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Marcone C, Pierro R, Palmieri C. Occurrence, Impact, and Multilocus Sequence Analysis of Alder Yellows Phytoplasma Infecting Common Alder and Italian Alder in Southern Italy. Microorganisms 2024; 12:1140. [PMID: 38930522 PMCID: PMC11205446 DOI: 10.3390/microorganisms12061140] [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: 03/20/2024] [Revised: 05/16/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Alder yellows (ALY) phytoplasma (16SrV-C) is associated with ALY, a disease of several Alnus (alder) species in Europe and A. rubra in North America. In all affected species, the symptoms are similar. However, latent infections are common. ALY phytoplasma includes different strains which may be occasionally transmitted to grapevines leading to some grapevine yellows diseases. In the current study, visual symptom assessment and PCR-based methods using universal and group-specific phytoplasma primers were used to update and extend knowledge on the occurrence, impact, and genetic diversity of ALY phytoplasma in declining and non-symptomatic A. glutinosa and A. cordata trees in the Basilicata and Campania regions of southern Italy. ALY phytoplasma was detected in 80% of alder trees examined. In symptomatic trees, no other cause of disease was observed. More than half of alder trees that tested phytoplasma-positive proved to be latently infected. A considerable genetic variability was observed among the newly recorded ALY phytoplasma strains in southern Italy in almost of the genes examined. These included 16S rRNA, 16S/23S rDNA spacer region, ribosomal protein rpsV (rpl22) and rpsC (rps3), map, imp, and groEL genes. Eleven new genotypes were identified at map gene sequence level. However, the genetic differences observed were not related to plant host species, geographical origin, and symptoms shown by infected alder trees. Also, this study indicates that ALY phytoplasma is more widespread than previously thought.
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Affiliation(s)
- Carmine Marcone
- Department of Pharmacy, University of Salerno, I-84084 Fisciano, Italy
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Bertaccini A. Plants and Phytoplasmas: When Bacteria Modify Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111425. [PMID: 35684198 PMCID: PMC9182842 DOI: 10.3390/plants11111425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 05/14/2023]
Abstract
Plant pathogen presence is very dangerous for agricultural ecosystems and causes huge economic losses. Phytoplasmas are insect-transmitted wall-less bacteria living in plants, only in the phloem tissues and in the emolymph of their insect vectors. They are able to manipulate several metabolic pathways of their hosts, very often without impairing their life. The molecular diversity described (49 'Candidatus Phytoplasma' species and about 300 ribosomal subgroups) is only in some cases related to their associated symptomatology. As for the other plant pathogens, it is necessary to verify their identity and recognize the symptoms associated with their presence to appropriately manage the diseases. However, the never-ending mechanism of patho-adaptation and the copresence of other pathogens makes this management difficult. Reducing the huge impact of phytoplasma-associated diseases in all the main crops and wild species is, however, relevant, in order to reduce their effects that are jeopardizing plant biodiversity.
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Affiliation(s)
- Assunta Bertaccini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, 40127 Bologna, Italy
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Soto N, Helmick EE, Harrison NA, Bahder BW. Genetic Variability of Palm Lethal Decline Phytoplasmas in the Caribbean Basin and Florida, U.S.A., Based on a Multilocus Analysis. PHYTOPATHOLOGY 2021; 111:2203-2212. [PMID: 34844420 DOI: 10.1094/phyto-04-21-0130-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Palm lethal decline phytoplasmas are an important group of plant pathogens that cause death in a variety of palm species throughout the Caribbean basin and the southeastern United States. The 16SrIV-D phytoplasma was introduced to the state of Florida, United States; it has since caused severe economic losses to the green industries of Florida and is threating natural ecosystems because of its ability to infect the native palm Sabal palmetto. In this study, the genetic variability of the 16SrIV-D phytoplasma was assessed over a 10-year period to determine if multiple introductions had occurred or if natural mutations were occurring. Furthermore, the genetic variability of the palm lethal decline phytoplasma group (16SrIV) was assessed with a multiple locus analysis using the 16S ribosomal RNA gene, the 16S-23S intergenic spacer region, and secA and groEL genes. Overall, no variability of the 16SrIV-D phytoplasma was documented in Florida over a 10-year period. The multilocus analysis showed support for three distinct species of the phytoplasma in the Caribbean basin that infect palms and further support that the 16SrIV-C from Tanzania is not closely related. Furthermore, 16SrIV-B and 16SrIV-D were found to be the same phytoplasma based on 100% identity between the two based on intergenic spacer region, secA, and groEL analysis. This study represents the first robust, multilocus analysis of palm-infecting phytoplasmas from the Caribbean and sheds light on the phylogeny and evolution of the group.
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Affiliation(s)
- Noemi Soto
- Department of Entomology and Nematology, University of Florida Fort Lauderdale Research and Education Center, Davie, FL 33314-7719
| | - Ericka E Helmick
- Department of Entomology and Nematology, University of Florida Fort Lauderdale Research and Education Center, Davie, FL 33314-7719
| | - Nigel A Harrison
- Department of Plant Pathology, University of Florida Fort Lauderdale Research and Education Center, Davie, FL 33314-7719
| | - Brian W Bahder
- Department of Entomology and Nematology, University of Florida Fort Lauderdale Research and Education Center, Davie, FL 33314-7719
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Detection of blueberry stunt phytoplasma in Eastern Canada using cpn60-based molecular diagnostic assays. Sci Rep 2021; 11:22118. [PMID: 34764366 PMCID: PMC8586236 DOI: 10.1038/s41598-021-01439-4] [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: 06/28/2021] [Accepted: 10/25/2021] [Indexed: 11/15/2022] Open
Abstract
Blueberry stunt phytoplasma (BBSP; ‘Candidatus Phytoplasma asteris’) is an insect-vectored plant pathogen that causes severe yield losses in blueberry (Vaccinium corymbosum), which is the most valuable fruit crop in Canada. Rapid, field-based diagnostic assays are desirable tools for the control of BBSP, as part of an integrated, proactive approach to production management termed biovigilance. We designed and validated a chaperonin-60 (cpn60)-targeted LAMP assay for detection of BBSP, providing a rapid, low cost, field-deployable diagnostic option. Our validation demonstrates that the assay is reproducible, with high analytical specificity and improved sensitivity when compared with 16S rRNA nested PCR. We applied the validated LAMP assay to nearly 2000 blueberry samples from Québec and Nova Scotia over three growing seasons (2016–2018). Our surveys revealed that BBSP is present in most sites across both provinces, though detection of the pathogen in individual plants varied in different tissues across sampling dates and across years, and evidence of spread between plants was limited. To quantify pathogen load in select plants, we designed additional qPCR and ddPCR assays, also based on cpn60. We found that pathogen load fluctuates in individual plants, both within and between growing seasons. Finally, we designed an interactive map to visualize the results of our surveys. These results provide a validated diagnostic assay that can be used as part of a biovigilance strategy for detecting and controlling infections caused by BBSP.
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Ajithkumar K, Savitha AS, Mahadevakumar S, Sreenivasa MY, Naik MK, Rajanna B, Sathyanarayana R, Singh PK. A new host record for Candidatus Phytoplasma cynodontis (16Sr XIV-A) associated with phyllody and fasciation of linseed (Linum usitatissimum) from India. Lett Appl Microbiol 2021; 73:672-681. [PMID: 34545601 DOI: 10.1111/lam.13561] [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: 08/15/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/27/2022]
Abstract
Linseed commonly called as flaxseed (Linum usitatissimum Linn.) is an important oilseed crop cultivated widely in Northern parts of Karnataka. During, 2019 (January-February), a characteristic disease was noticed with symptoms that resembled phytoplasma or like disease symptoms. The incidence was ranged from 6·5 to 16·5% in the experimental station of Raichur Agricultural University. The typical symptoms observed were virescence of floral parts, fasciation of the inflorescence axis, phyllody, stunted and flattened stem with reduced leaves. Symptomatic and healthy samples were collected and processed for molecular detection of phytoplasma. Total DNA was isolated from four infected plants and two healthy plants. The 16S rDNA region was amplified using P1/P7 followed by R16F2n/R16R2 primer pair which showed the amplification of expected amplicon size from all four infected samples. Furthermore, the SecA gene was amplified using SecA1/SecA3 primers. The PCR amplified products were subjected for direct sequencing from both directions and the consensus sequences were obtained and nBLAST search analysis revealed that the 16Sr RNA and SecA sequences were sharing maximum similarity (100%) with the reference sequence of Ca. P. cynodontis. The sequences were analysed phylogenetically by constructing a Phylogram independently by NJ method along with reference sequence of 16S rRNA region and SecA region retrieved from GenBank database showed that the phytoplasma sequence from linseed phyllody of the present study placed in a distinct clade along with reference sequence of "Ca. P. cynodontis" thus confirming the identity phylogenetically. Furthermore, iPhyClassifier and virtual RFLP proved that the phytoplasma belonged to 16SrXIV (subgroup A) phytoplasma. Previously linseed is known to be associated with 16SrII-D phytoplasma but the association of the 16SrXIV-A group of phytoplasma is not reported so far. Therefore, this is the new host record for Ca. P. cynodontis (16SrXIV-A) phytoplasma associated with linseed stem fasciation, phyllody from India.
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Affiliation(s)
- K Ajithkumar
- AICRP on Linseed, Main Agricultural Research Station, University of Agricultural Sciences, Raichur, India
| | - A S Savitha
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, Raichur, India
| | - S Mahadevakumar
- Applied Phytopathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru, India
| | - M Y Sreenivasa
- Phytopathology Laboratory, Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru, India
| | - M K Naik
- University of Agricultural and Horticultural Sciences, Shivamogga, India
| | - B Rajanna
- AICRP on Linseed, Main Agricultural Research Station, University of Agricultural Sciences, Raichur, India
| | | | - P K Singh
- CSA University of Agriculture & Technology, Kanpur, Uttar Pradesh, India
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Wei W, Trivellone V, Dietrich CH, Zhao Y, Bottner-Parker KD, Ivanauskas A. Identification of Phytoplasmas Representing Multiple New Genetic Lineages from Phloem-Feeding Leafhoppers Highlights the Diversity of Phytoplasmas and Their Potential Vectors. Pathogens 2021; 10:352. [PMID: 33809759 PMCID: PMC8002289 DOI: 10.3390/pathogens10030352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 01/18/2023] Open
Abstract
Phytoplasmas are obligate transkingdom bacterial parasites that infect a variety of plant species and replicate in phloem-feeding insects in the order Hemiptera, mainly leafhoppers (Cicadellidae). The insect capacity in acquisition, transmission, survival, and host range directly determines the epidemiology of phytoplasmas. However, due to the difficulty of insect sampling and the lack of follow-up transmission trials, the confirmed phytoplasma insect hosts are still limited compared with the identified plant hosts. Recently, quantitative polymerase chain reaction (qPCR)-based quick screening of 227 leafhoppers collected in natural habitats unveiled the presence of previously unknown phytoplasmas in six samples. In the present study, 76 leafhoppers, including the six prescreened positive samples, were further examined to identify and characterize the phytoplasma strains by semi-nested PCR. A total of ten phytoplasma strains were identified in leafhoppers from four countries including South Africa, Kyrgyzstan, Australia, and China. Based on virtual restriction fragment length polymorphism (RFLP) analysis, these ten phytoplasma strains were classified into four distinct ribosomal (16Sr) groups (16SrI, 16SrIII, 16SrXIV, and 16SrXV), representing five new subgroups (16SrI-AO, 16SrXIV-D, 16SrXIV-E, 16SrXIV-F, and 16SrXV-C). The results strongly suggest that the newly identified phytoplasma strains not only represent new genetic subgroup lineages, but also extend previously undiscovered geographical distributions. In addition, ten phytoplasma-harboring leafhoppers belonged to seven known leafhopper species, none of which were previously reported insect vectors of phytoplasmas. The findings from this study provide fresh insight into genetic diversity, geographical distribution, and insect host range of phytoplasmas. Further transmission trials and screening of new potential host plants and weed reservoirs in areas adjacent to collection sites of phytoplasma harboring leafhoppers will contribute to a better understanding of phytoplasma transmission and epidemiology.
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Affiliation(s)
- Wei Wei
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (Y.Z.); (K.D.B.-P.); (A.I.)
| | - Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA; (V.T.); (C.H.D.)
| | - Christopher H. Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA; (V.T.); (C.H.D.)
| | - Yan Zhao
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (Y.Z.); (K.D.B.-P.); (A.I.)
| | - Kristi D. Bottner-Parker
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (Y.Z.); (K.D.B.-P.); (A.I.)
| | - Algirdas Ivanauskas
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (Y.Z.); (K.D.B.-P.); (A.I.)
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Schneider B, Hüttel B, Zübert C, Kube M. Genetic variation, phylogenetic relationship and spatial distribution of 'Candidatus Phytoplasma ulmi' strains in Germany. Sci Rep 2020; 10:21864. [PMID: 33318538 PMCID: PMC7736341 DOI: 10.1038/s41598-020-78745-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/23/2020] [Indexed: 11/09/2022] Open
Abstract
A recent survey in Germany revealed the wide presence of 'Candidatus Phytoplasma ulmi' in native elm stands. Accessions were studied for their genetic variability and phylogenetic relationship based on the conserved groEL and the variable imp gene. While the groEL sequences revealed a high intraspecific homology of more than 99%, the homology of the imp gene dropped to 71% between distantly related sequences. Twenty-nine groEL and 74 imp genotypes were distinguished based on polymorphic sites. Phylogenetic analysis of the groEL gene clustered all 'Ca. P. ulmi' strains and separated them from related phytoplasmas of the 16SrV group. The inferred phylogeny of the imp gene resulted in a different tree topology and separated the 'Ca. P. ulmi' genotypes into two clusters, one closely related to the flavescence dorée phytoplasma strain FD-D (16SrV-D), the other affiliated with the flavescence dorée phytoplasma strains FD-C and FD70 and the alder yellows phytoplasma (16SrV-C). In both phylograms, 'Ca. P. ulmi' genotypes from Scots elm trees formed a coherent cluster, while genotypes from European white elms and field elms grouped less strictly. The regional distribution pattern was congruent for some of the groEL and imp genotypes, but a strict linkage for all genotypes was not apparent.
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Affiliation(s)
- B Schneider
- Thuenen-Institute of Forest Genetics, 15377, Waldsieversdorf, Germany.
| | - B Hüttel
- Max Planck Institute for Plant Breeding Research, Max Planck Genome Centre Cologne, 50829, Cologne, Germany
| | - C Zübert
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599, Stuttgart, Germany
| | - M Kube
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599, Stuttgart, Germany
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Muirhead K, Pérez-López E, Bahder BW, Hill JE, Dumonceaux T. The CpnClassiPhyR Is a Resource for cpn60 Universal Target-Based Classification of Phytoplasmas. PLANT DISEASE 2019; 103:2494-2497. [PMID: 31453748 DOI: 10.1094/pdis-03-19-0454-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytoplasmas are plant-pathogenic bacteria that are associated with yield losses in many crop plants worldwide. Phytoplasma strain differentiation is accomplished using in silico restriction fragment length polymorphism (RFLP) analysis of 16S ribosomal RNA-encoding gene sequences, which has resulted in the definition of ribosomal groups and subgroups of phytoplasmas. Due to limitations associated with this approach, a complementary classification scheme was recently developed based on RFLP analysis of the single-copy, protein-encoding gene chaperonin-60 (cpn60). We present the CpnClassiPhyR, software that facilitates phytoplasma strain classification using both RFLP and automated phylogenetic analysis of cpn60 sequences. This software is available through a web interface at http://cpnclassiphyr.ca.
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Affiliation(s)
| | - Edel Pérez-López
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Brian W Bahder
- University of Florida Fort Lauderdale Research and Education Center
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tim Dumonceaux
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
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Pérez-López E, Dumonceaux TJ. Detection and identification of the heterogeneous novel subgroup 16SrXIII-(A/I)I phytoplasma associated with strawberry green petal disease and Mexican periwinkle virescence. Int J Syst Evol Microbiol 2016; 66:4406-4415. [DOI: 10.1099/ijsem.0.001365] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Edel Pérez-López
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de Las Culturas Veracruzanas, Xalapa, Veracruz, Mexico
| | - Tim J. Dumonceaux
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
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Pérez-López E, Olivier CY, Luna-Rodríguez M, Dumonceaux TJ. Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences. Int J Syst Evol Microbiol 2016; 66:5600-5613. [PMID: 27667728 PMCID: PMC5244502 DOI: 10.1099/ijsem.0.001501] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas are unculturable, phytopathogenic bacteria that cause economic losses worldwide. As unculturable micro-organisms, phytoplasma taxonomy has been based on the use of the 16S rRNA-encoding gene to establish 16Sr groups and subgroups based on the restriction fragment length polymorphism (RFLP) pattern resulting from the digestion of amplicon (in vitro) or sequence (in silico) with seventeen restriction enzymes. Problems such as heterogeneity of the ribosomal operon and the inability to differentiate closely related phytoplasma strains has motivated the search for additional markers capable of providing finer differentiation of phytoplasma strains. In this study we developed and validated a scheme to classify phytoplasmas based on the use of cpn60 universal target (cpn60 UT) sequences. Ninety-six cpn60 UT sequences from strains belonging to 19 16Sr subgroups were subjected to in silico RFLP using pDRAW32 software, resulting in 25 distinctive RFLP profiles. Based on these results we delineated cpn60 UT groups and subgroups, and established a threshold similarity coefficient for groups and subgroups classifying all the strains analysed in this study. The nucleotide identity among the reference strains, the correspondence between in vitro and in silico RFLP, and the phylogenetic relationships of phytoplasma strains based on cpn60 UT sequences are also discussed.
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Affiliation(s)
- Edel Pérez-López
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de Las Culturas Veracruzanas Xalapa, Veracruz, México
| | - Chrystel Y. Olivier
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Mauricio Luna-Rodríguez
- Laboratorio de Alta Tecnología de Xalapa - DGI, Universidad Veracruzana, Médicos 5, Unidad del Bosque Xalapa, Veracruz, México
| | - Tim J. Dumonceaux
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Correspondence Tim J. Dumonceaux
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