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Kałużna M, Prokić A, Obradović A, Weldon WA, Stockwell VO, Pothier JF. Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1254107. [PMID: 37780515 PMCID: PMC10535005 DOI: 10.3389/fpls.2023.1254107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023]
Abstract
Xanthomonas arboricola pv. corylina (Xac; formerly Xanthomonas campestris pv. corylina) is the causal agent of the bacterial blight of hazelnuts, a devastating disease of trees in plant nurseries and young orchards. Currently, there are no PCR assays to distinguish Xac from all other pathovars of X. arboricola. A comparative genomics approach with publicly available genomes of Xac was used to identify unique sequences, conserved across the genomes of the pathogen. We identified a 2,440 bp genomic region that was unique to Xac and designed identification and detection systems for conventional PCR, qPCR (SYBR® Green and TaqMan™), and loop-mediated isothermal amplification (LAMP). All PCR assays performed on genomic DNA isolated from eight X. arboricola pathovars and closely related bacterial species confirmed the specificity of designed primers. These new multi-platform molecular diagnostic tools may be used by plant clinics and researchers to detect and identify Xac in pure cultures and hazelnut tissues rapidly and accurately.
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Affiliation(s)
- Monika Kałużna
- The National Institute of Horticultural Research, Skierniewice, Poland
| | - Andjelka Prokić
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Aleksa Obradović
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Virginia O. Stockwell
- United States Department of Agriculture, Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, United States
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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Bartolini B, Gruber CE, Koopmans M, Avšič T, Bino S, Christova I, Grunow R, Hewson R, Korukluoglu G, Lemos CM, Mirazimi A, Papa A, Sanchez-Seco MP, Sauer AV, Zeller H, Nisii C, Capobianchi MR, Ippolito G, Reusken CB, Di Caro A. Laboratory management of Crimean-Congo haemorrhagic fever virus infections: perspectives from two European networks. ACTA ACUST UNITED AC 2020; 24. [PMID: 30722811 PMCID: PMC6386216 DOI: 10.2807/1560-7917.es.2019.24.5.1800093] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background Crimean-Congo haemorrhagic fever virus (CCHFV) is considered an emerging infectious disease threat in the European Union. Since 2000, the incidence and geographic range of confirmed CCHF cases have markedly increased, following changes in the distribution of its main vector, Hyalomma ticks. Aims To review scientific literature and collect experts’ opinion to analyse relevant aspects of the laboratory management of human CCHF cases and any exposed contacts, as well as identify areas for advancement of international collaborative preparedness and laboratory response plans. Methods We conducted a literature review on CCHF molecular diagnostics through an online search. Further, we obtained expert opinions on the key laboratory aspects of CCHF diagnosis. Consulted experts were members of two European projects, EMERGE (Efficient response to highly dangerous and emerging pathogens at EU level) and EVD-LabNet (Emerging Viral Diseases-Expert Laboratory Network). Results Consensus was reached on relevant and controversial aspects of CCHF disease with implications for laboratory management of human CCHF cases, including biosafety, diagnostic algorithm and advice to improve lab capabilities. Knowledge on the diffusion of CCHF can be obtained by promoting syndromic approach to infectious diseases diagnosis and by including CCHFV infection in the diagnostic algorithm of severe fevers of unknown origin. Conclusion No effective vaccine and/or therapeutics are available at present so outbreak response relies on rapid identification and appropriate infection control measures. Frontline hospitals and reference laboratories have a crucial role in the response to a CCHF outbreak, which should integrate laboratory, clinical and public health responses.
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Affiliation(s)
- Barbara Bartolini
- 'L. Spallanzani' National Institute for Infectious Diseases IRCCS (INMI), WHO Collaborating Center for Clinical Care, Diagnosis, Response and Training on Highly Infectious Diseases, Rome, Italy
| | - Cesare Em Gruber
- 'L. Spallanzani' National Institute for Infectious Diseases IRCCS (INMI), WHO Collaborating Center for Clinical Care, Diagnosis, Response and Training on Highly Infectious Diseases, Rome, Italy
| | - Marion Koopmans
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, The Netherlands
| | - Tatjana Avšič
- Institute of Microbiology and Immunology, Faculty of Medicine, Ljubljana, Slovenia
| | - Sylvia Bino
- Control of Infectious Diseases Department Institute of Public Health, Tirana, Albania
| | - Iva Christova
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Roger Hewson
- Public Health England, National Infection Service WHO Collaborating Centre for Virus Reference and Research (Special Pathogens), Porton Down, Salisbury, United Kingdom
| | | | - Cinthia Menel Lemos
- Consumers, Health, Agriculture and Food Executive Agency (CHAFEA), Luxembourg, Luxembourg
| | - Ali Mirazimi
- Department of Laboratory Medicine, Clinical Microbiology, Karolinska Institute and Karolinska University Hospital, Solna, Sweden.,National Veterinary Institute, Uppsala, Sweden.,Public Health agency of Sweden, Solna, Sweden
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Aisha V Sauer
- European Commission, Directorate General for Health and Food Safety, Unit for Crisis Management and Preparedness in Health, Luxembourg, Luxembourg
| | - Hervè Zeller
- European Center for Disease Prevention and Control, Office of the Chief Scientist, Stockholm, Sweden
| | - Carla Nisii
- 'L. Spallanzani' National Institute for Infectious Diseases IRCCS (INMI), WHO Collaborating Center for Clinical Care, Diagnosis, Response and Training on Highly Infectious Diseases, Rome, Italy
| | - Maria Rosaria Capobianchi
- 'L. Spallanzani' National Institute for Infectious Diseases IRCCS (INMI), WHO Collaborating Center for Clinical Care, Diagnosis, Response and Training on Highly Infectious Diseases, Rome, Italy
| | - Giuseppe Ippolito
- 'L. Spallanzani' National Institute for Infectious Diseases IRCCS (INMI), WHO Collaborating Center for Clinical Care, Diagnosis, Response and Training on Highly Infectious Diseases, Rome, Italy
| | - Chantal B Reusken
- Authors contributed equally to the work and share last authorship.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.,Erasmus MC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, The Netherlands
| | - Antonino Di Caro
- Authors contributed equally to the work and share last authorship.,'L. Spallanzani' National Institute for Infectious Diseases IRCCS (INMI), WHO Collaborating Center for Clinical Care, Diagnosis, Response and Training on Highly Infectious Diseases, Rome, Italy
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Mohammadi A, Bagherichimeh S, Perry MC, Fazel A, Tevlin E, Huibner S, Tharao W, Coburn B, Kaul R. The impact of cervical cytobrush sampling on cervico-vaginal immune parameters and microbiota relevant to HIV susceptibility. Sci Rep 2020; 10:8514. [PMID: 32444843 PMCID: PMC7244754 DOI: 10.1038/s41598-020-65544-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/06/2020] [Indexed: 01/01/2023] Open
Abstract
The immunology and microbiota of the female genital tract (FGT) are key determinants of HIV susceptibility. Cervical cytobrush sampling is a relatively non-invasive method permitting the longitudinal assessment of endocervical immune cells, but effects on FGT immunology are unknown. Blood, cervico-vaginal secretions and cervical cytobrushes were collected from sexually transmitted infection (STI)-free women at baseline and after either 6 hours or 48 hours. Endocervical immune cell subsets were assessed by flow cytometry, and pro-inflammatory cytokines by multiplex ELISA. The density of Lactobacillus species and key bacterial vaginosis-associated bacterial taxa were determined by qPCR. Paired changes were assessed before and after cytobrush sampling. After 6 hours there were significant increases in CD4 + T cell, antigen presenting cell (APC) and neutrophil numbers; APC elevations persisted at 48 hours, while neutrophil and CD4 + T cell numbers returned to baseline. In addition, pro-inflammatory cytokine levels were increased at 6 hours and returned to baseline by 48 hours. No significant changes were observed in the absolute abundance of Lactobacillus species or BV-associated bacteria at either time point. Overall, cytobrush sampling altered genital immune parameters at 6 hours, but only APC number increases persisted at 48 hours. This should be considered in longitudinal analyses of FGT immunology.
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Affiliation(s)
- A Mohammadi
- Department of Medicine, University of Toronto, Toronto, Canada.
| | - S Bagherichimeh
- Department of Medicine, University of Toronto, Toronto, Canada
| | - M C Perry
- Department of Immunology, University of Toronto, Toronto, Canada
| | - A Fazel
- Department of Medicine, University of Toronto, Toronto, Canada
| | - E Tevlin
- Women's Health in Women's Hands Community Health Center, Toronto, Canada
| | - S Huibner
- Department of Medicine, University of Toronto, Toronto, Canada
| | - W Tharao
- Women's Health in Women's Hands Community Health Center, Toronto, Canada
| | - B Coburn
- Department of Immunology, University of Toronto, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - R Kaul
- Department of Medicine, University of Toronto, Toronto, Canada. .,Department of Immunology, University of Toronto, Toronto, Canada.
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Artika IM, Wiyatno A, Ma'roef CN. Pathogenic viruses: Molecular detection and characterization. INFECTION GENETICS AND EVOLUTION 2020; 81:104215. [PMID: 32006706 PMCID: PMC7106233 DOI: 10.1016/j.meegid.2020.104215] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization. The continous emergence and re-emergence of pathogenic viruses has become a major threat to public health. PCR-based techniques together with DNA sequencing technology have provided highly sensitive and specific methods to determine virus circulation. Southeast Asia is considered to be vulnerable to potential outbreaks of pathogenic viruses. A number of pathogenic viruses have been reported to circulate in this region. The 2019 novel coronavirus has also been identified in Southeast Asia. Development of local capacity to rapidly identify new viruses is very important.
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Affiliation(s)
- I Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia; Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor 16680, Indonesia.
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
| | - Chairin Nisa Ma'roef
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta 10430, Indonesia
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Gruber CEM, Bartolini B, Castilletti C, Mirazimi A, Hewson R, Christova I, Avšič T, Grunow R, Papa A, Sánchez-Seco MP, Kopmans M, Ippolito G, Capobianchi MR, Reusken CBEM, Di Caro A. Geographical Variability Affects CCHFV Detection by RT-PCR: A Tool for In-Silico Evaluation of Molecular Assays. Viruses 2019; 11:E953. [PMID: 31623214 PMCID: PMC6833031 DOI: 10.3390/v11100953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 10/15/2019] [Indexed: 01/21/2023] Open
Abstract
The Crimean-Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient's travel history and geographic distribution of the different CCHFV strains.
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Affiliation(s)
- Cesare E M Gruber
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Barbara Bartolini
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Concetta Castilletti
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Ali Mirazimi
- Public Health agency of Sweden, 17182 Solna, Sweden.
- National veterinary Institute, 75189 Uppsala, Sweden.
- Department of laboratory Medicine, Clinical Microbiology, Karolinska Institute and Karolinska, 17177 Stockholm, Sweden.
| | - Roger Hewson
- Public Health England, National Infection Service WHO Collaborating Centre for Virus Reference and Research (Special Pathogens) Porton Down, Salisbury SP40JG, UK.
| | - Iva Christova
- National Reference Laboratory on Vector-Borne Pathogens, Leptospira and Listeria, Microbiology Department, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria.
| | - Tatjana Avšič
- Faculty of Medicine, Institute of Microbiology and Immunology, 1000 Ljubljana, Slovenia.
| | - Roland Grunow
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, 13353 Berlin, Germany.
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - María P Sánchez-Seco
- National Centre of Microbiology, Institute of Health "Carlos III", Majadahonda, 28220 Madrid, Spain.
| | - Marion Kopmans
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for arbovirus and viral hemorrhagic fever reference and research, 3015 CN Rotterdam, The Netherlands.
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Maria R Capobianchi
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
| | - Chantal B E M Reusken
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for arbovirus and viral hemorrhagic fever reference and research, 3015 CN Rotterdam, The Netherlands.
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands.
| | - Antonino Di Caro
- National Institute for Infectious Diseases (INMI) "L. Spallanzani" IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy.
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