrevibacter and Bifidobacterium and also of 11 other species (4 at a higher relative abundance in the exposed group and 7 at a higher relative abundance in the control group). Correlations were made between microbiome data and immunopathology measurements and it was noted that changes in the microbial composition correlated with miRNA-155, miR-146b and IFN-ɣ. In summary, this study illustrates the impact of exposure to MAP on the ruminant faecal microbiome with a number of species that may have relevance in veterinary medicine for tracking exposure to MAP.
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Affiliation(s)
- Chloe Matthews
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
| | - Aaron M Walsh
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Bryan Markey
- School of Veterinary Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, P61 C996 Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, T12 R229 Cork, Ireland
| | - Jim O' Mahony
- Department of Biological Sciences, Munster Technological University, Bishopstown, T12 P928 Cork, Ireland
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Hailu E, Cantillon D, Madrazo C, Rose G, Wheeler PR, Golby P, Adnew B, Gagneux S, Aseffa A, Gordon SV, Comas I, Young DB, Waddell SJ, Larrouy-Maumus G, Berg S. Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex. Microb Genom 2023; 9. [PMID: 37171244 PMCID: PMC10272862 DOI: 10.1099/mgen.0.001011] [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] [Indexed: 05/13/2023] Open
Abstract
Lineage 7 (L7) emerged in the phylogeny of the Mycobacterium tuberculosis complex (MTBC) subsequent to the branching of 'ancient' lineage 1 and prior to the Eurasian dispersal of 'modern' lineages 2, 3 and 4. In contrast to the major MTBC lineages, the current epidemiology suggests that prevalence of L7 is highly confined to the Ethiopian population, or when identified outside of Ethiopia, it has mainly been in patients of Ethiopian origin. To search for microbiological factors that may contribute to its restricted distribution, we compared the genome of L7 to the genomes of globally dispersed MTBC lineages. The frequency of predicted functional mutations in L7 was similar to that documented in other lineages. These include mutations characteristic of modern lineages - such as constitutive expression of nitrate reductase - as well as mutations in the VirS locus that are commonly found in ancient lineages. We also identified and characterized multiple lineage-specific mutations in L7 in biosynthesis pathways of cell wall lipids, including confirmed deficiency of methoxy-mycolic acids due to a stop-gain mutation in the mmaA3 gene that encodes a methoxy-mycolic acid synthase. We show that the abolished biosynthesis of methoxy-mycolates of L7 alters the cell structure and colony morphology on selected growth media and impacts biofilm formation. The loss of these mycolic acid moieties may change the host-pathogen dynamic for L7 isolates, explaining the limited geographical distribution of L7 and contributing to further understanding the spread of MTBC lineages across the globe.
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Affiliation(s)
- Elena Hailu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Daire Cantillon
- Present address: Department of Tropical Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Brighton and Sussex Centre for Global Health Research, Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, UK
| | - Carlos Madrazo
- Biomedicine Institute of Valencia, Spanish Research Council (IBV-CSIC), Valencia, Spain
| | - Graham Rose
- Present address: North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, London, UK
- Francis Crick Institute, London, UK
| | | | - Paul Golby
- Animal and Plant Health Agency, Weybridge, UK
| | | | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Iñaki Comas
- Biomedicine Institute of Valencia, Spanish Research Council (IBV-CSIC), Valencia, Spain
| | - Douglas B Young
- Francis Crick Institute, London, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Simon J Waddell
- Brighton and Sussex Centre for Global Health Research, Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Stefan Berg
- Present address: Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Animal and Plant Health Agency, Weybridge, UK
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Flores-Villalva S, Reid C, Remot A, Gordon SV, Meade KG. Long term dietary vitamin D 3 supplementation impacts both microbicidal and inflammatory responses to ex-vivo Mycobacterium bovis BCG challenge in dairy calves. Vet Immunol Immunopathol 2023; 258:110575. [PMID: 36848773 DOI: 10.1016/j.vetimm.2023.110575] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/19/2023] [Indexed: 02/22/2023]
Abstract
Vitamin D deficiency (VDD) is associated with enhanced susceptibility to multiple respiratory diseases in humans, including tuberculosis. However, the consequences of VDD for disease susceptibility in calves are unknown. Previously we developed a model to drive divergent circulating 25OHD concentrations in cattle, where animals were supplemented with vitamin D3 (vit D3) from birth to 7 months of age. Calves in the control group (Ctl) received a diet containing a standard vit D3 concentration, whereas the vit D group (VitD) received a diet with the highest vit D3 concentration allowed under EU guidelines. Here, we assessed the microbicidal activity and immunoregulatory effect of divergent 25OHD circulating levels to Mycobacterium bovis BCG challenge ex-vivo. Blood samples from Ctl and VitD calves were taken at 1-, 3- and 7-months of age. 25OHD concentrations were significantly different at 7 months (but not at 1 or 3 months) with animals from the VitD group having higher serum levels. Differences in microbicidal activity followed the same pattern, with no significant differences observed at 1 and 3 months, but at 7 months a significant increase in the percentage of bacteria killed was detected. Furthermore, analysis of the reactive oxygen species (ROS) and nitric oxide (NO) in serum showed a higher production of ROS and NO in VitD-supplemented calves. In contrast, serum concentrations of IL-1β and IL-8 were significantly lower. A similar anti-inflammatory profile was observed after gene expression analysis, with a significant downregulation of a cluster of genes including IL1B, IL1R1, CXCL1, CXCL2, CXCL5, MMP9 and COX2 and an upregulation of CXCR1, CX3CR1 and NCF1, in VitD calves after BCG challenge relative to Ctl animals. Collectively, these results suggest that dietary vit D3 boosts antimicrobial and innate immune responses and thereby could improve host anti-mycobacterial immunity.
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Affiliation(s)
- Susana Flores-Villalva
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland; CENID Fisiología, INIFAP. Querétaro, Mexico
| | - Cian Reid
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aude Remot
- INRAE, Université de Tours, Nouzilly, France
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran G Meade
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; Institute of Food and Health, University College Dublin, Belfield, Dublin 4, Ireland.
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8
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Flores-Villalva S, Remot A, Carreras F, Winter N, Gordon SV, Meade KG. Vitamin D induced microbicidal activity against Mycobacterium bovis BCG is dependent on the synergistic activity of bovine peripheral blood cell populations. Vet Immunol Immunopathol 2023; 256:110536. [PMID: 36586390 DOI: 10.1016/j.vetimm.2022.110536] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/17/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
A growing appreciation is emerging of the beneficial role of vitamin D for health and resistance against infectious diseases, including tuberculosis. However, research has predominantly focused on murine and human species and functional data in bovines is limited. Therefore, the objective of this study was to assess the microbicidal activity and immunoregulatory effect of the vitamin D metabolite 1,25(OH)2D3 on bovine peripheral blood leukocytes (PBL) in response to Mycobacterium bovis BCG (BCG) infection using a combination of functional assays and gene expression profiling. Blood from Holstein-Friesian bull calves with low circulating levels of 25(OH)D was stimulated with 1,25(OH)2D3 for 2 h, and then infected with M. bovis BCG. Results showed that 1,25(OH)2D3 supplementation significantly increased BCG killing by on average 16 %, although responses varied between 1 % and 38 % killing. Serial cell subset depletion was then performed on PBL prior to 1,25(OH)2D3 incubation and BCG infected as before to analyse the contribution of major cell types to mycobacterial growth control. Specific antibodies and either magnetic cell separation or density gradient centrifugation of monocytes, granulocytes, CD3+, CD4+, and CD8+ T lymphocytes were used to capture each cell subset. Results showed that depletion of granulocytes had the greatest impact on BCG growth, leading to a significant enhancement of bacterial colonies. In contrast, depletion of CD4+ or CD8+ T cells individually, or in combination (CD3+), had no impact on mycobacterial growth control. In agreement with our previous data, 1,25(OH)2D3 significantly increased bacterial killing in PBL, in monocyte depleted samples, and a similar trend was observed in the granulocyte depleted subset. In addition, specific analysis of sorted neutrophils treated with 1,25(OH)2D3 showed an enhanced microbicidal activity against both BCG and a virulent strain of M. bovis. Lastly, data showed that 1,25(OH)2D3 stimulation increased reactive oxygen species (ROS) production and the expression of genes encoding host defence peptides (HDP) and pathogen recognition receptors (PRRs), factors that play an important role in the microbicidal activity against mycobacteria. In conclusion, the vitamin D metabolite 1,25(OH)2D3 improves antimycobacterial killing in bovine PBLs via the synergistic activity of monocytes and granulocytes and enhanced activation of innate immunity.
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Affiliation(s)
- Susana Flores-Villalva
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland; CENID Fisiología, INIFAP, Querétaro, Mexico
| | - Aude Remot
- INRAE, Université de Tours, ISP, F-37380 Nouzilly, France
| | | | | | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran G Meade
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; Institute of Food and Health, University College Dublin, Belfield, Dublin 4, Ireland.
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9
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Graham HA, Doherty ML, More SJ, Gordon SV, Gormley EP, Mooney CT, Hanlon AJ, Mullan SM, Leonard FC, McAloon CG. Advancing national animal health and welfare policy. Am J Vet Res 2022; 83:ajvr.22.10.0179. [DOI: 10.2460/ajvr.22.10.0179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Helen A. Graham
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Michael L. Doherty
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Simon J. More
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Eamonn P. Gormley
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Carmel T. Mooney
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Alison J. Hanlon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Siobhan M. Mullan
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Finola C. Leonard
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Conor G. McAloon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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10
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Ma R, Gordon SV. Pyruvate supplementation and Mycobacterium bovis: A caveat. Tuberculosis (Edinb) 2022; 136:102257. [PMID: 36115126 DOI: 10.1016/j.tube.2022.102257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland.
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11
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Correia CN, McHugo GP, Browne JA, McLoughlin KE, Nalpas NC, Magee DA, Whelan AO, Villarreal-Ramos B, Vordermeier HM, Gormley E, Gordon SV, MacHugh DE. High-resolution transcriptomics of bovine purified protein derivative-stimulated peripheral blood from cattle infected with Mycobacterium bovis across an experimental time course. Tuberculosis (Edinb) 2022; 136:102235. [DOI: 10.1016/j.tube.2022.102235] [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: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
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12
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Ma R, Farrell D, Gonzalez G, Browne JA, Nakajima C, Suzuki Y, Gordon SV. Corrigendum: The TbD1 Locus Mediates a Hypoxia-Induced Copper Response in Mycobacterium bovis. Front Microbiol 2022; 13:947450. [PMID: 35783437 PMCID: PMC9245040 DOI: 10.3389/fmicb.2022.947450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Gabriel Gonzalez
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - John A. Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Chie Nakajima
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- *Correspondence: Stephen V. Gordon
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Kerins A, Farrell D, Gordon SV. Defining the pknH Transcriptional Network in the Animal Tuberculosis bacillus, Mycobacterium bovis. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Mycobacterium tuberculosiscomplex (MTBC) is a group of bacteria that show more than 99% genetic identity, yet they diverge in their host preference and the severity of associated disease. Mycobacterium bovis causes the disease in cattle and poses an economic challenge, with the cost of Irelands TB Eradication Scheme predicted to exceed €90 million in 2020.
The aim was to focus on the RD900 and pknH gene network in MTBC members. ThepknH gene encodes a transmembrane serine threonine protein kinase, that plays a role in the regulation of signalling pathways in the mycobacterial cell and has been linked to virulence. The RD900 or “region of difference 900” contains the tbD2 and pknH2 genes. The part of the genome that contains this region varies substantially across MTBC members.
The results of RNA-seq analysis showed that there are statistically significant levels of differential gene expression in wildtype and knock-in M. bovis strains.
The RD900 analysis across the MTBC showed that there is variation in this important genomic region. Analysis carried out by Mata et al. 2020, showed that this RD900 region had been independently lost in different MTBC lineages and strains. M. bovis has retained the RD900 region and this is believed to be linked to its increased virulence.
The majority of the M . africanum strains were found to possess the standard pknH, tbD2, pknH2, embR gene arrangement as is found in M. africanum GM041182, the strain that is typically used as a reference.
Based on work of Mata et al., 2020.
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Ma R, Farrell D, Gonzalez G, Browne JA, Nakajima C, Suzuki Y, Gordon SV. The TbD1 Locus Mediates a Hypoxia-Induced Copper Response in Mycobacterium bovis. Front Microbiol 2022; 13:817952. [PMID: 35495699 PMCID: PMC9048740 DOI: 10.3389/fmicb.2022.817952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) contains the causative agents of tuberculosis (TB) in mammals. The archetypal members of the MTBC, Mycobacterium tuberculosis and Mycobacterium bovis, cause human tuberculosis and bovine tuberculosis, respectively. Although M. tuberculosis and M. bovis share over 99.9% genome identity, they show distinct host adaptation for humans and animals; hence, while the molecular basis of host adaptation is encoded in their genomes, the mechanistic basis of host tropism is still unclear. Exploration of the in vitro phenotypic consequences of known genetic difference between M. bovis and M. tuberculosis offers one route to explore genotype–phenotype links that may play a role in host adaptation. The TbD1 (“Mycobacterium tuberculosis deletion 1 region”) locus encompasses the mmpS6 and mmpL6 genes. TbD1 is absent in M. tuberculosis “modern” lineages (Lineages 2, 3, and 4) but present in “ancestral” M. tuberculosis (Lineages 1 and 7), Mycobacterium africanum lineages (Lineages 5 and 6), newly identified M. tuberculosis lineages (Lineages 8 and 9), and animal adapted strains, such as M. bovis. The function of TbD1 has previously been investigated in M. tuberculosis, where conflicting data has emerged on the role of TbD1 in sensitivity to oxidative stress, while the underlying mechanistic basis of such a phenotype is unclear. In this study, we aimed to shed further light on the role of the TbD1 locus by exploring its function in M. bovis. Toward this, we constructed an M. bovis TbD1 knockout (ΔTbD1) strain and conducted comparative transcriptomics to define global gene expression profiles of M. bovis wild-type (WT) and the ΔTbD1 strains under in vitro culture conditions (rolling and standing cultures). This analysis revealed differential induction of a hypoxia-driven copper response in WT and ΔTbD1 strains. In vitro phenotypic assays demonstrated that the deletion of TbD1 sensitized M. bovis to H2O2 and hypoxia-specific copper toxicity. Our study provides new information on the function of the TbD1 locus in M. bovis and its role in stress responses in the MTBC.
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Affiliation(s)
- Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Gabriel Gonzalez
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - John A. Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Chie Nakajima
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- UCD Conway Institute, University College Dublin, Dublin, Ireland
- *Correspondence: Stephen V. Gordon,
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15
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Taylor EN, Beckmann M, Markey BK, Gordon SV, Hewinson G, Rooke D, Mur LAJ. Metabolomic changes in Mycobacterium avium subsp. paratuberculosis (MAP) challenged Holstein-Friesian cattle highlight the role of serum amino acids as indicators of immune system activation. Metabolomics 2022; 18:21. [PMID: 35320420 PMCID: PMC8942901 DOI: 10.1007/s11306-022-01876-w] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/23/2022] [Indexed: 10/26/2022]
Abstract
INTRODUCTION Paratuberculosis, commonly known as Johne's disease, is a chronic granulomatous infection of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Clinical signs, including reduced milk yields, weight loss and diarrhoea, are typically absent until 2 to 6 years post exposure. OBJECTIVES To identify metabolomic changes profiles of MAP challenged Holstein-Friesian (HF) cattle and correlate identified metabolites to haematological and immunological parameters. METHODS At approximately 6 weeks of age, calves (n = 9) were challenged with 3.8 × 109 cells of MAP (clinical isolate CIT003) on 2 consecutive days. Additional unchallenged calves (n = 9) formed the control group. The study used biobanked serum from cattle sampled periodically from 3- to 33-months post challenge. The assessment of sera using flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) for high throughput, sensitive, non-targeted metabolite fingerprinting highlighted differences in metabolite levels between the two groups. RESULTS In total, 25 metabolites which were differentially accumulated in MAP challenged cattle were identified, including 20 which displayed correlation to haematology parameters, particularly monocyte levels. CONCLUSION The targeted metabolites suggest shifts in amino acid metabolism that could reflect immune system activation linked to MAP and as well as differences in phosphocholine levels which could reflect activation of the Th1 (tending towards pro-inflammatory) immune response. If verified by future work, selected metabolites could be used as biomarkers to diagnose and manage MAP infected cattle.
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Affiliation(s)
| | | | - Bryan K Markey
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Glyn Hewinson
- Centre of Excellence for Bovine Tuberculosis, Aberystwyth University, Ceredigion, UK
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16
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Russell L, Whyte P, Zintl A, Gordon SV, Markey B, de Waal T, Nolan S, O'Flaherty V, Abram F, Richards K, Fenton O, Bolton D. The Survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in Sandy and Clay Loam Textured Soils When Applied in Bovine Slurry or Unpasteurised Digestate and the Run-Off Rate for a Test Bacterium, Listeria innocua, When Applied to Grass in Slurry and Digestate. Front Sustain Food Syst 2022. [DOI: 10.3389/fsufs.2022.806920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study investigated the survival of Salmonella Senftenberg, Escherichia coli O157:H7, Listeria monocytogenes, Enterococcus faecalis and Clostridium sporogenes in sandy and clay loam textured soils when applied in bovine slurry or unpasteurised digestate, using laboratory based inoculation studies. The run-off rate for a test bacterium, Listeria innocua, when applied to grass in slurry and digestate, was also examined using field studies. Bovine slurry and digestate were inoculated with the target bacteria to a final concentration of 106 log10 cfu/g or spores/g, thoroughly mixed into soil samples and incubated at 4°C or 14°C. Samples were removed periodically and the surviving cells enumerated using AOAC or equivalent methods. The loss of viability/culturability phase followed first order kinetics and T90 values ranged from 11.9 to 166.7 d at 4°C and from 6.0 to 156 d at 14°C. With the exception of E. coli O157:H7 and E. faecalis in sandy loam textured soil at 14°C (T90 values were significantly (P < 0.05) higher in slurry) the type of soil texture or application material (slurry or digestate) did not affect survival rates. In the field study, 12 grass covered micro-plots were prepared. L. innocua was applied in digestate and bovine slurry and rainfall was simulated at a target rate of ~11 mm per plot per h−1. Rainfall simulation (30 min) took place after 24, 48 h, 14 d and 30 d. Run-off samples were tested for the L. innocua strain using Brilliance Listeria agar supplemented with streptomycin sulphate (1,000 μg/ml) at 37°C for 48 h, as were soil samples after 30, 58, 86 and 112 d. Significantly (P < 0.05) lower counts were obtained in the run-off from digestate after 1, 2 and 30 d as compared to slurry. It was concluded that the type of organic fertiliser does not affect the bacterial survival rates in sandy and clay soils, with the exception of E. coli O157:H7 and E. faecalis in sandy loam textured soil at 14°C. Furthermore, bacteria may be retained better in the soil-digestate matrices during rainfall although additional research is required to further validate and provide the scientific basis for this observation.
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17
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Lorente-Leal V, Farrell D, Romero B, Álvarez J, de Juan L, Gordon SV. Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization. Front Vet Sci 2022; 8:780018. [PMID: 34970617 PMCID: PMC8712436 DOI: 10.3389/fvets.2021.780018] [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: 09/20/2021] [Accepted: 11/25/2021] [Indexed: 11/29/2022] Open
Abstract
Whole genome sequencing (WGS) and allied variant calling pipelines are a valuable tool for the control and eradication of infectious diseases, since they allow the assessment of the genetic relatedness of strains of animal pathogens. In the context of the control of tuberculosis (TB) in livestock, mainly caused by Mycobacterium bovis, these tools offer a high-resolution alternative to traditional molecular methods in the study of herd breakdown events. However, despite the increased use and efforts in the standardization of WGS methods in human tuberculosis around the world, the application of these WGS-enabled approaches to control TB in livestock is still in early development. Our study pursued an initial evaluation of the performance and agreement of four publicly available pipelines for the analysis of M. bovis WGS data (vSNP, SNiPgenie, BovTB, and MTBseq) on a set of simulated Illumina reads generated from a real-world setting with high TB prevalence in cattle and wildlife in the Republic of Ireland. The overall performance of the evaluated pipelines was high, with recall and precision rates above 99% once repeat-rich and problematic regions were removed from the analyses. In addition, when the same filters were applied, distances between inferred phylogenetic trees were similar and pairwise comparison revealed that most of the differences were due to the positioning of polytomies. Hence, under the studied conditions, all pipelines offer similar performance for variant calling to underpin real-world studies of M. bovis transmission dynamics.
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Affiliation(s)
- Víctor Lorente-Leal
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain.,Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Beatriz Romero
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain.,Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Julio Álvarez
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain.,Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucía de Juan
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain.,Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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18
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Lundahl MLE, Mitermite M, Ryan DG, Case S, Williams NC, Yang M, Lynch RI, Lagan E, Lebre FM, Gorman AL, Stojkovic B, Bracken AP, Frezza C, Sheedy FJ, Scanlan EM, O'Neill LAJ, Gordon SV, Lavelle EC. Macrophage innate training induced by IL-4 and IL-13 activation enhances OXPHOS driven anti-mycobacterial responses. eLife 2022; 11:74690. [PMID: 36173104 PMCID: PMC9555863 DOI: 10.7554/elife.74690] [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: 10/13/2021] [Accepted: 09/28/2022] [Indexed: 01/05/2023] Open
Abstract
Macrophages are a highly adaptive population of innate immune cells. Polarization with IFNγ and LPS into the 'classically activated' M1 macrophage enhances pro-inflammatory and microbicidal responses, important for eradicating bacteria such as Mycobacterium tuberculosis. By contrast, 'alternatively activated' M2 macrophages, polarized with IL-4, oppose bactericidal mechanisms and allow mycobacterial growth. These activation states are accompanied by distinct metabolic profiles, where M1 macrophages favor near exclusive use of glycolysis, whereas M2 macrophages up-regulate oxidative phosphorylation (OXPHOS). Here, we demonstrate that activation with IL-4 and IL-13 counterintuitively induces protective innate memory against mycobacterial challenge. In human and murine models, prior activation with IL-4/13 enhances pro-inflammatory cytokine secretion in response to a secondary stimulation with mycobacterial ligands. In our murine model, enhanced killing capacity is also demonstrated. Despite this switch in phenotype, IL-4/13 trained murine macrophages do not demonstrate M1-typical metabolism, instead retaining heightened use of OXPHOS. Moreover, inhibition of OXPHOS with oligomycin, 2-deoxy glucose or BPTES all impeded heightened pro-inflammatory cytokine responses from IL-4/13 trained macrophages. Lastly, this work identifies that IL-10 attenuates protective IL-4/13 training, impeding pro-inflammatory and bactericidal mechanisms. In summary, this work provides new and unexpected insight into alternative macrophage activation states in the context of mycobacterial infection.
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Affiliation(s)
- Mimmi LE Lundahl
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland,School of Chemistry, Scanlan Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Morgane Mitermite
- School of Veterinary Medicine, UCD Veterinary Sciences Centre, University College DublinDublinIreland
| | - Dylan Gerard Ryan
- School of Biochemistry and Immunology, Inflammation Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland,Hutchison/MRC Research centre, MRC Cancer Unit, University of CambridgeCambridgeUnited Kingdom
| | - Sarah Case
- School of Biochemistry and Immunology, Macrophage Homeostasis Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Niamh C Williams
- School of Biochemistry and Immunology, Inflammation Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Ming Yang
- Hutchison/MRC Research centre, MRC Cancer Unit, University of CambridgeCambridgeUnited Kingdom
| | - Roisin I Lynch
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Eimear Lagan
- School of Genetics and Microbiology, Department of Genetics, Trinity College DublinDublinIreland
| | - Filipa M Lebre
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Aoife L Gorman
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Bojan Stojkovic
- School of Veterinary Medicine, UCD Veterinary Sciences Centre, University College DublinDublinIreland
| | - Adrian P Bracken
- School of Genetics and Microbiology, Department of Genetics, Trinity College DublinDublinIreland
| | - Christian Frezza
- Hutchison/MRC Research centre, MRC Cancer Unit, University of CambridgeCambridgeUnited Kingdom
| | - Frederick J Sheedy
- School of Biochemistry and Immunology, Macrophage Homeostasis Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Eoin M Scanlan
- School of Chemistry, Scanlan Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Luke AJ O'Neill
- School of Biochemistry and Immunology, Inflammation Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
| | - Stephen V Gordon
- School of Veterinary Medicine, UCD Veterinary Sciences Centre, University College DublinDublinIreland
| | - Ed C Lavelle
- School of Biochemistry and Immunology, Adjuvant Research Group, Trinity Biomedical Sciences Institute, Trinity College DublinDublinIreland
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19
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Collins ÁB, Floyd S, Gordon SV, More SJ. Prevalence of Mycobacterium bovis in milk on dairy cattle farms: An international systematic literature review and meta-analysis. Tuberculosis (Edinb) 2022; 132:102166. [PMID: 35091379 DOI: 10.1016/j.tube.2022.102166] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 12/30/2022]
Abstract
Bovine tuberculosis, caused by Mycobacterium bovis (M. bovis), is a globally distributed chronic disease of animals. The bacteria can be transmitted to humans via the consumption of unpasteurised (raw) milk, thus representing an important public health risk. To investigate the risk of zoonotic transmission of M. bovis via raw milk, this study systematically reviewed published studies to estimate the prevalence of M. bovis in on-farm bulk-tank milk (BTM) and individual cow's milk (IM) by meta-analysis. In total, 1,339 articles were identified through seven electronic databases and initially screened using titles and abstracts. The quality of 108 potentially relevant articles was assessed using full texts, and 67 articles comprising 83 studies (76 IM and 7 BTM), were included in the meta-analysis. The prevalence of M. bovis in IM and BTM was summarised according to the diagnostic test used, and the tuberculin skin test (TST) infection status of the individual cows (for IM) or herds (for BTM). Heterogeneity was quantified using the I-squared statistic. Prediction intervals (95% PIs) were also estimated. For IM, the overall prevalence was summarised at 5% (95%CI: 3%-7%). In TST positive cows, prevalence was summarised at 8% (95%CI: 4%-13%). For BTM, the overall prevalence independent of individual herd TST infection status was summarised at 5% (95%CI: 0%-21%). There was considerable heterogeneity evident among the included studies, while PIs were also wide. Inconsistency in the quality of reporting was also observed resulting in missing information, such as the TST infection status of the individual animal/herd. No study reported the number of M. bovis bacteria in test-positive milk samples. Several studies reported the detection of M. tuberculosis and M. africanum in milk. Despite international efforts to control tuberculosis, this study highlights the risk of zoonotic transmission of M. bovis via unpasteurised milk and dairy products made using raw milk.
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Affiliation(s)
- Áine B Collins
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, D04 W6F6, Ireland; Department of Agriculture Food and the Marine, Government of Ireland, Kildare Street, Dublin, D02 WK12, Ireland.
| | - Sian Floyd
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom.
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, D04 W6F6, Ireland.
| | - Simon J More
- Centre for Veterinary Epidemiology and Risk Analysis, University College Dublin, Dublin, D04 W6F6, Ireland; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom.
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20
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Rossi G, Crispell J, Brough T, Lycett SJ, White PCL, Allen A, Ellis RJ, Gordon SV, Harwood R, Palkopoulou E, Presho EL, Skuce R, Smith GC, Kao RR. Phylodynamic analysis of an emergent
Mycobacterium bovis
outbreak in an area with no previously known wildlife infections. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gianluigi Rossi
- Roslin Institute and R(D)SVS University of Edinburgh Edinburgh UK
| | - Joseph Crispell
- School of Veterinary Medicine University College Dublin Dublin Ireland
| | - Tanis Brough
- Advice Services Team Service Delivery Directorate APHA Penrith UK
| | | | | | - Adrian Allen
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | - Richard J. Ellis
- Surveillance and Laboratory Services Department APHA Addlestone UK
| | - Stephen V. Gordon
- School of Veterinary Medicine University College Dublin Dublin Ireland
- Conway Institute University College Dublin Dublin Ireland
| | | | | | - Eleanor L. Presho
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | - Robin Skuce
- Bacteriology Branch Veterinary Sciences Division Agri‐food and Biosciences Institute Belfast UK
| | | | - Rowland R. Kao
- Roslin Institute and R(D)SVS University of Edinburgh Edinburgh UK
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21
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Ó Maoldomhnaigh C, Cox DJ, Phelan JJ, Mitermite M, Murphy DM, Leisching G, Thong L, O'Leary SM, Gogan KM, McQuaid K, Coleman AM, Gordon SV, Basdeo SA, Keane J. Lactate Alters Metabolism in Human Macrophages and Improves Their Ability to Kill Mycobacterium tuberculosis. Front Immunol 2021; 12:663695. [PMID: 34691015 PMCID: PMC8526932 DOI: 10.3389/fimmu.2021.663695] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 02/03/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
In order to mount an appropriate immune response to infection, the macrophage must alter its metabolism by increasing aerobic glycolysis and concomitantly decreasing oxidative phosphorylation; a process known as the Warburg effect. Consequently, lactate, the end-product of glycolysis, accumulates in the extracellular environment. The subsequent effect of lactate on surrounding macrophages is poorly understood. Mycobacterium tuberculosis (Mtb), the causative organism of Tuberculosis (TB), is phagocytosed by macrophages in the airways. Mtb infected macrophages upregulate aerobic glycolysis and effector functions to try to kill the bacteria. Our lab has previously shown that human macrophages produce lactate in response to infection with Mtb. Although lactate has largely been considered a waste product of aerobic glycolysis, we hypothesised that the presence of extracellular lactate would impact subsequent immunometabolic responses and modulate macrophage function. We demonstrate that the presence of exogenous lactate has an immediate effect on the cellular metabolism of resting human macrophages; causing a decrease in extracellular acidification rate (ECAR; analogous to the rate of glycolysis) and an increase in the oxygen consumption rate (OCR; analogous to oxidative phosphorylation). When lactate-treated macrophages were stimulated with Mtb or LPS, glycolysis proceeds to increase immediately upon stimulation but oxidative phosphorylation remains stable compared with untreated cells that display a decrease in OCR. This resulted in a significantly reduced ECAR/OCR ratio early in response to stimulation. Since altered metabolism is intrinsically linked to macrophage function, we examined the effect of lactate on macrophage cytokine production and ability to kill Mtb. Lactate significantly reduced the concentrations of TNF and IL-1β produced by human macrophages in response to Mtb but did not alter IL-10 and IL-6 production. In addition, lactate significantly improved bacillary clearance in human macrophages infected with Mtb, through a mechanism that is, at least in part, mediated by promoting autophagy. These data indicate that lactate, the product of glycolysis, has a negative feedback effect on macrophages resulting in an attenuated glycolytic shift upon subsequent stimulation and reduced pro-inflammatory cytokine production. Interestingly, this pro-resolution effect of lactate is associated with increased capacity to kill Mtb.
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Affiliation(s)
- Cilian Ó Maoldomhnaigh
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Donal J Cox
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - James J Phelan
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Morgane Mitermite
- School of Veterinary Medicine and Conway Institute, University College Dublin, Dublin, Ireland
| | - Dearbhla M Murphy
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Gina Leisching
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Lorraine Thong
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Seónadh M O'Leary
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Karl M Gogan
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Kate McQuaid
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Amy M Coleman
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Stephen V Gordon
- School of Veterinary Medicine and Conway Institute, University College Dublin, Dublin, Ireland
| | - Sharee A Basdeo
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Joseph Keane
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St James's Hospital, Trinity College Dublin, The University of Dublin, Dublin, Ireland
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22
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Roycroft E, Fitzgibbon MM, Kelly DM, Scully M, McLaughlin AM, Flanagan PR, Gordon SV, Rogers TR, Keane J, O Meara M. The largest prison outbreak of TB in Western Europe investigated using whole-genome sequencing. Int J Tuberc Lung Dis 2021; 25:491-497. [PMID: 34049612 DOI: 10.5588/ijtld.21.0033] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: In March 2011, the Department of Public Health East in Ireland were notified of two cases of TB in two prisoners sharing a cell. We define the resulting outbreak and highlight the role of public health and laboratory-based molecular epidemiology in mapping and control of a prison outbreak.METHODS: Cases were identified through clinical presentation, contact tracing, case-finding exercise or enhanced laboratory surveillance. Mycobacterium tuberculosis isolates were genotyped and underwent whole-genome sequencing (WGS).RESULTS: Of the 34 cases of TB linked to the outbreak, 27 were prisoners (79%), 4 prison officers (12%) and 3 community cases (9%). M. tuberculosis was isolated from 31 cases (culture positivity: 91%). A maximum of six single-nucleotide polymorphisms separated the isolates, with 22 being identical, suggestive of a highly infectious 'super-spreader´ within the prison. Isolates belonged to the Beijing sub-lineage, and were susceptible to first-line anti-TB agents. A case-finding exercise incidentally detected a prisoner with multidrug-resistant TB. Of the 143 prison officers screened, 52% had latent TB infection. Litigation costs exceeded five million euros.CONCLUSION: This constitutes the largest prison outbreak of TB in Western Europe investigated using WGS. A robust prison entry TB screening and education programme is required to effect better TB control, and prevent future outbreaks and attendant litigation.
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Affiliation(s)
- E Roycroft
- Irish Mycobacteria Reference Laboratory, St James´s Hospital, Dublin, Ireland, Department of Clinical Microbiology, Trinity College Dublin, St James´s Hospital Campus, Dublin, Ireland
| | - M M Fitzgibbon
- Irish Mycobacteria Reference Laboratory, St James´s Hospital, Dublin, Ireland, Department of Clinical Microbiology, Trinity College Dublin, St James´s Hospital Campus, Dublin, Ireland
| | - D M Kelly
- Department of Public Health East, Health Service Executive, Dublin, Ireland
| | - M Scully
- Department of Public Health East, Health Service Executive, Dublin, Ireland
| | - A M McLaughlin
- Department of Respiratory Medicine, St James´s Hospital, Dublin, Ireland
| | - P R Flanagan
- Irish Mycobacteria Reference Laboratory, St James´s Hospital, Dublin, Ireland, Department of Clinical Microbiology, Trinity College Dublin, St James´s Hospital Campus, Dublin, Ireland
| | - S V Gordon
- UCD School of Veterinary Medicine and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland
| | - T R Rogers
- Irish Mycobacteria Reference Laboratory, St James´s Hospital, Dublin, Ireland, Department of Clinical Microbiology, Trinity College Dublin, St James´s Hospital Campus, Dublin, Ireland
| | - J Keane
- Department of Respiratory Medicine, St James´s Hospital, Dublin, Ireland
| | - M O Meara
- Department of Public Health East, Health Service Executive, Dublin, Ireland
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23
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Akapelwa ML, Kapalamula TF, Ouchi-Aizu Y, Hang'ombe BM, Nishiuchi Y, Gordon SV, Solo ES, Tamaru A, Nishimura T, Hasegawa N, Morimoto K, Fukushima Y, Suzuki Y, Nakajima C. Evaluation of IS1245 LAMP in Mycobacterium avium and the influence of host-related genetic diversity on its application. Diagn Microbiol Infect Dis 2021; 101:115494. [PMID: 34391980 DOI: 10.1016/j.diagmicrobio.2021.115494] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
Early detection and treatment are paramount for the timely control of Mycobacterium avium infections. Herein, we designed a LAMP assay targeting a widely used species-specific marker IS1245 for the rapid detection of M. avium and evaluated its applicability using human (n = 137) and pig (n = 91) M. avium isolates from Japan. The developed assay could detect as low as 1 genome copy of M. avium DNA within 30 minutes. All 91 (100%) M. avium isolates from pigs were detected positive while all other tested bacterial species were negative. Interestingly, among the 137 clinical M. avium isolates, 41 (30%) were undetectable with this LAMP assay as they lacked IS1245, the absence of which was revealed by PCR and whole-genome sequencing. These findings highlighted genotypic differences in M. avium strains from humans and pigs in Japan and how this diversity can influence the applicability of a detection tool across different geographic areas and hosts.
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Affiliation(s)
- Mwangala Lonah Akapelwa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Thoko Flav Kapalamula
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Yuki Ouchi-Aizu
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Bernard Mudenda Hang'ombe
- Department of ParaClinicals, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia; Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Eddie Samuneti Solo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Aki Tamaru
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | | | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Kozo Morimoto
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan.
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan.
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24
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Remot A, Carreras F, Coupé A, Doz-Deblauwe É, Boschiroli ML, Browne JA, Marquant Q, Descamps D, Archer F, Aseffa A, Germon P, Gordon SV, Winter N. Mycobacterial Infection of Precision-Cut Lung Slices Reveals Type 1 Interferon Pathway Is Locally Induced by Mycobacterium bovis but Not M. tuberculosis in a Cattle Breed. Front Vet Sci 2021; 8:696525. [PMID: 34307535 PMCID: PMC8299756 DOI: 10.3389/fvets.2021.696525] [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: 04/16/2021] [Accepted: 06/02/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis exacts a terrible toll on human and animal health. While Mycobacterium tuberculosis (Mtb) is restricted to humans, Mycobacterium bovis (Mb) is present in a large range of mammalian hosts. In cattle, bovine TB (bTB) is a noticeable disease responsible for important economic losses in developed countries and underestimated zoonosis in the developing world. Early interactions that take place between mycobacteria and the lung tissue early after aerosol infection govern the outcome of the disease. In cattle, these early steps remain poorly characterized. The precision-cut lung slice (PCLS) model preserves the structure and cell diversity of the lung. We developed this model in cattle in order to study the early lung response to mycobacterial infection. In situ imaging of PCLS infected with fluorescent Mb revealed bacilli in the alveolar compartment, in adjacent or inside alveolar macrophages, and in close contact with pneumocytes. We analyzed the global transcriptional lung inflammation signature following infection of PCLS with Mb and Mtb in two French beef breeds: Blonde d'Aquitaine and Charolaise. Whereas, lungs from the Blonde d'Aquitaine produced high levels of mediators of neutrophil and monocyte recruitment in response to infection, such signatures were not observed in the Charolaise in our study. In the Blonde d'Aquitaine lung, whereas the inflammatory response was highly induced by two Mb strains, AF2122 isolated from cattle in the UK and Mb3601 circulating in France, the response against two Mtb strains, H37Rv, the reference laboratory strain, and BTB1558, isolated from zebu in Ethiopia, was very low. Strikingly, the type I interferon pathway was only induced by Mb but not Mtb strains, indicating that this pathway may be involved in mycobacterial virulence and host tropism. Hence, the PCLS model in cattle is a valuable tool to deepen our understanding of early interactions between lung host cells and mycobacteria. It revealed striking differences between cattle breeds and mycobacterial strains. This model could help in deciphering biomarkers of resistance vs. susceptibility to bTB in cattle as such information is still critically needed for bovine genetic selection programs and would greatly help the global effort to eradicate bTB.
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Affiliation(s)
- Aude Remot
- INRAE, Université de Tours, Nouzilly, France
| | | | | | | | - Maria L Boschiroli
- Paris-Est University, National Reference Laboratory for Tuberculosis, Animal Health Laboratory, Anses, Maisons-Alfort, France
| | - John A Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | | | - Fabienne Archer
- INRAE, UMR754, Viral Infections and Comparative Pathology, IVPC, Univ Lyon, Université Claude Bernard Lyon 1, EPHE, Lyon, France
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Stephen V Gordon
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Dublin, Ireland
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25
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McLoughlin KE, Correia CN, Browne JA, Magee DA, Nalpas NC, Rue-Albrecht K, Whelan AO, Villarreal-Ramos B, Vordermeier HM, Gormley E, Gordon SV, MacHugh DE. RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course. Front Vet Sci 2021; 8:662002. [PMID: 34124223 PMCID: PMC8193354 DOI: 10.3389/fvets.2021.662002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Bovine tuberculosis, caused by infection with members of the Mycobacterium tuberculosis complex, particularly Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including RNA sequencing, has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analysed the transcriptome of bovine whole peripheral blood samples collected at −1 week pre-infection and +1, +2, +6, +10, and +12 weeks post-infection time points. Differentially expressed genes were catalogued and evaluated at each post-infection time point relative to the −1 week pre-infection time point and used for the identification of putative candidate host transcriptional biomarkers for M. bovis infection. Differentially expressed gene sets were also used for examination of cellular pathways associated with the host response to M. bovis infection, construction of de novo gene interaction networks enriched for host differentially expressed genes, and time-series analyses to identify functionally important groups of genes displaying similar patterns of expression across the infection time course. A notable outcome of these analyses was identification of a 19-gene transcriptional biosignature of infection consisting of genes increased in expression across the time course from +1 week to +12 weeks post-infection.
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Affiliation(s)
- Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Kevin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Adam O Whelan
- TB Immunology and Vaccinology Team, Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Bernardo Villarreal-Ramos
- TB Immunology and Vaccinology Team, Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - H Martin Vordermeier
- TB Immunology and Vaccinology Team, Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Eamonn Gormley
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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26
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Hall TJ, Mullen MP, McHugo GP, Killick KE, Ring SC, Berry DP, Correia CN, Browne JA, Gordon SV, MacHugh DE. Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria. BMC Genomics 2021; 22:343. [PMID: 33980141 PMCID: PMC8117616 DOI: 10.1186/s12864-021-07643-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background Bovine TB (bTB), caused by infection with Mycobacterium bovis, is a major endemic disease affecting global cattle production. The key innate immune cell that first encounters the pathogen is the alveolar macrophage, previously shown to be substantially reprogrammed during intracellular infection by the pathogen. Here we use differential expression, and correlation- and interaction-based network approaches to analyse the host response to infection with M. bovis at the transcriptome level to identify core infection response pathways and gene modules. These outputs were then integrated with genome-wide association study (GWAS) data sets to enhance detection of genomic variants for susceptibility/resistance to M. bovis infection. Results The host gene expression data consisted of RNA-seq data from bovine alveolar macrophages (bAM) infected with M. bovis at 24 and 48 h post-infection (hpi) compared to non-infected control bAM. These RNA-seq data were analysed using three distinct computational pipelines to produce six separate gene sets: 1) DE genes filtered using stringent fold-change and P-value thresholds (DEG-24: 378 genes, DEG-48: 390 genes); 2) genes obtained from expression correlation networks (CON-24: 460 genes, CON-48: 416 genes); and 3) genes obtained from differential expression networks (DEN-24: 339 genes, DEN-48: 495 genes). These six gene sets were integrated with three bTB breed GWAS data sets by employing a new genomics data integration tool—gwinteR. Using GWAS summary statistics, this methodology enabled detection of 36, 102 and 921 prioritised SNPs for Charolais, Limousin and Holstein-Friesian, respectively. Conclusions The results from the three parallel analyses showed that the three computational approaches could identify genes significantly enriched for SNPs associated with susceptibility/resistance to M. bovis infection. Results indicate distinct and significant overlap in SNP discovery, demonstrating that network-based integration of biologically relevant transcriptomics data can leverage substantial additional information from GWAS data sets. These analyses also demonstrated significant differences among breeds, with the Holstein-Friesian breed GWAS proving most useful for prioritising SNPS through data integration. Because the functional genomics data were generated using bAM from this population, this suggests that the genomic architecture of bTB resilience traits may be more breed-specific than previously assumed. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07643-w.
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Affiliation(s)
- Thomas J Hall
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Michael P Mullen
- Bioscience Research Institute, Athlone Institute of Technology, Dublin Road, Athlone, Westmeath, N37 HD68, Ireland
| | - Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Kate E Killick
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,Present address: Genuity Science, Cherrywood Business Park. Loughlinstown, Dublin, D18 K7W4, Ireland
| | - Siobhán C Ring
- Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Cork, P72 X050, Ireland
| | - Donagh P Berry
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland
| | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.
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27
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Kapalamula TF, Chizimu J, Belotindos L, Akapelwa M, Shrestha D, Nyenje ME, Munyeme M, Hang'ombe BM, Mkakosya RS, Gordon SV, Nakajima C, Suzuki Y. Molecular epidemiology of Mycobacterium bovis in central parts of Malawi. Transbound Emerg Dis 2021; 69:1577-1588. [PMID: 33900039 DOI: 10.1111/tbed.14127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/13/2021] [Accepted: 04/21/2021] [Indexed: 11/28/2022]
Abstract
Bovine tuberculosis (bTB) is a neglected disease that affects cattle and humans. The burden of bTB is higher in developing countries as compared to industrialized countries. The reasons behind this discrepancy include the fact that bTB control measures, such as testing and slaughter of infected cattle and pasteurization of milk, are not usually practised in developing countries largely because of their high cost. To improve our understanding of bTB in developing countries, molecular typing studies are essential, in particular in terms of transmission dynamics, infection sources and knowledge of circulating strains of the principal causative agent, Mycobacterium bovis. In this study, we applied a suite of molecular typing techniques encompassing deletion analysis, spoligotyping and MIRU-VNTR to isolates recovered from samples collected during the routine post-mortem of cattle at the cold storage abattoir in Lilongwe, Malawi. Out of 63 isolates, 51 (81%) belonged to the European 1. M. bovis clonal complex. Spoligotyping identified 8 profiles, with SB0131 being the predominant type (56% of isolates). Spoligotypes SB0273 and SB0425 were identified in 14% and 13%, respectively, of the isolates. MIRU-VNTR showed a high discriminatory power of 0.959 and differentiated the 8 spoligotypes to 31 genotypes. The high diversity of M. bovis within the study area suggests the infection has been circulating in the area for a considerable period of time, likely facilitated by the lack of effective control measures. We also observed genetic similarities between isolates from Malawi (this study) to isolates described in previous studies in Zambia and Mozambique, suggesting transmission links in this region. The information provided by this study provides much needed evidence for the formulation of improved bTB control strategies.
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Affiliation(s)
- Thoko Flav Kapalamula
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Joseph Chizimu
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Lawrence Belotindos
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mwangala Akapelwa
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Dipti Shrestha
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mirriam Ethel Nyenje
- Community Health Sciences Unit, National Tuberculosis Reference Laboratory, Lilongwe, Malawi
| | - Musso Munyeme
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Bernard Mudenda Hang'ombe
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | | | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Chie Nakajima
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
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28
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Queval CJ, Fearns A, Botella L, Smyth A, Schnettger L, Mitermite M, Wooff E, Villarreal-Ramos B, Garcia-Jimenez W, Heunis T, Trost M, Werling D, Salguero FJ, Gordon SV, Gutierrez MG. Macrophage-specific responses to human- and animal-adapted tubercle bacilli reveal pathogen and host factors driving multinucleated cell formation. PLoS Pathog 2021; 17:e1009410. [PMID: 33720986 PMCID: PMC7993774 DOI: 10.1371/journal.ppat.1009410] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 11/19/2020] [Revised: 03/25/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) is a group of related pathogens that cause tuberculosis (TB) in mammals. MTBC species are distinguished by their ability to sustain in distinct host populations. While Mycobacterium bovis (Mbv) sustains transmission cycles in cattle and wild animals and causes zoonotic TB, M. tuberculosis (Mtb) affects human populations and seldom causes disease in cattle. The host and pathogen determinants underlying host tropism between MTBC species are still unknown. Macrophages are the main host cell that encounters mycobacteria upon initial infection, and we hypothesised that early interactions between the macrophage and mycobacteria influence species-specific disease outcome. To identify factors that contribute to host tropism, we analysed blood-derived primary human and bovine macrophages (hMϕ or bMϕ, respectively) infected with Mbv and Mtb. We show that Mbv and Mtb reside in different cellular compartments and differentially replicate in hMϕ whereas both Mbv and Mtb efficiently replicate in bMϕ. Specifically, we show that out of the four infection combinations, only the infection of bMϕ with Mbv promoted the formation of multinucleated giant cells (MNGCs), a hallmark of tuberculous granulomas. Mechanistically, we demonstrate that both MPB70 from Mbv and extracellular vesicles released by Mbv-infected bMϕ promote macrophage multinucleation. Importantly, we extended our in vitro studies to show that granulomas from Mbv-infected but not Mtb-infected cattle contained higher numbers of MNGCs. Our findings implicate MNGC formation in the contrasting pathology between Mtb and Mbv for the bovine host and identify MPB70 from Mbv and extracellular vesicles from bMϕ as mediators of this process. The identification of host and pathogen factors contributing to host-pathogen interaction is crucial to understand the pathogenesis and dissemination of tuberculosis. This is particularly the case in deciphering the mechanistic basis for host-tropism across the MTBC. Here, we show that in vitro, M. bovis but not M. tuberculosis induces multinucleated cell formation in bovine macrophages. We identified host and pathogen mechanistic drivers of multinucleated cell formation: MPB70 as the M. bovis factor and bovine macrophage extracellular vesicles. Using a cattle experimental infection model, we confirmed differential multinucleated cell formation in vivo. Thus, we have identified host and pathogen factors that contribute to host tropism in human/bovine tuberculosis. Additionally, this work provides an explanation for the long-standing association of multinucleated cells with tuberculosis pathogenesis.
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Affiliation(s)
| | | | | | - Alicia Smyth
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Dublin, Ireland
| | | | - Morgane Mitermite
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Esen Wooff
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Bernardo Villarreal-Ramos
- Animal and Plant Health Agency, Addlestone, United Kingdom
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Waldo Garcia-Jimenez
- Department of Pathology an Infectious Diseases. School of Veterinary Medicine. University of Surrey, Guildford, United Kingdom
| | - Tiaan Heunis
- Biosciences Institute, Newcastle University, Newcastle, United Kingdom
| | - Matthias Trost
- Biosciences Institute, Newcastle University, Newcastle, United Kingdom
| | - Dirk Werling
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield Hertfordshire, United Kingdom
| | - Francisco J. Salguero
- Department of Pathology an Infectious Diseases. School of Veterinary Medicine. University of Surrey, Guildford, United Kingdom
- National Infection Service, Public Health England (PHE), Porton Down, Salisbury, United Kingdom
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Dublin, Ireland
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Cahill C, O’Connell F, Gogan KM, Cox DJ, Basdeo SA, O’Sullivan J, Gordon SV, Keane J, Phelan JJ. The Iron Chelator Desferrioxamine Increases the Efficacy of Bedaquiline in Primary Human Macrophages Infected with BCG. Int J Mol Sci 2021; 22:ijms22062938. [PMID: 33805837 PMCID: PMC8001338 DOI: 10.3390/ijms22062938] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
For over 50 years, patients with drug-sensitive and drug-resistant tuberculosis have undergone long, arduous, and complex treatment processes with several antimicrobials. With the prevalence of drug-resistant strains on the rise and new therapies for tuberculosis urgently required, we assessed whether manipulating iron levels in macrophages infected with mycobacteria offered some insight into improving current antimicrobials that are used to treat drug-resistant tuberculosis. We investigated if the iron chelator, desferrioxamine, can support the function of human macrophages treated with an array of second-line antimicrobials, including moxifloxacin, bedaquiline, amikacin, clofazimine, linezolid and cycloserine. Primary human monocyte-derived macrophages were infected with Bacillus Calmette-Guérin (BCG), which is pyrazinamide-resistant, and concomitantly treated for 5 days with desferrioxamine in combination with each one of the second-line tuberculosis antimicrobials. Our data indicate that desferrioxamine used as an adjunctive treatment to bedaquiline significantly reduced the bacterial load in human macrophages infected with BCG. Our findings also reveal a link between enhanced bactericidal activity and increases in specific cytokines, as the addition of desferrioxamine increased levels of IFN-γ, IL-6, and IL-1β in BCG-infected human monocyte-derived macrophages (hMDMs) treated with bedaquiline. These results provide insight, and an in vitro proof-of-concept, that iron chelators may prove an effective adjunctive therapy in combination with current tuberculosis antimicrobials.
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Affiliation(s)
- Christina Cahill
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, St James’s Hospital, 8 Dublin, Ireland; (C.C.); (K.M.G.); (D.J.C.); (S.A.B.); (J.K.)
| | - Fiona O’Connell
- Department of Surgery, Trinity Translational Medicine Institute, Trinity College Dublin, St James’s Hospital, 8 Dublin, Ireland; (F.O.); (J.O.)
| | - Karl M. Gogan
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, St James’s Hospital, 8 Dublin, Ireland; (C.C.); (K.M.G.); (D.J.C.); (S.A.B.); (J.K.)
| | - Donal J. Cox
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, St James’s Hospital, 8 Dublin, Ireland; (C.C.); (K.M.G.); (D.J.C.); (S.A.B.); (J.K.)
| | - Sharee A. Basdeo
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, St James’s Hospital, 8 Dublin, Ireland; (C.C.); (K.M.G.); (D.J.C.); (S.A.B.); (J.K.)
| | - Jacintha O’Sullivan
- Department of Surgery, Trinity Translational Medicine Institute, Trinity College Dublin, St James’s Hospital, 8 Dublin, Ireland; (F.O.); (J.O.)
| | - Stephen V. Gordon
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, 4 Dublin, Ireland;
| | - Joseph Keane
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, St James’s Hospital, 8 Dublin, Ireland; (C.C.); (K.M.G.); (D.J.C.); (S.A.B.); (J.K.)
| | - James J. Phelan
- TB Immunology Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, St James’s Hospital, 8 Dublin, Ireland; (C.C.); (K.M.G.); (D.J.C.); (S.A.B.); (J.K.)
- Correspondence: ; Tel.: +353-18963265
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Kapalamula TF, Thapa J, Akapelwa ML, Hayashida K, Gordon SV, Hang' ombe BM, Munyeme M, Solo ES, Bwalya P, Nyenje ME, Tamaru A, Suzuki Y, Nakajima C. Development of a loop-mediated isothermal amplification (LAMP) method for specific detection of Mycobacterium bovis. PLoS Negl Trop Dis 2021; 15:e0008996. [PMID: 33493196 PMCID: PMC7833227 DOI: 10.1371/journal.pntd.0008996] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/14/2020] [Indexed: 11/24/2022] Open
Abstract
Bovine tuberculosis (TB) caused by Mycobacterium bovis is a significant health threat to cattle and a zoonotic threat for humans in many developing countries. Rapid and accurate detection of M. bovis is fundamental for controlling the disease in animals and humans, and for the proper treatment of patients as one of the first-line anti-TB drug, pyrazinamide, is ineffective against M. bovis. Currently, there are no rapid, simplified and low-cost diagnostic methods that can be easily integrated for use in many developing countries. Here, we report the development of a loop-mediated isothermal amplification (LAMP) assay for specific identification of M. bovis by targeting the region of difference 4 (RD4), a 12.7 kb genomic region that is deleted solely in M. bovis. The assay's specificity was evaluated using 139 isolates comprising 65 M. bovis isolates, 40 M. tuberculosis isolates, seven M. tuberculosis complex reference strains, 22 non-tuberculous mycobacteria and five other bacteria. The established LAMP detected only M. bovis isolates as positive and no false positives were observed using the other mycobacteria and non-mycobacteria tested. Our LAMP assay detected as low as 10 copies of M. bovis genomic DNA within 40 minutes. The procedure of LAMP is simple with an incubation at a constant temperature. Results are observed with the naked eye by a color change, and there is no need for expensive equipment. The established LAMP can be used for the detection of M. bovis infections in cattle and humans in resource-limited areas. Although bovine tuberculosis in humans has been eliminated in developed countries, the disease remains a challenge in many developing countries. Routine laboratory methods used to identify tuberculosis (TB) in high-burden countries do not distinguish between the two main causes of TB in humans, namely Mycobacterium tuberculosis and M. bovis. In addition, M. bovis is naturally resistant to one of the first-line drugs used to treat TB called pyrazinamide; therefore, accurate diagnosis of M. bovis is important for proper selection of anti TB drugs. In cattle, surveillance for M. bovis infection is important to obtain data on bovine TB burden and hence provide a basis for the establishment and/or improvement of control programs. In this study, a loop-mediated isothermal amplification (LAMP) based method was developed to identify M. bovis. This LAMP method detected M. bovis within 40 minutes following incubation at constant temperature (66°C) in a battery-powered incubator and results could be read with the naked eye following development of a color change. Our results elaborate a rapid and low-cost LAMP based method for detection and surveillance of M. bovis infection in cattle and humans in resource-limited, endemic areas.
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Affiliation(s)
- Thoko Flav Kapalamula
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Jeewan Thapa
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mwangala Lonah Akapelwa
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kyoko Hayashida
- Division of Collaborations and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Contsrol, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Stephen V. Gordon
- International Collaboration Unit, Research Center for Zoonosis Contsrol, Hokkaido University, Sapporo, Hokkaido, Japan
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Bernard Mudenda Hang' ombe
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Musso Munyeme
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Eddie Samuneti Solo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Precious Bwalya
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Mirriam Ethel Nyenje
- Community Health Sciences Unit, National Tuberculosis Reference Laboratory, Lilongwe, Malawi
| | - Aki Tamaru
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Contsrol, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Contsrol, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail:
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Lundahl M, Lynch DM, Barnes D, McSweeney L, Gorman A, Lebre F, Gordon SV, Lavelle EC, Scanlan EM. Mycobacterial para-Hydroxybenzoic Acid-Derivatives ( pHBADs) and Related Structures Induce Macrophage Innate Memory. ACS Chem Biol 2020; 15:2415-2421. [PMID: 32786261 DOI: 10.1021/acschembio.0c00378] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Macrophages are key immune cells for combatting Mycobacterium tuberculosis. However, M. tuberculosis possesses means to evade macrophage bactericidal responses by, for instance, secretion of the immunomodulatory para-hydroxybenzoic acid derivatives (pHBADs). While these molecules have been implicated in inhibiting macrophage responses in an acute context, little is known about their ability to reprogram macrophages via induction of long-term innate memory. Since innate memory has been highlighted as a promising strategy to augment bactericidal immune responses against M. tuberculosis, investigating corresponding immune evasion mechanisms is highly relevant. Our results reveal for the first time that pHBAD I and related molecules (unmethylated pHBAD I and the hexose l-rhamnose) reduce macrophage bactericidal mechanisms in both the short- and the long-term. Moreover, we demonstrate how methyl-p-anisate hinders bactericidal responses soon after exposure yet results in enhanced pro-inflammatory responses in the long-term. This work highlights new roles for these compounds in M. tuberculosis pathogenesis.
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Affiliation(s)
- Mimmi Lundahl
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College, Pearse St, D02 R590 Dublin 2, Ireland
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin 2, Ireland
| | - Dylan M. Lynch
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College, Pearse St, D02 R590 Dublin 2, Ireland
| | - Danielle Barnes
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College, Pearse St, D02 R590 Dublin 2, Ireland
| | - Lauren McSweeney
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College, Pearse St, D02 R590 Dublin 2, Ireland
| | - Aoife Gorman
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin 2, Ireland
| | - Filipa Lebre
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin 2, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, D02 R590 Dublin, Ireland
| | - Ed C. Lavelle
- Adjuvant Research Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin 2, Ireland
| | - Eoin M. Scanlan
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College, Pearse St, D02 R590 Dublin 2, Ireland
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Crispell J, Cassidy S, Kenny K, McGrath G, Warde S, Cameron H, Rossi G, MacWhite T, White PCL, Lycett S, Kao RR, Moriarty J, Gordon SV. Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland. Microb Genom 2020; 6:mgen000388. [PMID: 32553050 PMCID: PMC7641417 DOI: 10.1099/mgen.0.000388] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
Control of bovine tuberculosis (bTB), caused by Mycobacterium bovis, in the Republic of Ireland costs €84 million each year. Badgers are recognized as being a wildlife source for M. bovis infection of cattle. Deer are thought to act as spillover hosts for infection; however, population density is recognized as an important driver in shifting their epidemiological role, and deer populations across the country have been increasing in density and range. County Wicklow represents one specific area in the Republic of Ireland with a high density of deer that has had consistently high bTB prevalence for over a decade, despite control operations in both cattle and badgers. Our research used whole-genome sequencing of M. bovis sourced from infected cattle, deer and badgers in County Wicklow to evaluate whether the epidemiological role of deer could have shifted from spillover host to source. Our analyses reveal that cattle and deer share highly similar M. bovis strains, suggesting that transmission between these species is occurring in the area. In addition, the high level of diversity observed in the sampled deer population suggests deer may be acting as a source of infection for local cattle populations. These findings have important implications for the control and ultimate eradication of bTB in Ireland.
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Affiliation(s)
- Joseph Crispell
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Data Science Campus, Office for National Statistics, Newport, UK
| | - Sophie Cassidy
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Kevin Kenny
- Central Veterinary Research Laboratory, Backweston, County Kildare, Ireland
| | - Guy McGrath
- UCD Centre for Veterinary Epidemiology and Risk Analysis (CVERA), School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Susan Warde
- Central Veterinary Research Laboratory, Backweston, County Kildare, Ireland
| | - Henrietta Cameron
- Central Veterinary Research Laboratory, Backweston, County Kildare, Ireland
| | - Gianluigi Rossi
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Teresa MacWhite
- Department of Agriculture, Food and the Marine, Backweston, County Kildare, Ireland
| | - Piran C. L. White
- Department of Environment and Geography, University of York, Wentworth Way, York YO10 5NG, UK
| | | | - Rowland R. Kao
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - John Moriarty
- Central Veterinary Research Laboratory, Backweston, County Kildare, Ireland
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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Farrell D, Crispell J, Gordon SV. Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome. Access Microbiol 2020; 2:acmi000129. [PMID: 32974593 PMCID: PMC7497835 DOI: 10.1099/acmi.0.000129] [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: 02/19/2020] [Accepted: 03/16/2020] [Indexed: 12/04/2022] Open
Abstract
Mycobacterium bovis AF2122/97 is the reference strain for the bovine tuberculosis bacillus. Here we report an update to the M. bovis AF2122/97 genome annotation to reflect 616 new protein identifications that replace many of the old hypothetical coding sequences and proteins of unknown function in the genome. These changes integrate information from functional assignments of orthologous coding sequences in the Mycobacterium tuberculosis H37Rv genome. We have also added 69 additional new gene names.
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Affiliation(s)
- Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- *Correspondence: Damien Farrell,
| | - Joseph Crispell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
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Shaughnessy RG, Farrell D, Stojkovic B, Browne JA, Kenny K, Gordon SV. Identification of microRNAs in bovine faeces and their potential as biomarkers of Johne's Disease. Sci Rep 2020; 10:5908. [PMID: 32246047 PMCID: PMC7125074 DOI: 10.1038/s41598-020-62843-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/20/2020] [Indexed: 01/01/2023] Open
Abstract
Extracellular microRNAs (miRNAs) are detectable in the peripheral blood and have been touted as potential biomarkers for a range of maladies. The presence and biomarker potential of miRNAs in other biofluids has been less thoroughly explored, particularly in the veterinary realm. Faecal miRNAs are a case in point; while they have been identified largely in rodents and humans, they have not been reported in cattle but may have prognostic or diagnostic value for Johne's Disease (JD) in cattle, a chronic granulomatous inflammation of the ileum caused by Mycobacterium avium subspecies paratuberculosis (MAP). The aim of this study was thus to characterise the bovine faecal miRNome and to determine the utility of these transcripts as biomarkers for JD. Real-time PCR arrays consisting of 752 miRNA targets, optimised for detection of human miRNA, were used to screen RNA purified from faecal samples obtained from confirmed JD clinical cases vs. healthy controls. Two hundred and fifty-eight miRNAs were detected in bovine faeces, three of which are potentially novel orthologs of known human miRNAs. Differential abundance of three miRNA was evident in animals with clinical JD as compared to healthy controls. Our study has therefore identified a variety of miRNAs in bovine faeces and has demonstrated their utility in differentiating healthy animals from those with late-stage JD, providing potential biomarkers for MAP infection and disease progression.
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Affiliation(s)
- Ronan G Shaughnessy
- School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland.,Biosensia, NovaUCD, Belfield Innovation Park, UCD, Dublin, Ireland
| | - Damien Farrell
- School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland
| | - Bojan Stojkovic
- School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland.,School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia
| | - John A Browne
- School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Kevin Kenny
- Department of Agriculture, Food and the Marine, Central Veterinary Research Laboratory, Stacumny Lane, Backweston, Co. Kildare, Ireland
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland. .,School of Medicine, University College Dublin, Dublin 4, Ireland. .,School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland. .,UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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Hall TJ, Vernimmen D, Browne JA, Mullen MP, Gordon SV, MacHugh DE, O’Doherty AM. Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection. Front Genet 2020; 10:1386. [PMID: 32117424 PMCID: PMC7020904 DOI: 10.3389/fgene.2019.01386] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 06/06/2019] [Accepted: 12/18/2019] [Indexed: 12/29/2022] Open
Abstract
Bovine tuberculosis is caused by infection with Mycobacterium bovis, which can also cause disease in a range of other mammals, including humans. Alveolar macrophages are the key immune effector cells that first encounter M. bovis and how the macrophage epigenome responds to mycobacterial pathogens is currently not well understood. Here, we have used chromatin immunoprecipitation sequencing (ChIP-seq), RNA-seq and miRNA-seq to examine the effect of M. bovis infection on the bovine alveolar macrophage (bAM) epigenome. We show that H3K4me3 is more prevalent, at a genome-wide level, in chromatin from M. bovis-infected bAM compared to control non-infected bAM; this was particularly evident at the transcriptional start sites of genes that determine programmed macrophage responses to mycobacterial infection (e.g. M1/M2 macrophage polarisation). This pattern was also supported by the distribution of RNA Polymerase II (Pol II) ChIP-seq results, which highlighted significantly increased transcriptional activity at genes demarcated by permissive chromatin. Identification of these genes enabled integration of high-density genome-wide association study (GWAS) data, which revealed genomic regions associated with resilience to infection with M. bovis in cattle. Through integration of these data, we show that bAM transcriptional reprogramming occurs through differential distribution of H3K4me3 and Pol II at key immune genes. Furthermore, this subset of genes can be used to prioritise genomic variants from a relevant GWAS data set.
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Affiliation(s)
- Thomas J. Hall
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
| | - Douglas Vernimmen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - John A. Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
| | - Michael P. Mullen
- Bioscience Research Institute, Athlone Institute of Technology, Athlone, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alan M. O’Doherty
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, College Dublin, Dublin, Ireland
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San LL, Aye KS, Nan Aye TO, Shwe MM, Fukushima Y, Gordon SV, Suzuki Y, Nakajima C. Erratum to "Insight into multidrug-resistant Beijing genotype Mycobacterium tuberculosis isolates in Myanmar" [Int. J. Infect. Dis. 76 (November) (2018) 109-119]. Int J Infect Dis 2019; 85:214. [PMID: 31376946 DOI: 10.1016/j.ijid.2019.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Lai Lai San
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Khin Saw Aye
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Thida Oo Nan Aye
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Mu Mu Shwe
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Yukari Fukushima
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland; Hokkaido University, GI-CoRE Global Station for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, GI-CoRE Global Station for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Hokkaido University, GI-CoRE Global Station for Zoonosis Control, Sapporo, Japan.
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Mendis C, Thevanesam V, Kumara A, Wickramasinghe S, Madegedara D, Gamage C, Gordon SV, Suzuki Y, Ratnatunga C, Nakajima C. Insight into genetic diversity of Mycobacterium tuberculosis in Kandy, Sri Lanka reveals predominance of the Euro-American lineage. Int J Infect Dis 2019; 87:84-91. [PMID: 31299365 DOI: 10.1016/j.ijid.2019.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Sri Lanka is a country where the molecular epidemiology of Mycobacterium tuberculosis (MTB) is poorly explored. Therefore, this study was performed to identify circulating lineages/sub-lineages of MTB and their transmission patterns. METHODS DNA was extracted from 89 isolates of MTB collected during 2012 and 2013 from new pulmonary tuberculosis patients in Kandy, Sri Lanka and analyzed by spoligotyping, large sequence polymorphism (LSP), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing, and drug resistance-associated gene sequencing. RESULTS The predominant lineage was lineage 4 (Euro-American, 45.9%), followed by lineage 1 (Indo-Oceanic, 29.4%), lineage 2 (East-Asian, 23.5%), and lineage 3 (Central-Asian, 1.2%). Among 26 spoligotype patterns, eight were undesignated or new types and seven of these belonged to lineage 4. Undesignated lineage 4/SIT124 (n=2/8) and SIT3234 (n=8/8) clustered together based on 24-locus MIRU-VNTR typing. The dominant sub-lineage was Beijing/SIT1 (n=19), with the isoniazid resistance katG G944C mutation (Ser315Thr) detected in two of them. CONCLUSIONS The population structure of MTB in Kandy, Sri Lanka was different from that in the South Asian region. The clonal expansion of locally evolved lineage 4/SIT3234 and detection of the pre-multidrug resistant Beijing isolates from new tuberculosis patients is alarming and will require continuous monitoring.
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Affiliation(s)
- Charitha Mendis
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Peradeniya, Sri Lanka
| | - Vasanthi Thevanesam
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Athula Kumara
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Susiji Wickramasinghe
- Department of Parasitology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | | | - Chandika Gamage
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan
| | - Champa Ratnatunga
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka.
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan.
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Thapa J, Maharjan B, Malla M, Fukushima Y, Poudel A, Pandey BD, Hyashida K, Gordon SV, Nakajima C, Suzuki Y. Direct detection of Mycobacterium tuberculosis in clinical samples by a dry methyl green loop-mediated isothermal amplification (LAMP) method. Tuberculosis (Edinb) 2019; 117:1-6. [PMID: 31378262 DOI: 10.1016/j.tube.2019.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/09/2019] [Accepted: 05/19/2019] [Indexed: 11/19/2022]
Abstract
The purpose of this study was to develop a simple visual methyl green (MeG) based dry loop-mediated isothermal amplification (LAMP) method for early detection of Mycobacterium tuberculosis (MTB) from clinical samples. We identified MeG as an indicator of a positive LAMP reaction, where a positive reaction gave a blue-green color while a negative reaction was colorless. The MeG MTB-LAMP system was further simplified by drying all reagents for ease of use, and was then validated for its ability to diagnose TB directly using Nepalese clinical samples. We evaluated the dry MeG MTB-LAMP with 69 new TB suspected samples from patients that did not have a confirmed history of TB treatment and found the sensitivity in culture positive samples as 92.8% (13/14) and specificity in culture negative samples as 96.3% (53/55). Our LAMP system has the potential to be a point of care test for early diagnosis of active TB in developing countries.
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Affiliation(s)
- Jeewan Thapa
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Hokkaido University, Kita-12 Nishi-5, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
| | - Bhagwan Maharjan
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan; German Nepal Tuberculosis Project, Kalimati, Kathmandu, Nepal; Healthy Nepal, Balkhu, Kathmandu, Nepal
| | - Meena Malla
- Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Ajay Poudel
- Department of Microbiology, Chitwan Medical College Teaching Hospital, Chitwan, Nepal
| | | | - Kyoko Hyashida
- Division of Collaboration and Education, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, D04 W6F6, Ireland; The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan; The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan; The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan.
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Maharjan B, Nakajima C, Isoda N, Thapa J, Poudel A, Shah Y, Yamaguchi T, Shrestha B, Hoffmann H, Avsar K, Shrestha A, Gordon SV, Suzuki Y. Genetic diversity and distribution dynamics of multidrug-resistant Mycobacterium tuberculosis isolates in Nepal. Sci Rep 2018; 8:16634. [PMID: 30413747 PMCID: PMC6226479 DOI: 10.1038/s41598-018-34306-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 02/24/2018] [Accepted: 10/11/2018] [Indexed: 01/06/2023] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is an emerging public health problem in Nepal. Despite the implementation of a successful TB control program in Nepal, notifications of MDR-TB are increasing, yet the reasons are unknown. The objective of this study was to understand the genetic diversity and epidemiological characteristics of MDR-Mycobacterium tuberculosis (MTB) isolates in Nepal. We isolated and genotyped 498 MDR-MTB isolates collected from April 2009 to March 2013 and analyzed the patients' background information. Our results showed that the lineage 2 (Beijing family) was the most predominant lineage (n = 241; 48.4%), followed by lineage 3 (n = 153, 30.7%). Lineage 4 was the third most prevalent (n = 73, 14.5%) followed by lineage 1 (n = 32, 6.4%). The lineages were significantly associated with geographic region, ethnic group, age and sex of patients. The Beijing genotype was found to have an important role in transmitting MDR-TB in Nepal and was significantly associated with the eastern region, mongoloid ethnic group and younger age group. We conclude that early diagnosis and treatment including molecular-epidemiological surveillance of MDR-TB cases will help to control transmission of MDR-TB in Nepal.
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Affiliation(s)
- Bhagwan Maharjan
- German Nepal TB Project (GENETUP/NATA), Kathmandu, Nepal.,Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan.,Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Hokkaido, Japan
| | - Norikazu Isoda
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Hokkaido, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan
| | - Ajay Poudel
- Department of Microbiology, Chitwan Medical College Teaching Hospital, Chitwan, Nepal
| | - Yogendra Shah
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan
| | - Tomoyuki Yamaguchi
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan
| | | | - Harald Hoffmann
- WHO-Supranational Reference Laboratory of Tuberculosis, Munich, Gauting, Germany.,KuratoriumTuberkulose in der Welt e.V, München-Gauting, Germany
| | - Korkut Avsar
- KuratoriumTuberkulose in der Welt e.V, München-Gauting, Germany.,Asklepios Klinik, Gauting, Germany
| | - Ashish Shrestha
- National Tuberculosis Center, Thimi, Bhaktapur, Nepal.,World Health Organization, Kathmandu, Nepal
| | - Stephen V Gordon
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Hokkaido, Japan.,UCD School of Veterinary Medicine, University College Dublin, Dublin, D04 W6F6, Ireland
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University, Research Center for Zoonosis Control, Hokkaido, Japan. .,Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Hokkaido, Japan.
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40
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Franceschelli JJ, Belardinelli JM, Tong P, Loftus B, Recio-Balsells A, Labadié GR, Gordon SV, Morbidoni HR. A katG S315T or an ahpC promoter mutation mediate Mycobacterium tuberculosis resistance to 2-thiophen carboxylic acid hydrazide, an inhibitor resembling the anti-tubercular drugs Isoniazid and Ethionamide. Tuberculosis (Edinb) 2018; 112:69-78. [PMID: 30205971 DOI: 10.1016/j.tube.2018.08.001] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 11/16/2022]
Abstract
Clinical isolates of Mycobacterium tuberculosis and Mycobacterium bovis are differentially susceptible to 2-Thiophen Hydrazide (TCH); however its mechanism of action or the reasons for that difference are unknown. We report herein that under our experimental conditions, TCH inhibits M. tuberculosis in solid but not in liquid medium, and that in spite of resembling Isoniazid and Ethionamide, it does not affect mycolic acid synthesis. To understand the mechanisms of action of TCH we isolated M. tuberculosis TCH resistant mutants which fell into two groups; one resistant to TCH and Isoniazid but not to Ethionamide or Triclosan, and the other resistant only to TCH with no, or marginal, cross resistance to Isoniazid. A S315T katG mutation conferred resistance to TCH while katG expression from a plasmid reduced M. tuberculosis MIC to this drug, suggesting a possible involvement of KatG in TCH activation. Whole genome sequencing of mutants from this second group revealed a single mutation in the alkylhydroperoxide reductase ahpC promoter locus in half of the mutants, while the remaining contained mutations in dispensable genes. This is the first report of the genetics underlying the action of TCH and of the involvement of ahpC as the sole basis for resistance to an anti-tubercular compound.
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Affiliation(s)
- Jorgelina J Franceschelli
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, 2000, Argentina
| | - Juan M Belardinelli
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, 2000, Argentina
| | - Ping Tong
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Brendan Loftus
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | - Stephen V Gordon
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.
| | - Hector R Morbidoni
- Laboratorio de Microbiología Molecular, Facultad de Ciencias Médicas, Universidad Nacional de Rosario, 2000, Argentina.
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41
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Correia CN, McLoughlin KE, Nalpas NC, Magee DA, Browne JA, Rue-Albrecht K, Gordon SV, MacHugh DE. RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses ( Equus caballus) and Cattle ( Bos taurus). Front Genet 2018; 9:278. [PMID: 30154823 PMCID: PMC6102425 DOI: 10.3389/fgene.2018.00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/09/2018] [Indexed: 12/15/2022] Open
Abstract
RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.
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Affiliation(s)
- Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Kevin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland
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42
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Malone KM, Rue-Albrecht K, Magee DA, Conlon K, Schubert OT, Nalpas NC, Browne JA, Smyth A, Gormley E, Aebersold R, MacHugh DE, Gordon SV. Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli. Microb Genom 2018; 4. [PMID: 29557774 PMCID: PMC5885015 DOI: 10.1099/mgen.0.000163] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [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] [Indexed: 01/30/2023] Open
Abstract
Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and M. tuberculosis H37Rv at both the global transcriptional and the translational level via RNA-sequencing and SWATH MS. Furthermore, a bovine alveolar macrophage infection time course model was used to investigate the shared and divergent host transcriptomic response to infection with M. tuberculosis H37Rv or M. bovis AF2122/97. Significant differential expression of virulence-associated pathways between the two bacilli was revealed, including the ESX-1 secretion system. A divergent transcriptional response was observed between M. tuberculosis H37Rv and M. bovis AF2122/97 infection of bovine alveolar macrophages, in particular cytosolic DNA-sensing pathways at 48 h post-infection, and highlights a distinct engagement of M. bovis with the bovine innate immune system. The work presented here therefore provides a basis for the identification of host innate immune mechanisms subverted by virulent host-adapted mycobacteria to promote their survival during the early stages of infection.
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Affiliation(s)
- Kerri M Malone
- 1UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,†Present address: European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kévin Rue-Albrecht
- 1UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,2Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.,‡Present address: Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Headington, Oxford OX3 7FY, UK
| | - David A Magee
- 2Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin Conlon
- 1UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Olga T Schubert
- 3Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland.,§Present address: Department of Human Genetics, University of California, Los Angeles, USA
| | - Nicolas C Nalpas
- 2Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.,¶Present address: Quantitative Proteomics and Proteome Centre Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - John A Browne
- 2Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Alicia Smyth
- 1UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eamonn Gormley
- 4Tuberculosis Diagnostics and Immunology Research Centre, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ruedi Aebersold
- 3Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich CH-8093, Switzerland
| | - David E MacHugh
- 2Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.,5UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stephen V Gordon
- 5UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,6UCD School of Medicine, University College Dublin, Dublin 4, Ireland.,1UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,7UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
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Abstract
Mycobacterium tuberculosis is an expert and deadly pathogen, causing the disease tuberculosis (TB) in humans. It has several notable features: the ability to enter non-replicating states for long periods and cause latent infection; metabolic remodelling during chronic infection; a thick, waxy cell wall; slow growth rate in culture; and intrinsic drug resistance and antibiotic tolerance. As a pathogen, M. tuberculosis has a complex relationship with its host, is able to replicate inside macrophages, and expresses diverse immunomodulatory molecules. M. tuberculosis currently causes over 1.8 million deaths a year, making it the world's most deadly human pathogen.
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Affiliation(s)
- Stephen V Gordon
- UCD College of Health and Agricultural Sciences, University College Dublin, Ireland.,UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Tanya Parish
- Infectious Disease Research Institute, 1616 Eastlake Avenue E, Suite 400, Seattle, WA 98102, USA
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Avanzi C, Del-Pozo J, Benjak A, Stevenson K, Simpson VR, Busso P, McLuckie J, Loiseau C, Lawton C, Schoening J, Shaw DJ, Piton J, Vera-Cabrera L, Velarde-Felix JS, McDermott F, Gordon SV, Cole ST, Meredith AL. Red squirrels in the British Isles are infected with leprosy bacilli. Science 2017; 354:744-747. [PMID: 27846605 DOI: 10.1126/science.aah3783] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/27/2016] [Indexed: 12/15/2022]
Abstract
Leprosy, caused by infection with Mycobacterium leprae or the recently discovered Mycobacterium lepromatosis, was once endemic in humans in the British Isles. Red squirrels in Great Britain (Sciurus vulgaris) have increasingly been observed with leprosy-like lesions on the head and limbs. Using genomics, histopathology, and serology, we found M. lepromatosis in squirrels from England, Ireland, and Scotland, and M. leprae in squirrels from Brownsea Island, England. Infection was detected in overtly diseased and seemingly healthy animals. Phylogenetic comparisons of British and Irish M. lepromatosis with two Mexican strains from humans show that they diverged from a common ancestor around 27,000 years ago, whereas the M. leprae strain is closest to one that circulated in Medieval England. Red squirrels are thus a reservoir for leprosy in the British Isles.
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Affiliation(s)
- Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jorge Del-Pozo
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Scotland, UK
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Karen Stevenson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Scotland, UK
| | - Victor R Simpson
- Wildlife Veterinary Investigation Centre, Chacewater, Cornwall, UK
| | - Philippe Busso
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Joyce McLuckie
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Scotland, UK
| | - Chloé Loiseau
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Colin Lawton
- School of Natural Sciences, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Janne Schoening
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Darren J Shaw
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Scotland, UK
| | - Jérémie Piton
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Lucio Vera-Cabrera
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, Monterrey, N.L., Mexico
| | - Jesùs S Velarde-Felix
- Laboratorio Interdisciplinario de Investigación Dermatológica, Servicio de Dermatología, Hospital Universitario, Monterrey, N.L., Mexico
| | - Fergal McDermott
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland.,UCD School of Medicine, University College Dublin, Belfield, Dublin, Ireland.,UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Anna L Meredith
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Scotland, UK.
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45
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Correia CN, Nalpas NC, McLoughlin KE, Browne JA, Gordon SV, MacHugh DE, Shaughnessy RG. Circulating microRNAs as Potential Biomarkers of Infectious Disease. Front Immunol 2017; 8:118. [PMID: 28261201 PMCID: PMC5311051 DOI: 10.3389/fimmu.2017.00118] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [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: 10/03/2016] [Accepted: 01/25/2017] [Indexed: 12/12/2022] Open
Abstract
microRNAs (miRNAs) are a class of small non-coding endogenous RNA molecules that regulate a wide range of biological processes by post-transcriptionally regulating gene expression. Thousands of these molecules have been discovered to date, and multiple miRNAs have been shown to coordinately fine-tune cellular processes key to organismal development, homeostasis, neurobiology, immunobiology, and control of infection. The fundamental regulatory role of miRNAs in a variety of biological processes suggests that differential expression of these transcripts may be exploited as a novel source of molecular biomarkers for many different disease pathologies or abnormalities. This has been emphasized by the recent discovery of remarkably stable miRNAs in mammalian biofluids, which may originate from intracellular processes elsewhere in the body. The potential of circulating miRNAs as biomarkers of disease has mainly been demonstrated for various types of cancer. More recently, however, attention has focused on the use of circulating miRNAs as diagnostic/prognostic biomarkers of infectious disease; for example, human tuberculosis caused by infection with Mycobacterium tuberculosis, sepsis caused by multiple infectious agents, and viral hepatitis. Here, we review these developments and discuss prospects and challenges for translating circulating miRNA into novel diagnostics for infectious disease.
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Affiliation(s)
- Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin , Dublin , Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland; University College Dublin, UCD Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland; University College Dublin, UCD Conway Institute of Biomolecular and Biomedical Research, Dublin, Ireland
| | - Ronan G Shaughnessy
- UCD School of Veterinary Medicine, University College Dublin , Dublin , Ireland
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46
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Auer A, Vande Burgt NH, Abram F, Barry G, Fenton O, Markey BK, Nolan S, Richards K, Bolton D, De Waal T, Gordon SV, O'Flaherty V, Whyte P, Zintl A. Agricultural anaerobic digestion power plants in Ireland and Germany: policy and practice. J Sci Food Agric 2017; 97:719-723. [PMID: 27553887 DOI: 10.1002/jsfa.8005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/31/2016] [Accepted: 08/21/2016] [Indexed: 06/06/2023]
Abstract
The process of anaerobic digestion (AD) is valued as a carbon-neutral energy source, while simultaneously treating organic waste, making it safer for disposal or use as a fertilizer on agricultural land. The AD process in many European nations, such as Germany, has grown from use of small, localized digesters to the operation of large-scale treatment facilities, which contribute significantly to national renewable energy quotas. However, these large AD plants are costly to run and demand intensive farming of energy crops for feedstock. Current policy in Germany has transitioned to support funding for smaller digesters, while also limiting the use of energy crops. AD within Ireland, as a new technology, is affected by ambiguous governmental policies concerning waste and energy. A clear governmental strategy supporting on-site AD processing of agricultural waste will significantly reduce Ireland's carbon footprint, improve the safety and bioavailability of agricultural waste, and provide an indigenous renewable energy source. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Agathe Auer
- University College of Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - Nathan H Vande Burgt
- University College of Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - Florence Abram
- National University of Ireland Galway School of Natural Sciences, Galway, Ireland
| | - Gerald Barry
- University College of Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - Owen Fenton
- TEAGASC, Environment Research Centre, Johnstown Castle, County Wexford, Ireland
| | - Bryan K Markey
- University College of Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - Stephen Nolan
- National University of Ireland Galway School of Natural Sciences, Galway, Ireland
| | - Karl Richards
- TEAGASC, Environment Research Centre, Johnstown Castle, County Wexford, Ireland
| | - Declan Bolton
- TEAGASC, Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Theo De Waal
- University College of Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - Stephen V Gordon
- University College of Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - Vincent O'Flaherty
- National University of Ireland Galway School of Natural Sciences, Galway, Ireland
| | - Paul Whyte
- University College of Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
| | - Annetta Zintl
- University College of Dublin School of Veterinary Medicine, Belfield, Dublin 4, Ireland
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Rahim Z, Thapa J, Fukushima Y, van der Zanden AGM, Gordon SV, Suzuki Y, Nakajima C. Tuberculosis Caused by Mycobacterium orygis in Dairy Cattle and Captured Monkeys in Bangladesh: a New Scenario of Tuberculosis in South Asia. Transbound Emerg Dis 2016; 64:1965-1969. [PMID: 27888587 DOI: 10.1111/tbed.12596] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 11/28/2022]
Abstract
Mycobacterium orygis, commonly known as the oryx bacillus and a newly proposed Mycobacterium tuberculosis complex subspecies, was isolated from 18 cattle in a dairy farm and two captured rhesus monkeys in a zoo in Bangladesh. All the infected animals had tuberculosis lesions in their lungs, suggesting transmission and infection with M. orygis by an airborne route. The 20 isolates were analysed using a range of conventional and molecular typing methods, and RD-deletion typing and sequencing of selected genes confirmed the isolates as M. orygis. Multiple-locus variable-number tandem repeat analysis (MLVA) allowed the isolates to be divided into three clusters based on the relatedness of their MLVA profiles. The two monkey isolates shared the same MLVA pattern with 15 of the cattle isolates, whereas the remaining three cattle isolates had different patterns, even though the latter animals had been kept in the same dairy farm. The diversity observed among isolates may suggest the bacteria have been established in this area for a long period. This study along with other recent findings that report the detection of M. orygis from animals as well as humans originating from South Asia potentially indicate endemic distribution of M. orygis in South Asia.
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Affiliation(s)
- Z Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - J Thapa
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Y Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - A G M van der Zanden
- Laboratory for Medical Microbiology and Public Health, Enschede, The Netherlands
| | - S V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Y Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - C Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
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Farrell D, Jones G, Pirson C, Malone K, Rue-Albrecht K, Chubb AJ, Vordermeier M, Gordon SV. Integrated computational prediction and experimental validation identifies promiscuous T cell epitopes in the proteome of Mycobacterium bovis. Microb Genom 2016; 2:e000071. [PMID: 28348866 PMCID: PMC5320590 DOI: 10.1099/mgen.0.000071] [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: 04/20/2016] [Accepted: 05/26/2016] [Indexed: 11/18/2022] Open
Abstract
The discovery of novel antigens is an essential requirement in devising new diagnostics or vaccines for use in control programmes against human tuberculosis (TB) and bovine tuberculosis (bTB). Identification of potential epitopes recognised by CD4+ T cells requires prediction of peptide binding to MHC class-II, an obligatory prerequisite for T cell recognition. To comprehensively prioritise potential MHC-II-binding epitopes from Mycobacterium bovis, the agent of bTB and zoonotic TB in humans, we integrated three binding prediction methods with the M. bovisproteome using a subset of human HLA alleles to approximate the binding of epitope-containing peptides to the bovine MHC class II molecule BoLA-DRB3. Two parallel strategies were then applied to filter the resulting set of binders: identification of the top-scoring binders or clusters of binders. Our approach was tested experimentally by assessing the capacity of predicted promiscuous peptides to drive interferon-γ secretion from T cells of M. bovis infected cattle. Thus, 376 20-mer peptides, were synthesised (270 predicted epitopes, 94 random peptides with low predictive scores and 12 positive controls of known epitopes). The results of this validation demonstrated significant enrichment (>24 %) of promiscuously recognised peptides predicted in our selection strategies, compared with randomly selected peptides with low prediction scores. Our strategy offers a general approach to the identification of promiscuous epitopes tailored to target populations where there is limited knowledge of MHC allelic diversity.
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Affiliation(s)
- Damien Farrell
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland
| | - Gareth Jones
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Christopher Pirson
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Kerri Malone
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland
| | - Kevin Rue-Albrecht
- 1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.,3School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Anthony J Chubb
- 4School of Medicine, University College Dublin, Dublin D4, Ireland
| | - Martin Vordermeier
- 2Department of Bacteriology, Animal and Plant Health Agency, New Haw, Surrey KT15 3NB, UK
| | - Stephen V Gordon
- 6School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland.,5Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin D4, Ireland.,1School of Veterinary Medicine, University College Dublin, Dublin D4, Ireland.,4School of Medicine, University College Dublin, Dublin D4, Ireland
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Rue-Albrecht K, McGettigan PA, Hernández B, Nalpas NC, Magee DA, Parnell AC, Gordon SV, MacHugh DE. GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data. BMC Bioinformatics 2016; 17:126. [PMID: 26968614 PMCID: PMC4788925 DOI: 10.1186/s12859-016-0971-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 02/25/2016] [Indexed: 02/06/2023] Open
Abstract
Background Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0971-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.,Centre for Pharmacology and Therapeutics, Division of Experimental Medicine, Imperial College London, Hammersmith Hospital, London, W12 0NN, UK
| | - Paul A McGettigan
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.,Novartis Pharmaceuticals, Elm Park Business Campus, Merrion Road, Dublin 4, Ireland
| | - Belinda Hernández
- UCD School of Mathematics and Statistics, Insight Centre for Data Analytics, University College Dublin, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.,Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | - Andrew C Parnell
- UCD School of Mathematics and Statistics, Insight Centre for Data Analytics, University College Dublin, Dublin 4, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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50
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Ní Cheallaigh C, Sheedy FJ, Harris J, Muñoz-Wolf N, Lee J, West K, McDermott EP, Smyth A, Gleeson LE, Coleman M, Martinez N, Hearnden CHA, Tynan GA, Carroll EC, Jones SA, Corr SC, Bernard NJ, Hughes MM, Corcoran SE, O'Sullivan M, Fallon CM, Kornfeld H, Golenbock D, Gordon SV, O'Neill LAJ, Lavelle EC, Keane J. A Common Variant in the Adaptor Mal Regulates Interferon Gamma Signaling. Immunity 2016; 44:368-79. [PMID: 26885859 PMCID: PMC4760121 DOI: 10.1016/j.immuni.2016.01.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 04/20/2015] [Accepted: 11/06/2015] [Indexed: 12/14/2022]
Abstract
Humans that are heterozygous for the common S180L polymorphism in the Toll-like receptor (TLR) adaptor Mal (encoded by TIRAP) are protected from a number of infectious diseases, including tuberculosis (TB), whereas those homozygous for the allele are at increased risk. The reason for this difference in susceptibility is not clear. We report that Mal has a TLR-independent role in interferon-gamma (IFN-γ) receptor signaling. Mal-dependent IFN-γ receptor (IFNGR) signaling led to mitogen-activated protein kinase (MAPK) p38 phosphorylation and autophagy. IFN-γ signaling via Mal was required for phagosome maturation and killing of intracellular Mycobacterium tuberculosis (Mtb). The S180L polymorphism, and its murine equivalent S200L, reduced the affinity of Mal for the IFNGR, thereby compromising IFNGR signaling in macrophages and impairing responses to TB. Our findings highlight a role for Mal outside the TLR system and imply that genetic variation in TIRAP may be linked to other IFN-γ-related diseases including autoimmunity and cancer.
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Affiliation(s)
- Clíona Ní Cheallaigh
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin and St. James's Hospital, D08 W9RT, Dublin, Ireland; Adjuvant Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland.
| | - Frederick J Sheedy
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin and St. James's Hospital, D08 W9RT, Dublin, Ireland
| | - James Harris
- Centre for Inflammatory Diseases, Southern Clinical School, Monash University Faculty of Medicine, Nursing and Health Sciences, Clayton, Victoria 3168, Australia
| | - Natalia Muñoz-Wolf
- Adjuvant Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Jinhee Lee
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Kim West
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Eva Palsson McDermott
- Inflammation Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Alicia Smyth
- UCD Schools of Veterinary Medicine, Medicine and Medical Science, and Biomolecular and Biomedical Science, and UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Laura E Gleeson
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin and St. James's Hospital, D08 W9RT, Dublin, Ireland
| | - Michelle Coleman
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin and St. James's Hospital, D08 W9RT, Dublin, Ireland
| | - Nuria Martinez
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Claire H A Hearnden
- Adjuvant Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Graham A Tynan
- Adjuvant Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Elizabeth C Carroll
- Adjuvant Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Sarah A Jones
- Centre for Inflammatory Diseases, Southern Clinical School, Monash University Faculty of Medicine, Nursing and Health Sciences, Clayton, Victoria 3168, Australia
| | - Sinéad C Corr
- Inflammation Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Nicholas J Bernard
- Inflammation Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Mark M Hughes
- Inflammation Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Sarah E Corcoran
- Inflammation Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Mary O'Sullivan
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin and St. James's Hospital, D08 W9RT, Dublin, Ireland
| | - Ciara M Fallon
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin and St. James's Hospital, D08 W9RT, Dublin, Ireland
| | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Douglas Golenbock
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Stephen V Gordon
- UCD Schools of Veterinary Medicine, Medicine and Medical Science, and Biomolecular and Biomedical Science, and UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Luke A J O'Neill
- Inflammation Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland
| | - Ed C Lavelle
- Adjuvant Research Group, School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40, Dublin, Ireland; Advanced Materials and BioEngineering Research (AMBER), Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College, D02 PN40, Dublin, Ireland.
| | - Joseph Keane
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin and St. James's Hospital, D08 W9RT, Dublin, Ireland
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