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Santos-Ribeiro D, Cunha C, Carvalho A. Humoral pathways of innate immune regulation in granuloma formation. Trends Immunol 2024; 45:419-427. [PMID: 38762333 DOI: 10.1016/j.it.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
Abstract
The humoral arm of mammalian innate immunity regulates several molecular mechanisms involved in resistance to pathogens, inflammation, and tissue repair. Recent studies highlight the crucial role played by humoral mediators in granulomatous inflammation. However the molecular mechanisms linking the function of these soluble molecules to the initiation and maintenance of granulomas remain elusive. We propose that humoral innate immunity coordinates fundamental physiological processes in macrophages which, in turn, initiate activation and transformation events that enable granuloma formation. We discuss the involvement of humoral mediators in processes such as immune activation, phagocytosis, metabolism, and tissue remodeling, and how these can dictate macrophage functionality during granuloma formation. These advances present opportunities for discovering novel disease factors and developing targeted, more effective treatments for granulomatous diseases.
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Affiliation(s)
- Diana Santos-Ribeiro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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Valencia-Trujillo D, Avila-Trejo AM, García-Reyes RL, Narváez-Díaz L, Segura del Pilar M, Mújica-Sánchez MA, Becerril-Vargas E, León-Juárez M, Mata-Miranda MM, Rivera-Gutiérrez S, Cerna-Cortés JF. Genetic Diversity of Mycobacterium tuberculosis Strains Isolated from HIV-Infected Patients in Mexico. Pathogens 2024; 13:428. [PMID: 38787280 PMCID: PMC11124049 DOI: 10.3390/pathogens13050428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
There has been very limited investigation regarding the genetic diversity of Mycobacterium tuberculosis (MTb) strains isolated from human immunodeficiency virus (HIV)-infected patients in Mexico. In this study, we isolated 93 MTb strains from pulmonary and extrapulmonary samples of HIV-infected patients treated in a public hospital in Mexico City to evaluate the genetic diversity using spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) typing (based on 24 loci). The cohort comprised 80 male and 13 female individuals. There was a positive correlation between a high HIV viral load (>100,000 copies) and extrapulmonary tuberculosis (TB) (r = 0.306, p = 0.008). Lineage 4 was the most frequent lineage (79 strains). In this lineage, we found the H clade (n = 24), including the Haarlem, H3, and H1 families; the T clade (n = 22), including T1 and T2; the X clade (n = 15), including X1 and X3; the LAM clade (n = 14), including LAM1, LAM2, LAM3, LAM6, and LAM9; the S clade (n = 2); Uganda (n = 1); and Ghana (n = 1). We also found 12 strains in the EAI clade belonging to lineage 1, including the EAI2-Manila and EAI5 families. Interestingly, we identified one strain belonging to the Beijing family, which is part of lineage 2. One strain could not be identified. This study reports high genetic diversity among MTb strains, highlighting the need for a molecular epidemiological surveillance system that can help to monitor the spread of these strains, leading to more appropriate measures for TB control in HIV-infected patients.
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Affiliation(s)
- Daniel Valencia-Trujillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Amanda Marineth Avila-Trejo
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Rocío Liliana García-Reyes
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| | - Luis Narváez-Díaz
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Mariela Segura del Pilar
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Mario Alberto Mújica-Sánchez
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Eduardo Becerril-Vargas
- Servicio de Microbiología Clínica, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México 14080, Mexico; (L.N.-D.); (M.S.d.P.); (M.A.M.-S.); (E.B.-V.)
| | - Moises León-Juárez
- Departamento de Inmunobioquímica, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Ciudad de México 11000, Mexico;
| | - Mónica Maribel Mata-Miranda
- Escuela Militar de Medicina, Centro Militar de Ciencias de la Salud, Secretaría de la Defensa Nacional, Ciudad de México 11200, Mexico; (A.M.A.-T.); (M.M.M.-M.)
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
| | - Jorge Francisco Cerna-Cortés
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (D.V.-T.); (R.L.G.-R.); (S.R.-G.)
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Yerezhepov D, Gabdulkayum A, Akhmetova A, Kozhamkulov U, Rakhimova S, Kairov U, Zhunussova G, Kalendar R, Akilzhanova A. Pulmonary tuberculosis epidemiology and genetics in Kazakhstan. Front Public Health 2024; 12:1340673. [PMID: 38706548 PMCID: PMC11066200 DOI: 10.3389/fpubh.2024.1340673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 04/08/2024] [Indexed: 05/07/2024] Open
Abstract
Background Tuberculosis (TB) is a major public health emergency in many countries, including Kazakhstan. Despite the decline in the incidence rate and having one of the highest treatment effectiveness in the world, the incidence rate of TB remains high in Kazakhstan. Social and environmental factors along with host genetics contribute to pulmonary tuberculosis (PTB) incidence. Due to the high incidence rate of TB in Kazakhstan, our research aimed to study the epidemiology and genetics of PTB in Kazakhstan. Materials and methods 1,555 participants were recruited to the case-control study. The epidemiology data was taken during an interview. Polymorphisms of selected genes were determined by real-time PCR using pre-designed TaqMan probes. Results Epidemiological risk factors like diabetes (χ2 = 57.71, p < 0.001), unemployment (χ2 = 81.1, p < 0.001), and underweight-ranged BMI (<18.49, χ2 = 206.39, p < 0.001) were significantly associated with PTB. VDR FokI (rs2228570) and VDR BsmI (rs1544410) polymorphisms were associated with an increased risk of PTB. A/A genotype of the TLR8 gene (rs3764880) showed a significant association with an increased risk of PTB in Asians and Asian males. The G allele of the rs2278589 polymorphism of the MARCO gene increases PTB susceptibility in Asians and Asian females. VDR BsmI (rs1544410) polymorphism was significantly associated with PTB in Asian females. A significant association between VDR ApaI polymorphism and PTB susceptibility in the Caucasian population of Kazakhstan was found. Conclusion This is the first study that evaluated the epidemiology and genetics of PTB in Kazakhstan on a relatively large cohort. Social and environmental risk factors play a crucial role in TB incidence in Kazakhstan. Underweight BMI (<18.49 kg/m2), diabetes, and unemployment showed a statistically significant association with PTB in our study group. FokI (rs2228570) and BsmI (rs1544410) polymorphisms of the VDR gene can be used as possible biomarkers of PTB in Asian males. rs2278589 polymorphism of the MARCO gene may act as a potential biomarker of PTB in Kazakhs. BsmI polymorphism of the VDR gene and rs2278589 polymorphism of the MARCO gene can be used as possible biomarkers of PTB risk in Asian females as well as VDR ApaI polymorphism in Caucasians.
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Affiliation(s)
- Dauren Yerezhepov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Aidana Gabdulkayum
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ruslan Kalendar
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
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Sousa LPB, Pinto LFB, Cruz VAR, Oliveira GA, Rojas de Oliveira H, Chud TS, Pedrosa VB, Miglior F, Schenkel FS, Brito LF. Genome-wide association and functional genomic analyses for various hoof health traits in North American Holstein cattle. J Dairy Sci 2024; 107:2207-2230. [PMID: 37939841 DOI: 10.3168/jds.2023-23806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023]
Abstract
Hoof diseases are a major welfare and economic issue in the global dairy cattle production industry, which can be minimized through improved management and breeding practices. Optimal genetic improvement of hoof health could benefit from a deep understanding of the genetic background and biological underpinning of indicators of hoof health. Therefore, the primary objectives of this study were to perform genome-wide association studies, using imputed high-density genetic markers data from North American Holstein cattle, for 8 hoof-related traits: digital dermatitis, sole ulcer, sole hemorrhage, white line lesion, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, and toe ulcer, and a hoof health index. De-regressed estimated breeding values from 25,580 Holstein animals were used as pseudo-phenotypes for the association analyses. The genomic quality control, genotype phasing, and genotype imputation were performed using the PLINK (version 1.9), Eagle (version 2.4.1), and Minimac4 software, respectively. The functional genomic analyses were performed using the GALLO R package and the DAVID platform. We identified 22, 34, 14, 22, 28, 33, 24, 43, and 15 significant markers for digital dermatitis, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, sole hemorrhage, sole ulcer, toe ulcer, white line lesion disease, and the hoof health index, respectively. The significant markers were located across all autosomes, except BTA10, BTA12, BTA20, BTA26, BTA27, and BTA28. Moreover, the genomic regions identified overlap with various previously reported quantitative trait loci for exterior, health, meat and carcass, milk, production, and reproduction traits. The enrichment analyses identified 44 significant gene ontology terms. These enriched genomic regions harbor various candidate genes previously associated with bone development, metabolism, and infectious and immunological diseases. These findings indicate that hoof health traits are highly polygenic and influenced by a wide range of biological processes.
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Affiliation(s)
- Luis Paulo B Sousa
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Luis Fernando B Pinto
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Valdecy A R Cruz
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Gerson A Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Hinayah Rojas de Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Tatiane S Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; PEAK, Madison, WI 53718
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Lactanet Canada, Guelph, ON, N1K 1E5, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Thiam F, Diop G, Coulonges C, Derbois C, Thiam A, Diouara AAM, Mbaye MN, Diop M, Nguer CM, Dieye Y, Mbengue B, Zagury JF, Deleuze JF, Dieye A. An elevated level of interleukin-17A in a Senegalese malaria cohort is associated with rs8193038 IL-17A genetic variant. BMC Infect Dis 2024; 24:275. [PMID: 38438955 PMCID: PMC10910704 DOI: 10.1186/s12879-024-09149-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 02/17/2024] [Indexed: 03/06/2024] Open
Abstract
Malaria infection is a multifactorial disease partly modulated by host immuno-genetic factors. Recent evidence has demonstrated the importance of Interleukin-17 family proinflammatory cytokines and their genetic variants in host immunity. However, limited knowledge exists about their role in parasitic infections such as malaria. We aimed to investigate IL-17A serum levels in patients with severe and uncomplicated malaria and gene polymorphism's influence on the IL-17A serum levels. In this research, 125 severe (SM) and uncomplicated (UM) malaria patients and 48 free malaria controls were enrolled. IL-17A serum levels were measured with ELISA. PCR and DNA sequencing were used to assess host genetic polymorphisms in IL-17A. We performed a multivariate regression to estimate the impact of human IL-17A variants on IL-17A serum levels and malaria outcomes. Elevated serum IL-17A levels accompanied by increased parasitemia were found in SM patients compared to UM and controls (P < 0.0001). Also, the IL-17A levels were lower in SM patients who were deceased than in those who survived. In addition, the minor allele frequencies (MAF) of two IL-17A polymorphisms (rs3819024 and rs3748067) were more prevalent in SM patients than UM patients, indicating an essential role in SM. Interestingly, the heterozygous rs8193038 AG genotype was significantly associated with higher levels of IL-17A than the homozygous wild type (AA). According to our results, it can be concluded that the IL-17A gene rs8193038 polymorphism significantly affects IL-17A gene expression. Our results fill a gap in the implication of IL-17A gene polymorphisms on the cytokine level in a malaria cohort. IL-17A gene polymorphisms also may influence cytokine production in response to Plasmodium infections and may contribute to the hyperinflammatory responses during severe malaria outcomes.
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Affiliation(s)
- Fatou Thiam
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal.
| | - Gora Diop
- Departement de Biologie Animale, Faculte Des Sciences Et Techniques, Unite Postulante de Biologie GenetiqueGenomique Et Bio-Informatique (G2B), Universite Cheikh Anta DIOP, Avenue Cheikh Anta DIOP, Dakar, BP: 5005, Senegal
- Pole d'Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, 36, Avenue Pasteur, Dakar, BP: 220, Senegal
| | - Cedric Coulonges
- Equipe GBA «GenomiqueBioinformatique & Applications», Conservatoire National Des Arts Et Metiers, 292, Rue Saint Martin, Paris Cedex 03, Paris, 75141, France
| | - Celine Derbois
- Centre National de Recherche en Génétique Humaine (CNRGH), Institut de Biologie François Jacob, 2 Rue Gaston Crémieux, CP 5721, Evry Cedex, 91057, France
| | - Alassane Thiam
- Pole d'Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, 36, Avenue Pasteur, Dakar, BP: 220, Senegal
| | - Abou Abdallah Malick Diouara
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
| | - Mame Ndew Mbaye
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
| | - Mamadou Diop
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
| | - Cheikh Momar Nguer
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
| | - Yakhya Dieye
- Groupe de Recherche Biotechnologies Appliquees & Bioprocedes Environnementaux, Ecole Superieure Polytechnique, Universite Cheikh Anta Diop de Dakar, Corniche Ouest, Dakar-Fann, BP: 5085, Senegal
- Pôle de Microbiologie, Institut Pasteur de Dakar, 36 Avenue Pasteur, Dakar, BP 220, Senegal
| | - Babacar Mbengue
- Service d'Immunologie, Faculté de Médecine, de Pharmacie Et d'Odontostomatologie, Université Cheikh Anta DIOP, Avenue Cheikh Anta DIOP, Dakar, BP: 5005, Senegal
| | - Jean-Francois Zagury
- Equipe GBA «GenomiqueBioinformatique & Applications», Conservatoire National Des Arts Et Metiers, 292, Rue Saint Martin, Paris Cedex 03, Paris, 75141, France
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génétique Humaine (CNRGH), Institut de Biologie François Jacob, 2 Rue Gaston Crémieux, CP 5721, Evry Cedex, 91057, France
| | - Alioune Dieye
- Service d'Immunologie, Faculté de Médecine, de Pharmacie Et d'Odontostomatologie, Université Cheikh Anta DIOP, Avenue Cheikh Anta DIOP, Dakar, BP: 5005, Senegal
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Thorpe J, Sawaengdee W, Ward D, Campos M, Wichukchinda N, Chaiyasirinroje B, Thanraka A, Chumpol J, Phelan JE, Campino S, Mahasirimongkol S, Clark TG. Multi-platform whole genome sequencing for tuberculosis clinical and surveillance applications. Sci Rep 2024; 14:5201. [PMID: 38431684 PMCID: PMC10908857 DOI: 10.1038/s41598-024-55865-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/28/2024] [Indexed: 03/05/2024] Open
Abstract
Whole genome sequencing (WGS) of Mycobacterium tuberculosis offers valuable insights for tuberculosis (TB) control. High throughput platforms like Illumina and Oxford Nanopore Technology (ONT) are increasingly used globally, although ONT is known for higher error rates and is less established for genomic studies. Here we present a study comparing the sequencing outputs of both Illumina and ONT platforms, analysing DNA from 59 clinical isolates in highly endemic TB regions of Thailand. The resulting sequence data were used to profile the M. tuberculosis pairs for their lineage, drug resistance and presence in transmission chains, and were compared to publicly available WGS data from Thailand (n = 1456). Our results revealed isolates that are predominantly from lineages 1 and 2, with consistent drug resistance profiles, including six multidrug-resistant strains; however, analysis of ONT data showed longer phylogenetic branches, emphasising the technologies higher error rate. An analysis incorporating the larger dataset identified fifteen of our samples within six potential transmission clusters, including a significant clade of 41 multi-drug resistant isolates. ONT's extended sequences also revealed strain-specific structural variants in pe/ppe genes (e.g. ppe50), which are candidate loci for vaccine development. Despite some limitations, our results show that ONT sequencing is a promising approach for TB genomic research, supporting precision medicine and decision-making in areas with less developed infrastructure, which is crucial for tackling the disease's significant regional burden.
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Affiliation(s)
- Joseph Thorpe
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Waritta Sawaengdee
- Department of Medical Sciences, Medical Genetics Center, Medical Life Sciences Institute, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Daniel Ward
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Monica Campos
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Nuanjun Wichukchinda
- Department of Medical Sciences, Medical Genetics Center, Medical Life Sciences Institute, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | | | - Aungkana Thanraka
- Department of Medical Technology, Chiangrai Prachanukroh Hospital, Chiang Rai, 57000, Thailand
| | - Jaluporn Chumpol
- The Office of Disease Prevention and Control 7, Khon Kaen, 40000, Thailand
| | - Jody E Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Surakameth Mahasirimongkol
- Department of Medical Sciences, Medical Genetics Center, Medical Life Sciences Institute, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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7
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Torrey EF. Did the human genome project affect research on Schizophrenia? Psychiatry Res 2024; 333:115691. [PMID: 38219345 DOI: 10.1016/j.psychres.2023.115691] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
The Human Genome Project was undertaken primarily to discover genetic causes and better treatments for human diseases. Schizophrenia was targeted since three of the project`s principal architects had a personal interest and also because, based on family, adoption, and twin studies, schizophrenia was widely believed to be a genetic disorder. Extensive studies using linkage analysis, candidate genes, genome wide association studies [GWAS], copy number variants, exome sequencing and other approaches have failed to identify causal genes. Instead, they identified almost 300 single nucleotide polymorphisms [SNPs] associated with altered risks of developing schizophrenia as well as some rare variants associated with increased risk in a small number of individuals. Risk genes play a role in the clinical expression of most diseases but do not cause the disease in the absence of other factors. Increasingly, observers question whether schizophrenia is strictly a genetic disorder. Beginning in 1996 NIMH began shifting its research resources from clinical studies to basic research based on the promise of the Human Genome Project. Consequently, three decades later NIMH's genetics investment has yielded almost nothing clinically useful for individuals currently affected. It is time to review NIMH`s schizophrenia research portfolio.
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Zhang SX, Lu ZH, Wang MT, Shen YP, Duan L, Guan SY, Chen MX, Lu Y, Yang M, Wang L, Yang GB, Lv WW, Wang JC, Zheng JX. Assessing the association between the circulating levels of inflammatory cytokines and the risk of tuberculosis: A bidirectional two-sample mendelian randomization study. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105524. [PMID: 37952650 DOI: 10.1016/j.meegid.2023.105524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND Numerous observational studies have previously reported an association between inflammatory cytokines and tuberculosis (TB). However, the causal relationship between these factors remains unclear. Consequently, we conducted two-sample Mendelian randomization (MR) analyses to ascertain the causal link between levels of inflammatory cytokines and the risk of TB. METHODS Single nucleotide polymorphisms (SNPs) robustly associated with the cytokines, located in or close to their coding gene. SNP was obtained from genome-wide association studies (GWAS) of 8293 individuals of Finnish. TB data was obtained from the UK Biobank, which included 46,293 individuals of European ancestry (comprising 2277 TB cases and 46,056 controls). Two-sample, bi-directional MR analyses using inverse-variance weighted (IVW) method as the primary analysis. Followed by comprehensive sensitivity analyses to validate the robustness of results. RESULT The study showed that the causal relationship between circulating levels of interleukin (IL)-7 and risk of TB (odds ratio [OR] = 1.001, 95% confidence intervals [CIs]: 1.000, 1.003. p = 0.047). No causal associations were observed between other influencing factors and the occurrence of TB. Furthermore, the analysis revealed that TB infection exhibited negative causal associations with macrophage inflammatory protein 1 alpha ([MIP-1α], OR = 0.007, 95% CI: 0.000, 0.192. p = 0.004), IL-2 (OR = 0.014, 95% CI: 0.010, 0.427. p = 0.014), interleukin-2 receptor alpha chain([IL-2rα], OR = 0.019, 95% CI: 0.001, 0.525. p = 0.019) and basic fibroblast growth factor ([bFGF], OR = 0.066, 95% CI: 0.006, 0.700. p = 0.024). CONCLUSION The study has illuminated the causal link between inflammatory cytokines and TB, thereby enhancing our comprehension of the potential mechanisms underlying TB pathogenesis. This discovery offers promising avenues for the identification of novel therapeutic targets in TB treatment. These insights may ultimately pave the way for more effective treatment approaches, thereby improving patient outcomes.
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Affiliation(s)
- Shun-Xian Zhang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research On Tropical Diseases, National Institute of Parasitic Diseases, Shanghai 200025, China; School of Global Health, Chinese Center for Tropical Diseases Research-Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhen-Hui Lu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Mei-Ti Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Yu-Ping Shen
- The Second affiliated Hospital of Zhejiang Chinese Medical University, Huangzhou 310012, China
| | - Lei Duan
- Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research On Tropical Diseases, National Institute of Parasitic Diseases, Shanghai 200025, China; School of Global Health, Chinese Center for Tropical Diseases Research-Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shi-Yang Guan
- Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Mu-Xin Chen
- Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research On Tropical Diseases, National Institute of Parasitic Diseases, Shanghai 200025, China; School of Global Health, Chinese Center for Tropical Diseases Research-Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yan Lu
- Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research On Tropical Diseases, National Institute of Parasitic Diseases, Shanghai 200025, China; School of Global Health, Chinese Center for Tropical Diseases Research-Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ming Yang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lei Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Guo-Bing Yang
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou 730000, China
| | - Wen-Wen Lv
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ji-Chun Wang
- Department of Science and Technology, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Jin-Xin Zheng
- Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research On Tropical Diseases, National Institute of Parasitic Diseases, Shanghai 200025, China; School of Global Health, Chinese Center for Tropical Diseases Research-Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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9
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Angchagun K, Boonklang P, Chomkatekaew C, Pakdeerat S, Wongsuwan G, Amornchai P, Wuthiekanun V, Panapipat S, Ngernseng T, Waithira N, Walton S, Limmathurotsakul D, Surawong A, Siriboon S, Chamnan P, Chantratita N, Dunachie S, Corander J, Davenport EE, Knight J, Parkhill J, Peacock SJ, Thomson NR, Day NP, Chewapreecha C. BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection. Wellcome Open Res 2023; 8:347. [PMID: 37928212 PMCID: PMC10624953 DOI: 10.12688/wellcomeopenres.19809.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 11/07/2023] Open
Abstract
Background Melioidosis is a frequently fatal disease caused by an environmental bacterium Burkholderia pseudomallei. The disease is prevalent in northeast Thailand, particularly among rice field farmers who are at risk of bacterial exposure through contact with contaminated soil and water. However, not all exposure results in disease, and infection can manifest diverse outcomes. We postulate that genetic factors, whether from the bacterium, the host or the combination of both, may influence disease outcomes. To address this hypothesis, we aim to collect, sequence, and analyse genetic data from melioidosis patients and controls, along with isolates of B. pseudomallei obtained from patients. Additionally, we will study the metagenomics of the household water supply for both patients and controls, including the presence of B. pseudomallei. Methods BurkHostGEN is an ongoing observational study being conducted at Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand. We are obtaining consent from 600 melioidosis patients and 700 controls, spanning both sexes, to collect 1 mL of blood for host DNA analysis, 3 mL of blood for RNA analysis, as well as 5 L of household water supply for metagenomic analysis. Additionally, we are isolating B. pseudomallei from the melioidosis patients to obtain bacterial DNA. This comprehensive approach will allow us to identify B. pseudomallei and their paired host genetic factors associated with disease acquisition and severity. Ethical approvals have been obtained for BurkHostGEN. Host and bacterial genetic data will be uploaded to European Genome-Phenome Archive (EGA) and European Nucleotide Archive (ENA), respectively. Conclusions BurkHostGEN holds the potential to discover bacterial and host genetic factors associated with melioidosis infection and severity of illness. It can also support various study designs, including biomarker validation, disease pathogenesis, and epidemiological analysis not only for melioidosis but also for other infectious diseases.
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Affiliation(s)
- Kesorn Angchagun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Phumrapee Boonklang
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Chalita Chomkatekaew
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Sukritpong Pakdeerat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Gumphol Wongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Premjit Amornchai
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Salwaluk Panapipat
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Thatsanun Ngernseng
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Naomi Waithira
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Steve Walton
- Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Anoree Surawong
- Sunpasitthiprasong Regional Hospital, Ubon Ratchathani, 34000, Thailand
| | | | - Parinya Chamnan
- Sunpasitthiprasong Regional Hospital, Ubon Ratchathani, 34000, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
| | - Susie Dunachie
- Nuffield Department of Medicine, Centre of Tropical Medicine and Global Health, University of Oxford, Oxford, England, OX3 7LG, UK
| | - Jukka Corander
- Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
- Institute of Basic Medical Sciences, Faculty of Medcine, University of Oslo, Oslo, Oslo, 0317, Norway
| | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, England, OX3 7BN, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, England, CB3 0ES, UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge, England, CB2 0SP, UK
| | | | - Nicholas P.J. Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
- Nuffield Department of Medicine, Centre of Tropical Medicine and Global Health, University of Oxford, Oxford, England, OX3 7LG, UK
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
- Wellcome Sanger Institute, Hinxton, England, CB10 1SA, UK
- Department of Clinical Medicine, Faculty of Tropical Medicine, Mahidol University, Salaya, Nakhon Pathom, 10400, Thailand
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10
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Xu ZM, Naret O, Oumelloul MA, Fellay J. G2GSnake: a Snakemake workflow for host-pathogen genomic association studies. BIOINFORMATICS ADVANCES 2023; 3:vbad142. [PMID: 37840906 PMCID: PMC10576169 DOI: 10.1093/bioadv/vbad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
Summary Joint analyses of paired host and pathogen genome sequences have the potential to enhance our understanding of host-pathogen interactions. A systematic approach to conduct such a joint analysis is through a "genome-to-genome" (G2G) association study, which involves testing for associations between all host and pathogen genetic variants. Significant associations reveal host genetic factors that might drive pathogen variation, highlighting biological mechanisms likely to be involved in host control and pathogen escape. Here, we present a Snakemake workflow that allows researchers to conduct G2G studies in a reproducible and scalable manner. In addition, we have developed an intuitive R Shiny application that generates custom summaries of the results, enabling users to derive relevant insights. Availability and implementation G2GSnake is freely available at: https://github.com/zmx21/G2GSnake under the MIT license.
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Affiliation(s)
- Zhi Ming Xu
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Olivier Naret
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Mariam Ait Oumelloul
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
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11
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Bisschop PIH, Frankena K, Milne GM, Ford T, McCallan L, Young FJ, Byrne AW. Relationship between ambient temperature at sampling and the interferon gamma test result for bovine tuberculosis in cattle. Vet Microbiol 2023; 283:109778. [PMID: 37216720 DOI: 10.1016/j.vetmic.2023.109778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]
Abstract
Bovine tuberculosis (bTB) is a disease of significant economic and zoonotic importance, therefore, optimising tests for the identification of Mycobacterium bovis infected cattle is essential. The Interferon Gamma (IFN-γ) Release Assay (IGRA) can diagnose M. bovis infected cattle at an early stage, is easy to perform and can be used alongside skin tests for confirmatory purposes or to increase diagnostic sensitivity. It is known that IGRA performance is sensitive to environmental conditions under which samples are taken and transported. In this study, the association between the ambient temperature on the day of bleeding and the subsequent IGRA result for bTB was quantified using field samples from Northern Ireland (NI). Results of 106,434 IGRA results (2013-2018) were associated with temperature data extracted from weather stations near tested cattle herds. Model dependent variables were the levels of IFN-γ triggered by avian purified protein derivative (PPDa), M. bovis PPD (PPDb), their difference (PPD(b-a)) as well as the final binary outcome (positive or negative for M. bovis infection). IFN-γ levels after both PPDa and PPDb stimulation were lowest at the extremes of the temperature distribution for NI. The highest IGRA positive probability (above 6%) was found on days with moderate maximum temperatures (6-16 °C) or moderate minimum temperatures (4-7 °C). Adjustment for covariates did not lead to major changes in the model estimates. These data suggest that IGRA performance can be affected when samples are taken at high or low temperatures. Whilst it is difficult to exclude physiological factors, the data nonetheless supports the temperature control of samples from bleeding through to laboratory to help mitigate post-collection confounders.
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Affiliation(s)
- P I H Bisschop
- Department of Animal Science, Adaptation Physiology group, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, the Netherlands
| | - K Frankena
- Department of Animal Science, Adaptation Physiology group, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, the Netherlands
| | - G M Milne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), 12 Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - T Ford
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), 12 Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - L McCallan
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), 12 Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - F J Young
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), 12 Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - A W Byrne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), 12 Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University, 19 Chlorine Gardens, Belfast BT9 5DL, UK
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