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Urtasun-Elizari JM, Ma R, Pickford H, Farrell D, Gonzalez G, Perets V, Nakajima C, Suzuki Y, MacHugh DE, Bhatt A, Gordon SV. Functional analysis of the Mycobacterium bovis AF2122/97 PhoPR system. Tuberculosis (Edinb) 2024; 148:102544. [PMID: 39018651 DOI: 10.1016/j.tube.2024.102544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
The PhoPR system is a master regulator in Mycobacterium tuberculosis. A key difference between M. tuberculosis and Mycobacterium bovis is a G71I substitution in the M. bovis PhoR orthologue. Functional studies of the M. bovis PhoPR system have generated conflicting findings, with some research suggesting that the M. bovis PhoPR is defective while others indicate it is functional. We sought to revisit the functionality of the M. bovis PhoPR system. To address this, we constructed a phoPR mutant in the reference strain M. bovis AF2122/97. We employed a combination of growth assays and transcriptomics analyses to assess the phenotype of the mutant vs wild type and complemented strains. We found that the M. bovis AF2122/97 ΔphoPR mutant showed a growth defect on solid and liquid media compared to the wild type and complemented strains. The transcriptome of the M. bovis AF2122/97 ΔphoPR mutant was also altered as compared to wild type, including differential expression of genes involved in lipid metabolism and secretion. Our work provides further insight into the activity of PhoPR in M. bovis and underlines the importance of the PhoPR system as a master regulator of gene expression in the Mycobacterium tuberculosis complex.
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Affiliation(s)
| | - Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Hayleah Pickford
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Gabriel Gonzalez
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan
| | - Viktor Perets
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Chie Nakajima
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| | - Yasuhiko Suzuki
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Centre for One Health, University College Dublin, Belfield, Dublin, Ireland
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan; UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Centre for One Health, University College Dublin, Belfield, Dublin, Ireland; UCD Centre for Experimental Pathogen Host Research, University College Dublin, Belfield, Dublin, Ireland.
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2
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Hall TJ, McHugo GP, Mullen MP, Ward JA, Killick KE, Browne JA, Gordon SV, MacHugh DE. Integrative and comparative genomic analyses of mammalian macrophage responses to intracellular mycobacterial pathogens. Tuberculosis (Edinb) 2024; 147:102453. [PMID: 38071177 DOI: 10.1016/j.tube.2023.102453] [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: 07/17/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 06/14/2024]
Abstract
Mycobacterium tuberculosis, the causative agent of human tuberculosis (hTB), is a close evolutionary relative of Mycobacterium bovis, which causes bovine tuberculosis (bTB), one of the most damaging infectious diseases to livestock agriculture. Previous studies have shown that the pathogenesis of bTB disease is comparable to hTB disease, and that the bovine and human alveolar macrophage (bAM and hAM, respectively) transcriptomes are extensively reprogrammed in response to infection with these intracellular mycobacterial pathogens. In this study, a multi-omics integrative approach was applied with functional genomics and GWAS data sets across the two primary hosts (Bos taurus and Homo sapiens) and both pathogens (M. bovis and M. tuberculosis). Four different experimental infection groups were used: 1) bAM infected with M. bovis, 2) bAM infected with M. tuberculosis, 3) hAM infected with M. tuberculosis, and 4) human monocyte-derived macrophages (hMDM) infected with M. tuberculosis. RNA-seq data from these experiments 24 h post-infection (24 hpi) was analysed using three computational pipelines: 1) differentially expressed genes, 2) differential gene expression interaction networks, and 3) combined pathway analysis. The results were integrated with high-resolution bovine and human GWAS data sets to detect novel quantitative trait loci (QTLs) for resistance to mycobacterial infection and resilience to disease. This revealed common and unique response macrophage pathways for both pathogens and identified 32 genes (12 bovine and 20 human) significantly enriched for SNPs associated with disease resistance, the majority of which encode key components of the NF-κB signalling pathway and that also drive formation of the granuloma.
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Affiliation(s)
- Thomas J Hall
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Michael P Mullen
- Bioscience Research Institute, Technological University of the Shannon, Athlone, Westmeath, N37 HD68, Ireland
| | - James A Ward
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Kate E Killick
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, 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, 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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3
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Jiménez-Martín D, García-Bocanegra I, Risalde MA, Napp S, Domínguez M, Romero B, Moreno I, Martínez R, Cano-Terriza D. Mycobacterium tuberculosis complex in domestic goats in Southern Spain. Prev Vet Med 2024; 227:106204. [PMID: 38604014 DOI: 10.1016/j.prevetmed.2024.106204] [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: 10/19/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
Tuberculosis (TB) is a zoonotic infectious disease caused by bacteria belonging to the Mycobacterium tuberculosis complex (MTC), which can affect a wide variety of domestic and wild animal species. Although the role of goats as a reservoir of MTC bacteria has been evidenced, information about the circulation of MTC strains in this species is still very scarce. The aim of the present study was to determine the seroprevalence, spatial distribution, risk factors and MTC spoligotypes circulating in goats from Andalusia (Southern Spain), the Spanish region with the largest goat census and a hotspot area of TB in both cattle and wild ungulates. A total of 2155 serum samples from 80 goat flocks were analyzed by an in-house ELISA using the P22 protein complex as a coating antigen. Antibodies against MTC were detected in 473 goats (21.9%, 95% CI: 20.2-23.7) and the true seroprevalence was 22.3% (95% CI: 20.6-24.1). Seropositivity was found in 72 (90.0%) of the 80 flocks analyzed. The generalized estimating equation model showed that the management system (higher seroprevalence on intensive and semi-intensive farms), and the presence of hospital pens inside the regular stables, were risk factors potentially associated with MTC exposure in goats in Southern Spain. The spatial analysis identified a significant spatial cluster (p < 0.001) in Eastern Andalusia. A total of 16 different MTC spoligotypes, including five of M. caprae and eleven of M. bovis, were identified in goats between 2015 and 2022 in the study area, with SB0157 as the most frequently isolated. The results obtained indicate widespread and non-homogeneous spatial distribution of MTC in goat herds from Southern Spain. The high individual and herd-level seroprevalence values found suggest that goats could play a significant role in the maintenance and transmission of MTC in the study area. Our results highlight the importance of implementing control measures in this species.
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Affiliation(s)
- Débora Jiménez-Martín
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba, Spain
| | - Ignacio García-Bocanegra
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain.
| | - María A Risalde
- CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain; Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Napp
- IRTA, Animal Health Research Centre (CReSA IRTA-UAB), Bellaterra, Spain
| | - Mercedes Domínguez
- Unidad de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Beatriz Romero
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET) y Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Inmaculada Moreno
- Unidad de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Remigio Martínez
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba, Spain
| | - David Cano-Terriza
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes ENZOEM, Universidad de Córdoba, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain
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4
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van Heule M, El-Sheikh Ali H, Monteiro HF, Scoggin K, Fedorka C, Weimer BC, Ball B, Daels P, Dini P. Characterization of the equine placental microbial population during nocardioform placentitis. Theriogenology 2024; 225:172-179. [PMID: 38810343 DOI: 10.1016/j.theriogenology.2024.05.025] [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: 02/02/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
Abstract
Nocardioform placentitis is a poorly understood disease of equine late gestation. The presence of nocardioform, filamentous branching gram-positive bacteria, has been linked to the disease, with Crossiella equi, Amycolatopsis spp., and Streptomyces spp. being the most frequently identified bacteria. However, these bacteria are not found in all clinical cases in addition to being isolated from healthy, normal postpartum placentas. To better understand this form of placentitis, we analyzed the microbial composition in the equine placenta (chorioallantois) of both healthy postpartum (control; n = 11) and nocardioform-affected samples (n = 22) using 16S rDNA sequencing. We found a lower Shannon index in nocardioform samples, a higher Chao1 index in nocardioform samples, and a difference in beta diversity between control and nocardioform samples (p < 0.05), suggesting the presence of dysbiosis during the disease. In the majority of the NP samples (77 %), one of the following genera-Amycolatopsis, Crossiella, Lentzea, an unidentified member of the Pseudonocardiaceae family, Mycobacterium, or Enterococcus -represented over 70 % of the relative abundance. Overall, the data suggest that a broader spectrum of potential opportunistic pathogens could be involved in nocardioform placentitis, extending beyond the traditionally recognized bacteria, resulting in a similar histomorphological profile.
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Affiliation(s)
- Machteld van Heule
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA; Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, University of Ghent, Merelbeke, 9800, Belgium
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40503, USA
| | - Hugo Fernando Monteiro
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Kirsten Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40503, USA
| | - Carleigh Fedorka
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40503, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Barry Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40503, USA
| | - Peter Daels
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, University of Ghent, Merelbeke, 9800, Belgium
| | - Pouya Dini
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
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5
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Refaya AK, Vetrivel U, Palaniyandi K. Genomic Characterization of IS 6110 Insertions in Mycobacterium orygis. Evol Bioinform Online 2024; 20:11769343241240558. [PMID: 38586439 PMCID: PMC10996354 DOI: 10.1177/11769343241240558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/04/2024] [Indexed: 04/09/2024] Open
Abstract
Mycobacterium orygis, a subspecies of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant concern in the context of One Health, with implications for zoonosis or zooanthroponosis or both. MTBC strains are characterized by the unique insertion element IS6110, which is widely used as a diagnostic marker. IS6110 transposition drives genetic modifications in MTBC, imparting genome plasticity and profound biological consequences. While IS6110 insertions are customarily found in the MTBC genomes, the evolutionary trajectory of strains seems to correlate with the number of IS6110 copies, indicating enhanced adaptability with increasing copy numbers. Here, we present a comprehensive analysis of IS6110 insertions in the M. orygis genome, utilizing ISMapper, and elucidate their genetic consequences in promoting successful host adaptation. Our study encompasses a panel of 67 paired-end reads, comprising 11 isolates from our laboratory and 56 sequences downloaded from public databases. Among these sequences, 91% exhibited high-copy, 4.5% low-copy, and 4.5% lacked IS6110 insertions. We identified 255 insertion loci, including 141 intragenic and 114 intergenic insertions. Most of these loci were either unique or shared among a limited number of isolates, potentially influencing strain behavior. Furthermore, we conducted gene ontology and pathway analysis, using eggNOG-mapper 5.0, on the protein sequences disrupted by IS6110 insertions, revealing 63 genes involved in diverse functions of Gene Ontology and 45 genes participating in various KEGG pathways. Our findings offer novel insights into IS6110 insertions, their preferential insertion regions, and their impact on metabolic processes and pathways, providing valuable knowledge on the genetic changes underpinning IS6110 transposition in M. orygis.
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Affiliation(s)
- Ahmed Kabir Refaya
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
| | - Umashankar Vetrivel
- Department of Virology & Biotechnology/Bioinformatics Division, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
| | - Kannan Palaniyandi
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
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6
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Blankson HNA, Kamara RF, Barilar I, Andres S, Conteh OS, Dallenga T, Foray L, Maurer F, Kranzer K, Utpatel C, Niemann S. Molecular determinants of multidrug-resistant tuberculosis in Sierra Leone. Microbiol Spectr 2024; 12:e0240523. [PMID: 38289066 PMCID: PMC10923214 DOI: 10.1128/spectrum.02405-23] [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: 06/28/2023] [Accepted: 10/28/2023] [Indexed: 03/06/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) management has become a serious global health challenge. Understanding its epidemic determinants on the regional level is crucial for developing effective control measures. We used whole genome sequencing data of 238 of Mycobacterium tuberculosis complex (MTBC) strains to determine drug resistance profiles, phylogeny, and transmission dynamics of MDR/rifampicin-resistant (RR) MTBC strains from Sierra Leone. Forty-two strains were classified as RR, 196 as MDR, 5 were resistant to bedaquiline (BDQ) and clofazimine (CFZ), but none was found to be resistant to fluoroquinolones. Sixty-one (26%) strains were resistant to all first-line drugs, three of which had additional resistance to BDQ/CFZ. The strains were classified into six major MTBC lineages (L), with strains of L4 being the most prevalent, 62% (n = 147), followed by L6 (Mycobacterium africanum) strains, (21%, n = 50). The overall clustering rate (using ≤d12 single-nucleotide polymorphism threshold) was 44%, stratified into 31 clusters ranging from 2 to 16 strains. The largest cluster (n = 16) was formed by sublineage 2.2.1 Beijing Ancestral 3 strains, which developed MDR several times. Meanwhile, 10 of the L6 strains had a primary MDR transmission. We observed a high diversity of drug resistance mutations, including borderline resistance mutations to isoniazid and rifampicin, and mutations were not detected by commercial assays. In conclusion, one in five strains investigated was resistant to all first-line drugs, three of which had evidence of BDQ/CFZ resistance. Implementation of interventions such as rapid diagnostics that prevent further resistance development and stop MDR-TB transmission chains in the country is urgently needed. IMPORTANCE A substantial proportion of MDR-TB strains in Sierra Leone were resistant against all first line drugs; however this makes the all-oral-six-month BPaLM regimen or other 6-9 months all oral regimens still viable, mainly because there was no FQ resistance.Resistance to BDQ was detected, as well as RR, due to mutations outside of the hotspot region. While the prevalence of those resistances was low, it is still cause for concern and needs to be closely monitored.
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Affiliation(s)
- Harriet N. A. Blankson
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Korle-Bu, Accra, Ghana
| | - Rashidatu Fouad Kamara
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Ousman S. Conteh
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Tobias Dallenga
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- Cellular Microbiology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Lynda Foray
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Florian Maurer
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Kranzer
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
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Holder T, Srinivasan S, McGoldrick A, Williams GA, Palmer S, Clarke J, O'Brien A, Conlan AJK, Juleff N, Vordermeier HM, Jones GJ, Kapur V. Temporal dynamics of the early immune response following Mycobacterium bovis infection of cattle. Sci Rep 2024; 14:2600. [PMID: 38297023 PMCID: PMC10831113 DOI: 10.1038/s41598-024-52314-x] [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: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
Bovine tuberculosis is an infectious disease of global significance that remains endemic in many countries. Mycobacterium bovis infection in cattle is characterized by a cell-mediated immune response (CMI) that precedes humoral responses, however the timing and trajectories of CMI and antibody responses determined by newer generation assays remain undefined. Here we used defined-antigen interferon-gamma release assays (IGRA) and an eleven-antigen multiplex ELISA (Enferplex TB test) alongside traditional tuberculin-based IGRA and IDEXX M. bovis antibody tests to assess immune trajectories following experimental M. bovis infection of cattle. The results show CMI responses developed as early as two-weeks post-infection, with all infected cattle testing positive three weeks post-infection. Interestingly, 6 of 8 infected animals were serologically positive with the Enferplex TB assay as early as 4 weeks post-infection. As expected, application of the tuberculin skin test enhanced subsequent serological reactivity. Infrequent M. bovis faecal shedding was observed but was uncorrelated with observed immune trajectories. Together, the results show that early antibody responses to M. bovis infection are detectable in some individuals and highlight an urgent need to identify biomarkers that better predict infection outcomes, particularly for application in low-and-middle income countries where test-and-slaughter based control methods are largely unfeasible.
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Affiliation(s)
- Thomas Holder
- Animal and Plant Health Agency, Bacteriology, Addlestone, UK
| | - Sreenidhi Srinivasan
- The Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | | | | | | | - John Clarke
- Enfer Scientific, Unit T, M7 Business Park, Newhall, Naas, County Kildare, Ireland
| | - Amanda O'Brien
- Enfer Scientific, Unit T, M7 Business Park, Newhall, Naas, County Kildare, Ireland
| | - Andrew J K Conlan
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nick Juleff
- The Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Gareth J Jones
- Animal and Plant Health Agency, Bacteriology, Addlestone, UK.
| | - Vivek Kapur
- The Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
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8
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Clough J, Schwab S, Mikac K. Gut Microbiome Profiling of the Endangered Southern Greater Glider ( Petauroides volans) after the 2019-2020 Australian Megafire. Animals (Basel) 2023; 13:3583. [PMID: 38003202 PMCID: PMC10668662 DOI: 10.3390/ani13223583] [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: 10/27/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.
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Affiliation(s)
- Jordyn Clough
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
| | - Sibylle Schwab
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Katarina Mikac
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
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9
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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] [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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10
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Rajbhandari RM, Napit R, Manandhar P, Raut R, Gurung A, Poudel A, Shrestha N, Sadaula A, Karmacharya D, Gortázar C, Alves PC, de la Fuente J, Queirós J. Phylogenomic analysis supports Mycobacterium tuberculosis transmission between humans and elephants. Front Vet Sci 2023; 10:1133823. [PMID: 37303725 PMCID: PMC10250650 DOI: 10.3389/fvets.2023.1133823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Tuberculosis is an infectious disease caused by a group of acid-fast bacilli known as Mycobacterium tuberculosis complex (MTC), which has a major impact on humans. Transmission of MTC across the human-animal interface has been demonstrated by several studies. However, the reverse zoonotic transmission from humans to animals (zooanthroponosis) has often been neglected. Methods In this study, we used Nanopore MinION and Illumina MiSeq approaches to sequence the whole genome of M. tuberculosis strains isolated from two deceased Asian elephants (Elephas maximus) and one human in Chitwan, Nepal. The evolutionary relationships and drug resistance capacity of these strains were assessed using the whole genome data generated by the stand-alone tool Tb-Profiler. Phylogenomic trees were also constructed using a non-synonymous SNP alignment of 2,596 bp, including 94 whole genome sequences representative of the previously described M. tuberculosis lineages from elephants worldwide (lineages 1 and 4) and from humans in Nepal (lineages 1, 2 and 3). Results and Discussion The new genomes achieved an average coverage of 99.6%, with an average depth of 55.67x. These M. tuberculosis strains belong to lineage 1 (elephant DG), lineage 2 (elephant PK) and lineage 4 (human), and none of them were found to have drug-resistant variants. The elephant-derived isolates were evolutionarily closely related to human-derived isolates previously described in Nepal, both in lineages 1 and 2, providing additional support for zooanthroponosis or bidirectional transmission between humans and elephants. The human-derived isolate clustered together with other published human isolates from Argentina, Russia and the United Kingdom in the lineage 4 clade. This complex multi-pathogen, multi-host system is challenging and highlights the need for a One Health approach to tuberculosis prevention and control at human-animal interface, particularly in regions where human tuberculosis is highly endemic.
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Affiliation(s)
- Rajesh Man Rajbhandari
- Departamento de Biologia, Faculdade de Ciencias da Universidade do Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado—BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM and CSIC), Ciudad Real, Spain
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | | | | | - Roji Raut
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | | | - Ajit Poudel
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | | | - Amir Sadaula
- National Trust for Nature Conservation, Biodiversity Conservation Center, Chitwan, Nepal
| | - Dibesh Karmacharya
- Center for Molecular Dynamics Nepal, Kathmandu, Nepal
- School of Biological Sciences, Faculty of Science, The University of Queensland, Brisbane, QLD, Australia
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM and CSIC), Ciudad Real, Spain
| | - Paulo Célio Alves
- Departamento de Biologia, Faculdade de Ciencias da Universidade do Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado—BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, Portugal
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM and CSIC), Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
| | - João Queirós
- Departamento de Biologia, Faculdade de Ciencias da Universidade do Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado—BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- EBM, Estação Biológica de Mértola, Praça Luís de Camões, Mértola, Portugal
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11
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Abstract
Immunity to infection has been extensively studied in humans and mice bearing naturally occurring or experimentally introduced germline mutations. Mouse studies are sometimes neglected by human immunologists, on the basis that mice are not humans and the infections studied are experimental and not natural. Conversely, human studies are sometimes neglected by mouse immunologists, on the basis of the uncontrolled conditions of study and small numbers of patients. However, both sides would agree that the infectious phenotypes of patients with inborn errors of immunity often differ from those of the corresponding mutant mice. Why is that? We argue that this important question is best addressed by revisiting and reinterpreting the findings of both mouse and human studies from a genetic perspective. Greater caution is required for reverse-genetics studies than for forward-genetics studies, but genetic analysis is sufficiently strong to define the studies likely to stand the test of time. Genetically robust mouse and human studies can provide invaluable complementary insights into the mechanisms of immunity to infection common and specific to these two species.
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Affiliation(s)
- Philippe Gros
- McGill University Research Center on Complex Traits, Department of Biochemistry, and Department of Human Genetics, McGill University, Montréal, Québec, Canada;
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute and St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, and University of Paris Cité, Imagine Institute and Necker Hospital for Sick Children, Paris, France
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12
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Jiménez-Martín D, Cano-Terriza D, Risalde MA, Napp S, Álvarez J, Fernández-Morente M, Fernández-Molera V, Moreno I, Infantes-Lorenzo JA, García-Bocanegra I. Seroepidemiology of tuberculosis in sheep in southern Spain. Prev Vet Med 2023; 215:105920. [PMID: 37094444 DOI: 10.1016/j.prevetmed.2023.105920] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/26/2023] [Accepted: 04/11/2023] [Indexed: 04/26/2023]
Abstract
Tuberculosis (TB) is a multi-host infectious disease caused by members of the Mycobacterium tuberculosis complex (MTC). In Mediterranean ecosystems, where multiple animal hosts of TB are present, identifying the role of the different species involved in the epidemiology of TB is a key point to be able to implement proper control measures. Sheep are susceptible to MTC infection but have traditionally been considered a spillover host. However, the occurrence of outbreaks involving sheep in recent years evidences the need to better understand the role of this small ruminant species in the epidemiology of the disease. Here, we aimed to determine the seroprevalence and risk factors associated with MTC seropositivity in sheep in Andalusia (southern Spain), a region with one of the highest prevalence of MTC infection in both cattle and wild ungulates. A total of 2266 sheep from 83 flocks were tested for antibodies against MTC using an in-house indirect ELISA. Anti-MTC antibodies were detected in 16 (0.7%) of the 2266 sheep (adjusted true prevalence 0.29%, 95% posterior probability interval 0.01-1.05). Seropositivity was found in 14.5% (12/83; 95%CI: 6.9-22.0) of the sheep farms analyzed. A semi-extensive management system was identified as a risk factor associated with MTC seropositivity in sheep farms (OR = 3.7; p < 0.038; 95%CI: 1.1-12.4) in the study area. To the best of the authors' knowledge, this is the first active TB surveillance study carried out to assess MTC exposure in sheep. Our results indicate MTC circulation in sheep farms in southern Spain. However, the low individual seroprevalence obtained suggests that sheep may play a limited role in the epidemiology of TB in this region. Serosurveillance programs could be a valuable tool to detect MTC circulation in sheep in risk scenarios or target farms, in order to optimize control measures on TB animal in multi-host Mediterranean ecosystems.
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Affiliation(s)
- Débora Jiménez-Martín
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Córdoba, Spain
| | - David Cano-Terriza
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain.
| | - María A Risalde
- CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain; Departamento de Anatomía y Anatomía Patológica Comparadas y Toxicología, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Napp
- IRTA, Animal Health Research Centre (CReSA IRTA-UAB), Bellaterra, Spain
| | - Julio Álvarez
- Centro de Vigilancia Sanitaria Veterinaria VISAVET, Universidad Complutense, Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | | | | | - Inmaculada Moreno
- Unidad de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - José A Infantes-Lorenzo
- Unidad de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ignacio García-Bocanegra
- Departamento de Sanidad Animal, Grupo de Investigación en Sanidad Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Universidad de Córdoba, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain
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13
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Gonzalo X, Yrah S, Broda A, Laurenson I, Claxton P, Kostrzewa M, Drobniewski F, Larrouy-Maumus G. Performance of lipid fingerprint by routine matrix-assisted laser desorption/ionization time of flight for the diagnosis of Mycobacterium tuberculosis complex species. Clin Microbiol Infect 2023; 29:387.e1-387.e6. [PMID: 36270589 DOI: 10.1016/j.cmi.2022.10.017] [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: 05/25/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Rapid detection of bacterial pathogens at species and sub-species levels is crucial for appropriate treatment, infection control, and public health management. Currently, one of the challenges in clinical microbiology is the discrimination of mycobacterial sub-species within the M. tuberculosis complex (MTBC). Our objective was to evaluate the ability of a biosafe mycobacterial lipid-based approach to identify MTBC cultures and sub-species. METHODS A blinded study was conducted using 90 mycobacterial clinical isolate strains comprising MTBC strains sub-cultured in Middlebrook 7H11 medium supplemented with 10% oleic-acid, dextrose, catalase growth supplement and incubated for up to 6 weeks at 37°C and using the following seven reference strains (M. tuberculosis H37Rv, M canettii, M. africanum, M. pinnipedii, M. caprae, M. bovis, and M. bovis BCG) grown under the same conditions, to set the reference lipid database and test it against the 90 MTBC clinical isolates. Cultured mycobacteria were heat-inactivated and loaded onto the matrix-assisted laser desorption/ionization target followed by the addition of the matrix. Acquisition of the data was performed using the positive ion mode. RESULTS Based on the identification of clear and defined lipid signatures from the seven reference strains, the method that we developed was fast (<10 minutes) and produced interpretable profiles for all but four isolates, caused by poor ionization giving an n = 86 with interpretable spectra. The sensitivity and specificity of the matrix-assisted laser desorption/ionization time of flight were 94.4 (95% CI, 86.4-98.5) and 94.4 (95% CI, 72.7-99.9), respectively. CONCLUSIONS Mycobacterial lipid profiling provides a means of rapid, safe, and accurate discrimination of species within the MTBC.
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Affiliation(s)
- Ximena Gonzalo
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shih Yrah
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Agnieszka Broda
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ian Laurenson
- Scottish Mycobacteria Reference Laboratory, Edinburgh, United Kingdom
| | - Pauline Claxton
- Scottish Mycobacteria Reference Laboratory, Edinburgh, United Kingdom
| | | | - Francis Drobniewski
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom.
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14
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Fernández-Veiga L, Fuertes M, Geijo MV, Pérez de Val B, Vidal E, Michelet L, Boschiroli ML, Gómez-Buendía A, Bezos J, Jones GJ, Vordermeier M, Juste RA, Garrido JM, Sevilla IA. Differences in skin test reactions to official and defined antigens in guinea pigs exposed to non-tuberculous and tuberculous bacteria. Sci Rep 2023; 13:2936. [PMID: 36806813 PMCID: PMC9941491 DOI: 10.1038/s41598-023-30147-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The single and comparative intradermal tuberculin tests (SITT and CITT) are official in vivo tests for bovine tuberculosis (TB) diagnosis using bovine and avian purified protein derivatives (PPD-B and PPD-A). Infection with bacteria other than Mycobacterium tuberculosis complex (MTC) can result in nonspecific reactions to these tests. We evaluated the performance of the skin test with PPDs and new defined antigens in the guinea pig model. A standard dose (SD) of Rhodococcus equi, Nocardia sp., M. nonchromogenicum, M. monacense, M. intracellulare, M. avium subsp. paratuberculosis, M. avium subsp. avium, M. avium subsp. hominissuis, M. scrofulaceum, M. persicum, M. microti, M. caprae and M. bovis, and a higher dose (HD) of M. nonchromogenicum, M. monacense, M. intracellulare, M. avium subsp. paratuberculosis were tested using PPD-B, PPD-A, P22, ESAT-6-CFP-10-Rv3615c peptide cocktail long (PCL) and fusion protein (FP). The SD of R. equi, Nocardia sp., M. nonchromogenicum, M. monacense, M. intracellulare and M. avium subsp. paratuberculosis did not cause any reactions. The HD of M. nonchromogenicum, M. monacense, M. intracellulare, and M. avium subsp. paratuberculosis and the SD of M. avium subsp. hominissuis, M. scrofulaceum and M. persicum, caused nonspecific reactions (SIT). A CITT interpretation would have considered M. avium complex and M. scrofulaceum groups negative, but not all individuals from M. nonchromogenicum HD, M. monacense HD and M. persicum SD groups. Only animals exposed to M. bovis and M. caprae reacted to PCL and FP. These results support the advantage of complementing or replacing PPD-B to improve specificity without losing sensitivity.
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Affiliation(s)
- Leire Fernández-Veiga
- Departamento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia Spain
| | - Miguel Fuertes
- Departamento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia Spain
| | - María V. Geijo
- Departamento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia Spain
| | - Bernat Pérez de Val
- grid.7080.f0000 0001 2296 0625IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia Spain ,grid.7080.f0000 0001 2296 0625Unitat Mixta d’investigació IRTA-UAB en Sanitat Animal, CReSA, Campus de la UAB, 08193 Bellaterra, Catalonia Spain
| | - Enric Vidal
- grid.7080.f0000 0001 2296 0625IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia Spain ,grid.7080.f0000 0001 2296 0625Unitat Mixta d’investigació IRTA-UAB en Sanitat Animal, CReSA, Campus de la UAB, 08193 Bellaterra, Catalonia Spain
| | - Lorraine Michelet
- grid.410511.00000 0001 2149 7878Laboratoire de Santé Animale, Unité Zoonoses Bactériennes, Agence Nationale de Sécurité Sanitaire de l’alimentation, de l’environnement et du Travail (ANSES), Université Paris-Est, 94701 Maisons-Alfort, France
| | - María Laura Boschiroli
- grid.410511.00000 0001 2149 7878Laboratoire de Santé Animale, Unité Zoonoses Bactériennes, Agence Nationale de Sécurité Sanitaire de l’alimentation, de l’environnement et du Travail (ANSES), Université Paris-Est, 94701 Maisons-Alfort, France
| | - Alberto Gómez-Buendía
- grid.4795.f0000 0001 2157 7667Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, 28040 Madrid, Spain ,grid.4795.f0000 0001 2157 7667Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Javier Bezos
- grid.4795.f0000 0001 2157 7667Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, 28040 Madrid, Spain ,grid.4795.f0000 0001 2157 7667Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Gareth J. Jones
- grid.422685.f0000 0004 1765 422XDepartment of Bacteriology, Animal and Plant Health Agency (APHA), Surrey, KT15 3NB UK
| | - Martin Vordermeier
- grid.422685.f0000 0004 1765 422XDepartment of Bacteriology, Animal and Plant Health Agency (APHA), Surrey, KT15 3NB UK
| | - Ramón A. Juste
- Departamento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia Spain
| | - Joseba M. Garrido
- Departamento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia Spain
| | - Iker A. Sevilla
- Departamento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia Spain
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15
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Padane A, Harouna Hamidou Z, Drancourt M, Saad J. CRISPR-Based Detection, Identification and Typing of Mycobacterium tuberculosis Complex Lineages. Microbiol Spectr 2023; 11:e0271722. [PMID: 36602330 PMCID: PMC9927308 DOI: 10.1128/spectrum.02717-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/11/2022] [Indexed: 01/06/2023] Open
Abstract
The polymerase chain reaction (PCR)-based detection of Mycobacterium tuberculosis (M. tuberculosis) complex (MTC) in clinical samples is a first-line approach by which to diagnose tuberculosis in clinical microbiology laboratories. In this study, the genome-wide profiling of 3,156 mycobacterial genomes using Roary determined the CRISPR-csm4 gene as specific for MTB. Real time (RT)-PCR and the PCR-sequencing of CRISPR-csm4, tested on a collection of 20 MTC and 5 nontuberculous mycobacteria, confirmed the 20 MTC isolates, whereas the 5 nontuberculous isolates were not detected. Further, 65 of the leftover clinical samples, including 25 GeneXpert-positive and 40 GeneXpert-negative samples, that were used to evaluate the CRISPR-csm4-MTB assay in the clinical microbiology laboratory setting yielded expected results in every case, further allowing for the identification of the M. tuberculosis Beijing lineage. RT-PCR and the PCR-sequencing of CRISPR-csm4 could be implanted in the clinical microbiology laboratory to complement the currently used assays, with the potential of increasing the specification of the MTC pathogens responsible for tuberculosis. IMPORTANCE The whole-genome sequence comparison of the Mycobacterium tuberculosis complex (MTC) genomic sequences that are available in the NCBI database identified a unique, specific gene to be used directly on clinical diagnostic samples to detect MTC against all species of mycobacteria and to differentiate between MTC species, lineages, and sublineages.
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Affiliation(s)
- A. Padane
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation (IRESSEF), Dakar, Sénégal
| | - Z. Harouna Hamidou
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - M. Drancourt
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - J. Saad
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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16
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Ortega J, de Juan L, Sevilla IA, Garrido JM, Roy Á, Velasco C, Romero B, Domínguez M, Pérez de Val B, Nebot C, Sáez-Llorente JL, Álvarez J, Bezos J. Effect of a recent parenteral dexamethasone and ketoprofen administration on the immunological diagnosis of tuberculosis in goats. Front Vet Sci 2022; 9:1042428. [DOI: 10.3389/fvets.2022.1042428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Caprine tuberculosis (TB) is a zoonosis caused by members of the Mycobacterium tuberculosis complex (MTBC). Caprine TB eradication programmes are based mainly on intradermal tuberculin tests and slaughterhouse surveillance. Different factors may affect the performance of the TB diagnostic tests used in caprine herds and, therefore, their ability to detect infected animals. The present study evaluates the effect of the fraudulent administration of two anti-inflammatory substances, dexamethasone and ketoprofen, on the performance of the TB diagnostic techniques used in goats, as well as the suitability of high performance liquid chromatography (HPLC) for their detection in hair samples. The animals (n = 90) were distributed in three groups: (1) a group treated with dexamethasone (n = 30); a second group treated with ketoprofen (n = 30); and a third non-treated control group (n = 30). Both dexamethasone and ketoprofen groups were subjected to intramuscular inoculation with the substances 48 h after the administration of bovine and avian purified protein derivatives (PPDs), that is, 24 h before the tests were interpreted. All the animals were subjected to the single and comparative intradermal tuberculin (SIT and CIT, respectively) tests, interferon-gamma release assay (IGRA) and P22 ELISA. The number of SIT test reactors was significantly lower in the dexamethasone (p = 0.001) and ketoprofen (p < 0.001) groups 72 h after the bovine PPD inoculation compared with the control group. A significantly higher number of positive reactors to IGRA was detected within the dexamethasone group (p = 0.016) 72 h after PPD administration compared to the control group. Dexamethasone and ketoprofen detection in either hair or serum samples was challenging when using HPLC since these substances were not detected in animals whose skin fold thickness (SFT) was reduced, what could be an issue if they are used for fraudulent purposes. In conclusion, the parenteral administration of dexamethasone or ketoprofen 48 h after the PPDs administration can significantly reduce the increase in SFT (mm) and subsequently the number of positive reactors to SIT test.
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17
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Neila C, Rebollada-Merino A, Bezos J, de Juan L, Domínguez L, Rodríguez-Bertos A. Extracellular matrix proteins (fibronectin, collagen III, and collagen I) immunoexpression in goat tuberculous granulomas (Mycobacterium caprae). Vet Res Commun 2022; 46:1147-1156. [PMID: 36136210 DOI: 10.1007/s11259-022-09996-3] [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: 01/10/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
The lesion resulting from the interaction between Mycobacterium and the host immune response is the tuberculous granuloma. Tuberculous granulomas, except in incipient stages, are partially or totally encapsulated by connective tissue. The aim of this study was to assess the immunoexpression of the extracellular matrix proteins fibronectin, collagen III, and collagen I in granulomas caused by Mycobacterium caprae in goats (Capra aegagrus hircus) to understand capsule development at different granuloma stages. For this purpose, a retrospective study of 56 samples of tuberculous granulomas in lung (n = 30) and mediastinal lymph node (n = 26) from 17 goats naturally infected with M. caprae in stages I (n = 15), II (n = 14) and III (n = 27) was carried out. Fibronectin immunoreaction was extracellular, fibrillar-reticular in the center of stage I, II and III granulomas and peripheral in stages II and III granulomas. Collagen III immunoexpression was extracellular and fibrillar in the center of stages I, II and III tuberculous granulomas in lung and mediastinal lymph node, and progressive expression was observed in the periphery of stages II and III granulomas. Finally, collagen I immunoexpression was extracellular and fibrillar, showing a progressive loss of central expression and an increase in peripheral expression in stage III granulomas compared to stage I granulomas. Immunoexpression of these extracellular matrix proteins could help understand fibrogenesis and dating in tuberculous granuloma in both animal models and humans.
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Affiliation(s)
- Carlos Neila
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040, Madrid, Spain
- Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - Agustín Rebollada-Merino
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040, Madrid, Spain
- Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - Javier Bezos
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - Lucía de Juan
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - Antonio Rodríguez-Bertos
- VISAVET Health Surveillance Centre, Complutense University of Madrid, 28040, Madrid, Spain.
- Department of Internal Medicine and Animal Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain.
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18
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Ncube P, Bagheri B, Goosen WJ, Miller MA, Sampson SL. Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals. Microorganisms 2022; 10:microorganisms10091845. [PMID: 36144447 PMCID: PMC9503773 DOI: 10.3390/microorganisms10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host–pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host–pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.
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19
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Villar M, Rajbhandari RM, Artigas-Jerónimo S, Contreras M, Sadaula A, Karmacharya D, Alves PC, Gortázar C, de la Fuente J. Differentially Represented Proteins in Response to Infection with Mycobacterium tuberculosis Identified by Quantitative Serum Proteomics in Asian Elephants. Pathogens 2022; 11:pathogens11091010. [PMID: 36145440 PMCID: PMC9505326 DOI: 10.3390/pathogens11091010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/27/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis is a major global concern. Tuberculosis in wildlife is a risk for zoonotic transmission and becoming one of the challenges for conservation globally. In elephants, the number of cases is likely rising. The aim of this study was to identify proteins related to tuberculosis infection in elephants, which could then be used for the development of diagnostic tools and/or vaccines. A serum proteomics approach was used to characterize differentially represented proteins in response to Mycobacterium tuberculosis in Asian elephants (Elaphas maximus). Blood samples were collected from eight elephants, four of which were antibody positive for tuberculosis and four were antibody negative. Proteomics analysis identified 26 significantly dysregulated proteins in response to tuberculosis. Of these, 10 (38%) were identified as immunoglobulin and 16 (62%) as non-immunoglobulin proteins. The results provided new information on the antibody response to mycobacterial infection and biomarkers associated with tuberculosis and protective response to mycobacteria in Asian elephants. Protective mechanisms included defense against infection (Alpha-1-B glycoprotein A1BG, Serpin family A member 1 SERPINA1, Transthyretin TTR), neuroprotection (TTR), and reduced risks of inflammation, infections, and cancer (SERPINA1, Keratin 10 KRT10). Using a translational biotechnology approach, the results provided information for the identification of candidate diagnostic, prognostic, and protective antigens for monitoring and control of tuberculosis in Asian elephants.
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Affiliation(s)
- Margarita Villar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain
- Biochemistry Section, Faculty of Science and Chemical Technologies, and Regional Centre for Biomedical Research (CRIB), University of Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Rajesh Man Rajbhandari
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain
- Center for Molecular Dynamics Nepal (CMDN), Thapathali Road 11, Kathmandu 44600, Nepal
- Dep. de Biologia, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, S/N, Edificio FC4, 4169-007 Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado—BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Sara Artigas-Jerónimo
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain
| | - Marinela Contreras
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain
| | - Amir Sadaula
- National Trust for Nature Conservation, Biodiversity Conservation Center, Sauraha, Chitwan 44204, Nepal
| | - Dibesh Karmacharya
- Center for Molecular Dynamics Nepal (CMDN), Thapathali Road 11, Kathmandu 44600, Nepal
| | - Paulo Célio Alves
- Dep. de Biologia, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, S/N, Edificio FC4, 4169-007 Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado—BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Estação Biológica de Mértola EBM, Praça Luís de Camões, Mértola, 7750-329 Mértola, Portugal
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain
- Correspondence: (C.G.); or (J.d.l.F.)
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
- Correspondence: (C.G.); or (J.d.l.F.)
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20
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Robinne S, Saad J, Morsli M, Hamidou ZH, Tazerart F, Drancourt M, Baron SA. Rapid Identification of Mycobacterium tuberculosis Complex Using Mass Spectrometry: A Proof of Concept. Front Microbiol 2022; 13:753969. [PMID: 35432257 PMCID: PMC9008353 DOI: 10.3389/fmicb.2022.753969] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria that form the Mycobacterium tuberculosis complex are responsible for deadly tuberculosis in animals and patients. Identification of these pathogens at the species level is of primary importance for treatment and source tracing and currently relies on DNA analysis, including whole genome sequencing (WGS), which requires a whole day. In this study, we report the unprecedented discrimination of M. tuberculosis complex species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), with WGS as the comparative reference standard. In the first step, optimized peptide extraction applied to 36 isolates otherwise identified in five of the 11 M. tuberculosis complex variants by WGS yielded 139 MALDI-TOF spectra, which were used to identify biomarkers of interest that facilitate differentiation between variants. In a second step, 70/80 (88%) other isolates were correctly classified by an algorithm based on specific peaks. This study is the first to report a MALDI-TOF-MS method for discriminating M. tuberculosis complex mycobacteria that is easily implemented in clinical microbiology laboratories.
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Affiliation(s)
- Simon Robinne
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Jamal Saad
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Madjid Morsli
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Zelika Harouna Hamidou
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - Fatah Tazerart
- IHU Méditerranée Infection, Marseille, France
- Institut des Sciences Vétérinaires, Université de Blida 1, Blida, Algeria
| | - Michel Drancourt
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- Aix-Marseille-University, IRD, MEPHI, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- *Correspondence: Sophie Alexandra Baron,
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21
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Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations. Nat Commun 2022; 13:1195. [PMID: 35256608 PMCID: PMC8901693 DOI: 10.1038/s41467-022-28562-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/25/2022] [Indexed: 12/30/2022] Open
Abstract
AbstractPrevious ancient DNA research has shown that Mycobacterium pinnipedii, which today causes tuberculosis (TB) primarily in pinnipeds, infected human populations living in the coastal areas of Peru prior to European colonization. Skeletal evidence indicates the presence of TB in several pre-colonial South and North American populations with minimal access to marine resources— a scenario incompatible with TB transmission directly from infected pinnipeds or their tissues. In this study, we investigate the causative agent of TB in ten pre-colonial, non-coastal individuals from South America. We reconstruct M. pinnipedii genomes (10- to 15-fold mean coverage) from three contemporaneous individuals from inland Peru and Colombia, demonstrating the widespread dissemination of M. pinnipedii beyond the coast, either through human-to-human and/or animal-mediated routes. Overall, our study suggests that TB transmission in the pre-colonial era Americas involved a more complex transmission pathway than simple pinniped-to-human transfer.
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22
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Gibson AJ, Passmore IJ, Faulkner V, Xia D, Nobeli I, Stiens J, Willcocks S, Clark TG, Sobkowiak B, Werling D, Villarreal-Ramos B, Wren BW, Kendall SL. Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq. Front Vet Sci 2021; 8:760717. [PMID: 35004921 PMCID: PMC8739905 DOI: 10.3389/fvets.2021.760717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Members of the Mycobacterium tuberculosis complex (MTBC) show distinct host adaptations, preferences and phenotypes despite being >99% identical at the nucleic acid level. Previous studies have explored gene expression changes between the members, however few studies have probed differences in gene essentiality. To better understand the functional impacts of the nucleic acid differences between Mycobacterium bovis and Mycobacterium tuberculosis, we used the Mycomar T7 phagemid delivery system to generate whole genome transposon libraries in laboratory strains of both species and compared the essentiality status of genes during growth under identical in vitro conditions. Libraries contained insertions in 54% of possible TA sites in M. bovis and 40% of those present in M. tuberculosis, achieving similar saturation levels to those previously reported for the MTBC. The distributions of essentiality across the functional categories were similar in both species. 527 genes were found to be essential in M. bovis whereas 477 genes were essential in M. tuberculosis and 370 essential genes were common in both species. CRISPRi was successfully utilised in both species to determine the impacts of silencing genes including wag31, a gene involved in peptidoglycan synthesis and Rv2182c/Mb2204c, a gene involved in glycerophospholipid metabolism. We observed species specific differences in the response to gene silencing, with the inhibition of expression of Mb2204c in M. bovis showing significantly less growth impact than silencing its orthologue (Rv2182c) in M. tuberculosis. Given that glycerophospholipid metabolism is a validated pathway for antimicrobials, our observations suggest that target vulnerability in the animal adapted lineages cannot be assumed to be the same as the human counterpart. This is of relevance for zoonotic tuberculosis as it implies that the development of antimicrobials targeting the human adapted lineage might not necessarily be effective against the animal adapted lineage. The generation of a transposon library and the first reported utilisation of CRISPRi in M. bovis will enable the use of these tools to further probe the genetic basis of survival under disease relevant conditions.
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Affiliation(s)
- Amanda J. Gibson
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Ian J. Passmore
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Valwynne Faulkner
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Dong Xia
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, United Kingdom
| | - Sam Willcocks
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ben Sobkowiak
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dirk Werling
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | | | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sharon L. Kendall
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom,*Correspondence: Sharon L. Kendall
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23
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Mazorra-Carrillo JL, Alcaraz-López OA, López-Rincón G, Villarreal-Ramos B, Gutiérrez-Pabello JA, Esquivel-Solís H. Host Serum Proteins as Potential Biomarkers of Bovine Tuberculosis Resistance Phenotype. Front Vet Sci 2021; 8:734087. [PMID: 34869715 PMCID: PMC8637331 DOI: 10.3389/fvets.2021.734087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/25/2021] [Indexed: 12/19/2022] Open
Abstract
Eradication of bovine tuberculosis (bTB) continues to be a worldwide challenge. The lack of reliable vaccines dampens the control and eradication programs of Mycobacterium bovis infection and spread. Selection and breeding of cattle resistant to M. bovis infection would greatly enhance the effectiveness of bTB eradication programs. Here, we have evaluated the potential of serum proteins as biomarkers of cattle resistance to bTB in Holstein-Friesian cows, 6-8-year-old, born and raised in similar conditions in herds with bTB prevalence >30%. Serum proteins obtained from uninfected cows (bTB-resistant; R) were compared to those from infected cows (bTB-susceptible; S), defined by a negative or positive bTB diagnosis, respectively. bTB diagnosis included: (i) single intradermal (caudal fold) tuberculin test, (ii) whole blood IFN-gamma test, (iii) gross visible lesions in lymph nodes and lungs by inspection at the abattoir, and (iv) a bacteriological culture for M. bovis. Using 2D-GE and LC-ESI-MS/MS, we found higher expression levels of primary amine oxidase (AO), complement component 5 (C5), and serotransferrin (TF) in R cattle than S cattle. In-house developed and standardized ELISAs for these novel biomarkers showed the best sensitivities of 72, 77, 77%, and specificities of 94, 94, 83%, for AO, C5, and TF, respectively. AUC-ROC (95% CI) values of 0.8935 (0.7906-0.9964), 0.9290 (0.8484-1.010), and 0.8580 (0.7291-0.9869) were obtained at cut-off points of 192.0, 176.5 ng/ml, and 2.1 mg/ml for AO, C5, and TF, respectively. These proteins are involved in inflammatory/immunomodulatory responses to infections and may provide a novel avenue of research to determine the mechanisms of protection against bTB. Overall, our results indicate that these proteins could be novel biomarkers to help identify cattle resistant to bTB, which in turn could be used to strengthen the effectiveness of existing eradication programs against bTB.
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Affiliation(s)
- Jorge Luis Mazorra-Carrillo
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | - Omar Antonio Alcaraz-López
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico.,Laboratorio de Investigación en Tuberculosis Bovina, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gonzalo López-Rincón
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | - Bernardo Villarreal-Ramos
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom.,Centre of Excellence for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - José A Gutiérrez-Pabello
- Laboratorio de Investigación en Tuberculosis Bovina, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo Esquivel-Solís
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
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24
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Zwyer M, Çavusoglu C, Ghielmetti G, Pacciarini ML, Scaltriti E, Van Soolingen D, Dötsch A, Reinhard M, Gagneux S, Brites D. A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics. OPEN RESEARCH EUROPE 2021; 1:100. [PMID: 37645186 PMCID: PMC10445919 DOI: 10.12688/openreseurope.14029.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 08/31/2023]
Abstract
Background: The bacteria that compose the Mycobacterium tuberculosis complex (MTBC) cause tuberculosis (TB) in humans and in different animals, including livestock. Much progress has been made in understanding the population structure of the human-adapted members of the MTBC by combining phylogenetics with genomics. Accompanying the discovery of new genetic diversity, a body of operational nomenclature has evolved to assist comparative and molecular epidemiological studies of human TB. By contrast, for the livestock-associated MTBC members, Mycobacterium bovis, M. caprae and M. orygis, there has been a lack of comprehensive nomenclature to accommodate new genetic diversity uncovered by emerging phylogenomic studies. We propose to fill this gap by putting forward a new nomenclature covering the main phylogenetic groups within M. bovis, M. caprae and M. orygis. Methods: We gathered a total of 8,736 whole-genome sequences (WGS) from public sources and 39 newly sequenced strains, and selected a subset of 829 WGS, representative of the worldwide diversity of M. bovis, M. caprae and M. orygis. We used phylogenetics and genetic diversity patterns inferred from WGS to define groups. Results: We propose to divide M. bovis, M. caprae and M. orygis in three main phylogenetic lineages, which we named La1, La2 and La3, respectively. Within La1, we identified several monophyletic groups, which we propose to classify into eight sublineages (La1.1-La1.8). These sublineages differed in geographic distribution, with some being geographically restricted and others globally widespread, suggesting different expansion abilities. To ease molecular characterization of these MTBC groups by the community, we provide phylogenetically informed, single nucleotide polymorphisms that can be used as barcodes for genotyping. These markers were implemented in KvarQ and TB-Profiler, which are platform-independent, open-source tools. Conclusions: Our results contribute to an improved classification of the genetic diversity within the livestock-associated MTBC, which will benefit future molecular epidemiological and evolutionary studies.
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Affiliation(s)
- Michaela Zwyer
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cengiz Çavusoglu
- Department of Medical Microbiology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
| | - Dick Van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands Antilles
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Anna Dötsch
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Miriam Reinhard
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Sebastien Gagneux
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Daniela Brites
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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25
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Lekko YM, Che-Amat A, Ooi PT, Omar S, Mohd-Hamdan DT, Linazah LS, Zakaria Z, Ramanoon SZ, Mazlan M, Jesse FFA, Abdul-Razak MFA, Jasni S, Abdul-Hamid N. Detection of Mycobacterium tuberculosis complex antibodies in free-ranged wild boar and wild macaques in selected districts in Selangor and reevaluation of tuberculosis serodetection in captive Asian elephants in Pahang, Peninsular Malaysia. J Vet Med Sci 2021; 83:1702-1707. [PMID: 34544936 PMCID: PMC8636890 DOI: 10.1292/jvms.21-0144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Tuberculosis (TB) is a chronic inflammatory and zoonotic disease caused by Mycobacterium tuberculosis complex (MTBC) members, affecting several domestic animals, wildlife
species and humans. The preliminary investigation was aimed to detect antibody against MTBC among indigenous wildlife which are free-ranged wild boar, free-ranged wild macaques and captive
Asian elephants in selected areas of Selangor and elephant conservation centre in Pahang, respectively. The results indicate that MTBC serodetection rate in wild boar was 16.7% (7.3–33.5 at
95% confidence interval (CI)) using an in-house ELISA bPPD IgG and 10% (3.5–25.6 at 95% CI) by DPP®VetTB assay, while the wild macaques and Asian elephant were seronegative. The
univariate analysis indicates no statistically significant difference in risk factors for sex and age of wild boar but there was a significant positive correlation
(P<0.05) between bovine TB in dairy cattle and wild boar seropositivity in the Sepang district.
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Affiliation(s)
- Yusuf Madaki Lekko
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Maiduguri, PMB 1069, Maiduguri, Borno State, Nigeria
| | - Azlan Che-Amat
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Peck Toung Ooi
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Sharina Omar
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Dhabitah Tatiyana Mohd-Hamdan
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Liya Syahila Linazah
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Zakirawaranis Zakaria
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Zubaidah Ramanoon
- Department of Farm and Exotic Animal Medicine and Surgery, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mazlina Mazlan
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Faez Firdaus Abdullah Jesse
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | | | - Sabri Jasni
- Department of Paraclinical, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, 16100 Kota Bharu, Kelantan, Malaysia
| | - Norhamizah Abdul-Hamid
- Selangor State Veterinary Services Department, Lot 2, Jalan Utas 15/7, Seksyen 15, 40630 Shah Alam, Selangor, Malaysia
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26
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De Maio F, Berisio R, Manganelli R, Delogu G. PE_PGRS proteins of Mycobacterium tuberculosis: A specialized molecular task force at the forefront of host-pathogen interaction. Virulence 2021; 11:898-915. [PMID: 32713249 PMCID: PMC7550000 DOI: 10.1080/21505594.2020.1785815] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
To the PE_PGRS protein subfamily belongs a group of surface-exposed mycobacterial antigens that in Mycobacterium tuberculosis (Mtb) H37Rv accounts to more than 65 genes, 51 of which are thought to express a functional protein. PE_PGRS proteins share a conserved structural architecture with three main domains: the N-terminal PE domain; the PGRS domain, that can vary in sequence and size and is characterized by the presence of multiple GGA-GGX amino acid repeats; the highly conserved sequence containing the GRPLI motif that links the PE and PGRS domains; the unique C-terminus end that can vary in size from few to up to ≈ 300 amino acids. pe_pgrs genes emerged in slow-growing mycobacteria and expanded and diversified in MTBC and few other pathogenic mycobacteria. Interestingly, despite sequence homology and apparent redundancy, PE_PGRS proteins seem to have evolved a peculiar function. In this review, we summarize the actual knowledge on this elusive protein family in terms of evolution, structure, and function, focusing on the role of PE_PGRS in TB pathogenesis. We provide an original hypothesis on the role of the PE domain and propose a structural model for the polymorphic PGRS domain that might explain how so similar proteins can have different physiological functions.
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Affiliation(s)
- Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" , Rome, Italy.,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore , Rome, Italy
| | - Rita Berisio
- Institute of Bio-Structures and Bio-Imaging - CNR-IBB , Naples, Italy
| | | | - Giovanni Delogu
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore , Rome, Italy.,Mater Olbia Hospital , Olbia, Italy
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27
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Pérez-González J, Carranza J, Martínez R, Benítez-Medina JM. Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis. Animals (Basel) 2021; 11:1630. [PMID: 34072907 PMCID: PMC8229303 DOI: 10.3390/ani11061630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.
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Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Córdoba, Spain;
| | - Remigio Martínez
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
| | - José Manuel Benítez-Medina
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
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28
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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] [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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29
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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] [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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30
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Zakham F, Sironen T, Vapalahti O, Kant R. Pan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains. Antibiotics (Basel) 2021; 10:antibiotics10050500. [PMID: 33924811 PMCID: PMC8145561 DOI: 10.3390/antibiotics10050500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/24/2021] [Accepted: 04/25/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) is an airborne communicable disease with high morbidity and mortality rates, especially in developing countries. The causal agents of TB belong to the complex Mycobacterium tuberculosis (MTBc), which is composed of different human and animal TB associated species. Some animal associated species have zoonotic potential and add to the burden of TB management. The BCG ("Bacillus Calmette-Guérin") vaccine is widely used for the prevention against TB, but its use is limited in immunocompromised patients and animals due to the adverse effects and disseminated life-threatening complications. In this study, we aimed to carry out a comparative genome analysis between the human adapted species including BCG vaccine strains to identify and pinpoint the conserved genes related to the virulence across all the species, which could add a new value for vaccine development. For this purpose, the sequences of 183 Mycobacterium tuberculosis (MTB) strains were retrieved from the freely available WGS dataset at NCBI. The species included: 168 sensu stricto MTB species with other human MTB complex associated strains: M. tuberculosis var. africanum (3), M. tuberculosis var. bovis (2 draft genomes) and 10 BCG species, which enabled the analysis of core genome which contains the conserved genes and some virulence factor determinants. Further, a phylogenetic tree was constructed including the genomes of human (183); animals MTB adapted strains (6) and the environmental Mycobacterium strain "M. canettii". Our results showed that the core genome consists of 1166 conserved genes among these species, which represents a small portion of the pangenome (7036 genes). The remaining genes in the pangenome (5870) are accessory genes, adding a high inter-species diversity. Further, the core genome includes several virulence-associated genes and this could explain the rare infectiousness potential of some attenuated vaccine strains in some patients. This study reveals that low number of conserved genes in human adapted MTBc species and high inter-species diversity of the pan-genome could be considered for vaccine candidate development.
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Affiliation(s)
- Fathiah Zakham
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (F.Z.); (T.S.); (O.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (F.Z.); (T.S.); (O.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (F.Z.); (T.S.); (O.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- HUSLAB, Hospital District of Helsinki and Uusimaa, 00260 Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (F.Z.); (T.S.); (O.V.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland
- Correspondence:
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31
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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] [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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32
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Carneiro PA, Zimpel CK, Pasquatti TN, Silva-Pereira TT, Takatani H, Silva CBDG, Abramovitch RB, Sa Guimaraes AM, Davila AMR, Araujo FR, Kaneene JB. Genetic Diversity and Potential Paths of Transmission of Mycobacterium bovis in the Amazon: The Discovery of M. bovis Lineage Lb1 Circulating in South America. Front Vet Sci 2021; 8:630989. [PMID: 33665220 PMCID: PMC7921743 DOI: 10.3389/fvets.2021.630989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/15/2021] [Indexed: 11/13/2022] Open
Abstract
Bovine tuberculosis (bTB) has yet to be eradicated in Brazil. Herds of cattle and buffalo are important sources of revenue to people living in the banks of the Amazon River basin. A better understanding of Mycobacterium bovis (M. bovis) populational structure and transmission dynamics affecting these animals can significantly contribute in efforts to improve their sanitary status. Herein, we sequenced the whole genome of 22 M. bovis isolates (15 from buffalo and 7 from cattle) from 10 municipalities in the region of the Lower Amazon River Basin in Brazil and performed phylogenomic analysis and Single Nucleotide Polymorphism (SNP)-based transmission inference to evaluate population structure and transmission networks. Additionally, we compared these genomes to others obtained in unrelated studies in the Marajó Island (n = 15) and worldwide (n = 128) to understand strain diversity in the Amazon and to infer M. bovis lineages. Our results show a higher genomic diversity of M. bovis genomes obtained in the Lower Amazon River region when compared to the Marajó Island, while no significant difference was observed between M. bovis genomes obtained from cattle and buffalo (p ≥ 0.05). This high genetic diversity is reflected by the weak phylogenetic clustering of M. bovis from the Lower Amazon River region based on geographic proximity and in the detection of only two putative transmission clusters in the region. One of these clusters is the first description of inter-species transmission between cattle and buffalo in the Amazon, bringing implications to the bTB control program. Surprisingly, two M. bovis lineages were detected in our dataset, namely Lb1 and Lb3, constituting the first description of Lb1 in South America. Most of the strains of this study (13/22) and all 15 strains of the Marajó Island carried no clonal complex marker, suggesting that the recent lineage classification better describe the diversity of M. bovis in the Amazon.
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Affiliation(s)
- Paulo Alex Carneiro
- Center for Comparative Epidemiology, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Amazonas State Federal Institute, Manaus, Brazil
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | | | - Taiana T. Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Haruo Takatani
- Agência de Defesa Agropecuaria Do Amazonas, Manaus, Brazil
| | | | - Robert B. Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Ana Marcia Sa Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alberto M. R. Davila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute and Graduate Program in Biodiversity and Health, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - John B. Kaneene
- Center for Comparative Epidemiology, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
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33
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Orgeur M, Frigui W, Pawlik A, Clark S, Williams A, Ates LS, Ma L, Bouchier C, Parkhill J, Brodin P, Brosch R. Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts. Microb Genom 2021; 7:000505. [PMID: 33529148 PMCID: PMC8208694 DOI: 10.1099/mgen.0.000505] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/16/2020] [Indexed: 01/03/2023] Open
Abstract
Mycobacterium microti is an animal-adapted member of the Mycobacterium tuberculosis complex (MTBC), which was originally isolated from voles, but has more recently also been isolated from other selected mammalian hosts, including occasionally from humans. Here, we have generated and analysed the complete genome sequences of five representative vole and clinical M. microti isolates using PacBio- and Illumina-based technologies, and have tested their virulence and vaccine potential in SCID (severe combined immune deficient) mouse and/or guinea pig infection models. We show that the clinical isolates studied here cluster separately in the phylogenetic tree from vole isolates and other clades from publicly available M. microti genome sequences. These data also confirm that the vole and clinical M. microti isolates were all lacking the specific RD1mic region, which in other tubercle bacilli encodes the ESX-1 type VII secretion system. Biochemical analysis further revealed marked phenotypic differences between isolates in type VII-mediated secretion of selected PE and PPE proteins, which in part were attributed to specific genetic polymorphisms. Infection experiments in the highly susceptible SCID mouse model showed that the clinical isolates were significantly more virulent than the tested vole isolates, but still much less virulent than the M. tuberculosis H37Rv control strain. The strong attenuation of the ATCC 35872 vole isolate in immunocompromised mice, even compared to the attenuated BCG (bacillus Calmette-Guérin) vaccine, and its historic use in human vaccine trials encouraged us to test this strain's vaccine potential in a guinea pig model, where it demonstrated similar protective efficacy as a BCG control, making it a strong candidate for vaccination of immunocompromised individuals in whom BCG vaccination is contra-indicated. Overall, we provide new insights into the genomic and phenotypic variabilities and particularities of members of an understudied clade of the MTBC, which all share a recent common ancestor that is characterized by the deletion of the RD1mic region.
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Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
| | - Wafa Frigui
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
| | - Alexandre Pawlik
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
| | - Simon Clark
- Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Ann Williams
- Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Louis S. Ates
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
- Amsterdam UMC, University of Amsterdam, Department of Experimental Immunology, Amsterdam institute for Infection & Immunity, Meibergdreef 9, Amsterdam, Netherlands
| | - Laurence Ma
- Institut Pasteur, Biomics, C2RT, Paris 75015, France
| | | | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Priscille Brodin
- CIIL - Center for Infection and Immunity of Lille, Université de Lille/CNRS UMR 9017/INSERM U1019/CHU Lille/Institut Pasteur de Lille, Lille 59000, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris 75015, France
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Jiménez-Ruano AC, Madrazo-Moya CF, Cancino-Muñoz I, Mejía-Ponce PM, Licona-Cassani C, Comas I, Muñiz-Salazar R, Zenteno-Cuevas R. Whole genomic sequencing based genotyping reveals a specific X3 sublineage restricted to Mexico and related with multidrug resistance. Sci Rep 2021; 11:1870. [PMID: 33479318 PMCID: PMC7820219 DOI: 10.1038/s41598-020-80919-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/08/2020] [Indexed: 01/26/2023] Open
Abstract
Whole genome sequencing (WGS) has been shown to be superior to traditional procedures of genotyping in tuberculosis (TB), nevertheless, reports of its use in drug resistant TB (DR-TB) isolates circulating in Mexico, are practically unknown. Considering the above the main of this work was to identify and characterize the lineages and genomic transmission clusters present in 67 DR-TB isolates circulating in southeastern Mexico. The results show the presence of three major lineages: L1 (3%), L2 (3%) and L4 (94%), the last one included 16 sublineages. Sublineage 4.1.1.3 (X3) was predominant in 18 (27%) of the isolates, including one genomic cluster, formed by eleven multidrug resistant isolates and sharing the SIT 3278, which seems to be restricted to Mexico. By the use of WGS, it was possible to identify the high prevalence of L4 and a high number of sublineages circulating in the region, also was recognized the presence of a novel X3 sublineage, formed exclusively by multidrug resistant isolates and with restrictive circulation in Mexico for at least the past 17 years.
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Affiliation(s)
- Ana Cristina Jiménez-Ruano
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México
- Instituto de Salud Pública, Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Animas, 91190, Xalapa, Veracruz, México
| | - Carlos Francisco Madrazo-Moya
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México
- Biomedical Institute of Valencia IBV-CSIC, Valencia, Spain
| | | | - Paulina M Mejía-Ponce
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Nuevo Leon, Mexico
| | | | - Iñaki Comas
- Biomedical Institute of Valencia IBV-CSIC, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Raquel Muñiz-Salazar
- Laboratorio de Epidemiología y Ecología y Molecular, Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Ensenada, Baja California, México
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City, Mexico
| | - Roberto Zenteno-Cuevas
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México.
- Instituto de Salud Pública, Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Animas, 91190, Xalapa, Veracruz, México.
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City, Mexico.
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Abstract
Mycobacterial infections are widely distributed in animals and cause considerable economic losses, especially in livestock animals. Bovine paratuberculosis and bovine tuberculosis, which are representative mycobacterial infections in cattle, are difficult to diagnose using current-generation diagnostics due to their relatively long incubation periods. Thus, alternative diagnostic tools are needed for the detection of mycobacterial infections in cattle. A biomarker is an indicator present in biological fluids that reflects the biological state of an individual during the progression of a specific disease. Therefore, biomarkers are considered a potential diagnostic tool for various diseases. Recently, the number of studies investigating biomarkers as tools for diagnosing mycobacterial infections has increased. In human medicine, many diagnostic biomarkers have been developed and applied in clinical practice. In veterinary medicine, however, many such developments are still in the early stages. In this review, we summarize the current progress in biomarker research related to the development of diagnostic biomarkers for mycobacterial infections in cattle.
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36
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Independent genomic polymorphisms in the PknH serine threonine kinase locus during evolution of the Mycobacterium tuberculosis Complex affect virulence and host preference. PLoS Pathog 2020; 16:e1009061. [PMID: 33347499 PMCID: PMC7785237 DOI: 10.1371/journal.ppat.1009061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/05/2021] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Species belonging to the Mycobacterium tuberculosis Complex (MTBC) show more than 99% genetic identity but exhibit distinct host preference and virulence. The molecular genetic changes that underly host specificity and infection phenotype within MTBC members have not been fully elucidated. Here, we analysed RD900 genomic region across MTBC members using whole genome sequences from 60 different MTBC strains so as to determine its role in the context of MTBC evolutionary history. The RD900 region comprises two homologous genes, pknH1 and pknH2, encoding a serine/threonine protein kinase PknH flanking the tbd2 gene. Our analysis revealed that RD900 has been independently lost in different MTBC lineages and different strains, resulting in the generation of a single pknH gene. Importantly, all the analysed M. bovis and M. caprae strains carry a conserved deletion within a proline rich-region of pknH, independent of the presence or absence of RD900. We hypothesized that deletion of pknH proline rich-region in M. bovis may affect PknH function, having a potential role in its virulence and evolutionary adaptation. To explore this hypothesis, we constructed two M. bovis ‘knock-in’ strains containing the M. tuberculosis pknH gene. Evaluation of their virulence phenotype in mice revealed a reduced virulence of both M. bovis knock-in strains compared to the wild type, suggesting that PknH plays an important role in the differential virulence phenotype of M. bovis vs M. tuberculosis. Tuberculosis is caused in humans and animals by organisms from the Mycobacterium tuberculosis Complex (MTBC), that share more than 99% genetic identity but exhibit distinct host preference and virulence. While Mycobacterium tuberculosis is the main causative agent of human TB, Mycobacterium bovis is responsible for bovine TB disease, that exacts a tremendous economic burden worldwide, as well as being a zoonotic threat. Unlike the human restriction of M. tuberculosis, M. bovis has a broader host range and it has been found to be more virulent than M. tuberculosis in different animal models. However, the molecular basis for host preference and virulence divergence between M. tuberculosis and M. bovis is not fully elucidated. Here we study the genetic variations of the genomic region RD900 in the context of MTBC phylogeny. RD900 contains two genes encoding orthologues of the serine/threonine kinase PknH, which is linked to the regulation of several bacterial processes including virulence. We found that M. bovis pknH genes show a conserved deletion that is not present in M. tuberculosis strains, and we evaluated the potential impact of these variations in the regulation of M. bovis vs M. tuberculosis virulence through the construction and in vivo characterization of M. bovis pknH mutant strains.
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37
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Didkowska A, Krajewska-Wędzina M, Bielecki W, Brzezińska S, Augustynowicz-Kopeć E, Olech W, Anusz K, Sridhara AA, Johnathan-Lee A, Elahi R, Miller MA, Ray Waters W, Lyashchenko KP. Antibody responses in European bison (Bison bonasus) naturally infected with Mycobacterium caprae. Vet Microbiol 2020; 253:108952. [PMID: 33370619 DOI: 10.1016/j.vetmic.2020.108952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, infects humans and animals causing lesions and disease like that of Mycobacterium bovis. The aim of this study was to evaluate antibody responses in European Bison (EB, Bison bonasus; a vulnerable species) naturally infected with M. caprae using dual path platform (DPP) BovidTB test and multi-antigen print immunoassay (MAPIA). Study cohorts consisted of naturally M. caprae-infected EB (n = 4), M. caprae-exposed but uninfected (n = 3), EB infected with non-tuberculous mycobacteria or other respiratory pathogens (n = 3), and negative controls (n = 19). M. caprae-infected EB were seropositive by both DPP and MAPIA; 3/4 were seropositive by DPP; and 4/4 were seropositive by MAPIA. One M. caprae-infected animal that developed generalized disease with most advanced gross lesions in the group produced the most robust antibody response. All 25 EB with no culture-confirmed M. caprae infection, including three animals exposed to M. caprae and three other animals infected with non-tuberculous pathogens, were seronegative on both tests. Antibody responses to M. caprae infection included IgM antibodies against MPB70/MPB83 and IgG antibodies to both MPB70/MPB83 and CFP10/ESAT-6. This study demonstrates the potential for use of serological assays in the ante-mortem diagnosis of M. caprae infection in EB.
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Affiliation(s)
- Anna Didkowska
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166, 02-787, Warsaw, Poland.
| | - Monika Krajewska-Wędzina
- Department of Microbiology, National Veterinary Research Institute, Partyzantów 57, 24-100, Puławy, Poland
| | - Wojciech Bielecki
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166, 02-787, Warsaw, Poland
| | - Sylwia Brzezińska
- Department of Microbiology, National Tuberculosis Reference Laboratory, National Tuberculosis and Lung Diseases Research Institute, Płocka 26, 01-138, Warsaw, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis Reference Laboratory, National Tuberculosis and Lung Diseases Research Institute, Płocka 26, 01-138, Warsaw, Poland
| | - Wanda Olech
- Institute of Animal Sciences, Warsaw University of Life Sciences - SGGW, Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Krzysztof Anusz
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences (SGGW), Nowoursynowska 166, 02-787, Warsaw, Poland
| | - Archana A Sridhara
- Chembio Diagnostic Systems, Inc., 3661 Horseblock Road, Medford, New York, 11763, USA
| | - Ashley Johnathan-Lee
- Chembio Diagnostic Systems, Inc., 3661 Horseblock Road, Medford, New York, 11763, USA
| | - Rubyat Elahi
- Chembio Diagnostic Systems, Inc., 3661 Horseblock Road, Medford, New York, 11763, USA
| | - Michele A Miller
- Department of Science and Technology-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa
| | - W Ray Waters
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, 1920 Dayton Avenue, Ames, Iowa, 50010, USA
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Guerra Maldonado JF, Vincent AT, Chenal M, Veyrier FJ. CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution. BMC Genomics 2020; 21:832. [PMID: 33243176 PMCID: PMC7690079 DOI: 10.1186/s12864-020-07232-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a result of natural selection. Using phylogeny and genome comparisons, evolutionary paths can be somehow retraced, with recent events being much easier to detect than older ones. For this reason, multiple tools are available to study the evolutionary events within genomes of single species, such as gene composition alterations, or subtler mutations such as SNPs. However, these tools are generally designed to compare similar genomes and require advanced skills in bioinformatics. We present CAPRIB, a unique tool developed in Java that allows to determine the amino acid changes, at the genus level, that correlate with phenotypic differences between two groups of organisms. RESULTS CAPRIB has a user-friendly graphical interface and uses databases in SQL, making it easy to compare several genomes without the need for programming or thorough knowledge in bioinformatics. This intuitive software narrows down a list of amino acid changes that are concomitant with a given phenotypic divergence at the genus scale. Each permutation found by our software is associated with two already described statistical values that indicate its potential impact on the protein's function, helping the user decide which promising candidates to further investigate. We show that CAPRIB is able to detect already known mutations and uncovers many more, and that this tool can be used to question molecular phylogeny. Finally, we exemplify the utility of CAPRIB by pinpointing amino acid changes that coincided with the emergence of slow-growing mycobacteria from their fast-growing counterparts. The software is freely available at https://github.com/BactSymEvol/Caprib . CONCLUSIONS CAPRIB is a new bioinformatics software aiming to make genus-scale comparisons accessible to all. With its intuitive graphical interface, this tool identifies key amino acid changes concomitant with a phenotypic divergence. By comparing fast and slow-growing mycobacteria, we shed light on evolutionary hotspots, such as the cytokinin pathway, that are interesting candidates for further experimentations.
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Affiliation(s)
- Juan F Guerra Maldonado
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Québec, Canada
| | - Antony T Vincent
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Québec, Canada
| | - Martin Chenal
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Québec, Canada
| | - Frederic J Veyrier
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, Bacterial Symbionts Evolution, Laval, Québec, Canada.
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39
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Infantes-Lorenzo JA, Romero B, Rodríguez-Bertos A, Roy A, Ortega J, de Juan L, Moreno I, Domínguez M, Domínguez L, Bezos J. Tuberculosis caused by Mycobacterium caprae in a camel (Camelus dromedarius). BMC Vet Res 2020; 16:435. [PMID: 33172453 PMCID: PMC7653750 DOI: 10.1186/s12917-020-02665-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Animal tuberculosis (TB) is distributed worldwide and has a wide range of wild and domestic reservoirs. Few studies concerning TB in camelids have been published in the last decade, particularly as regards Old World Camelids (OWC), but the increase in reports of TB outbreaks in these species in recent years suggests a high susceptibility to the infection. CASE PRESENTATION We studied a dromedary camel (Camelus dromedarius) herd (n = 24) in which a Mycobacterium caprae infection was detected. The TB infection was confirmed in one animal at necropsy through the detection of TB lesions, mainly in the abdominal organs, and the subsequent isolation of M. caprae (SB0157 spoligotype). The whole herd was additionally tested using cellular and humoral based diagnostic techniques. The intradermal tuberculin test results were compared with those obtained using P22 ELISA for the detection of specific antibodies against the M. tuberculosis complex. The TB infected animal was a positive reactor to both the intradermal tuberculin tests and P22 ELISA, while the others were negative to all the diagnostic tests. CONCLUSION The present study found M. caprae infection in OWC. This is the first report of M. caprae infection in an OWC not living in a zoo. Since the animal was born in the herd and fed with goat's milk, this practice was suspected to be the potential source of TB infection, which was not confirmed in the other animals present in the herd. Moreover, our results highlight that the intradermal tuberculin test and the P22 ELISA could be valuable tools for the diagnosis of TB in OWC.
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Affiliation(s)
- J A Infantes-Lorenzo
- Servicio de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - B Romero
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - A Rodríguez-Bertos
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain.,Department of Animal Medicine and Surgery, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - A Roy
- BIOFABRI S.L., Porriño, Pontevedra, Spain
| | - J Ortega
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - L de Juan
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - I Moreno
- Servicio de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - M Domínguez
- Servicio de Inmunología Microbiana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - L Domínguez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain.,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain
| | - J Bezos
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain. .,Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, 28040, Madrid, Spain.
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40
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Kanipe C, Palmer MV. Mycobacterium bovis and you: A comprehensive look at the bacteria, its similarities to Mycobacterium tuberculosis, and its relationship with human disease. Tuberculosis (Edinb) 2020; 125:102006. [PMID: 33032093 DOI: 10.1016/j.tube.2020.102006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/21/2020] [Accepted: 09/29/2020] [Indexed: 12/16/2022]
Abstract
While Mycobacterium tuberculosis is the primary cause of tuberculosis in people, multiple other mycobacteria are capable of doing so. With the World Health Organization's goal of a 90% reduction in tuberculosis by 2035, all tuberculous mycobacteria need to be addressed. Understanding not only the similarities, but importantly the differences between the different species is crucial if eradication is ever to be achieved. Mycobacterium bovis, while typically thought of as a disease of cattle, remains a possible source of human infection worldwide. Although this species' genome differs from Mycobacterium tuberculosis by only 0.05%, significant differences are present, creating unique challenges to address. This review focuses on features which distinguish this bacterium from Mycobacterium tuberculosis, including differences in origin, structure, environmental persistence, host preferences, infection and disease, host immune response, diagnostics and treatment.
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Affiliation(s)
- Carly Kanipe
- Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA; Immunobiology Graduate Program, Iowa State University, Ames, IA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA.
| | - Mitchell V Palmer
- Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
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41
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Chin KL, Sarmiento ME, Mustapha ZA, Jani J, Jamal NB, Stanis CS, Acosta A. Identification of a Mycobacterium tuberculosis-specific gene marker for diagnosis of tuberculosis using semi-nested melt-MAMA qPCR (lprM-MAMA). Tuberculosis (Edinb) 2020; 125:102003. [PMID: 33099253 DOI: 10.1016/j.tube.2020.102003] [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: 11/20/2019] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) is the deadliest of infectious diseases. TB diagnosis, based on sputum microscopy, culture, and nucleic acid amplification tests (NAATs) to identify its main causative agent, Mycobacterium tuberculosis (MTB), remains challenging. The current available NAATs, endorsed by World Health Organization (WHO), can differentiate MTB from some MTB complex (MTBC) members. Using bioinformatics, we identified a single nucleotide polymorphism (SNP) in lprM (Rv1970) gene that differentiate MTB from other MTBC members. A forward mismatch amplification mutation assay (MAMA) primer was designed for the targeted mutation and was used in a semi-nested melt-MAMA qPCR (lprM-MAMA). Using the optimized protocol, lprM-MAMA was positive with all MTB reference and clinical strains, and negative with other MTBC members, non-tuberculous mycobacteria (NTM) and other non-mycobacterial (NM) reference strains. The limit of detection (LOD) of lprM-MAMA was 76.29 fg. Xpert® MTB/RIF (Xpert)-positive sputum samples were also positive by lprM-MAMA, except for samples classified as having "very low" bacterial load by Xpert. Xpert-negative sputum samples were also negative by lprM-MAMA. In conclusion, lprM-MAMA demonstrated to be a useful tool for specific MTB diagnosis. Further evaluation with higher number of reference strains, including NTM and NM; and sputum samples are required to determine its potential for clinical application.
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Affiliation(s)
- Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia.
| | - Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Zainal Arifin Mustapha
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Jaeyres Jani
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Norfazirah Binti Jamal
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Cheronie Shely Stanis
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia.
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42
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Comprehensive analysis of protein acetyltransferases of human pathogen Mycobacterium tuberculosis. Biosci Rep 2020; 39:221456. [PMID: 31820790 PMCID: PMC6923341 DOI: 10.1042/bsr20191661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB), a leading infectious disease caused by Mycobacterium tuberculosis strain, takes four human lives every minute globally. Paucity of knowledge on M. tuberculosis virulence and antibiotic resistance is the major challenge for tuberculosis control. We have identified 47 acetyltransferases in the M. tuberculosis, which use diverse substrates including antibiotic, amino acids, and other chemical molecules. Through comparative analysis of the protein file of the virulent M. tuberculosis H37Rv strain and the avirulent M. tuberculosis H37Ra strain, we identified one acetyltransferase that shows significant variations with N-terminal deletion, possibly influencing its physicochemical properties. We also found that one acetyltransferase has three types of post-translation modifications (lysine acetylation, succinylation, and glutarylation). The genome context analysis showed that many acetyltransferases with their neighboring genes belong to one operon. By data mining from published transcriptional profiles of M. tuberculosis exposed to diverse treatments, we revealed that several acetyltransferases may be functional during M. tuberculosis infection. Insights obtained from the present study can potentially provide clues for developing novel TB therapeutic interventions.
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43
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Ihedioha O, Potter AA, Chen JM. Poor stimulation of bovine dendritic cells by Mycobacterium bovis culture supernatant and surface extract is associated with decreased activation of ERK and NF- κB and higher expression of SOCS1 and 3. Innate Immun 2020; 26:537-546. [PMID: 32513050 PMCID: PMC7491241 DOI: 10.1177/1753425920929759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The cell envelope of pathogenic mycobacteria interfaces with the host. As such, the interaction of bacterial products localized at or released from the cell surface with the host’s immune system can determine the fate of the bacterium in its host. In this study, the effects of three different types of Mycobacterium bovis cell envelope fractions—purified protein derivative, total cell wall lipids and culture supernatant and surface extract—on bovine dendritic cells were assessed. We found that the culture supernatant and surface extract fraction induced little to no production of the pro-inflammatory cytokines TNF-α and IL-12 in bovine dendritic cells. Moreover, this muted response was associated with poor activation of ERK and NF-κB, both of which are critical for the pro-inflammatory response. Furthermore, culture supernatant and surface extract treatment increased the expression of suppressor of cytokine signaling 1 and 3, both of which are negative regulators of pro-inflammatory signaling, in bovine dendritic cells. These observations taken together suggest the M. bovis culture supernatant and surface extract fraction contain immunomodulatory molecules that may aid in M. bovis pathogenesis.
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Affiliation(s)
- Olivia Ihedioha
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Canada.,Vaccine and Infectious Disease Organization, International Vaccine Centre, University of Saskatchewan, Canada
| | - Andrew A Potter
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Canada.,Vaccine and Infectious Disease Organization, International Vaccine Centre, University of Saskatchewan, Canada
| | - Jeffrey M Chen
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Canada.,Vaccine and Infectious Disease Organization, International Vaccine Centre, University of Saskatchewan, Canada
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44
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Pérez I, Uranga S, Sayes F, Frigui W, Samper S, Arbués A, Aguiló N, Brosch R, Martín C, Gonzalo-Asensio J. Live attenuated TB vaccines representing the three modern Mycobacterium tuberculosis lineages reveal that the Euro-American genetic background confers optimal vaccine potential. EBioMedicine 2020; 55:102761. [PMID: 32361249 PMCID: PMC7195525 DOI: 10.1016/j.ebiom.2020.102761] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 01/11/2023] Open
Abstract
Background Human tuberculosis (TB) is caused by a plethora of Mycobacterium tuberculosis complex (MTBC) strains belonging to seven phylogenetic branches. Lineages 2, 3 and 4 are considered “modern” branches of the MTBC responsible for the majority of worldwide TB. Since the current BCG vaccine confers variable protection against pulmonary TB, new candidates are investigated. MTBVAC is the unique live attenuated vaccine based on M. tuberculosis in human clinical trials. Methods MTBVAC was originally constructed by unmarked phoP and fadD26 deletions in a clinical isolate belonging to L4. Here we construct new vaccines based on isogenic gene deletions in clinical isolates of the L2 and L3 modern lineages. These three vaccine candidates were characterized at molecular level and also in animal experiments of protection and safety. Findings Safety studies in immunocompromised mice showed that MTBVAC-L2 was less attenuated than BCG Pasteur, while the original MTBVAC was found even more attenuated than BCG and MTBVAC-L3 showed an intermediate phenotype. The three MTBVAC candidates showed similar or superior protection compared to BCG in immunocompetent mice vaccinated with each MTBVAC candidate and challenged with three representative strains of the modern lineages. Interpretation MTBVAC vaccines, based on double phoP and fadD26 deletions, protect against TB independently of the phylogenetic linage used as template strain for their construction. Nevertheless, lineage L4 confers the best safety profile. Funding European Commission (TBVAC2020, H2020-PHC-643381), Spanish Ministry of Science (RTI2018-097625-B-I00), Instituto de Salud Carlos III (PI18/0336), Gobierno de Aragón/Fondo Social Europeo and the French National Research Council (ANR-10-LABX-62-IBEID, ANR-16-CE35-0009, ANR-16-CE15-0003).
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Affiliation(s)
- Irene Pérez
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Santiago Uranga
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Fadel Sayes
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris, France
| | - Wafa Frigui
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris, France
| | - Sofía Samper
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Unidad de Investigación Translacional, Instituto Aragonés de Ciencias de la Salud, Instituto de Investigación Sanitaria Aragón, Zaragoza, Spain
| | - Ainhoa Arbués
- Present adress: Medical Parasitology & Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Nacho Aguiló
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris, France
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Zaragoza, Spain.
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45
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Palmer MV, Thacker TC, Rabideau MM, Jones GJ, Kanipe C, Vordermeier HM, Ray Waters W. Biomarkers of cell-mediated immunity to bovine tuberculosis. Vet Immunol Immunopathol 2019; 220:109988. [PMID: 31846797 DOI: 10.1016/j.vetimm.2019.109988] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/15/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
Abstract
Whole blood based assays, particularly interferon gamma (IFN-γ) release assays (IGRAs), are used for the diagnosis of both bovine and human tuberculosis (TB). The aim of the current study was to evaluate a panel of cytokines and chemokines for potential use as diagnostic readouts indicative of Mycobacterium bovis (M. bovis) infection in cattle. A gene expression assay was used to determine the kinetics of the response to M. bovis purified protein derivative and a fusion protein consisting of ESAT-6, CFP10, and Rv3615c upon aerosol infection with ∼104 cfu of M. bovis. The panel of biomarkers included: IFN-γ, CXCL9, CXCL10, CCL2, CCL3, TNF-α, IL-1α, IL-1β, IL-1Ra, IL-22, IL-21 and IL-13. Protein levels of IFN-γ, CXCL9, and CXCL10 were determined by ELISA. Findings suggest that CXCL9, CXCL10, IL-21, IL-13, and several acute phase cytokines may be worth pursuing as diagnostic biomarkers of M. bovis infection in cattle.
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Affiliation(s)
- Mitchell V Palmer
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, Iowa, USA.
| | - Tyler C Thacker
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, Iowa, USA
| | - Meaghan M Rabideau
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, Iowa, USA
| | - Gareth J Jones
- TB Immunology and Vaccinology, Department of Bacteriology, Animal and Plant Health Agency, New Haw, Addlestone, Surry UK
| | - Carly Kanipe
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, Iowa, USA; Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - H Martin Vordermeier
- TB Immunology and Vaccinology, Department of Bacteriology, Animal and Plant Health Agency, New Haw, Addlestone, Surry UK
| | - W Ray Waters
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture (USDA), Ames, Iowa, USA
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Sevilla IA, Arnal MC, Fuertes M, Martín E, Comenge J, Elguezabal N, Fernández de Luco D, Garrido JM. Tuberculosis outbreak caused by Mycobacterium caprae in a rabbit farm in Spain. Transbound Emerg Dis 2019; 67:431-441. [PMID: 31539200 DOI: 10.1111/tbed.13366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/16/2019] [Accepted: 09/06/2019] [Indexed: 12/14/2022]
Abstract
Animal tuberculosis remains a great source of socioeconomic and health concern worldwide. Its main causative agents, Mycobacterium bovis and Mycobacterium caprae, have been isolated from many different domestic and wild animals. Naturally, occurring tuberculosis is extremely rare in rabbits, and implication of M. caprae has never been reported earlier. This study describes a severe tuberculosis outbreak caused by M. caprae in a Spanish farm of rabbits raised for meat for human consumption. The disease was first identified in a cachectic dam, and then it was confirmed in ten does with similar clinical signs. Subsequently, a depopulation operation was ordered for public health, animal welfare and environmental reasons. To broaden knowledge of spontaneous tuberculosis in rabbits, a study focused on pathological, epidemiological and diagnostic aspects was carried out on 51 does and 16 kittens after receiving the necessary authorizations. These animals were subjected to a modified intradermal test. After being euthanized, rabbits were examined for the presence of visible tuberculosis-compatible lesions. Lung, kidney, caecal appendix and sacculus rotundus samples underwent microbiological and anatomopathological analysis. Infection was revealed by at least one of the methods used in 71% of dams and in 44% of kittens. The intradermal test was shown to be a good indicator of infection. Lung was the tissue for which more animals were positive but renal and intestinal tissues were also affected in many cases. Apparently, M. caprae spread mainly through the aerogenous route. Infection was pathologically characterized by the absence of evident fibrous capsules surrounding granulomas. A spoligotype (SB0415) frequently found in this area was considered responsible for the outbreak but the source could not be established. Regardless of the exceptional nature of animal tuberculosis in this host, rabbit industry might not escape from its effects and therefore, current biosafety and surveillance strategies should also consider this disease.
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Affiliation(s)
- Iker A Sevilla
- Departmento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio, Spain
| | - María Cruz Arnal
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Miguel Fuertes
- Departmento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio, Spain
| | | | | | - Natalia Elguezabal
- Departmento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio, Spain
| | - Daniel Fernández de Luco
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Joseba M Garrido
- Departmento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio, Spain
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Ejeh EF, Undiandeye A, Akinseye VO, Okon KO, Kazeem HM, Kudi CA, Cadmus SIB. Diagnostic performance of GeneXpert and Ziehl-Neelson microscopy in the detection of tuberculosis in Benue State, Nigeria. ALEXANDRIA JOURNAL OF MEDICINE 2019. [DOI: 10.1016/j.ajme.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Enenche Francis Ejeh
- Department of Veterinary Microbiology, University of Maiduguri, Nigeria
- Pulmonary, Department of Medicine, Critical Care & Sleep Medicine Unit, University of California, San Diego, USA
- Department of Veterinary Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | | | - Victor O. Akinseye
- Department of Chemical Sciences, Faculty of Science, Augustine University Ilara-Epe, Lagos State, Nigeria
| | - Kenneth O. Okon
- Department of Medical Microbiology, Federal Medical Centre, Makurdi, Nigeria
| | - Haruna M. Kazeem
- Department of Veterinary Microbiology, Ahmadu Bello University, Zaria, Nigeria
| | | | - Simeon Idowu B. Cadmus
- Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Nigeria
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48
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Brites D, Loiseau C, Menardo F, Borrell S, Boniotti MB, Warren R, Dippenaar A, Parsons SDC, Beisel C, Behr MA, Fyfe JA, Coscolla M, Gagneux S. A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex. Front Microbiol 2018; 9:2820. [PMID: 30538680 PMCID: PMC6277475 DOI: 10.3389/fmicb.2018.02820] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/02/2018] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely related to the human-adapted Mycobacterium africanum Lineage 6 than to other animal-adapted strains. Furthermore, we identified four main animal-adapted MTBC clades that might correspond to four main host shifts; two of these clades are hypothesized to reflect independent cattle domestication events. Contrary to what would be expected from an obligate pathogen, MTBC nucleotide diversity was not positively correlated with host phylogenetic distances, suggesting that host tropism in the animal-adapted MTBC seems to be driven by contact rates and demographic aspects of the host population rather by than host relatedness. By combining phylogenomics with ecological data, we propose an evolutionary scenario in which the ancestor of Lineage 6 and all animal-adapted MTBC ecotypes was a generalist pathogen that subsequently adapted to different host species. This study provides a new phylogenetic framework to better understand the evolution of the different ecotypes of the MTBC and guide future work aimed at elucidating the molecular mechanisms underlying host range.
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Affiliation(s)
- Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna: Centro Nazionale di Referenza per la Tubercolosi Bovina, Brescia, Italy
| | - Robin Warren
- SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Anzaan Dippenaar
- SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Sven David Charles Parsons
- SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Marcel A Behr
- McGill International TB Centre, Infectious Diseases and Immunity in Global Health, McGill University Health Centre and Research Institute, Montréal, QC, Canada
| | - Janet A Fyfe
- Mycobacterium Reference Laboratory, Victoria Infectious Diseases Reference Laboratory, Peter Doherty Institute, Melbourne, VIC, Australia
| | - Mireia Coscolla
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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49
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DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
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50
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Ates LS, Dippenaar A, Sayes F, Pawlik A, Bouchier C, Ma L, Warren RM, Sougakoff W, Majlessi L, van Heijst JWJ, Brossier F, Brosch R. Unexpected Genomic and Phenotypic Diversity of Mycobacterium africanum Lineage 5 Affects Drug Resistance, Protein Secretion, and Immunogenicity. Genome Biol Evol 2018; 10:1858-1874. [PMID: 30010947 PMCID: PMC6071665 DOI: 10.1093/gbe/evy145] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium africanum consists of Lineages L5 and L6 of the Mycobacterium tuberculosis complex (MTBC) and causes human tuberculosis in specific regions of Western Africa, but is generally not transmitted in other parts of the world. Since M. africanum is evolutionarily closely placed between the globally dispersed Mycobacterium tuberculosis and animal-adapted MTBC-members, these lineages provide valuable insight into M. tuberculosis evolution. Here, we have collected 15 M. africanum L5 strains isolated in France over 4 decades. Illumina sequencing and phylogenomic analysis revealed a previously underappreciated diversity within L5, which consists of distinct sublineages. L5 strains caused relatively high levels of extrapulmonary tuberculosis and included multi- and extensively drug-resistant isolates, especially in the newly defined sublineage L5.2. The specific L5 sublineages also exhibit distinct phenotypic characteristics related to in vitro growth, protein secretion and in vivo immunogenicity. In particular, we identified a PE_PGRS and PPE-MPTR secretion defect specific for sublineage L5.2, which was independent of PPE38. Furthermore, L5 isolates were able to efficiently secrete and induce immune responses against ESX-1 substrates contrary to previous predictions. These phenotypes of Type VII protein secretion and immunogenicity provide valuable information to better link genome sequences to phenotypic traits and thereby understand the evolution of the MTBC.
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Affiliation(s)
- Louis S Ates
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Anzaan Dippenaar
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Fadel Sayes
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Alexandre Pawlik
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Christiane Bouchier
- Department of Genomes and Genetics, Institut Pasteur, Genomics Platform, Paris, France
| | - Laurence Ma
- Department of Genomes and Genetics, Institut Pasteur, Genomics Platform, Paris, France
| | - Robin M Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wladimir Sougakoff
- Sorbonne Universités, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Team 13 (Bacteriology), Paris, France
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries (NRC MyRMA), Hôpitaux Universitaires Pitié-Salpêtrière – Charles Foix, Paris, France
| | - Laleh Majlessi
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Jeroen W J van Heijst
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Florence Brossier
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Sorbonne Universités, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Team 13 (Bacteriology), Paris, France
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries (NRC MyRMA), Hôpitaux Universitaires Pitié-Salpêtrière – Charles Foix, Paris, France
| | - Roland Brosch
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
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